Microorganisms

12 pages, 1954 KiB

Open AccessArticle

Increased Prevalence of Salmonella Infantis Isolated from Raw Chicken and Turkey Products in the United States Is Due to a Single Clonal Lineage Carrying the pESI Plasmid

by Elizabeth A. McMillan, Margaret D. Weinroth and Jonathan G. Frye

Microorganisms 2022, 10(7), 1478; https://doi.org/10.3390/microorganisms10071478 - 21 Jul 2022

Cited by 18 | Viewed by 2956

Abstract

Infantis has recently become one of the most common serotypes of Salmonella isolated in the U.S. from raw meat samples collected in processing facilities and in retail stores. Investigations have determined that the majority of these isolates contain the pESI plasmid, but there [...] Read more.

Infantis has recently become one of the most common serotypes of Salmonella isolated in the U.S. from raw meat samples collected in processing facilities and in retail stores. Investigations have determined that the majority of these isolates contain the pESI plasmid, but there has not been a large-scale investigation of the chromosome of these isolates. Here, we investigated 3276 whole-genome sequences of Salmonella Infantis with and without the pESI plasmid to understand chromosomal differences between plasmid carriage groups. S. Infantis genomes arranged into multiple clades with a single clade containing the isolates carrying the plasmid. Fifty-eight SNPs were identified in complete linkage disequilibrium between isolates that did and did not carry the plasmid. However, there were no unique genes present only in the genomes of isolates containing the plasmid. On average, isolates with the plasmid did contain more insertion sequences than those without (p < 0.05). Given that S. Infantis isolates carrying pESI form a single clade, it can be inferred that the increase in carriage of this plasmid in the U.S. is due to rapid clonal expansion of a single strain rather than as a result of multiple transfer events. As this S. Infantis clone does not contain any unique chromosomal genes, its proliferation appears to be due to pESI plasmid-encoded genes that may be advantageous in the chickens and turkeys or in their environment. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Increased Virulence of Salmonella)

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13 pages, 2089 KiB

Open AccessArticle

Characterization of Clostridioides difficile Strains from an Outbreak Using MALDI-TOF Mass Spectrometry

by Adriana Calderaro, Mirko Buttrini, Benedetta Farina, Sara Montecchini, Monica Martinelli, Maria Cristina Arcangeletti, Carlo Chezzi and Flora De Conto

Microorganisms 2022, 10(7), 1477; https://doi.org/10.3390/microorganisms10071477 - 21 Jul 2022

Cited by 5 | Viewed by 2732

Abstract

The epidemiology of Clostridioides difficile infection (CDI) has changed over the last two decades, due to the emergence of C. difficile strains with clinical relevance and responsible for nosocomial outbreaks with severe outcomes. This study reports an outbreak occurred in a Long-term Care [...] Read more.

The epidemiology of Clostridioides difficile infection (CDI) has changed over the last two decades, due to the emergence of C. difficile strains with clinical relevance and responsible for nosocomial outbreaks with severe outcomes. This study reports an outbreak occurred in a Long-term Care Unit from February to March 2022 and tracked by using a Matrix-Assisted Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) typing approach (T-MALDI); subsequently, a characterization of the toxigenic and antimicrobial susceptibility profiles of the C. difficile isolates was performed. A total of 143 faecal samples belonging to 112 patients was evaluated and C. difficile DNA was detected in 51 samples (46 patients). Twenty-nine C. difficile isolates were obtained, and three different clusters were revealed by T-MALDI. The most representative cluster accounted 22 strains and was considered to be epidemic, in agreement with PCR-Ribotyping. Such epidemic strains were susceptible to vancomycin (MIC ≤ 0.5 mg/mL) and metronidazole (MIC ≤ 1 mg/mL), but not to moxifloxacin (MIC > 32 mg/mL). Moreover, they produced only the Toxin A and, additionally, the binary toxin. To our knowledge, this is the first reported outbreak referable to a tcdA+/tcdB-/cdt+ genotypic profile. In light of these results, T-MALDI is a valid and rapid approach for discovering and tracking outbreaks. Full article

(This article belongs to the Special Issue Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogenic Microorganisms 2.0)

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12 pages, 2384 KiB

Open AccessArticle

Streptococcus pyogenes NAD+-Glycohydrolase Reduces Skeletal Muscle βNAD+ Levels Independently of Streptolysin O

by Eric R. McIndoo, Emily Price, Cheri L. Lamb, Christopher S. Dayton, Clifford R. Bayer, Dennis L. Stevens, Amy E. Bryant and Sarah E. Hobdey

Microorganisms 2022, 10(7), 1476; https://doi.org/10.3390/microorganisms10071476 - 21 Jul 2022

Viewed by 1905

Abstract

Necrotizing soft tissue infections caused by Streptococcus pyogenes (group A streptococcus [GAS]) are characterized by rapid and extensive necrosis of fascia and muscle. Molecular epidemiological studies have demonstrated a positive correlation between GAS isolates that cause invasive infections and the production of S. [...] Read more.

Necrotizing soft tissue infections caused by Streptococcus pyogenes (group A streptococcus [GAS]) are characterized by rapid and extensive necrosis of fascia and muscle. Molecular epidemiological studies have demonstrated a positive correlation between GAS isolates that cause invasive infections and the production of S. pyogenes NAD+-glycohydrolase (SPN), an NADase secreted by GAS, but the effect of SPN on muscle cells has not been described. Thus, using standard βNAD+ and ATP quantification assays, we investigated the effects of SPN on cultured human skeletal muscle cell (SkMC) βNAD+ and ATP with and without streptolysin O (SLO)–a secreted cholesterol-dependent cytolysin known to act synergistically with SPN. We found that culture supernatants from GAS strains producing SLO and SPN depleted intracellular βNAD+ and ATP, while exotoxins from a GAS strain producing SLO and an enzymatically-inactive form of SPN had no effect on βNAD+ or ATP. Addition of purified, enzymatically-active SPN to NADase-negative culture supernatants or sterile media reconstituted βNAD+ depletion but had no effect ATP levels. Further, SPN-mediated βNAD+ depletion could be augmented by SLO or the homologous cholesterol-dependent cytolysin, perfringolysin O (PFO). Remarkably, SPN-mediated βNAD+ depletion was SkMC-specific, as purified SPN had minimal effect on epithelial cell βNAD+. Taken together, this study identifies a previously unrecognized role for SPN as a major disruptor of skeletal muscle βNAD+. Such activity could contribute to the rapid and widespread myonecrosis characteristic of severe GAS soft tissue infections. Full article

(This article belongs to the Special Issue Gram Positive Toxins Producing Organisms)

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11 pages, 1704 KiB

Open AccessArticle

The Combination of Molnupiravir with Nirmatrelvir or GC376 Has a Synergic Role in the Inhibition of SARS-CoV-2 Replication In Vitro

by Anna Gidari, Samuele Sabbatini, Elisabetta Schiaroli, Sabrina Bastianelli, Sara Pierucci, Chiara Busti, Lucia Comez, Valeria Libera, Antonio Macchiarulo, Alessandro Paciaroni, Ilaria Vicenti, Maurizio Zazzi and Daniela Francisci

Microorganisms 2022, 10(7), 1475; https://doi.org/10.3390/microorganisms10071475 - 21 Jul 2022

Cited by 28 | Viewed by 3138

Abstract

Introduction: The development of effective vaccines has partially mitigated the trend of the SARS-CoV-2 pandemic; however, the need for orally administered antiviral drugs persists. This study aims to investigate the activity of molnupiravir in combination with nirmatrelvir or GC376 on SARS-CoV-2 to verify [...] Read more.

Introduction: The development of effective vaccines has partially mitigated the trend of the SARS-CoV-2 pandemic; however, the need for orally administered antiviral drugs persists. This study aims to investigate the activity of molnupiravir in combination with nirmatrelvir or GC376 on SARS-CoV-2 to verify the synergistic effect. Methods: The SARS-CoV-2 strains 20A.EU, BA.1 and BA.2 were used to infect Vero E6 in presence of antiviral compounds alone or in combinations using five two-fold serial dilution of compound concentrations ≤EC90. After 48 and 72 h post-infection, viability was performed using MTT reduction assay. Supernatants were collected for plaque-assay titration. All experiments were performed in triplicate, each being repeated at least three times. The synergistic score was calculated using Synergy Finder version 2. Results: All compounds reached micromolar EC90. Molnupiravir and GC376 showed a synergistic activity at 48 h with an HSA score of 19.33 (p < 0.0001) and an additive activity at 72 h with an HSA score of 8.61 (p < 0.0001). Molnupiravir and nirmatrelvir showed a synergistic activity both at 48 h and 72 h with an HSA score of 14.2 (p = 0.01) and 13.08 (p < 0.0001), respectively. Conclusion: Molnupiravir associated with one of the two protease-inhibitors nirmatrelvir and GC376 showed good additive-synergic activity in vitro. Full article

(This article belongs to the Special Issue COVID-19/SARS-CoV-2 Therapeutic Options Development: From Bench to Bedside)

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15 pages, 2094 KiB

Open AccessArticle

Beneficial Shifts in Gut Microbiota by Lacticaseibacillus rhamnosus R0011 and Lactobacillus helveticus R0052 in Alcoholic Hepatitis

by Haripriya Gupta, Sung Hun Kim, Seul Ki Kim, Sang Hak Han, Hak Cheol Kwon and Ki Tae Suk

Microorganisms 2022, 10(7), 1474; https://doi.org/10.3390/microorganisms10071474 - 21 Jul 2022

Cited by 12 | Viewed by 2665

Abstract

Gut microbiota performs indispensable functions in the pathophysiology of alcoholic hepatitis (AH). We investigated the effects of Lacticaseibacillus rhamnosus R0011 and Lactobacillus helveticus for gut microbial restoration toward eubiosis in patients with AH. A multicenter, double-blind, and randomized trial was conducted. Probiotics (n [...] Read more.

Gut microbiota performs indispensable functions in the pathophysiology of alcoholic hepatitis (AH). We investigated the effects of Lacticaseibacillus rhamnosus R0011 and Lactobacillus helveticus for gut microbial restoration toward eubiosis in patients with AH. A multicenter, double-blind, and randomized trial was conducted. Probiotics (n = 44) and placebo (n = 45) groups received, during 7 days, L. rhamnosus R0011/L. helveticus R0052 at 120 mg/day and placebo. All patients were hospitalized to ensure abstinence. Liver function, lipopolysaccharide level, and stool analysis were evaluated in patients before and after 7 days of treatment. At baseline, the dominant bacteria were Gram-negative in both groups which decreased after the probiotics treatment and exhibited a significant reduction in lipopolysaccharide level (p < 0.001). The probiotics ameliorated the Child–Pugh scores (p < 0.001). Furthermore, the probiotics group showed a decline in the levels of alanine aminotransferase and gamma-glutamyltranspeptidase (p < 0.05). The probiotics changed the gut microbial composition at various taxonomical levels. The proportion of Bacteroidetes (147%) was increased after 7 days of probiotics supplementation while Proteobacteria (30%) and Fusobacteria (0%) were decreased. Administration of L. rhamnosus R0011 and L. helveticus R0052 conceivably associated with restoration of gut microbiome in AH patients and improved AH by modulating the gut–liver axis. Full article

(This article belongs to the Special Issue Dialogue of Probiotics with the Host)

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14 pages, 2315 KiB

Open AccessArticle

Factors Influencing the Production of Extracellular Polysaccharides by the Green Algae Dictyosphaerium chlorelloides and Their Isolation, Purification, and Composition

by Olga Kronusová, Petr Kaštánek, Görkem Koyun, František Kaštánek and Tomáš Brányik

Microorganisms 2022, 10(7), 1473; https://doi.org/10.3390/microorganisms10071473 - 21 Jul 2022

Cited by 8 | Viewed by 2434

Abstract

The freshwater green microalgae, Dictyosphaerium chlorelloides (CCALA 330), has the ability to produce extracellular polysaccharides (EPS). Conditions for optimum growth and EPS overproduction were determined in laboratory-scale tubular photobioreactors (PBR) with a working volume of 300 mL. Multiple limitations in nutrient supply were [...] Read more.

The freshwater green microalgae, Dictyosphaerium chlorelloides (CCALA 330), has the ability to produce extracellular polysaccharides (EPS). Conditions for optimum growth and EPS overproduction were determined in laboratory-scale tubular photobioreactors (PBR) with a working volume of 300 mL. Multiple limitations in nutrient supply were proven to be an effective method for EPS overproduction. Salinity stress was also applied to the culture, but no significant increase in EPS production was observed. The effects of different nitrogen sources were examined and the microalgae exhibited the fastest growth and EPS production in medium containing ammonium nitrate. Under determined optimal conditions, EPS concentration reached 10 g/L (71% of the total biomass) and a total biomass of 14 g/L at the end of 17 days cultivation. Pilot-scale cultivation was also carried out in a column type airlift photobioreactor (PBR) with a working volume of 60 L. A new and efficient methodology was developed for separating cells from the EPS-containing culture broth. Due to the strong attachment between cells and EPS, high-pressure homogenization was carried out before a centrifugation process. The EPS in the supernatant was subsequently purified using ultrafiltration. The green microalgae Dictyosphaerium chlorelloides may therefore be appropriate for the commercial production of EPS. Full article

(This article belongs to the Topic Microorganisms in Aquatic Environments)

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16 pages, 2581 KiB

Open AccessArticle

Discrimination and Characterization of Escherichia coli Originating from Clinical Cases of Femoral Head Necrosis in Broilers by MALDI-TOF Mass Spectrometry Confirms Great Heterogeneity of Isolates

by Marina Nees, Michael Hess and Claudia Hess

Microorganisms 2022, 10(7), 1472; https://doi.org/10.3390/microorganisms10071472 - 20 Jul 2022

Viewed by 1771

Abstract

Escherichia coli, a major pathogen in poultry production, is involved in femoral head necrosis (FHN) in broiler birds. So far, the characterization and relationship of isolates in context with this disease are mainly based on phenotypic and genotypic characteristics. Previously, an involvement [...] Read more.

Escherichia coli, a major pathogen in poultry production, is involved in femoral head necrosis (FHN) in broiler birds. So far, the characterization and relationship of isolates in context with this disease are mainly based on phenotypic and genotypic characteristics. Previously, an involvement of diverse E. coli isolates was reported. MALDI-TOF MS has been successfully applied investigating the clonality of different bacteria. Therefore, its application to characterize a well-defined selection of E. coli isolates beyond the species level was tested. The isolates were derived from clinical cases of FHN as well as from healthy birds. Reproducibility studies to perform a standardized protocol were done, and LB agar as well as the usage of fresh bacterial cultures proved most appropriate. No distinct clustering in context with the origin of isolates, association with lesions, serotype, or PFGE profile was found. Most of the isolates belonging to phylogroup B2 revealed a characteristic peak shift at 9716 m/z and could be attributed to the same MALDI-TOF MS cluster. The present study confirmed the previously found pheno- and genotypic heterogeneity of E. coli involved in FHN on the proteomic level. The study also highlights the need for standardized protocols when using MALDI-TOF MS for bacterial typing, especially beyond species level. Full article

(This article belongs to the Special Issue Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogenic Microorganisms)

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23 pages, 1479 KiB

Open AccessArticle

iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments

by José Diogo Neves dos Santos, Susana Afonso João, Jesús Martín, Francisca Vicente, Fernando Reyes and Olga Maria Lage

Microorganisms 2022, 10(7), 1471; https://doi.org/10.3390/microorganisms10071471 - 20 Jul 2022

Cited by 8 | Viewed by 3725

Abstract

Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from [...] Read more.

Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an “one strain many compounds” approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products. Full article

(This article belongs to the Special Issue Ecology, Diversity and Functions of Members of the Planctomycetes, Verrucomicrobia and Clamydia (PVC) Superphylum)

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18 pages, 3052 KiB

Open AccessArticle

Adaptation of Brucella melitensis Antimicrobial Susceptibility Testing to the ISO 20776 Standard and Validation of the Method

by Alina Tscherne, Enrico Mantel, Talar Boskani, Sylwia Budniak, Mandy Elschner, Antonio Fasanella, Siri L. Feruglio, Domenico Galante, Christian G. Giske, Roland Grunow, Judit Henczko, Christin Hinz, Wojciech Iwaniak, Daniela Jacob, Agnieszka Kedrak-Jablonska, Veronica K. Jensen, Tone B. Johansen, Gunnar Kahlmeter, Viviana Manzulli, Erika Matuschek, Falk Melzer, Maria S. Nuncio, Joseph Papaparaskevas, Ana Pelerito, Margrete Solheim, Susanne Thomann, Athanasios Tsakris, Tara Wahab, Marcin Weiner, Lothar Zoeller and Sabine Zange Show full author list Hide full author list

Microorganisms 2022, 10(7), 1470; https://doi.org/10.3390/microorganisms10071470 - 20 Jul 2022

Cited by 7 | Viewed by 3202

Abstract

Brucellosis, mainly caused by Brucella (B.) melitensis, is associated with a risk of chronification and relapses. Antimicrobial susceptibility testing (AST) standards for B. melitensis are not available, and the agent is not yet listed in the EUCAST breakpoint tables. CLSI recommendations for [...] Read more.

Brucellosis, mainly caused by Brucella (B.) melitensis, is associated with a risk of chronification and relapses. Antimicrobial susceptibility testing (AST) standards for B. melitensis are not available, and the agent is not yet listed in the EUCAST breakpoint tables. CLSI recommendations for B. melitensis exist, but they do not fulfill the requirements of the ISO 20776 standard regarding the culture medium and the incubation conditions. Under the third EU Health Programme, laboratories specializing in the diagnostics of highly pathogenic bacteria in their respective countries formed a working group within a Joint Action aiming to develop a suitable method for the AST of B. melitensis. Under the supervision of EUCAST representatives, this working group adapted the CLSI M45 document to the ISO 20776 standard after testing and validation. These adaptations included the comparison of various culture media, culture conditions and AST methods. A Standard Operation Procedure was derived and an interlaboratory validation was performed in order to evaluate the method. The results showed pros and cons for both of the two methods but also indicate that it is not necessary to abandon Mueller–Hinton without additives for the AST of B. melitensis. Full article

(This article belongs to the Special Issue Emerging Themes in Brucella and Brucellosis)

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18 pages, 2927 KiB

Open AccessArticle

Lactobacillus salivarius SNK-6 Activates Intestinal Mucosal Immune System by Regulating Cecal Microbial Community Structure in Laying Hens

by Yuchen Liu, Lianhong Li, Huaxiang Yan, Zhonghua Ning and Zhong Wang

Microorganisms 2022, 10(7), 1469; https://doi.org/10.3390/microorganisms10071469 - 20 Jul 2022

Cited by 8 | Viewed by 2120

Abstract

The production performance and disease resistance of laying hens decrease obviously with age. This study aimed to investigate the effects of supplementary Lactobacillus salivarius (L. salivarius) SNK-6 on laying performance, the immune-related gene expression in cecal tonsil, and the cecal microbial [...] Read more.

The production performance and disease resistance of laying hens decrease obviously with age. This study aimed to investigate the effects of supplementary Lactobacillus salivarius (L. salivarius) SNK-6 on laying performance, the immune-related gene expression in cecal tonsil, and the cecal microbial composition of laying hens. Here, 384 Xinyang black commercial hens (55 weeks old) were randomly allocated to three groups under the same husbandry and dietary regimes: basal diet (Con), the low L. salivarius SNK-6 group (T1: 1.0 × 10⁶ CFU/g), and the high L. salivarius SNK-6 group (T2: 1.0 × 10⁷ CFU/g). The results showed that the feed intake and broken-egg rate in the T1 group were significantly higher than the Con group (p < 0.05). Meanwhile, expressions of intestinal mucosal immune-related genes were significantly upregulated. The 16S rRNA gene sequencing indicated that supplementary L. salivarius SNK-6 had no significant difference in α -diversity and only displayed a trend difference in the β-diversity of cecal microbiota (p = 0.07). LEfSe and random forest were further used to identify bacteria family Enterobacteriaceae, order RF39, genera Ochrobactrum, and Eubacterium as biomarkers between the Con and T1 groups. Genera Ochrobactrum, which had high relative abundance and nodal degree in the T1 and T2 groups, showed a significant positive correlation with the expression of TLR-6, IL-10, MHC-II, and CD40 in cecal tonsils and might play a critical role in activating the host intestinal mucosal immune responses. Overall, dietary supplementary L. salivarius SNK-6 can display an immunomodulatory function, possibly by regulating cecal microbial composition. However, the changes in immune responses may be at the expenditure of corresponding production performance, which needs to be weighed up in practical application. Full article

(This article belongs to the Section Veterinary Microbiology)

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16 pages, 1634 KiB

Open AccessArticle

Culturable Screening of Plant Growth-Promoting and Biocontrol Bacteria in the Rhizosphere and Phyllosphere of Wild Rice

by Zongmu Yao, Yalin Chen, Shouyang Luo, Jilin Wang, Jiafan Zhang, Jianfeng Zhang, Chunjie Tian and Lei Tian

Microorganisms 2022, 10(7), 1468; https://doi.org/10.3390/microorganisms10071468 - 20 Jul 2022

Cited by 6 | Viewed by 2643

Abstract

Wild rice is an important improved resource for cultivated rice and its unique ability to resist biotic and abiotic stress has attracted the attention of many scholars. The microbial community structure in the rhizosphere and leaf area of different rice varieties is also [...] Read more.

Wild rice is an important improved resource for cultivated rice and its unique ability to resist biotic and abiotic stress has attracted the attention of many scholars. The microbial community structure in the rhizosphere and leaf area of different rice varieties is also different, which may be one of the reasons for the difference in stress resistance between wild rice and cultivated rice. Forty-six bacteria were screened from the rhizosphere and phyllospheric of four different wild rice varieties. The results of functions of the screened strains showed that 18 strains had a good inhibitory effect on rice blast, and 33 strains had the ability to dissolve phosphorus, potassium, or fix nitrogen. Through potted experiment, the three bacterial strains, 499G2 (Peribacillus simplex), 499G3 (Bacillus velezensis), and 499G4 (B. megaterium) have a positive effect on the growth of cultivated rice in addition to the resistance to rice blast. The contents of total nitrogen, total phosphorus, total potassium, indole acetic acid (IAA), and chlorophyll in plant leaves were increased. In addition, in the verification test of rice blast infection, the application of inoculants can significantly reduce the content of malondialdehyde (MDA), increase the content of soluble sugar, and increase the activity of plant antioxidant enzymes, which may thereby improve rice in resisting to rice blast. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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15 pages, 5166 KiB

Open AccessArticle

The Common and Unique Pattern of Microbiome Profiles among Saliva, Tissue, and Stool Samples in Patients with Crohn’s Disease

by Seung Yong Shin, Sounkou Kim, Ji Won Choi, Sang-Bum Kang, Tae Oh Kim, Geom Seog Seo, Jae Myung Cha, Jaeyoung Chun, Yunho Jung, Jong Pil Im, Ki Bae Bang, Chang Hwan Choi, Soo-Kyung Park and Dong Il Park

Microorganisms 2022, 10(7), 1467; https://doi.org/10.3390/microorganisms10071467 - 20 Jul 2022

Cited by 4 | Viewed by 2637

Abstract

This study aimed to elucidate common and unique microbiome patterns in saliva, intestinal tissue biopsy, and stool samples from patients with Crohn’s disease (CD). Saliva, tissue, and stool samples from patients with CD were prospectively collected. Quantitative and phylogenetic analyses of 16s rRNA [...] Read more.

This study aimed to elucidate common and unique microbiome patterns in saliva, intestinal tissue biopsy, and stool samples from patients with Crohn’s disease (CD). Saliva, tissue, and stool samples from patients with CD were prospectively collected. Quantitative and phylogenetic analyses of 16s rRNA sequencing data were performed with bioinformatical pipelines. A total of 30 patients were enrolled in this study. The composition of major microbial taxa was similar between tissue and stool samples. A total of 11 of the 20 most abundant microbiota were found in both samples. The microbial community in saliva was significantly distinct from that in tissue and stool. The major species of microbiota and their composition also differed significantly from those of tissue and stool samples. However, Streptococcus and Prevotella are common genera in saliva, tissue, and stool microbiome. The abundance of Streptococcus, Pantoea, and Actinomyces from the saliva sample group were significantly different, varying with the location of the inflammation. Saliva has a distinct microbial community compared with tissues and stools in patients with CD. Prevotella and Streptococcus, which are commonly observed in saliva, stool, and tissue, can be considered a potential biomarker related to the diagnosis or prognosis of CD. Full article

(This article belongs to the Special Issue Role of Beneficial Microbiota in the Prevention and Treatment of Disease)

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14 pages, 2524 KiB

Open AccessArticle

Role of Dissimilative Pathway of Komagataella phaffii (Pichia pastoris): Formaldehyde Toxicity and Energy Metabolism

by Julio Berrios, Chrispian W. Theron, Sébastien Steels, Belén Ponce, Edgar Velastegui, Cristina Bustos, Claudia Altamirano and Patrick Fickers

Microorganisms 2022, 10(7), 1466; https://doi.org/10.3390/microorganisms10071466 - 20 Jul 2022

Cited by 12 | Viewed by 3074

Abstract

Komagataella phaffii (aka Pichia pastoris) is a yeast able to grow in methanol as the sole carbon and energy source. This substrate is converted into formaldehyde, a toxic intermediary that can either be assimilated to biomass or dissimilated to CO₂ through [...] Read more.

Komagataella phaffii (aka Pichia pastoris) is a yeast able to grow in methanol as the sole carbon and energy source. This substrate is converted into formaldehyde, a toxic intermediary that can either be assimilated to biomass or dissimilated to CO₂ through the enzymes formaldehyde dehydrogenase (FLD) and formate dehydrogenase, also producing energy in the form of NADH. The dissimilative pathway has been described as an energy producing and a detoxifying route, but conclusive evidence has not been provided for this. In order to elucidate this theory, we generated mutants lacking the FLD activity (Δfld1) and used flux analysis to evaluate the metabolic impact of this disrupted pathway. Unexpectedly, we found that the specific growth rate of the Δfld1 strain was only slightly lower (92%) than the control. In contrast, the sensitivity to formaldehyde pulses (up to 8mM) was significantly higher in the Δfld1 mutant strain and was associated with a higher maintenance energy. In addition, the intracellular flux estimation revealed a high metabolic flexibility of K. phaffii in response to the disrupted pathway. Our results suggest that the role of the dissimilative pathway is mainly to protect the cells from the harmful effect of formaldehyde, as they were able to compensate for the energy provided from this pathway when disrupted. Full article

(This article belongs to the Section Microbial Biotechnology)

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18 pages, 7118 KiB

Open AccessArticle

A Comprehensive View of Microbial Communities in the Laundering Cycle Suggests a Preventive Effect of Soil Bacteria on Malodour Formation

by Marc-Kevin Zinn, Hans-Curt Flemming and Dirk Bockmühl

Microorganisms 2022, 10(7), 1465; https://doi.org/10.3390/microorganisms10071465 - 20 Jul 2022

Cited by 8 | Viewed by 2743

Abstract

Microorganisms are an important factor in the wash-and-use cycle of textiles since they can cause unwanted aesthetic effects, such as malodour formation, and even pose health risks. In this regard, a comprehensive view of the microbial communities in washing machines and consideration of [...] Read more.

Microorganisms are an important factor in the wash-and-use cycle of textiles since they can cause unwanted aesthetic effects, such as malodour formation, and even pose health risks. In this regard, a comprehensive view of the microbial communities in washing machines and consideration of the microbial contamination of used textiles is needed to understand the formation of malodour and evaluate the infection risk related to laundering. So far, neither the compositions of washing machine biofilms leading to the formation of or protection against malodour have been investigated intensively, nor have microbial communities on used towels been analysed after normal use. Our results link the qualitative and quantitative analysis of microbial communities in washing machines and on used towels with the occurrence of malodour and thus not only allow for a better risk evaluation but also suggest bacterial colonizers of washing machines that might prevent malodour formation. It was shown that soil bacteria such as Rhizobium, Agrobacterium, Bosea, and Microbacterium in particular are found in non-odourous machines, and that Rhizobium species are able to prevent malodour formation in an in vitro model. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 3172 KiB

Open AccessArticle

Exploiting the Potential of Bioreactors for Creating Spatial Organization in the Soil Microbiome: A Strategy for Increasing Sustainable Agricultural Practices

by Carlos Fernando Gutiérrez, Nicolás Rodríguez-Romero, Siobhon Egan, Elaine Holmes and Janeth Sanabria

Microorganisms 2022, 10(7), 1464; https://doi.org/10.3390/microorganisms10071464 - 20 Jul 2022

Cited by 3 | Viewed by 3080

Abstract

Industrial production of synthetic nitrogen fertilizers and their crop application have caused considerable environmental impacts. Some eco-friendly alternatives try to solve them but raise some restrictions. We tested a novel method to produce a nitrogen bioinoculant by enriching a soil microbial community in [...] Read more.

Industrial production of synthetic nitrogen fertilizers and their crop application have caused considerable environmental impacts. Some eco-friendly alternatives try to solve them but raise some restrictions. We tested a novel method to produce a nitrogen bioinoculant by enriching a soil microbial community in bioreactors supplying N₂ by air pumping. The biomass enriched with diazotrophic bacteria was diluted and applied to N-depleted and sterilized soil of tomato plants. We estimated microbial composition and diversity by 16S rRNA metabarcoding from soil and bioreactors at different run times and during plant uprooting. Bioreactors promoted the N-fixing microbial community and revealed a hided diversity. One hundred twenty-four (124) operational taxonomic units (OTUs) were assigned to bacteria with a greater Shannon diversity during the reactor’s steady state. A total of 753 OTUs were found in the rhizospheres with higher biodiversity when the lowest concentration of bacteria was applied. The apparent bacterial abundance in the batch and continuous bioreactors suggested a more specific functional ecological organization. We demonstrate the usefulness of bioreactors to evidence hidden diversity in the soil when it passes through bioreactors. By obtaining the same growth of inoculated plants and the control with chemical synthesis fertilizers, we evidence the potential of the methodology that we have called directed bioprospecting to grow a complex nitrogen-fixing microbial community. The simplicity of the reactor’s operation makes its application promising for developing countries with low technological progress. Full article

(This article belongs to the Special Issue Microbial Biotechnology in Agriculture)

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12 pages, 326 KiB

Open AccessOpinion

“Don’t Look Up” Your Science—Herd Immunity or Herd Mentality?

by Botond Z. Igyártó

Microorganisms 2022, 10(7), 1463; https://doi.org/10.3390/microorganisms10071463 - 20 Jul 2022

Cited by 2 | Viewed by 8563

Abstract

This analysis piece will attempt to examine some of the critical pandemic-related measures implemented in the United States from an immunological perspective and pinpoint caveats that should have been considered before their implementation. I also discuss alternative measures grounded in scientific data that [...] Read more.

This analysis piece will attempt to examine some of the critical pandemic-related measures implemented in the United States from an immunological perspective and pinpoint caveats that should have been considered before their implementation. I also discuss alternative measures grounded in scientific data that were not thoroughly explored and likely could have helped fight the pandemic. Full article

(This article belongs to the Special Issue COVID-19: Antivirals and Vaccines)

14 pages, 3296 KiB

Open AccessEditor’s ChoiceArticle

In Vitro and In Silico Analysis of the Inhibitory Activity of EGCG-Stearate against Herpes Simplex Virus-2

by James D. Stamos, Lee H. Lee, Calvin Taylor, Tony Elias and Sandra D. Adams

Microorganisms 2022, 10(7), 1462; https://doi.org/10.3390/microorganisms10071462 - 20 Jul 2022

Cited by 4 | Viewed by 3696

Abstract

About half a billion people worldwide are infected with herpes simplex virus-2 (HSV-2). Prolonged treatment with acyclovir (ACV) and its analogs leads to the development of resistant strains. The aim of this study was to investigate the antiviral potential of epigallocatechin gallate (EGCG) [...] Read more.

About half a billion people worldwide are infected with herpes simplex virus-2 (HSV-2). Prolonged treatment with acyclovir (ACV) and its analogs leads to the development of resistant strains. The aim of this study was to investigate the antiviral potential of epigallocatechin gallate (EGCG) from Camellia sinensis and a stable analog EGCG-stearate (EGCG-S) against HSV-2 in cultured Vero cells. Cell viability and cell proliferation assays were used to determine the non-cytotoxic concentrations on cultured Vero cells. HSV-2 with a green fluorescent protein (GFP) fusion protein of VP26 virions were treated with non-cytotoxic concentrations of EGCG and EGCG-S. The effects on infectivity and mechanisms were determined by plaque assay, attachment and penetration assays, confocal microscopy, qPCR, and in silico modeling analysis. Our results demonstrate that treatment of HSV-2 virions with EGCG and EGCG-S at a concentration of 75 µM showed greater than 99.9% inhibition by inhibiting the attachment of HSV-2 virions to host cells. The bioinformatic analysis indicated high binding affinity of EGCG-S for glycoprotein D; thus EGCG-S may block fusion of HSV-2 and the cell membrane, preventing entry of HSV-2 into the cell. Full article

(This article belongs to the Special Issue Emerging Viruses and Antiviral Drugs)

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3 pages, 219 KiB

Open AccessEditorial

Special Issue: Type III Secretion Systems in Human/Animal Pathogenic Bacteria

by Joaquín Bernal-Bayard and Francisco Ramos-Morales

Microorganisms 2022, 10(7), 1461; https://doi.org/10.3390/microorganisms10071461 - 20 Jul 2022

Viewed by 1711

Abstract

Type III secretion systems (T3SSs) are molecular devices that are essential for the communication of many Gram-negative bacteria with their eukaryotic hosts [...] Full article

(This article belongs to the Special Issue Type III Secretion Systems in Human/Animal Pathogenic Bacteria)

18 pages, 4049 KiB

Open AccessArticle

Conidial Emulsion Formulation and Thermal Storability of Metarhizium anisopliae against Red Palm Weevil, Rhynchophorusferrugineus Olivier (Coleoptera: Dryophthoridae)

by Cheong Jia Lei, Najihah Abdul Halim, Norhayu Asib, Azlina Zakaria and Wahizatul Afzan Azmi

Microorganisms 2022, 10(7), 1460; https://doi.org/10.3390/microorganisms10071460 - 19 Jul 2022

Cited by 11 | Viewed by 2981

Abstract

Industrial crops including coconut palm and other palm species are seriously infested by red palm weevil (RPW), resulting in significant economic damage globally. Therefore, this study aimed to develop a mycoinsecticide utilizing conidia of Metarhizium anisopliae to control RPW and sought to investigate [...] Read more.

Industrial crops including coconut palm and other palm species are seriously infested by red palm weevil (RPW), resulting in significant economic damage globally. Therefore, this study aimed to develop a mycoinsecticide utilizing conidia of Metarhizium anisopliae to control RPW and sought to investigate a new emulsion formulation for the influences of storage temperature and heat stress on conidia germination in an oil-in-glycerol emulsion system. The mycoinsecticide is an emulsion formulation which comprises an oil carrier, non-ionic surfactants, water, and glycerol, which was optimized by premixing the oil and non-ionic surfactant in different weight ratios (1:0, 9:1, 8:2, 7:3, 6:4, 5:5, 4: 6, 3: 7, 2:8, 1:9, and 0:1). From three selected oil-in-glycerol formulations, F25 was more stable in storage and had a smaller particle size (between 154.3 and 236.4 nm in diameter) and stable zeta potential (above + 30 mV) with low surface tension (29.83 ± 0.24 mN/m to 30.72 ± 0.11 mN/m at room temperature. Extended conidial viability was observed at 4 °C overall; the emulsion formulation maintained 12–15% conidial viability until the eighth week at room temperature. Heat of over 30 °C showed an inhibitory effect on conidial germination. This study revealed that the oil-in-glycerol formulation was stable and able to prolong conidial shelf life as compared to non-formulated conidia. Full article

(This article belongs to the Special Issue Microorganisms as Biocontrol Agents)

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14 pages, 2046 KiB

Open AccessArticle

Metagenomic Analysis of the Species Composition and Seasonal Distribution of Marine Dinoflagellate Communities in Four Korean Coastal Regions

by Jinik Hwang, Hee Woong Kang, Seung Joo Moon, Jun-Ho Hyung, Eun Sun Lee and Jaeyeon Park

Microorganisms 2022, 10(7), 1459; https://doi.org/10.3390/microorganisms10071459 - 19 Jul 2022

Cited by 3 | Viewed by 2118

Abstract

Biomonitoring of dinoflagellate communities in marine ecosystems is essential for efficient water quality management and limiting ecosystem disturbances. Current identification and monitoring of toxic dinoflagellates, which cause harmful algal blooms, primarily involves light or scanning electron microscopy; however, these techniques are limited in [...] Read more.

Biomonitoring of dinoflagellate communities in marine ecosystems is essential for efficient water quality management and limiting ecosystem disturbances. Current identification and monitoring of toxic dinoflagellates, which cause harmful algal blooms, primarily involves light or scanning electron microscopy; however, these techniques are limited in their ability to monitor dinoflagellates and plankton, leaving an incomplete analysis. In this study, we analyzed the species composition and seasonal distribution of the dinoflagellate communities in four Korean coastal regions using 18S rRNA amplicon sequencing. The results showed significantly high diversity in the dinoflagellate communities in all regions and seasons. Furthermore, we found seasonally dominant species and causative species of harmful algal blooms (Cochlodinium sp., Alexandrium sp., Dinophysis sp., and Gymnodinium sp.). Moreover, dominant species were classified by region and season according to the difference in geographical and environmental parameters. The molecular analysis of the dinoflagellate community based on metagenomics revealed more diverse species compositions that could not be identified by microscopy and revealed potentially harmful or recently introduced dinoflagellate species. In conclusion, metagenomic analysis of dinoflagellate communities was more precise and obtained results faster than microscopic analysis, and could improve the existing monitoring techniques for community analysis. Full article

(This article belongs to the Special Issue Dinoflagellate Biology: Using Molecular Approaches to Unlock Their Ecology and Evolution

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21 pages, 2463 KiB

Open AccessArticle

Soil pH, Calcium Content and Bacteria as Major Factors Responsible for the Distribution of the Known Fraction of the DNA Bacteriophage Populations in Soils of Luxembourg

by Perrine Florent, Henry-Michel Cauchie, Malte Herold, Stéphan Jacquet and Leslie Ogorzaly

Microorganisms 2022, 10(7), 1458; https://doi.org/10.3390/microorganisms10071458 - 19 Jul 2022

Cited by 6 | Viewed by 3098

Abstract

Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence [...] Read more.

Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence of bacteriophages is now recognized; however, it has been mainly studied under experimental conditions. This study aimed to determine whether the abiotic factors well-known to influence bacteriophage persistence also control the natural distribution of the known DNA bacteriophage populations. To this end, soil from eight study sites including forests and grasslands located in the Attert River basin (Grand Duchy of Luxembourg) were sampled, covering different soil and land cover characteristics. Shotgun metagenomics, reference-based bioinformatics and statistical analyses allowed characterising the diversity of known DNA bacteriophage and bacterial communities. After combining soil properties with the identified DNA bacteriophage populations, our in-situ study highlighted the influence of pH and calcium cations on the diversity of the known fraction of the soil DNA bacteriophages. More interestingly, significant relationships were established between bacteriophage and bacterial populations. This study provides new insights into the importance of abiotic and biotic factors in the distribution of DNA bacteriophages and the natural ecology of terrestrial bacteriophages. Full article

(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)

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27 pages, 1445 KiB

Open AccessReview

Impact of Environmental Pollutants on Gut Microbiome and Mental Health via the Gut–Brain Axis

by Samradhi Singh, Poonam Sharma, Namrata Pal, Manoj Kumawat, Swasti Shubham, Devojit Kumar Sarma, Rajnarayan R. Tiwari, Manoj Kumar and Ravinder Nagpal

Microorganisms 2022, 10(7), 1457; https://doi.org/10.3390/microorganisms10071457 - 19 Jul 2022

Cited by 47 | Viewed by 11449

Abstract

Over the last few years, the microbiome has emerged as a high-priority research area to discover missing links between brain health and gut dysbiosis. Emerging evidence suggests that the commensal gut microbiome is an important regulator of the gut–brain axis and plays a [...] Read more.

Over the last few years, the microbiome has emerged as a high-priority research area to discover missing links between brain health and gut dysbiosis. Emerging evidence suggests that the commensal gut microbiome is an important regulator of the gut–brain axis and plays a critical role in brain physiology. Engaging microbiome-generated metabolites such as short-chain fatty acids, the immune system, the enteric nervous system, the endocrine system (including the HPA axis), tryptophan metabolism or the vagus nerve plays a crucial role in communication between the gut microbes and the brain. Humans are exposed to a wide range of pollutants in everyday life that impact our intestinal microbiota and manipulate the bidirectional communication between the gut and the brain, resulting in predisposition to psychiatric or neurological disorders. However, the interaction between xenobiotics, microbiota and neurotoxicity has yet to be completely investigated. Although research into the precise processes of the microbiota–gut–brain axis is growing rapidly, comprehending the implications of environmental contaminants remains challenging. In these milieus, we herein discuss how various environmental pollutants such as phthalates, heavy metals, Bisphenol A and particulate matter may alter the intricate microbiota–gut–brain axis thereby impacting our neurological and overall mental health. Full article

(This article belongs to the Special Issue Host-Associated Microbiome and the Diet-Gut-Brain Axis)

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13 pages, 2581 KiB

Open AccessArticle

Effects of Inhibitors Generated by Dilute Phosphoric Acid Plus Steam-Exploded Poplar on Saccharomyces cerevisiae Growth

by Yanan Wang, Peng Zhan, Lishu Shao, Lin Zhang and Yan Qing

Microorganisms 2022, 10(7), 1456; https://doi.org/10.3390/microorganisms10071456 - 19 Jul 2022

Cited by 3 | Viewed by 1685

Abstract

The pretreatment of lignocellulosic biomass is important for efficient bioethanol conversion, but causes undesirable by-products that inhibit microbial growth, conversely affecting the bioconversion efficiency. In this study, the main inhibitors derived from dilute phosphoric acid plus steam-exploded poplar wood were identified as 0.22 [...] Read more.

The pretreatment of lignocellulosic biomass is important for efficient bioethanol conversion, but causes undesirable by-products that inhibit microbial growth, conversely affecting the bioconversion efficiency. In this study, the main inhibitors derived from dilute phosphoric acid plus steam-exploded poplar wood were identified as 0.22 g/L furfural, 3.63 g/L acetic acid, 0.08 g/L syringaldehyde, etc., indicating the green nature and low toxicity of the pretreatment process. The effects of the three typical inhibitors (furfural, acetic acid, and syringaldehyde) on Saccharomyces cerevisiae 1517RM growth were analyzed and shown to prolong the lag phase of microbial growth to different degrees. In all the inhibitor groups, the ergosterol secretion was boosted, indicating low cell membrane fluidity and robustness of the strain to an adverse environment. The cell electronegativity and morphology of S. cerevisiae 1517RM also changed under different growth conditions, which was helpful for monitoring the physicochemical properties of cells. Furfural, acetic acid, and syringaldehyde had a synergistic effect on each other, providing an important reference to improving the subsequent ethanol fermentation process. Full article

(This article belongs to the Special Issue Microbes for Production of Biofuels and Bio-Products 2.0)

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22 pages, 5146 KiB

Open AccessArticle

Yeast Diversity during Spontaneous Fermentations and Oenological Characterisation of Indigenous Saccharomyces cerevisiae for Potential as Wine Starter Cultures

by Yu Chen, Jiao Jiang, Yaoyao Song, Xiaomin Zang, Guoping Wang, Yingfang Pei, Yuyang Song, Yi Qin and Yanlin Liu

Microorganisms 2022, 10(7), 1455; https://doi.org/10.3390/microorganisms10071455 - 19 Jul 2022

Cited by 18 | Viewed by 2598

Abstract

Diversity of regional yeast can be influenced by geography, grape cultivars and the use of SO₂, but at single vineyard scale in China, the impact of these factors on yeast population, particularly Saccharomyces cerevisiae, is not well studied. Here, we characterised [...] Read more.

Diversity of regional yeast can be influenced by geography, grape cultivars and the use of SO₂, but at single vineyard scale in China, the impact of these factors on yeast population, particularly Saccharomyces cerevisiae, is not well studied. Here, we characterised yeast species and dynamics during spontaneous fermentations with/without SO₂ using eight typical grape cultivars from Yuma vineyard in Ningxia wine region of China. Results show that distribution and abundance of yeast species varied by grape varieties, fermentation stage and SO₂ treatment. A number of 290 S. cerevisiae isolates were further classified into 33 genotypes by Interdelta fingerprinting. A prevailing role of grape varieties in shaping the genetic divergence of S. cerevisiae in Yuma vineyard was observed, as compared to the impacts of fermentation stage and SO₂ treatment. Pre-selected S. cerevisiae strains were subjected to vinification with Cabernet Sauvignon and Chardonnay. All strains completed fermentations but the physiochemical parameters and volatile profiles of wines were strain-specific. Some indigenous S. cerevisiae yielded more desirable aroma compounds compared to the commercial strains, among which NX16 and NX18 outcompeted others, therefore having potential for use as starters. This study provides comprehensive analysis on yeast diversity at vineyard scale in Ningxia. Information on the vinification using indigenous S. cerevisiae is of great value for improving Ningxia wine regionality. Full article

(This article belongs to the Section Food Microbiology)

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24 pages, 2395 KiB

Open AccessReview

Mycobacterium abscessus: It’s Complex

by Hazem F. M. Abdelaal, Edward D. Chan, Lisa Young, Susan L. Baldwin and Rhea N. Coler

Microorganisms 2022, 10(7), 1454; https://doi.org/10.3390/microorganisms10071454 - 19 Jul 2022

Cited by 24 | Viewed by 9530

Abstract

Mycobacterium abscessus (M. abscessus) is an opportunistic pathogen usually colonizing abnormal lung airways and is often seen in patients with cystic fibrosis. Currently, there is no vaccine available for M. abscessus in clinical development. The treatment of M. abscessus-related pulmonary [...] Read more.

Mycobacterium abscessus (M. abscessus) is an opportunistic pathogen usually colonizing abnormal lung airways and is often seen in patients with cystic fibrosis. Currently, there is no vaccine available for M. abscessus in clinical development. The treatment of M. abscessus-related pulmonary diseases is peculiar due to intrinsic resistance to several commonly used antibiotics. The development of either prophylactic or therapeutic interventions for M. abscessus pulmonary infections is hindered by the absence of an adequate experimental animal model. In this review, we outline the critical elements related to M. abscessus virulence mechanisms, host–pathogen interactions, and treatment challenges associated with M. abscessus pulmonary infections. The challenges of effectively combating this pathogen include developing appropriate preclinical animal models of infection, developing proper diagnostics, and designing novel strategies for treating drug-resistant M. abscessus. Full article

(This article belongs to the Special Issue Novel Models Targetting Vaccines and Drugs for M. tuberculosis, M. avium and M. absessus Infection)

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12 pages, 1226 KiB

Open AccessArticle

Evaluation of Intestinal Microbial Metabolites in Preterm Infants with Different Initial Feeding Methods by In Vitro Fermentation Modeling System

by Yunwei Li, Jingjing Jiang, Liying Zhu, Xin Wang, Weilin Wan, Danhua Wang and Zhenghong Li

Microorganisms 2022, 10(7), 1453; https://doi.org/10.3390/microorganisms10071453 - 19 Jul 2022

Viewed by 1937

Abstract

We aim to explore the intestinal microbial metabolites in preterm infants with noninvasive methods and analyze the effects of initial feeding methods. Preterm infants with gestational weeks lower than 34 were recruited for fecal sample collection every 7 days. Fecal pH, ammonia, bile [...] Read more.

We aim to explore the intestinal microbial metabolites in preterm infants with noninvasive methods and analyze the effects of initial feeding methods. Preterm infants with gestational weeks lower than 34 were recruited for fecal sample collection every 7 days. Fecal pH, ammonia, bile acid, and secretory IgA (sIgA) were tested. A 1:10 fecal slurry was inoculated into different culture media containing different carbohydrates as the only carbon source: lactose (LAT), fructooligosaccharide (FOS), galactooligosaccharide (GOS), and 2′-fucosyllactose (FL2). After 24 h of anaerobic culture through an in vitro fermentation system, air pressure difference, carbohydrate degradation rate, and short-chain fatty acids (SCFAs) content in fermentation pots were measured. Preterm infants were assigned into two groups: group A, preterm infants fed by human milk, including mother’s own milk and donor human milk (DHM); group B, preterm infants fed by preterm formula at first 3 days and fed by human milk (including mother’s own milk and DHM) from day 4 to discharge. Group A included 90 samples and group B included 70 samples. Group A had lower fecal pH (p = 0.023), ammonia (p = 0.001), and bile acids (p = 0.025). Group B also had higher fecal sIgA levels, both in OD (p = 0.046) and concentration (p < 0.0001) methods. Carbohydrates degradation rates in group A were higher than group B, especially in LAT medium (p = 0.017) and GOS medium (p = 0.005). Gas production amount had no significant difference in all four media. Several different SCFAs in four kinds of different culture media in group A were higher than in group B, but valeric acid was lower in group A. The initial feeding methods may affect the preterm infants’ intestinal microecology and microbial metabolites for at least several weeks. Full article

(This article belongs to the Special Issue Gut Microbiome Modulation and Its Consequences to Infant Development)

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7 pages, 544 KiB

Open AccessProtocol

Effectiveness and Efficacy of Thermoformed and 3D Printed Aligners in Correcting Malocclusion (Spacing) and Its Impact on Periodontal Oral Health and Oral Microbiome: A Double-Blinded Parallel Randomized Controlled Multicenter Clinical Trial

by Shahnawaz Khijmatgar, Margherita Tumedei, Massimo Del Fabbro and Gianluca Martino Tartaglia

Microorganisms 2022, 10(7), 1452; https://doi.org/10.3390/microorganisms10071452 - 19 Jul 2022

Cited by 2 | Viewed by 2133

Abstract

Aligners are the common devices used in orthodontics for the correction of malocclusion. Various materials and techniques are employed to fabricate aligners. One of those includes thermoformed and 3D aligners. These aligners can be worn for several days, and their impact on periodontal [...] Read more.

Aligners are the common devices used in orthodontics for the correction of malocclusion. Various materials and techniques are employed to fabricate aligners. One of those includes thermoformed and 3D aligners. These aligners can be worn for several days, and their impact on periodontal health is not known. Therefore, the aim of our protocol is to determine the effectiveness of these aligners in correcting malocclusion and their impact on periodontal health and oral microbiome. A double-blinded randomized controlled clinical trial with a total of n = 60 patients will be included with n = 30 in each group (Test: 3D printed aligners and Control: Thermoformed). The evaluation of oral health indices such as basic periodontal examination (BPE), periodontal screening and recording (PSR) that provide the status of periodontal health will be recorded. The oral microbiome assessment will be conducted with polymerase chain reaction (PCR). The primary endpoint will be the correction of malocclusion, and the secondary end point will be the status of periodontal health and oral microbiome. The duration of follow-up for each group will be 7 days for periodontal health and oral microbiome and 6 months for the space closure of 5 mm by 3D and thermoformed aligners. Full article

(This article belongs to the Special Issue Customized Minimally Invasive Protocols for the Clinical and Microbiological Management of the Oral Microbiota)

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14 pages, 11773 KiB

Open AccessArticle

A Chikungunya Virus Multiepitope Recombinant Protein Expressed from the Binary System Insect Cell/Recombinant Baculovirus Is Useful for Laboratorial Diagnosis of Chikungunya

by Leonardo Assis da Silva, Monique da Rocha Queiroz Lima, Brenda Rabello de Camargo, Dyeferson Kened da Silva Coelho Guimarães, Anabele Azevedo Lima Barbastefano, Raquel Curtinhas de Lima, Paulo Vieira Damasco, Rivaldo Venâncio da Cunha, Luiz José de Souza, Elzinandes Leal de Azeredo, Luzia Maria de-Oliveira-Pinto, Tatsuya Nagata, Daniel M. P. Ardisson-Araújo, Flavia Barreto dos Santos and Bergmann Morais Ribeiro

Microorganisms 2022, 10(7), 1451; https://doi.org/10.3390/microorganisms10071451 - 18 Jul 2022

Cited by 3 | Viewed by 2298

Abstract

Chikungunya virus (CHIKV) is an arbovirus currently distributed worldwide, causing a disease that shares clinical signs and symptoms with other illnesses, such as dengue and Zika and leading to a challenging clinical differential diagnosis. In Brazil, CHIKV emerged in 2014 with the simultaneous [...] Read more.

Chikungunya virus (CHIKV) is an arbovirus currently distributed worldwide, causing a disease that shares clinical signs and symptoms with other illnesses, such as dengue and Zika and leading to a challenging clinical differential diagnosis. In Brazil, CHIKV emerged in 2014 with the simultaneous introduction of both Asian and East/Central/South African (ECSA) genotypes. Laboratorial diagnosis of CHIKV is mainly performed by molecular and serological assays, with the latter more widely used. Although many commercial kits are available, their costs are still high for many underdeveloped and developing countries where the virus circulates. Here we described the development and evaluation of a multi-epitope recombinant protein-based IgG-ELISA (MULTREC IgG-ELISA) test for the specific detection of anti-CHIKV antibodies in clinical samples, as an alternative approach for laboratorial diagnosis. The MULTREC IgG-ELISA showed 86.36% of sensitivity and 100% of specificity, and no cross-reactivity with other exanthematic diseases was observed. The recombinant protein was expressed from the binary system insect cell/baculovirus using the crystal-forming baculoviral protein polyhedrin as a carrier of the target recombinant protein to facilitate recovery. The crystals were at least 10 times smaller in size and had an amorphous shape when compared to the polyhedrin wild-type crystal. The assay uses a multi-epitope antigen, representing two replicates of 18 amino acid sequences from the E2 region and a sequence of 17 amino acids from the nsP3 region of CHIKV. The recombinant protein was highly expressed, easy to purify and has demonstrated its usefulness in confirming chikungunya exposure, indeed showing a good potential tool for epidemiological surveillance. Full article

(This article belongs to the Special Issue Arboviruses)

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13 pages, 847 KiB

Open AccessReview

Viral Vector Vaccine Development and Application during the COVID-19 Pandemic

by Shaofeng Deng, Hui Liang, Pin Chen, Yuwan Li, Zhaoyao Li, Shuangqi Fan, Keke Wu, Xiaowen Li, Wenxian Chen, Yuwei Qin, Lin Yi and Jinding Chen

Microorganisms 2022, 10(7), 1450; https://doi.org/10.3390/microorganisms10071450 - 18 Jul 2022

Cited by 48 | Viewed by 12436

Abstract

With the accumulation of mutations in SARS-CoV-2 and the continuous emergence of new variants, the importance of developing safer and effective vaccines has become more prominent in combating the COVID-19 pandemic. Both traditional and genetically engineered vaccines have contributed to the prevention and [...] Read more.

With the accumulation of mutations in SARS-CoV-2 and the continuous emergence of new variants, the importance of developing safer and effective vaccines has become more prominent in combating the COVID-19 pandemic. Both traditional and genetically engineered vaccines have contributed to the prevention and control of the pandemic. However, in recent years, the trend of vaccination research has gradually transitioned from traditional to genetically engineered vaccines, with the development of viral vector vaccines attracting increasing attention. Viral vector vaccines have several unique advantages compared to other vaccine platforms. The spread of Omicron has also made the development of intranasal viral vector vaccines more urgent, as the infection site of Omicron is more prominent in the upper respiratory tract. Therefore, the present review focuses on the development of viral vector vaccines and their application during the COVID-19 pandemic. Full article

(This article belongs to the Special Issue Recent Advances in Antivirals for Emerging Viruses 2.0)

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9 pages, 956 KiB

Open AccessCommunication

Achromobacter Species: An Emerging Cause of Community-Onset Bloodstream Infections

by Burcu Isler, David L. Paterson, Patrick N. A. Harris, Weiping Ling, Felicity Edwards, Claire M. Rickard, Timothy J. Kidd, Ian Gassiep and Kevin B. Laupland

Microorganisms 2022, 10(7), 1449; https://doi.org/10.3390/microorganisms10071449 - 18 Jul 2022

Cited by 7 | Viewed by 1891

Abstract

Background: Case reports and small series indicate that Achromobacter species bloodstream infection (BSI) is most commonly a complication of hospitalization among patients with chronic lung disease. The aim of the present study was to determine the incidence, risk factors, and outcomes of Achromobacter [...] Read more.

Background: Case reports and small series indicate that Achromobacter species bloodstream infection (BSI) is most commonly a complication of hospitalization among patients with chronic lung disease. The aim of the present study was to determine the incidence, risk factors, and outcomes of Achromobacter sp. BSI in an Australian population. Methods: Retrospective, laboratory-based surveillance was conducted in Queensland, Australia (population ≈ 5 million) during 2000–2019. Clinical and outcome data were obtained by linkage to state hospital admissions and vital statistics databases. BSI diagnosed within the community or within the first two calendar days of stay in hospital were classified as community-onset. Community-onset BSIs were grouped into community-associated and healthcare-associated. Results: During more than 86 million person-years of surveillance, 210 incidents of Achromobacter sp. BSI occurred among 195 individuals for an overall age-and sex-standardized annual incidence of 2.6 per million residents. Older individuals and males were at highest risk (2.9 vs. 2.0 per million, IRR for males 1.5; 95% CI, 1.1–1.9; p = 0.008). Most (153; 73%) cases were of community-onset of which 100 (48%) and 53 (25%) were healthcare- and community-associated, respectively. An increasing proportion of community-onset cases were observed during twenty years of surveillance. Underlying medical illnesses were common with median (interquartile range) Charlson Comorbidity Index (CCI) scores of 3 (1–5). CCI scores of 0, 1, 2, and 3+ were observed in 37 (18%), 27 (13%), 40 (19%), and 105 (50%) of cases, respectively. All but one of the cases were admitted to hospital for a median (interquartile range) length of stay of 12 (5–34) days. All-cause case–fatality rates in hospital by day 30 and by day 90 were 30 (14%), 28 (13%), and 42 (20%), respectively. The 90-day case–fatality rate increased with increasing comorbidity and was 3% (1/37), 11% (3/27), 25% (10/40), and 27% (28/105) among those with Charlson Comorbidity Indices of 0, 1, 2, and 3+, respectively (p = 0.004). Conclusions: Although comorbidity is an important determinant of risk, most Achromobacter sp. BSI are of community-onset and one-fifth of cases occur in patients without significant underlying chronic co-morbidities. This study highlights the value of population-based methodologies to define the epidemiology of an infectious disease. Full article

(This article belongs to the Special Issue Achromobacter spp: New Insights in Epidemiology, Pathogenicity, and Antimicrobial Therapy)

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