Microorganisms

17 pages, 16644 KiB

Open AccessArticle

A Systematic Approach to Bacterial Phylogeny Using Order Level Sampling and Identification of HGT Using Network Science

by Ehdieh Khaledian, Kelly A. Brayton and Shira L. Broschat

Microorganisms 2020, 8(2), 312; https://doi.org/10.3390/microorganisms8020312 - 24 Feb 2020

Cited by 9 | Viewed by 4707

Reconstructing and visualizing phylogenetic relationships among living organisms is a fundamental challenge because not all organisms share the same genes. As a result, the first phylogenetic visualizations employed a single gene, e.g., rRNA genes, sufficiently conserved to be present in all organisms but [...] Read more.

Reconstructing and visualizing phylogenetic relationships among living organisms is a fundamental challenge because not all organisms share the same genes. As a result, the first phylogenetic visualizations employed a single gene, e.g., rRNA genes, sufficiently conserved to be present in all organisms but divergent enough to provide discrimination between groups. As more genome data became available, researchers began concatenating different combinations of genes or proteins to construct phylogenetic trees believed to be more robust because they incorporated more information. However, the genes or proteins chosen were based on ad hoc approaches. The large number of complete genome sequences available today allows the use of whole genomes to analyze relationships among organisms rather than using an ad hoc set of genes. We present a systematic approach for constructing a phylogenetic tree based on simultaneously clustering the complete proteomes of 360 bacterial species. From the homologous clusters, we identify 49 protein sequences shared by 99% of the organisms to build a tree. Of the 49 sequences, 47 have homologous sequences in both archaea and eukarya. The clusters are also used to create a network from which bacterial species with horizontally-transferred genes from other phyla are identified. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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17 pages, 1446 KiB

Open AccessArticle

Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds

by Xin Tai, Rui Li, Bao Zhang, Hao Yu, Xiao Kong, Zhihui Bai, Ye Deng, Lan Jia and Decai Jin

Microorganisms 2020, 8(2), 311; https://doi.org/10.3390/microorganisms8020311 - 24 Feb 2020

Cited by 23 | Viewed by 4031

Abstract

Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little [...] Read more.

Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems. Full article

(This article belongs to the Special Issue Wastewater Microbiology)

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15 pages, 2338 KiB

Open AccessArticle

A Potent Burkholderia Endophyte against Boxwood Blight Caused by Calonectria pseudonaviculata

by Ping Kong and Chuanxue Hong

Microorganisms 2020, 8(2), 310; https://doi.org/10.3390/microorganisms8020310 - 24 Feb 2020

Cited by 26 | Viewed by 3589

Abstract

Calonectria pseudonaviculata (Cps) poses an increasing threat to boxwood, a major nursery crop and iconic landscape plant worldwide. Here, we report on a potent biocontrol agent that produces small sage green (SSG) colonies on potato dextrose agar. SSG is a bacterial [...] Read more.

Calonectria pseudonaviculata (Cps) poses an increasing threat to boxwood, a major nursery crop and iconic landscape plant worldwide. Here, we report on a potent biocontrol agent that produces small sage green (SSG) colonies on potato dextrose agar. SSG is a bacterial strain recovered from Justin Brouwers boxwood leaves with unusual response to Cps inoculation. Water-soaked symptoms developed on leaves 2 days after inoculation then disappeared a few days later. This endophyte affected several major steps of the boxwood blight disease cycle. SSG at 10⁷ cfu/mL lysed all conidia in mixed broth culture. SSG at 10⁸ cfu/mL reduced blight incidence by >98% when applied one day before or 3 h after boxwood were inoculated with Cps. Its control efficacy decreased with decreasing bacterial concentration to 10³ cfu/mL and increasing lead time up to 20 days. When applied on diseased leaf litter under boxwood plants, SSG reduced Cps sporulation and consequently mitigated blight incidence by 90%. SSG was identified as a new member of the Burkholderia cepacia complex with distinct characters from known clinical strains. With these protective, curative, and sanitizing properties, this Burkholderia endophyte offers great promise for sustainable blight management at production and in the landscape. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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9 pages, 1161 KiB

Open AccessArticle

Polyphasic Characterisation of Cedecea colo sp. nov., a New Enteric Bacterium Isolated from the Koala Hindgut

by Jarryd M. Boath, Sudip Dakhal, Thi Thu Hao Van, Robert J. Moore, Chaitali Dekiwadia and Ian G. Macreadie

Microorganisms 2020, 8(2), 309; https://doi.org/10.3390/microorganisms8020309 - 24 Feb 2020

Cited by 9 | Viewed by 4128

Abstract

The Cedecea genus is comprised of six rarely isolated species within the Enterobacteriaceae family. Representatives are Gram-negative motile bacilli, and are typically oxidase-negative, lipase-positive and resistant to colistin and cephalothin. In this study, a putative novel Cedecea species (designated strain ZA_0188^T), [...] Read more.

The Cedecea genus is comprised of six rarely isolated species within the Enterobacteriaceae family. Representatives are Gram-negative motile bacilli, and are typically oxidase-negative, lipase-positive and resistant to colistin and cephalothin. In this study, a putative novel Cedecea species (designated strain ZA_0188^T), isolated from the koala hindgut, was characterised using a polyphasic taxonomic approach. Maximum average nucleotide identity (ANI) and 16S ribosomal RNA (rRNA) similarity scores well below thresholds of species demarcation were reported, at 81.1% and 97.9%, respectively. Multilocus phylogenetic analysis indicated strain ZA_0188^T was most similar to but divergent from recognised Cedecea species. The isolate’s genomic G+C content was determined as 53.0 mol%, >1% lower than previously reported in Cedecea. Phenotypically, strain ZA_0188^T was distinct from recognised Cedecea species such as colistin- and cephalothin-sensitive, lipase-, sorbitol-, sucrose-, and Voges-Proskauer-negative, and melibiose-, arabinose-, arginine-, and rhamnose-positive. In preliminary experiments, strain ZA_0188^T exhibited cellulase activity and high-level tolerance to eucalyptus oil compared to other enteric species surveyed. Collectively, these findings suggest that strain ZA_0188^T represents a novel enteric species, for which the name Cedecea colo is proposed. Full article

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28 pages, 2656 KiB

Open AccessReview

The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems

by Jesse R. Willis and Toni Gabaldón

Microorganisms 2020, 8(2), 308; https://doi.org/10.3390/microorganisms8020308 - 23 Feb 2020

Cited by 256 | Viewed by 42026

Abstract

The human oral cavity is home to an abundant and diverse microbial community (i.e., the oral microbiome), whose composition and roles in health and disease have been the focus of intense research in recent years. Thanks to developments in sequencing-based approaches, such as [...] Read more.

The human oral cavity is home to an abundant and diverse microbial community (i.e., the oral microbiome), whose composition and roles in health and disease have been the focus of intense research in recent years. Thanks to developments in sequencing-based approaches, such as 16S ribosomal RNA metabarcoding, whole metagenome shotgun sequencing, or meta-transcriptomics, we now can efficiently explore the diversity and roles of oral microbes, even if unculturable. Recent sequencing-based studies have charted oral ecosystems and how they change due to lifestyle or disease conditions. As studies progress, there is increasing evidence of an important role of the oral microbiome in diverse health conditions, which are not limited to diseases of the oral cavity. This, in turn, opens new avenues for microbiome-based diagnostics and therapeutics that benefit from the easy accessibility of the oral cavity for microbiome monitoring and manipulation. Yet, many challenges remain ahead. In this review, we survey the main sequencing-based methodologies that are currently used to explore the oral microbiome and highlight major findings enabled by these approaches. Finally, we discuss future prospects in the field. Full article

(This article belongs to the Special Issue Oral Microbiota in Health and Disease)

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16 pages, 2684 KiB

Open AccessArticle

Bacterial Community Structure of Pinus Thunbergii Naturally Infected by the Nematode Bursaphelenchus Xylophilus

by Yang Ma, Zhao-Lei Qu, Bing Liu, Jia-Jin Tan, Fred O. Asiegbu and Hui Sun

Microorganisms 2020, 8(2), 307; https://doi.org/10.3390/microorganisms8020307 - 23 Feb 2020

Cited by 21 | Viewed by 3549

Abstract

Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function [...] Read more.

Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p < 0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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9 pages, 238 KiB

Open AccessOpinion

Microbiological Safety and the Management of Microbial Resources in Artisanal Foods and Beverages: The Need for a Transdisciplinary Assessment to Conciliate Actual Trends and Risks Avoidance

by Vittorio Capozzi, Mariagiovanna Fragasso and Pasquale Russo

Microorganisms 2020, 8(2), 306; https://doi.org/10.3390/microorganisms8020306 - 22 Feb 2020

Cited by 50 | Viewed by 5151

Abstract

Current social and environmental trends explain the rising popularity of artisanal fermented foods and beverages. In contrast with their marketing success, several studies underline a lack of regulations necessary to claim differences occurred from the farm to the fork and to certify high [...] Read more.

Current social and environmental trends explain the rising popularity of artisanal fermented foods and beverages. In contrast with their marketing success, several studies underline a lack of regulations necessary to claim differences occurred from the farm to the fork and to certify high quality and safety standards. Microbial-based fermentative processes represent the crucial phase in the production of fermented foods and beverages. Nevertheless, what are the effects of the application of the “artisanal” category to the management of food fermentations? This opinion paper is built up on this issue by analyzing microbial aspects, instances of innovation, safety issues, and possible solutions. Evidence indicates: (i) a global curiosity to exploit food fermentations as drivers of innovation in artisanal contexts and (ii) an increasing interest of the artisanal producers into management of fermentation that relies on native microbial consortia. Unfortunately, this kind of revamp of “artisanal food microbiology,” rather than re-establishing artisanal content, can restore the scarce hygienic conditions that characterized underdeveloped food systems. We highlight that in the scientific literature, it is possible to underline existing approaches that, surpassing the dichotomy between relying on spontaneous fermentation and the use of commercial starter cultures, depict a “third way” to conjugate interest in enhancing the artisanal attributes with the need for correct management of microbial-related risks in the final products. Full article

(This article belongs to the Special Issue Artisanal Foods: Challenges for Microbiological Control and Safety)

29 pages, 1075 KiB

Open AccessReview

Pathogenicity and Virulence Factors of Fusarium graminearum Including Factors Discovered Using Next Generation Sequencing Technologies and Proteomics

by Molemi E. Rauwane, Udoka V. Ogugua, Chimdi M. Kalu, Lesiba K. Ledwaba, Adugna A. Woldesemayat and Khayalethu Ntushelo

Microorganisms 2020, 8(2), 305; https://doi.org/10.3390/microorganisms8020305 - 22 Feb 2020

Cited by 39 | Viewed by 8422

Abstract

Fusarium graminearum is a devasting mycotoxin-producing pathogen of grain crops. F. graminearum has been extensively studied to understand its pathogenicity and virulence factors. These studies gained momentum with the advent of next-generation sequencing (NGS) technologies and proteomics. NGS and proteomics have enabled the [...] Read more.

Fusarium graminearum is a devasting mycotoxin-producing pathogen of grain crops. F. graminearum has been extensively studied to understand its pathogenicity and virulence factors. These studies gained momentum with the advent of next-generation sequencing (NGS) technologies and proteomics. NGS and proteomics have enabled the discovery of a multitude of pathogenicity and virulence factors of F. graminearum. This current review aimed to trace progress made in discovering F. graminearum pathogenicity and virulence factors in general, as well as pathogenicity and virulence factors discovered using NGS, and to some extent, using proteomics. We present more than 100 discovered pathogenicity or virulence factors and conclude that although a multitude of pathogenicity and virulence factors have already been discovered, more work needs to be done to take advantage of NGS and its companion applications of proteomics. Full article

(This article belongs to the Special Issue Fusarium: Mycotoxins, Taxonomy and Pathogenicity)

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17 pages, 1363 KiB

Open AccessArticle

Daily Intake of Paraprobiotic Lactobacillus amylovorus CP1563 Improves Pre-Obese Conditions and Affects the Gut Microbial Community in Healthy Pre-Obese Subjects: A Double-Blind, Randomized, Placebo-Controlled Study

by Tomonori Sugawara, Daisuke Sawada, Sae Yanagihara, Yumeko Aoki, Isao Takehara, Hirosuke Sugahara, Tatsuhiko Hirota, Yasunori Nakamura and Susumu Ishikawa

Microorganisms 2020, 8(2), 304; https://doi.org/10.3390/microorganisms8020304 - 22 Feb 2020

Cited by 18 | Viewed by 4598

Abstract

Despite the fact that gut microbiota is closely associated with obesity, few studies have focused on the influences of paraprobiotics as food ingredients on both obesity prevention and the gut microbial community. In this study, we evaluated the effects of fragmented Lactobacillus amylovorus [...] Read more.

Despite the fact that gut microbiota is closely associated with obesity, few studies have focused on the influences of paraprobiotics as food ingredients on both obesity prevention and the gut microbial community. In this study, we evaluated the effects of fragmented Lactobacillus amylovorus CP1563 (CP1563) as a paraprobiotic for obesity prevention and investigated its effects on the gut microbial community in pre-obese subjects. One hundred sixty-nine healthy subjects with a body mass index from 25.0 to 29.9 kg/m² ingested beverages with or without the fragmented CP1563 containing 10-hydroxyoctadecanoic acid (10-HOA) for 12 weeks. The changes in abdominal, total, visceral, and subcutaneous fatty areas were significantly lower in the CP1563-10-HOA group than in the placebo group at 12 weeks. Furthermore, 16S rRNA gene sequencing of fecal DNA revealed that the changes in the abundances of the genera Roseburia and Lachnospiraceae;g were significantly greater in the CP1563-10-HOA group than in the placebo group, and the changes in the abundances of the genus Collinsella was significantly smaller in the CP1563-10HOA group than in the placebo group. Our results showed that continuous ingestion of the fragmented CP1563 containing 10-HOA reduced abdominal body fat and affected the gut microbial community in pre-obese healthy subjects. Our findings may contribute to the understanding of the relationship between the anti-obesity effect of paraprobiotics and gut microbiota. Full article

(This article belongs to the Section Medical Microbiology)

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11 pages, 618 KiB

Open AccessCommunication

Preliminary Survey of Alternaria Toxins Reduction during Fermentation of Whole Wheat Dough

by Elizabet Janić Hajnal, Lato Pezo, Dejan Orčić, Ljubiša Šarić, Dragana Plavšić, Jovana Kos and Jasna Mastilović

Microorganisms 2020, 8(2), 303; https://doi.org/10.3390/microorganisms8020303 - 21 Feb 2020

Cited by 7 | Viewed by 2698

Abstract

The aim of this study was to investigate the fate of the most common Alternaria toxins found in wheat—tenuazonic acid (TeA), alternariol (AOH), and alternariol monomethyl ether (AME) during sourdough processing. For this purpose, spiked whole wheat flour, 3% sourdough starter, 0.5% of [...] Read more.

The aim of this study was to investigate the fate of the most common Alternaria toxins found in wheat—tenuazonic acid (TeA), alternariol (AOH), and alternariol monomethyl ether (AME) during sourdough processing. For this purpose, spiked whole wheat flour, 3% sourdough starter, 0.5% of baker’s yeast, and 105% of water calculated on flour weight as a base were used as raw materials. Spiked whole wheat dough was fermented for 4 h, 8 h, 12 h, 24 h, and 48 h at 25 °C, and at each point the fermented dough samples were taken, frozen, lyophilized, grounded, and stored until further analysis. To study the effect of sourdough processing on TeA, AOH and AME content, the validated method of high-performance liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) for these mycotoxins was used. Mathematical models of Alternaria toxins reduction were developed in the form of Four Parameter Logistic Regression function. The maximum reduction of TeA, AOH, and AME levels was archived at 48 h of dough fermentation at 25 °C compared with dough after kneading (0 h). Under these conditions, a reduction of the toxin levels of 60.3 %, 41.5%, and 24.1% was observed for TeA, AOH, and AME, respectively. Full article

(This article belongs to the Special Issue Microbial Safety of Fermented Products)

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19 pages, 1083 KiB

Open AccessArticle

Carotenoids from Cyanobacteria: A Biotechnological Approach for the Topical Treatment of Psoriasis

by Graciliana Lopes, Duarte Clarinha and Vitor Vasconcelos

Microorganisms 2020, 8(2), 302; https://doi.org/10.3390/microorganisms8020302 - 21 Feb 2020

Cited by 57 | Viewed by 5941

Abstract

In this study, five cyanobacteria strains (Alkalinema aff. pantanalense LEGE15481, Cyanobium gracile LEGE12431, Nodosilinea (Leptolyngbya) antarctica LEGE13457, Cuspidothrix issatschenkoi LEGE03282 and Leptolyngbya-like sp. LEGE13412) from the Blue Biotechnology and Ecotoxicology Culture Collection (LEGE CC) of CIIMAR were explored for [...] Read more.

In this study, five cyanobacteria strains (Alkalinema aff. pantanalense LEGE15481, Cyanobium gracile LEGE12431, Nodosilinea (Leptolyngbya) antarctica LEGE13457, Cuspidothrix issatschenkoi LEGE03282 and Leptolyngbya-like sp. LEGE13412) from the Blue Biotechnology and Ecotoxicology Culture Collection (LEGE CC) of CIIMAR were explored for their biotechnological potential in the treatment of psoriasis. Different extracts were characterized for their pigment profile by HPLC-PDA. The antioxidant potential of the extracts was assessed against the superoxide anion radical (O₂^•-). Their anti-inflammatory and antiproliferative potential was assessed in vitro using the macrophages RAW 264.7 and the human keratinocytes HaCaT as cell-line models, respectively. Terrestrial and freshwater strains presented the highest carotenoid content (33193−63926 μg/g dry extract), with all-trans-β-carotene, zeaxanthin, echinenone and lutein derivatives being the most abundant carotenoids. Acetone was the most effective solvent for pigment extraction. The acetone extracts presented the lowest IC₅₀ values (0.29−0.38 mg dry extract/mL) regarding O₂^•- scavenging, and revealed anti-inflammatory potential, with N. antarctica LEGE13457, A. pantanalense LEGE15481 and Leptolyngbya-like sp. LEGE13412 reducing the nitric oxide (NO) in RAW 264.7 cell culture medium in about 25% (p < 0.05). With the exception of A. pantanalense LEGE15481, all the extracts significantly reduced keratinocyte proliferation (p < 0.05), demonstrating a selective toxicity among the different cell lines. Overall, Leptolyngbya-like sp. LEGE13412 and N. antarctica LEGE13457 seem promising for further exploitation in the framework of psoriasis, due to their antioxidant, anti-inflammatory and antiproliferative potential. Full article

(This article belongs to the Special Issue Microbial Pigments)

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19 pages, 3467 KiB

Open AccessArticle

Identification of Species and Subspecies of Lactic Acid Bacteria Present in Spanish Cheeses Type “Torta” by MALDI-TOF MS and pheS gene Analyses

by Fernando Sánchez-Juanes, Vanessa Teixeira-Martín, José Manuel González-Buitrago, Encarna Velázquez and José David Flores-Félix

Microorganisms 2020, 8(2), 301; https://doi.org/10.3390/microorganisms8020301 - 21 Feb 2020

Cited by 29 | Viewed by 4987

Abstract

Several artisanal cheeses are elaborated in European countries, being commonly curdled with rennets of animal origin. However, in some Spanish regions some cheeses of type “Torta” are elaborated using Cynara cardunculus L. rennets. Two of these cheeses, “Torta del Casar” and “Torta de [...] Read more.

Several artisanal cheeses are elaborated in European countries, being commonly curdled with rennets of animal origin. However, in some Spanish regions some cheeses of type “Torta” are elaborated using Cynara cardunculus L. rennets. Two of these cheeses, “Torta del Casar” and “Torta de Trujillo”, are elaborated in Cáceres province with ewe’s raw milk and matured over at least 60 days without starters. In this work, we identified the lactic acid bacteria present in these cheeses using MALDI-TOF MS and pheS gene analyses, which showed they belong to the species Lactobacillus curvatus, Lactobacillus diolivorans, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus rhamnosus, Lactococcus lactis and Leuconostoc mesenteroides. The pheS gene analysis also allowed the identification of the subspecies La. plantarum subsp. plantarum, La. paracasei subsp. paracasei and Le. mesenteroides subsp. jonggajibkimchii. Low similarity values were found in this gene for some currently accepted subspecies of Lc. lactis and for the two subspecies of La. plantarum, and values near to 100% for the subspecies of Le. mesenteroides and La. paracasei. These results, which were confirmed by the calculated ANIb and dDDH values of their whole genomes, showed the need to revise the taxonomic status of these species and their subspecies. Full article

(This article belongs to the Special Issue Feature Papers in Food Microbiology)

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17 pages, 5604 KiB

Open AccessArticle

Functions of Enyolreductase (ER) Domains of PKS Cluster in Lipid Synthesis and Enhancement of PUFAs Accumulation in Schizochytrium limacinum SR21 Using Triclosan as a Regulator of ER

by Xueping Ling, Hao Zhou, Qinghua Yang, Shengyang Yu, Jun Li, Zhipeng Li, Ning He, Cuixue Chen and Yinghua Lu

Microorganisms 2020, 8(2), 300; https://doi.org/10.3390/microorganisms8020300 - 21 Feb 2020

Cited by 25 | Viewed by 4829

Abstract

The polyketide synthase (PKS) cluster genes are supposed to synthesize polyunsaturated fatty acids (PUFAs) in S. limacinum. In this study, two enyolreductase (ER) genes located on PKS cluster were knocked out through homologous recombination to explore their functions. The knock-out of [...] Read more.

The polyketide synthase (PKS) cluster genes are supposed to synthesize polyunsaturated fatty acids (PUFAs) in S. limacinum. In this study, two enyolreductase (ER) genes located on PKS cluster were knocked out through homologous recombination to explore their functions. The knock-out of OrfB-ER (located on OrfB subunit) decreased lipid content and had obvious decrease on PUFAs content, indicating OrfB-ER domain played a vital role on PUFAs synthesis; the knock-out of OrfC-ER (located on OrfC subunit) decreased SFAs content and increased total lipid content, indicating OrfC-ER domain was likely to be related with SFAs synthesis, and lipid production could be improved by down-regulating OrfC-ER domain expression. Therefore, the addition of triclosan as a reported regulator of ER domain induced the increase of PUFAs production by 51.74% and lipids yield by 47.63%. Metabolic analysis indicated triclosan played its role through inhibiting the expression of OrfC-ER to reduce the feedback inhibition of SFAs and further to enhance NADPH synthesis for lipid production, and by weakening mevalonate pathway and tricarboxylic acid (TCA) cycle to shift precursors for lipid and PUFAs synthesis. This research illuminates functions of two ER domains in S. limacinum and provides a potential targets for improving lipid production. Full article

(This article belongs to the Section Microbial Biotechnology)

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18 pages, 2714 KiB

Open AccessArticle

The interaction between Carbohydrates and the Antimicrobial Peptide P-113Tri is Involved in the Killing of Candida albicans

by Guan-Yu Lin, Chuan-Fa Chang and Chung-Yu Lan

Microorganisms 2020, 8(2), 299; https://doi.org/10.3390/microorganisms8020299 - 21 Feb 2020

Cited by 8 | Viewed by 3604

Abstract

The emergence of drug resistance to Candida albicans is problematic in the clinical setting. Therefore, developing new antifungal drugs is in high demand. Our previous work indicated that the antimicrobial peptide P-113Tri exhibited higher antifungal activity against planktonic cells, biofilm cells, and clinical [...] Read more.

The emergence of drug resistance to Candida albicans is problematic in the clinical setting. Therefore, developing new antifungal drugs is in high demand. Our previous work indicated that the antimicrobial peptide P-113Tri exhibited higher antifungal activity against planktonic cells, biofilm cells, and clinical isolates of Candida species compared to its parental peptide P-113. In this study, we further investigated the difference between these two peptides in their mechanisms against C. albicans. Microscopic examination showed that P-113 rapidly gained access to C. albicans cells. However, most of the P-113Tri remained on the cell surface. Moreover, using a range of cell wall-defective mutants and competition assays, the results indicated that phosphomannan and N-linked mannan in the cell wall are important for peptide binding to C. albicans cells. Furthermore, the addition of exogenous phosphosugars reduced the efficacy of the peptide, suggesting that negatively charged phosphosugars also contributed to the peptide binding to the cell wall polysaccharides. Finally, using a glycan array, P-113Tri, but not P-113, can bind to other glycans commonly present on other microbial and mammalian cells. Together, these results suggest that P-113 and P-113Tri have fundamental differences in their interaction with C. albicans and candidacidal activities. Full article

(This article belongs to the Special Issue Antimicrobial Peptides: Therapeutic Potentials)

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7 pages, 1272 KiB

Open AccessArticle

A Rare Glimpse into the Past of the Anthrax Pathogen Bacillus anthracis

by Peter Braun, Mandy Knüpfer, Markus Antwerpen, Dagmar Triebel and Gregor Grass

Microorganisms 2020, 8(2), 298; https://doi.org/10.3390/microorganisms8020298 - 21 Feb 2020

Cited by 2 | Viewed by 4360

Abstract

The bacterium Bacillus anthracis is the causative agent of the zoonotic disease anthrax. While genomics of extant B. anthracis isolates established in-depth phylogenomic relationships, there is scarce information on the historic genomics of the pathogen. Here, we characterized the oldest documented B. anthracis [...] Read more.

The bacterium Bacillus anthracis is the causative agent of the zoonotic disease anthrax. While genomics of extant B. anthracis isolates established in-depth phylogenomic relationships, there is scarce information on the historic genomics of the pathogen. Here, we characterized the oldest documented B. anthracis specimen. The inactive 142-year-old material originated from a bovine diseased in Chemnitz (Germany) in 1878 and is contemporary with the seminal studies of Robert Koch on B. anthracis. A specifically developed isolation method yielded high-quality DNA from this specimen for genomic sequencing. The bacterial chromosome featuring 242 unique base-characters placed it into a major phylogenetic clade of B. anthracis (B.Branch CNEVA), which is typical for central Europe today. Our results support the notion that the CNEVA-clade represents part of the indigenous genetic lineage of B. anthracis in this part of Europe. This work emphasizes the value of historic specimens as precious resources for reconstructing the past phylogeny of the anthrax pathogen. Full article

(This article belongs to the Special Issue An Update on Anthrax)

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21 pages, 548 KiB

Open AccessReview

Safety Aspects of Genetically Modified Lactic Acid Bacteria

by Tina Vida Plavec and Aleš Berlec

Microorganisms 2020, 8(2), 297; https://doi.org/10.3390/microorganisms8020297 - 21 Feb 2020

Cited by 81 | Viewed by 11015

Abstract

Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of [...] Read more.

Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of various systems for their engineering. Together with novel approaches such as CRISPR-Cas, the established systems for engineering now allow significant improvements to LAB strains. Nevertheless, genetically modified LAB (GM-LAB) still encounter disapproval and are under extensive regulatory requirements. This review presents data on the prospects for LAB to obtain ‘generally recognized as safe’ (GRAS) status. Genetic modification of LAB is discussed, together with problems that can arise from their engineering, including their dissemination into the environment and the spread of antibiotic resistance markers. Possible solutions that would allow the use of GM-LAB are described, such as biocontainment, alternative selection markers, and use of homologous DNA. The use of GM-LAB as cell factories in closed systems that prevent their environmental release is the least problematic aspect, and this is also discussed. Full article

(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)

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16 pages, 2178 KiB

Open AccessArticle

DNA Methylation Changes Induced by Cold in Psychrophilic and Psychrotolerant Naganishia Yeast Species

by Benedetta Turchetti, Gianpiero Marconi, Ciro Sannino, Pietro Buzzini and Emidio Albertini

Microorganisms 2020, 8(2), 296; https://doi.org/10.3390/microorganisms8020296 - 20 Feb 2020

Cited by 10 | Viewed by 3783

Abstract

The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold [...] Read more.

The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold stress) and at optimum temperatures again, were performed. After Methylation Sensitive Amplified Polymorphism (MSAP) fingerprints a total of 550 and 423 clear and reproducible fragments were amplified from N. antarctica and N. albida strains, respectively. The two Naganishia strains showed a different response in terms of level of DNA methylation during cold stress and recovery from cold stress. The percentage of total methylated fragments in psychrophilic N. antarctica did not show any significant change. On the contrary, the methylation of psychrotolerant N. albida exhibited a nonsignificant increase during the incubation at 4 °C and continued during the recovery step, showing a significant difference if compared with control condition, resembling an uncontrolled response to cold stress. A total of 12 polymorphic fragments were selected, cloned, and sequenced. Four fragments were associated to genes encoding for elongation factor G and for chitin synthase export chaperon. To the best of our knowledge, this is the first study on DNA methylation in the response to cold stress carried out by comparing a psychrophilic and a psychrotolerant yeast species. Full article

(This article belongs to the Special Issue Non-Conventional Yeasts)

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14 pages, 3987 KiB

Open AccessArticle

Proteomic and Transcriptional Profiles of Human Stem Cell-Derived β Cells Following Enteroviral Challenge

by Julius O. Nyalwidhe, Agata Jurczyk, Basanthi Satish, Sambra Redick, Natasha Qaisar, Melanie I. Trombly, Pranitha Vangala, Riccardo Racicot, Rita Bortell, David M. Harlan, Dale L. Greiner, Michael A. Brehm, Jerry L. Nadler and Jennifer P. Wang

Microorganisms 2020, 8(2), 295; https://doi.org/10.3390/microorganisms8020295 - 20 Feb 2020

Cited by 6 | Viewed by 3887

Abstract

Enteroviral infections are implicated in islet autoimmunity and type 1 diabetes (T1D) pathogenesis. Significant β-cell stress and damage occur with viral infection, leading to cells that are dysfunctional and vulnerable to destruction. Human stem cell-derived β (SC-β) cells are insulin-producing cell clusters that [...] Read more.

Enteroviral infections are implicated in islet autoimmunity and type 1 diabetes (T1D) pathogenesis. Significant β-cell stress and damage occur with viral infection, leading to cells that are dysfunctional and vulnerable to destruction. Human stem cell-derived β (SC-β) cells are insulin-producing cell clusters that closely resemble native β cells. To better understand the events precipitated by enteroviral infection of β cells, we investigated transcriptional and proteomic changes in SC-β cells challenged with coxsackie B virus (CVB). We confirmed infection by demonstrating that viral protein colocalized with insulin-positive SC-β cells by immunostaining. Transcriptome analysis showed a decrease in insulin gene expression following infection, and combined transcriptional and proteomic analysis revealed activation of innate immune pathways, including type I interferon (IFN), IFN-stimulated genes, nuclear factor-kappa B (NF-κB) and downstream inflammatory cytokines, and major histocompatibility complex (MHC) class I. Finally, insulin release by CVB4-infected SC-β cells was impaired. These transcriptional, proteomic, and functional findings are in agreement with responses in primary human islets infected with CVB ex vivo. Human SC-β cells may serve as a surrogate for primary human islets in virus-induced diabetes models. Because human SC-β cells are more genetically tractable and accessible than primary islets, they may provide a preferred platform for investigating T1D pathogenesis and developing new treatments. Full article

(This article belongs to the Special Issue Enterovirus and Type 1 Diabetes)

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10 pages, 1031 KiB

Open AccessArticle

Occurrence, Diversity of Listeria spp. Isolates from Food and Food-Contact Surfaces and the Presence of Virulence Genes

by Franca Rossi, Carmela Amadoro, Daniele Conficoni, Valerio Giaccone and Giampaolo Colavita

Microorganisms 2020, 8(2), 294; https://doi.org/10.3390/microorganisms8020294 - 20 Feb 2020

Cited by 7 | Viewed by 3007

Abstract

This study evaluates the hazards posed by foodborne bacteria of the Listeria genus by analyzing the occurrence, diversity and virulence of Listeria spp.in food and food-manufacturing plants. Seventy-five isolates obtained from the routine analysis of 653 samples taken by three diagnostic laboratories in [...] Read more.

This study evaluates the hazards posed by foodborne bacteria of the Listeria genus by analyzing the occurrence, diversity and virulence of Listeria spp.in food and food-manufacturing plants. Seventy-five isolates obtained from the routine analysis of 653 samples taken by three diagnostic laboratories in Northern Italy were genotypically differentiated by Repetitive Extragenic Palindrome (rep) PCR, with the GTG5 primer identified by sequencing the 16S rRNA gene and examined by specific PCR tests for the presence of L. monocytogenes virulence determinants occasionally found to occur in other species of the genus. Within this sample, 76% (n = 57) isolates were identified as L. innocua, 16% (n = 12) as L. monocytogenes, 6.6% (n = 5) as L. welshimeri and 1.3% (n = 1) as L. seeligeri. All L. monocytogenes isolates belonged to the serotype 1/2a and were predicted to be virulent for the presence of the inlJ internalin gene. Potentially virulent strains of L. innocua, L. seeligeri and L. welshimeri, carrying the L. monocytogenesinlA gene and/or hly gene, were identified, and most isolates were found to possess the toxin–antitoxin system mazEF for efficient adaptation to heat shock. Results indicated the need to reinforce food-contamination-prevention measures against all Listeria species by defining efficiently their environmental distribution. Full article

(This article belongs to the Special Issue Transmission and Detection of Food and Environmental Pathogens)

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14 pages, 3232 KiB

Open AccessArticle

Discovery of Two Brominated Oxindole Alkaloids as Staphylococcal DNA Gyrase and Pyruvate Kinase Inhibitors via Inverse Virtual Screening

by Ahmed M. Sayed, Hani A. Alhadrami, Seham S. El-Hawary, Rabab Mohammed, Hossam M. Hassan, Mostafa E. Rateb, Usama Ramadan Abdelmohsen and Walid Bakeer

Microorganisms 2020, 8(2), 293; https://doi.org/10.3390/microorganisms8020293 - 20 Feb 2020

Cited by 35 | Viewed by 4491

Abstract

In the present study, a small marine-derived natural products library was assessed for antibacterial potential. Among 36 isolated compounds, a number of bis-indole derivatives exhibited growth-inhibitory activity towards Gram-positive strains (Bacillus subtilis and multidrug-resistant Staphylococcus aureus). 5- and 6-trisindoline (5-Tris [...] Read more.

In the present study, a small marine-derived natural products library was assessed for antibacterial potential. Among 36 isolated compounds, a number of bis-indole derivatives exhibited growth-inhibitory activity towards Gram-positive strains (Bacillus subtilis and multidrug-resistant Staphylococcus aureus). 5- and 6-trisindoline (5-Tris and 6-Tris) were the most active derivatives (minimum inhibitory concentration, MIC, 4–8 µM) that were subsequently selected for anti-biofilm activity evaluation. Only 5-Tris was able to inhibit the staphylococcal biofilm formation starting at a 5 µM concentration. In order to investigate their possible molecular targets, both natural products were subjected to in silico inverse virtual screening. Among 20 target proteins, DNA gyrase and pyruvate kinase were the most likely to be involved in the observed antibacterial and anti-biofilm activities of both selected natural products. The in vitro validation and in silico binding mode studies revealed that 5-Tris could act as a dual enzyme inhibitor (IC₅₀ 11.4 ± 0.03 and 6.6 ± 0.05 µM, respectively), while 6-Tris was a low micromolar gyrase-B inhibitor (IC₅₀ 2.1 ± 0.08 µM), indicating that the bromine position plays a crucial role in the determination of the antibacterial lead compound inhibitory activity. Full article

(This article belongs to the Special Issue Natural Antimicrobial Compounds)

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18 pages, 2025 KiB

Open AccessArticle

Construction of a Tetracycline Degrading Bacterial Consortium and Its Application Evaluation in Laboratory-Scale Soil Remediation

by Xueling Wu, Yichao Gu, Xiaoyan Wu, Xiangyu Zhou, Han Zhou, Charles Amanze, Li Shen and Weimin Zeng

Microorganisms 2020, 8(2), 292; https://doi.org/10.3390/microorganisms8020292 - 20 Feb 2020

Cited by 31 | Viewed by 4511

Abstract

As an environmental pollutant, tetracycline (TC) can persist in the soil for years and damage the ecosystem. So far, many methods have been developed to handle the TC contamination. Microbial remediation, which involves the use of microbes to biodegrade the pollutant, is considered [...] Read more.

As an environmental pollutant, tetracycline (TC) can persist in the soil for years and damage the ecosystem. So far, many methods have been developed to handle the TC contamination. Microbial remediation, which involves the use of microbes to biodegrade the pollutant, is considered cost-efficient and more suitable for practical application in soil. This study isolated several strains from TC-contaminated soil and constructed a TC-degrading bacterial consortium containing Raoultella sp. XY-1 and Pandoraea sp. XY-2, which exhibited better growth and improved TC degradation efficiency compared with single strain (81.72% TC was biodegraded within 12 days in Lysogeny broth (LB) medium). Subsequently, lab-scale soil remediation was conducted to evaluate its effectiveness in different soils and the environmental effects it brought. Results indicated that the most efficient TC degradation was recorded at 30 °C and in soil sample Y which had relatively low initial TC concentration (around 35 mg/kg): TC concentration decreased by 43.72% within 65 days. Soil properties were affected, for instance, at 30 °C, the pH value of soil sample Y increased to near neutral, and soil moisture content (SMC) of both soils declined. Analysis of bacterial communities at the phylum level showed that Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi were the four dominant phyla, and the relative abundance of Proteobacteria significantly increased in both soils after bioremediation. Further analysis of bacterial communities at the genus level revealed that Raoultella sp. XY-1 successfully proliferated in soil, while Pandoraea sp. XY-2 was undetectable. Moreover, bacteria associated with nitrogen cycling, biodegradation of organic pollutants, soil biochemical reactions, and plant growth were affected, causing the decline in soil bacterial diversity. Variations in the relative abundance of tetracycline resistance genes (TRGs) and mobile gene elements (MGEs) were investigated, the results obtained indicated that tetD, tetG, tetX, intI1, tnpA-04, and tnpA-05 had higher relative abundance in original soils, and the relative abundance of most TRGs and MGEs declined after the microbial remediation. Network analysis indicated that tnpA may dominate the transfer of TRGs, and Massilia, Alkanibacter, Rhizomicrobium, Xanthomonadales, Acidobacteriaceae, and Xanthomonadaceae were possible hosts of TRGs or MGEs. This study comprehensively evaluated the effectiveness and the ecological effects of the TC-degrading bacterial consortium in soil environment. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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11 pages, 3257 KiB

Open AccessArticle

A Rotational Slurry Bioreactor Accelerates Biodegradation of A-Fuel in Oil-Contaminated Soil Even under Low Temperature Conditions

by Yuna Miyoshi, Jo Okada, Tomotaka Urata, Masaki Shintani and Kazuhide Kimbara

Microorganisms 2020, 8(2), 291; https://doi.org/10.3390/microorganisms8020291 - 20 Feb 2020

Cited by 8 | Viewed by 3406

Abstract

An effective bioaugmentation system for oil-contaminated soil under low-temperature conditions was developed with a rotational slurry bioreactor. Mixtures of two Rhodococcus oil-degraders, strain A and C, which are officially permitted to be used in bioaugmentation in Japan, were inoculated and A-fuel oil was [...] Read more.

An effective bioaugmentation system for oil-contaminated soil under low-temperature conditions was developed with a rotational slurry bioreactor. Mixtures of two Rhodococcus oil-degraders, strain A and C, which are officially permitted to be used in bioaugmentation in Japan, were inoculated and A-fuel oil was added to a final concentration of 2500 and 5000 mg/kg-slurry. Decomposition tests were carried out for the inoculated samples and non-inoculated samples by rotating at 15 °C, the annual average temperature of Japan. The residue of A-fuel oil and the number of bacteria were measured every two days. After 6 days of treatment, more than 95% of the oil was removed in the inoculated samples, which was more than three times faster than a previous degradation experiment without rotation. A semi-continuous treatment was performed by removing 90% of the treated slurry, then adding the same amount of contaminated slurry into the system without additional degraders. Ninety-four percent of A-fuel oil was successfully degraded after 6 days by this repeated treatment. This could drastically reduce the cost of preparing the degraders. Strikingly, semi-continuous treatment showed oil removal in the non-inoculated samples, indicating that the rotational slurry conditions could efficiently promote biodegradation by indigenous degraders. Our rotational slurry bioreactor accelerated the removal of oil contamination without adding further degraders provides an efficient and cost-effective method of removal of A-fuel oil using a semi-continuous system, which can be used in practical applications in areas with a cooler climate. Full article

(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)

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15 pages, 730 KiB

Open AccessReview

Scientific Prospects for Cannabis-Microbiome Research to Ensure Quality and Safety of Products

by Vladimir Vujanovic, Darren R. Korber, Silva Vujanovic, Josko Vujanovic and Suha Jabaji

Microorganisms 2020, 8(2), 290; https://doi.org/10.3390/microorganisms8020290 - 20 Feb 2020

Cited by 31 | Viewed by 11685

Abstract

Cannabis legalization has occurred in several countries worldwide. Along with steadily growing research in Cannabis healthcare science, there is an increasing interest for scientific-based knowledge in plant microbiology and food science, with work connecting the plant microbiome and plant health to product quality [...] Read more.

Cannabis legalization has occurred in several countries worldwide. Along with steadily growing research in Cannabis healthcare science, there is an increasing interest for scientific-based knowledge in plant microbiology and food science, with work connecting the plant microbiome and plant health to product quality across the value chain of cannabis. This review paper provides an overview of the state of knowledge and challenges in Cannabis science, and thereby identifies critical risk management and safety issues in order to capitalize on innovations while ensuring product quality control. It highlights scientific gap areas to steer future research, with an emphasis on plant-microbiome sciences committed to using cutting-edge technologies for more efficient Cannabis production and high-quality products intended for recreational, pharmaceutical, and medicinal use. Full article

(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)

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11 pages, 3045 KiB

Open AccessArticle

Human Cytomegalovirus (HCMV) Reactivation in the Mammary Gland Induces a Proinflammatory Cytokine Shift in Breast Milk

by Tabea Rabe, Katrin Lazar, Christoffer Cambronero, Rangmar Goelz and Klaus Hamprecht

Microorganisms 2020, 8(2), 289; https://doi.org/10.3390/microorganisms8020289 - 20 Feb 2020

Cited by 21 | Viewed by 4879

Abstract

A locally restricted human cytomegalovirus (HCMV) reactivation in the mammary gland commonly occurs in nearly every IgG-seropositive breastfeeding mother. This unique phenomenon can therefore be used to study the reactivation process in an immunocompetent healthy host. Breast milk contains a variety of immunoactive [...] Read more.

A locally restricted human cytomegalovirus (HCMV) reactivation in the mammary gland commonly occurs in nearly every IgG-seropositive breastfeeding mother. This unique phenomenon can therefore be used to study the reactivation process in an immunocompetent healthy host. Breast milk contains a variety of immunoactive compounds, including immune cells, antibodies, growth factors, and cytokines supporting the newborn’s immature immune system. To characterize the impact of HCMV reactivation on breast milk cytokines, we analyzed longitudinal breast milk samples of four IgG-seropositive and three IgG-seronegative mothers of preterm infants using Proximity Extension Assay (PEA) technology (Olink Proteomics, Uppsala, Sweden). Cytokine profiling revealed elevated cytokine levels in IgG-seropositive mothers’ milk whey. Reactivating mothers showed higher levels of CC-chemokines (MCP-2, CCL19, and CCL20) and CXC-chemokines (IL-8, CXCL9, CXCL10, and CXCL11), such as the proinflammatory cytokine IL-17C, glycoprotein CD5, and TNFSF14. HCMV reactivation seems to influence the cytokine profile in human breast milk. This work could open the door for further studies analyzing distinct relations of the cytokine network as well as phenotypical and functional T cell properties in background of HCMV DNA dynamics in early lactation. Full article

(This article belongs to the Special Issue Cytomegalovirus: Biology and Infection)

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21 pages, 1260 KiB

Open AccessArticle

Antimicrobial Resistance in Members of the Bacterial Bovine Respiratory Disease Complex Isolated from Lung Tissue of Cattle Mortalities Managed with or without the Use of Antimicrobials

by Kim Stanford, Rahat Zaheer, Cassidy Klima, Tim McAllister, Delores Peters, Yan D. Niu and Brenda Ralston

Microorganisms 2020, 8(2), 288; https://doi.org/10.3390/microorganisms8020288 - 20 Feb 2020

Cited by 35 | Viewed by 4563

Abstract

Over a two-year period, Mannheimia haemolytica (MH; n = 113), Pasteurella multocida (PM; n = 47), Histophilus somni (HS; n = 41) and Mycoplasma bovis (MB; n = 227) were isolated from bovine lung tissue at necropsy from cattle raised conventionally (CON, n [...] Read more.

Over a two-year period, Mannheimia haemolytica (MH; n = 113), Pasteurella multocida (PM; n = 47), Histophilus somni (HS; n = 41) and Mycoplasma bovis (MB; n = 227) were isolated from bovine lung tissue at necropsy from cattle raised conventionally (CON, n = 29 feedlots) or without antimicrobials [natural (NAT), n = 2 feedlots]. Excluding MB, isolates were assayed by PCR to detect the presence of 13 antimicrobial resistance (AMR) genes and five core genes associated with integrative and conjugative elements (ICEs). Antimicrobial susceptibility phenotypes and minimum inhibitory concentrations (MICs, µg/mL) were determined for a subset of isolates (MH, n = 104; PM, n = 45; HS, n = 23; and MB, n = 61) using Sensititre analyses. A subset of isolates (n = 21) was also evaluated by whole-genome sequencing (WGS) based on variation in AMR phenotype. All five ICE core genes were detected in PM and HS by PCR, but only 3/5 were present in MH. Presence of mco and tnpA ICE core genes in MH was associated with higher MICs (p < 0.05) for all tetracyclines, and 2/3 of all macrolides, aminoglycosides and fluoroquinolones evaluated. In contrast, association of ICE core genes with MICs was largely restricted to macrolides for PM and to individual tetracyclines and macrolides for HS. For MH, the average number of AMR genes markedly increased (p < 0.05) in year 2 of the study due to the emergence of a strain that was PCR positive for all 13 PCR-tested AMR genes as well as two additional AMR genes (aadA31 and bla_ROB-1) detected by WGS. Conventional management of cattle increased (p < 0.05) MICs of tilmicosin and tulathromycin for MH; neomycin and spectinomycin for PM; and gamithromycin and tulathromycin for MB. The average number of PCR-detected AMR genes in PM was also increased (p < 0.05) in CON mortalities. This study demonstrates increased AMR especially to macrolides by bovine respiratory disease organisms in CON as compared to NAT feedlots and a rapid increase in AMR following dissemination of strain(s) carrying ICE-associated multidrug resistance. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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12 pages, 980 KiB

Open AccessArticle

Colistin-Resistant Acinetobacter Baumannii Bacteremia: A Serious Threat for Critically Ill Patients

by Georgios Papathanakos, Ioannis Andrianopoulos, Athanasios Papathanasiou, Efthalia Priavali, Despoina Koulenti and Vasilios Koulouras

Microorganisms 2020, 8(2), 287; https://doi.org/10.3390/microorganisms8020287 - 20 Feb 2020

Cited by 41 | Viewed by 5498

Abstract

The prevalence of acinetobacter baumannii (AB) as a cause of hospital infections has been rising. Unfortunately, emerging colistin resistance limits therapeutic options and affects the outcome. The aim of the study was to confirm our clinically-driven hypothesis that intensive care unit (ICU) patients [...] Read more.

The prevalence of acinetobacter baumannii (AB) as a cause of hospital infections has been rising. Unfortunately, emerging colistin resistance limits therapeutic options and affects the outcome. The aim of the study was to confirm our clinically-driven hypothesis that intensive care unit (ICU) patients with AB resistant-to-colistin (ABCoR) bloodstream infection (BSI) develop fulminant septic shock and die. We conducted a 28-month retrospective observational study including all patients developing AB infection on ICU admission or during ICU stay. From 622 screened patients, 31 patients with BSI sepsis were identified. Thirteen (41.9%) patients had ABCoR BSI and 18/31 (58.1%) had colistin-susceptible (ABCoS) BSI. All ABCoR BSI patients died; of them, 69% (9/13) presented with fulminant septic shock and died within the first 3 days from its onset. ABCoR BSI patients compared to ABCoS BSI patients had higher mortality (100% vs. 50%, respectively (p = 0.001)), died sooner (p = 0.006), had lower pH (p = 0.004) and higher lactate on ICU admission (p = 0.0001), and had higher APACHE II (p = 0.01) and Charlson Comorbidity Index scores (p = 0.044). In conclusion, we documented that critically ill patients with ABCoR BSI exhibit fulminant septic shock with excessive mortality. Our results highlight the emerging clinical problem of AB colistin resistance among ICU patients. Full article

(This article belongs to the Special Issue Multidrug-Resistant Pathogens)

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22 pages, 3095 KiB

Open AccessArticle

pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion

by Nina Lackner, Andreas O. Wagner, Rudolf Markt and Paul Illmer

Microorganisms 2020, 8(2), 286; https://doi.org/10.3390/microorganisms8020286 - 20 Feb 2020

Cited by 19 | Viewed by 3846

Abstract

pH is a central environmental factor influencing CH₄ production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0–8.5, phosphate buffered) and the application of a phosphate buffer per [...] Read more.

pH is a central environmental factor influencing CH₄ production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0–8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH₄ production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH₄ production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions. Full article

(This article belongs to the Special Issue Anaerobic Digestion)

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17 pages, 3884 KiB

Open AccessArticle

The Effect of Posaconazole, Itraconazole and Voriconazole in the Culture Medium on Aspergillus fumigatus Triazole Resistance

by Martyna Mroczyńska, Ewelina Kurzyk, Magdalena Śliwka-Kaszyńska, Urszula Nawrot, Marta Adamik and Anna Brillowska-Dąbrowska

Microorganisms 2020, 8(2), 285; https://doi.org/10.3390/microorganisms8020285 - 19 Feb 2020

Cited by 4 | Viewed by 3154

Abstract

Triazoles are the only compounds used as antibiotics in both medicine and agriculture. The presence of triazoles in the environment can contribute to the acquisition of azole resistance among isolates of Aspergillus fumigatus. The objective of this study was to investigate the [...] Read more.

Triazoles are the only compounds used as antibiotics in both medicine and agriculture. The presence of triazoles in the environment can contribute to the acquisition of azole resistance among isolates of Aspergillus fumigatus. The objective of this study was to investigate the effect of A. fumigatus exposure to triazoles on susceptibility to these compounds. Seventeen triazole-resistant and 21 triazole-sensitive A. fumigatus isolates were examined. The isolates were transferred 20 times on the Sabouraud medium supplemented with posaconazole, itraconazole or voriconazole, followed by five times on the medium not supplemented. The minimum inhibitory concentrations of antimycotics were examined according to the EUCAST broth microdilution method after the 20th transfer and also the 25th transfer. In addition, the expression levels of genes mdr1, mdr2, mdr3, atrF, cyp51A and cyp51B were determined. Cultivation of A. fumigatus on media supplemented with posaconazole, itraconazole and voriconazole resulted in the acquisition of resistance to the tested triazoles of all examined isolates. After recultivation on Sabouraud without azoles, most of the isolates lost their acquired resistance. The long-term use of triazole compounds in agriculture may result in the occurrence of triazole resistant A. fumigatus isolates in the environment, not only by induction or selection of mutations in the cyp51A gene, but also by contribution to changes in the gene expression. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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13 pages, 2154 KiB

Open AccessArticle

Degradation Potential of the Nonylphenol Monooxygenase of Sphingomonas sp. NP5 for Bisphenols and Their Structural Analogs

by Masahiro Takeo, Junichi Akizuki, Aika Kawasaki and Seiji Negoro

Microorganisms 2020, 8(2), 284; https://doi.org/10.3390/microorganisms8020284 - 19 Feb 2020

Cited by 21 | Viewed by 3852

Abstract

The nonylphenol-degrading bacterium Sphingomonas sp. strain NP5 has a very unique monooxygenase that can attack a wide range of 4-alkylphenols with a branched side chain. Due to the structural similarity, it can also attack bisphenolic compounds, which are very important materials for the [...] Read more.

The nonylphenol-degrading bacterium Sphingomonas sp. strain NP5 has a very unique monooxygenase that can attack a wide range of 4-alkylphenols with a branched side chain. Due to the structural similarity, it can also attack bisphenolic compounds, which are very important materials for the synthesis of plastics and resins, but many of them are known to or suspected to have endocrine disrupting effects to fish and animals. In this study, to clarify the substrate specificity of the enzyme (NmoA) for bisphenolic compounds, degradation tests using the cell suspension of Pseudomonas putida harboring the nonylphenol monooxygenase gene (nmoA) were conducted. The cell suspension degraded several bisphenols including bisphenol F, bisphenol S, 4,4′-dihydroxybenzophenone, 4,4′-dihydroxydiphenylether, and 4,4′-thiodiphenol, indicating that this monooxygenase has a broad substrate specificity for compounds with a bisphenolic structure. Full article

(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)

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22 pages, 2417 KiB

Open AccessArticle

Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus

by Mathieu K. Licht, Aaron M. Nuss, Marcel Volk, Anne Konzer, Michael Beckstette, Bork A. Berghoff and Gabriele Klug

Microorganisms 2020, 8(2), 283; https://doi.org/10.3390/microorganisms8020283 - 19 Feb 2020

Cited by 17 | Viewed by 4476

Abstract

Photosynthetic bacteria have to deal with the risk of photooxidative stress that occurs in presence of light and oxygen due to the photosensitizing activity of (bacterio-) chlorophylls. Facultative phototrophs of the genus Rhodobacter adapt the formation of photosynthetic complexes to oxygen and light [...] Read more.

Photosynthetic bacteria have to deal with the risk of photooxidative stress that occurs in presence of light and oxygen due to the photosensitizing activity of (bacterio-) chlorophylls. Facultative phototrophs of the genus Rhodobacter adapt the formation of photosynthetic complexes to oxygen and light conditions, but cannot completely avoid this stress if environmental conditions suddenly change. R. capsulatus has a stronger pigmentation and faster switches to phototrophic growth than R. sphaeroides. However, its photooxidative stress response has not been investigated. Here, we compare both species by transcriptomics and proteomics, revealing that proteins involved in oxidation–reduction processes, DNA, and protein damage repair play pivotal roles. These functions are likely universal to many phototrophs. Furthermore, the alternative sigma factors RpoE and RpoH_II are induced in both species, even though the genetic localization of the rpoE gene, the RpoE protein itself, and probably its regulon, are different. Despite sharing the same habitats, our findings also suggest individual strategies. The crtIB-tspO operon, encoding proteins for biosynthesis of carotenoid precursors and a regulator of photosynthesis, and cbiX, encoding a putative ferrochelatase, are induced in R. capsulatus. This specific response might support adaptation by maintaining high carotenoid-to-bacteriochlorophyll ratios and preventing the accumulation of porphyrin-derived photosensitizers. Full article

(This article belongs to the Special Issue Advances in the Biology of Phototrophic Bacteria)

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