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23 pages, 1876 KB  
Article
Red Pepper Powder Enhances Antioxidant and Immune Functions in the Sea Urchin Strongylocentrotus intermedius: Potential as a Functional Feed in Aquaculture
by Jiadong Guo, Yuntian Zhang, Yi Chen, Yupeng Zhang, Rongwei Zhang, Yuzhe Han, Xiaoran Zhao and Tongjun Ren
Antioxidants 2025, 14(10), 1173; https://doi.org/10.3390/antiox14101173 - 26 Sep 2025
Viewed by 676
Abstract
Driven by the concept of sustainable aquaculture, natural feed additives with growth-promoting, antioxidant, and immune-enhancing properties have become a key research focus. This study assessed the effects of dietary red pepper powder (Capsicum annuum) supplementation at 0%, 0.5%, 1.0%, and 2.0% [...] Read more.
Driven by the concept of sustainable aquaculture, natural feed additives with growth-promoting, antioxidant, and immune-enhancing properties have become a key research focus. This study assessed the effects of dietary red pepper powder (Capsicum annuum) supplementation at 0%, 0.5%, 1.0%, and 2.0% over 50 days on the growth, digestive function, immune and antioxidant capacities, intestinal microbiota, and gene expression in Strongylocentrotus intermedius (S. intermedius). The results indicated that red pepper powder significantly promoted growth and decreased the feed conversion ratio (FCR) (p < 0.05), with the 1.0% group showing the highest growth rate. Additionally, supplementation improved gonadal coloration and increased crude protein and lipid contents in the gonads, particularly in the 1.0% and 2.0% groups (p < 0.05). Supplementation with 1.0% and 2.0% red pepper powder enhanced digestive, immune, and antioxidant enzyme activities, while reducing malondialdehyde (MDA) levels, indicating lower lipid peroxidation. α-diversity analysis revealed the highest ACE, Chao, and Shannon indices and the lowest Simpson index in the 1.0% group, indicating greater microbial diversity. Community analysis revealed that in the red pepper powder treatment groups, beneficial bacteria, such as Firmicutes and Unclassified_f__Rhodobacteraceae, increased in relative abundance, while potential pathogens like Arcobacter, and Epsilonbacteraeota were less abundant. Red pepper powder supplementation upregulated key immune- and antioxidant-related genes while downregulating pro-inflammatory and stress-associated genes. Overall, optimal dietary supplementation of red pepper powder, particularly at 1.0%, enhanced antioxidant and immune functions, optimized intestinal microbiota, mitigated oxidative stress, and consequently promoted growth, improved gonadal quality, and strengthened overall health in S. intermedius. Full article
(This article belongs to the Special Issue Antioxidants Benefits in Aquaculture—3rd Edition)
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15 pages, 881 KB  
Article
Prevalence and Resistance Patterns of Campylobacter spp. and Arcobacter spp. in Portuguese Water Bodies
by Igor Venâncio, Inês Martins, Rodrigo M. Martins, Mónica Oleastro and Susana Ferreira
Water 2025, 17(18), 2767; https://doi.org/10.3390/w17182767 - 18 Sep 2025
Viewed by 453
Abstract
Campylobacter spp. and Arcobacter spp. are recognized etiological agents of gastroenteritis worldwide. While poultry is their best-known reservoir, human exposure can also occur via environmental pathways, particularly through contaminated water sources, which play a significant role in their transmission dynamics. In addition to [...] Read more.
Campylobacter spp. and Arcobacter spp. are recognized etiological agents of gastroenteritis worldwide. While poultry is their best-known reservoir, human exposure can also occur via environmental pathways, particularly through contaminated water sources, which play a significant role in their transmission dynamics. In addition to their pathogenicity and widespread environmental prevalence, increasing antibiotic resistance has contributed to the global emergence of multidrug-resistant strains, hindering effective treatment. Here, the distribution and antibiotic resistance potential of Campylobacter spp. and Arcobacter spp. isolates collected from water bodies in Portugal were investigated. Water samples were collected from rivers, their tributaries, and springs, at 25 sites over a six-month period. Campylobacter spp. were isolated from 13.3% of the samples, whereas Arcobacter spp. were detected in 57.6% of the samples. Of the 27 isolated Campylobacter isolates, 44.0% were resistant to at least one antibiotic, while only one strain exhibited a multidrug-resistant (MDR) phenotype. In contrast, 98.9% of the 177 Arcobacter isolates were resistant to at least one antibiotic, with 15.8% classified as MDR. These findings contribute to the surveillance of Campylobacter spp. and Arcobacter spp., highlighting the critical role of aquatic environments in their epidemiology and supporting the need to incorporate waterborne transmission pathways into integrated surveillance and control strategies within the One Health framework. Full article
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22 pages, 826 KB  
Review
Inactivation of Emerging Opportunistic Foodborne Pathogens Cronobacter spp. and Arcobacter spp. on Fresh Fruit and Vegetable Products: Effects of Emerging Chemical and Physical Methods in Model and Real Food Systems—A Review
by Junior Bernardo Molina-Hernandez, Beatrice Cellini, Fatemeh Shanbeh Zadeh, Lucia Vannini, Pietro Rocculi and Silvia Tappi
Foods 2025, 14(14), 2463; https://doi.org/10.3390/foods14142463 - 14 Jul 2025
Viewed by 1441
Abstract
The consumption of fresh fruit and vegetables is essential for a healthy diet as they contain a diverse composition of vitamins, minerals, fibre, and bioactive compounds. However, cross-contamination during harvest and post-harvest poses a high risk of microbial contamination. Therefore, handling fruit and [...] Read more.
The consumption of fresh fruit and vegetables is essential for a healthy diet as they contain a diverse composition of vitamins, minerals, fibre, and bioactive compounds. However, cross-contamination during harvest and post-harvest poses a high risk of microbial contamination. Therefore, handling fruit and vegetables during processing and contact with wet equipment and utensil surfaces is an ideal environment for microbial contamination and foodborne illness. Nevertheless, less attention has been paid to some emerging pathogens that are now increasingly recognised as transmissible to humans through contaminated fruit and vegetables, such as Arcobacter and Cronobacter species in various products, which are the main risk in fruit and vegetables. Cronobacter and Arcobacter spp. are recognised food-safety hazards because they pose a risk of foodborne disease, especially in vulnerable groups such as newborns and immunocompromised individuals. Cronobacter spp. have been linked to severe infant conditions—notably meningitis and sepsis—most often traced to contaminated powdered infant formula. Although Arcobacter spp. have been less extensively studied, they have also been associated with foodborne disease, chiefly from dairy products and meat. With this in mind, this review provides an overview of the main chemical and physical sanitisation methods in terms of their ability to reduce the contamination of fresh fruit and vegetable products caused by two emerging pathogens: Arcobacter and Cronobacter. Emerging chemical (organic acid compounds, extracts, and essential oils) and physical methods (combination of UV-C with electrolysed water, ultrasound, and cold atmospheric plasma) offer innovative and environmentally friendly alternatives to traditional approaches. These methods often utilise natural materials, less toxic solvents, and novel techniques, resulting in more sustainable processes compared with traditional methods that may use harsh chemicals and environmentally harmful processes. This review provides the fruit and vegetable industry with a general overview of possible decontamination alternatives to develop optimal and efficient processes that ensure food safety. Full article
(This article belongs to the Section Food Engineering and Technology)
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18 pages, 3598 KB  
Article
Molecular and Genetic Characterization of Arcobacter Species Isolated from Chicken Feces and Chicken Giblets from Grenada, West Indies
by Jacqueline Paige Coughlin, Andy Alhassan, Alfred Chikweto, Rohini Roopnarine and Bhumika Sharma
Microorganisms 2025, 13(7), 1495; https://doi.org/10.3390/microorganisms13071495 - 26 Jun 2025
Viewed by 1491
Abstract
This study aimed to isolate and genetically characterize Arcobacter species from broiler chickens sampled at three slaughterhouses in Grenada, West Indies. A total of 126 samples—including cloacal swabs, intestinal contents, and meat—from 42 birds were cultured using a chromogenic agar medium. Arcobacter spp. [...] Read more.
This study aimed to isolate and genetically characterize Arcobacter species from broiler chickens sampled at three slaughterhouses in Grenada, West Indies. A total of 126 samples—including cloacal swabs, intestinal contents, and meat—from 42 birds were cultured using a chromogenic agar medium. Arcobacter spp. were detected in 21.4% (9/42) of the birds. Among the sample types, meat exhibited the highest prevalence at 14.3% (6/42), followed by fecal samples at 7.1% (3/42) and cloacal swabs at 2.4% (1/42). Genus- and species-specific polymerase chain reaction assays on 33 isolates identified five Arcobacter species: A. butzleri, A. cryaerophilus, and A. skirrowii (each 18.2%), as well as A. cibarius and A. thereius (each 6.1%). Genetic diversity was further assessed via Enterobacterial Repetitive Intergenic Consensus–polymerase chain reaction, which revealed 13 distinct genotypic fingerprints forming six clusters, with a high discriminatory power (D = 0.96). This study represents the first documented isolation and molecular characterization of five Arcobacter species from broiler chickens in Grenada across multiple sample types. These findings underscore the zoonotic implications of isolating Arcobacter spp., particularly in contaminated poultry meat destined for human consumption. The presence of Arcobacter spp. in poultry carcasses poses a significant public health concern. To mitigate this public health risk, recommendations include surveillance for the presence of this pathogen in Hazard Analysis and Critical Control Points plans or other tools used to identify pathogens compromising food safety and public health. Full article
(This article belongs to the Section Food Microbiology)
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12 pages, 1115 KB  
Article
Evidence of Exposure to Multiple Zoonotic Pathogens in Humans in Lusaka, Zambia: Insights from Metagenomic Next-Generation Sequencing
by Samuel Munalula Munjita, John Tembo, Walter Muleya and Matthew Bates
Zoonotic Dis. 2025, 5(2), 13; https://doi.org/10.3390/zoonoticdis5020013 - 16 May 2025
Viewed by 997
Abstract
Zoonotic diseases present a growing public health challenge, particularly in sub-Saharan Africa (SSA) due to close interactions between humans and animals and poor diagnostic capacity. This pilot study investigated human exposure to zoonotic pathogens in Zambia among 47 suspected COVID-19 patients from whom [...] Read more.
Zoonotic diseases present a growing public health challenge, particularly in sub-Saharan Africa (SSA) due to close interactions between humans and animals and poor diagnostic capacity. This pilot study investigated human exposure to zoonotic pathogens in Zambia among 47 suspected COVID-19 patients from whom nasopharyngeal samples were collected between November 2020 and February 2021 at two major COVID-19 referral centers in Lusaka. Using metagenomic next-generation sequencing (mNGS), the study identified a diverse range of pathogens, including bacterial, fungal, viral, and parasitic species. The prevalence of zoonotic pathogens was 57.4%. Noteworthy zoonoses included Bacillus anthracis, Sporothrix schenckii, Listeria monocytogenes, Yersinia pestis, Streptococcus suis, Vibrio parahaemolyticus, Brucella melitensis, Rickettsia prowazekii, Shewanella algae, Rickettsia japonica, Coxiella burnetii, Leptospira borgpetersenii, Erysipelothrix rhusiopathiae, Brucella abortus, Bartonella quintana, Banna virus, Vibrio alginolyticus, Bartonella clarridgeiae, Rickettsia canadensis, Leishmania braziliensis, Trypanosoma brucei, Pasteurella multocida, and Arcobacter butzleri. Despite moderate diversity in the microbial community, no significant demographic or health-related factors, including age, gender, or comorbidities such as HIV, were found to be statistically associated with zoonotic pathogen infection. The findings provide valuable data on the presence of zoonotic pathogens in humans in Zambia and highlight the need for more comprehensive research into zoonotic diseases in both clinical and non-clinical settings. Full article
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19 pages, 2362 KB  
Article
Respiratory and Enteric Bacterial Pathogens in Municipal Wastewater: A Potential Risk of Infection to Workers
by Evida Poopedi, Tanusha Singh and Annancietar Gomba
Water 2025, 17(2), 268; https://doi.org/10.3390/w17020268 - 18 Jan 2025
Cited by 1 | Viewed by 1974
Abstract
Investigating human pathogens in wastewater is crucial for identifying and predicting potential occupational health risks faced by wastewater treatment plant (WWTP) workers. This study aimed to determine the occurrence and levels of Legionella pneumophila, Mycobacterium spp., Arcobacter butzleri, and Aeromonas hydrophila [...] Read more.
Investigating human pathogens in wastewater is crucial for identifying and predicting potential occupational health risks faced by wastewater treatment plant (WWTP) workers. This study aimed to determine the occurrence and levels of Legionella pneumophila, Mycobacterium spp., Arcobacter butzleri, and Aeromonas hydrophila in untreated municipal wastewater. Grab influent, activated sludge, and secondary settling tank (SST) effluent samples were collected bi-weekly over 6 months from 5 WWTPs in Tshwane, South Africa. Mycobacterium spp., A. butzleri, and A. hydrophila were detected using quantitative PCR (qPCR), while Legionella was detected using both a culture method and qPCR. The four pathogens were identified in most samples at varying levels. Legionella pneumophila had a positivity rate of 92%, ranging from 2 to 5.4 log10 MPN/100 mL. Detection rates of Legionella spp., L. pneumophila, and L. pneumophila serogroup 1 were 97%, 75%, and 69%, respectively, with up to 5.3 log10 gene copies (GC)/mL. Importantly, this study demonstrates molecular typing of L. pneumophila serogroup 1 in wastewater, a topic that has been rarely documented. Mycobacterium spp. were detected in all samples at varying levels (log10 GC/mL) in influent (2.8–7.6), activated sludge (4.8–8.9), and SST effluent (3.8–8.9) samples. Arcobacter butzleri and A. hydrophila were detected in 96% and 82% of the samples, respectively, with GC levels in influent, activated sludge, and SST effluent ranging from 0.8 to 6.6, 1.5 to 6.5, and 0.7 to 6.6 log10 GC/mL for A. butzleri, and similar levels for A. hydrophila. These findings underscore the presence of respiratory and enteric pathogens at various treatment points, suggesting potential occupational exposure for WWTP workers. This emphasises the need for microbiological risk assessments (RAs) or reviewing existing RAs and implementing necessary control measures to protect WWTP workers. Full article
(This article belongs to the Section Wastewater Treatment and Reuse)
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22 pages, 11558 KB  
Article
Chemical Composition and Antibacterial Effect of Clove and Thyme Essential Oils on Growth Inhibition and Biofilm Formation of Arcobacter spp. and Other Bacteria
by Leona Hofmeisterová, Tomáš Bajer, Maciej Walczak and David Šilha
Antibiotics 2024, 13(12), 1232; https://doi.org/10.3390/antibiotics13121232 - 20 Dec 2024
Cited by 2 | Viewed by 3329
Abstract
Background: In recent years, significant resistance of microorganisms to antibiotics has been observed. A biofilm is a structure that significantly aids the survival of the microbial population and also significantly affects its resistance. Methods: Thyme and clove essential oils (EOs) were subjected to [...] Read more.
Background: In recent years, significant resistance of microorganisms to antibiotics has been observed. A biofilm is a structure that significantly aids the survival of the microbial population and also significantly affects its resistance. Methods: Thyme and clove essential oils (EOs) were subjected to chemical analysis using gas chromatography coupled to mass spectrometry (GC-MS) and gas chromatography with a flame ionization detector (GC-FID). Furthermore, the antimicrobial effect of these EOs was tested in both the liquid and vapor phases using the volatilization method. The effect of the EOs on growth parameters was monitored using an RTS-8 bioreactor. However, the effect of the EOs on the biofilm formation of commonly occurring bacteria with pathogenic potential was also monitored, but for less described and yet clinically important strains of Arcobacter spp. Results: In total, 37 and 28 compounds were identified in the thyme and clove EO samples, respectively. The most common were terpenes and also derivatives of phenolic substances. Both EOs exhibited antimicrobial activity in the liquid and/or vapor phase against at least some strains. The determined antimicrobial activity of thyme and clove oil was in the range of 32–1024 µg/mL in the liquid phase and 512–1024 µg/mL in the vapor phase, respectively. The results of the antimicrobial effect are also supported by similar conclusions from monitoring growth curves using the RTS bioreactor. The effect of EOs on biofilm formation differed between strains. Biofilm formation of Pseudomonas aeruginosa was completely suppressed in an environment with a thyme EO concentration of 1024 µg/mL. On the other hand, increased biofilm formation was found, e.g., in an environment of low concentration (1–32 µg/mL). Conclusions: The potential of using natural matrices as antimicrobials or preservatives is evident. The effect of these EOs on biofilm formation, especially Arcobacter strains, is described for the first time. Full article
(This article belongs to the Special Issue Microbial Biofilms: Identification, Resistance and Novel Drugs)
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13 pages, 1880 KB  
Article
Depuration of Aliarcobacter butzleri and Malaciobacter molluscorum in Comparison with Escherichia coli in Mussels (Mytilus galloprovincialis) and Oysters (Crassostrea gigas)
by Nuria Salas-Massó, Ana Fernández-Bravo, Edgar Bertomeu, Karl B. Andree, Maria José Figueras and Dolors Furones
Pathogens 2024, 13(11), 973; https://doi.org/10.3390/pathogens13110973 - 7 Nov 2024
Cited by 1 | Viewed by 1192
Abstract
Arcobacter-related species are considered emerging food-borne and waterborne pathogens, with shellfish being a suggested reservoir. In a published study that investigated 204 shellfish samples and 476 isolates, the species Arcobacter butzleri (now known as Aliarcobacter butzleri) and Arcobacter molluscorum (now known [...] Read more.
Arcobacter-related species are considered emerging food-borne and waterborne pathogens, with shellfish being a suggested reservoir. In a published study that investigated 204 shellfish samples and 476 isolates, the species Arcobacter butzleri (now known as Aliarcobacter butzleri) and Arcobacter molluscorum (now known as Malaciobacter molluscorum) have been isolated as the most dominant species. However, the efficiency of depuration for eliminating A. butzleri and M. molluscorum in comparison with Escherichia coli from mussels and oysters is unknown and is therefore the objective of this investigation. The shellfish depuration process was evaluated in the laboratory, in summer and winter, using mussels and oysters collected from the Ebro Delta harvesting areas after performing a natural contamination and an artificial contamination using the same conditions for both mollusk and seasons. The natural contamination was performed by exposing the shellfish to a freshwater channel that receives untreated sewage from the village of Poble Nou (PNC) and that had a salinity of 10.7–16.8‰. The artificial contamination exposed the shellfish to A. butzleri and E. coli (in one tank) and to M. molluscorum and E. coli in another tank under controlled conditions of salinity (34.5‰) and temperature (20 °C summer and 14 °C winter). When evaluating the reduction in the bacteria load (every 24 h) throughout 120 h, the naturally contaminated shellfish at the PNC showed a higher reduction than the shellfish contaminated at the laboratory, with the exception of M. molluscorum, that at 24 h could not be detected in summer, neither in mussels nor in oysters. This may be attributed to the fact that the bacteria from the PNC were less adapted to the conditions of high salinity (34.5‰) in which the depuration process was performed. Although temperature did not statistically make a difference in depuration, at 20 °C a higher elimination of all bacteria was recorded relative to 14 °C. In general, E. coli survived more in mussels than in oysters, and M. molluscorum suffered in both mollusks a higher reduction than A. butzleri. New studies are required to determine further the safety of bivalves regarding the presence of Arcobacter-related species. Full article
(This article belongs to the Special Issue Current Research on Host–Pathogen Interaction in 2024)
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13 pages, 4061 KB  
Review
Arcobacteraceae: An Exploration of Antibiotic Resistance Featuring the Latest Research Updates
by Davide Buzzanca, Elisabetta Chiarini and Valentina Alessandria
Antibiotics 2024, 13(7), 669; https://doi.org/10.3390/antibiotics13070669 - 18 Jul 2024
Cited by 5 | Viewed by 2551
Abstract
The Arcobacteraceae bacterial family includes species isolated from animals and related food products. Moreover, these species have been found in other ecological niches, including water. Some species, particularly Arcobacter butzleri and Arcobacter cryaerophilus, have been isolated from human clinical cases and linked [...] Read more.
The Arcobacteraceae bacterial family includes species isolated from animals and related food products. Moreover, these species have been found in other ecological niches, including water. Some species, particularly Arcobacter butzleri and Arcobacter cryaerophilus, have been isolated from human clinical cases and linked to gastrointestinal symptoms. The presence of antibiotic-resistant strains is a concern for public health, considering the possible zoonoses and foodborne infections caused by contaminated food containing bacteria resistant to antibiotic treatments. This review aims to highlight the importance of antibiotic resistance in Arcobacter spp. isolates from several sources, including information about antibiotic classes to which this bacterium has shown resistance. Arcobacter spp. demonstrated a wide spectrum of antibiotic resistance, including several antibiotic resistance genes. Antibiotic resistance genomic traits include efflux pumps and mutations in antibiotic target proteins. The literature shows a high proportion of Arcobacter spp. that are multidrug-resistant. However, studies in the literature have primarily focused on the evaluation of antibiotic resistance in A. butzleri and A. cryaerophilus, as these species are frequently isolated from various sources. These aspects underline the necessity of studies focused on several Arcobacter species that could potentially be isolated from several sources. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Zoonoses, 2nd Edition)
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17 pages, 5477 KB  
Article
Comparative Analysis of Bacterial Information of Biofilms and Activated Sludge in Full-Scale MBBR-IFAS Systems
by Xiaolin Zhou, Haicheng Liu, Xing Fan, Xuyi Wang, Xuejun Bi, Lihua Cheng, Shujuan Huang, Fangchao Zhao and Tang Yang
Microorganisms 2024, 12(6), 1121; https://doi.org/10.3390/microorganisms12061121 - 31 May 2024
Cited by 1 | Viewed by 1718
Abstract
This study extensively analyzed the bacterial information of biofilms and activated sludge in oxic reactors of full-scale moving bed biofilm reactor-integrated fixed-film activated sludge (MBBR-IFAS) systems. The bacterial communities of biofilms and activated sludge differed statistically (R = 0.624, p < 0.01). The [...] Read more.
This study extensively analyzed the bacterial information of biofilms and activated sludge in oxic reactors of full-scale moving bed biofilm reactor-integrated fixed-film activated sludge (MBBR-IFAS) systems. The bacterial communities of biofilms and activated sludge differed statistically (R = 0.624, p < 0.01). The denitrifying genera Ignavibacterium, Phaeodactylibacter, Terrimonas, and Arcobacter were more abundant in activated sludge (p < 0.05), while comammox Nitrospira was more abundant in biofilms (p < 0.05), with an average relative abundance of 8.13%. Nitrospira and Nitrosomonas had weak co-occurrence relationships with other genera in the MBBR-IFAS systems. Potential function analysis revealed no differences in pathways at levels 1 and 2 based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) between biofilms and activated sludge. However, in terms of pathways at level 3, biofilms had more potential in 26 pathways, including various organic biodegradation and membrane and signal transportation pathways. In comparison, activated sludge had more potential in only five pathways, including glycan biosynthesis and metabolism. With respect to nitrogen metabolism, biofilms had greater potential for nitrification (ammonia oxidation) (M00528), and complete nitrification (comammox) (M00804) concretely accounted for methane/ammonia monooxygenase (K10944, K10945, and K10946) and hydroxylamine dehydrogenase (K10535). This study provides a theoretical basis for MBBR-IFAS systems from the perspective of microorganisms. Full article
(This article belongs to the Section Microbial Biotechnology)
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26 pages, 17083 KB  
Article
Microbial Metagenomes and Host Transcriptomes Reveal the Dynamic Changes of Rumen Gene Expression, Microbial Colonization and Co-Regulation of Mineral Element Metabolism in Yaks from Birth to Adulthood
by Yili Liu, Liangliang Ma, Daojie Riqing, Jiu Qu, Jiyong Chen, Danzeng Zhandu, Biao Li and Mingfeng Jiang
Animals 2024, 14(9), 1365; https://doi.org/10.3390/ani14091365 - 30 Apr 2024
Cited by 2 | Viewed by 2814
Abstract
Yaks are the main pillar of plateau animal husbandry and the material basis of local herdsmen’s survival. The level of mineral elements in the body is closely related to the production performance of yaks. In this study, we performed a comprehensive analysis of [...] Read more.
Yaks are the main pillar of plateau animal husbandry and the material basis of local herdsmen’s survival. The level of mineral elements in the body is closely related to the production performance of yaks. In this study, we performed a comprehensive analysis of rumen epithelial morphology, transcriptomics and metagenomics to explore the dynamics of rumen functions, microbial colonization and functional interactions in yaks from birth to adulthood. Bacteria, eukaryotes, archaea and viruses colonized the rumen of yaks from birth to adulthood, with bacteria being the majority. Bacteroidetes and Firmicutes were the dominant phyla in five developmental stages, and the abundance of genus Lactobacillus and Fusobacterium significantly decreased with age. Glycoside hydrolase (GH) genes were the most highly represented in five different developmental stages, followed by glycosyltransferases (GTs) and carbohydrate-binding modules (CBMs), where the proportion of genes coding for CBMs increased with age. Integrating host transcriptome and microbial metagenome revealed 30 gene modules related to age, muscle layer thickness, nipple length and width of yaks. Among these, the MEmagenta and MEturquoise were positively correlated with these phenotypic traits. Twenty-two host genes involved in transcriptional regulation related to metal ion binding (including potassium, sodium, calcium, zinc, iron) were positively correlated with a rumen bacterial cluster 1 composed of Alloprevotella, Paludibacter, Arcobacter, Lactobacillus, Bilophila, etc. Therefore, these studies help us to understand the interaction between rumen host and microorganisms in yaks at different ages, and further provide a reliable theoretical basis for the development of feed and mineral element supplementation for yaks at different ages. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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58 pages, 5337 KB  
Review
Opportunistic Pathogens in Drinking Water Distribution Systems—A Review
by Mark W. LeChevallier, Toby Prosser and Melita Stevens
Microorganisms 2024, 12(5), 916; https://doi.org/10.3390/microorganisms12050916 - 30 Apr 2024
Cited by 36 | Viewed by 12188
Abstract
In contrast to “frank” pathogens, like Salmonella entrocolitica, Shigella dysenteriae, and Vibrio cholerae, that always have a probability of disease, “opportunistic” pathogens are organisms that cause an infectious disease in a host with a weakened immune system and rarely in [...] Read more.
In contrast to “frank” pathogens, like Salmonella entrocolitica, Shigella dysenteriae, and Vibrio cholerae, that always have a probability of disease, “opportunistic” pathogens are organisms that cause an infectious disease in a host with a weakened immune system and rarely in a healthy host. Historically, drinking water treatment has focused on control of frank pathogens, particularly those from human or animal sources (like Giardia lamblia, Cryptosporidium parvum, or Hepatitis A virus), but in recent years outbreaks from drinking water have increasingly been due to opportunistic pathogens. Characteristics of opportunistic pathogens that make them problematic for water treatment include: (1) they are normally present in aquatic environments, (2) they grow in biofilms that protect the bacteria from disinfectants, and (3) under appropriate conditions in drinking water systems (e.g., warm water, stagnation, low disinfectant levels, etc.), these bacteria can amplify to levels that can pose a public health risk. The three most common opportunistic pathogens in drinking water systems are Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa. This report focuses on these organisms to provide information on their public health risk, occurrence in drinking water systems, susceptibility to various disinfectants, and other operational practices (like flushing and cleaning of pipes and storage tanks). In addition, information is provided on a group of nine other opportunistic pathogens that are less commonly found in drinking water systems, including Aeromonas hydrophila, Klebsiella pneumoniae, Serratia marcescens, Burkholderia pseudomallei, Acinetobacter baumannii, Stenotrophomonas maltophilia, Arcobacter butzleri, and several free-living amoebae including Naegleria fowleri and species of Acanthamoeba. The public health risk for these microbes in drinking water is still unclear, but in most cases, efforts to manage Legionella, mycobacteria, and Pseudomonas risks will also be effective for these other opportunistic pathogens. The approach to managing opportunistic pathogens in drinking water supplies focuses on controlling the growth of these organisms. Many of these microbes are normal inhabitants in biofilms in water, so the attention is less on eliminating these organisms from entering the system and more on managing their occurrence and concentrations in the pipe network. With anticipated warming trends associated with climate change, the factors that drive the growth of opportunistic pathogens in drinking water systems will likely increase. It is important, therefore, to evaluate treatment barriers and management activities for control of opportunistic pathogen risks. Controls for primary treatment, particularly for turbidity management and disinfection, should be reviewed to ensure adequacy for opportunistic pathogen control. However, the major focus for the utility’s opportunistic pathogen risk reduction plan is the management of biological activity and biofilms in the distribution system. Factors that influence the growth of microbes (primarily in biofilms) in the distribution system include, temperature, disinfectant type and concentration, nutrient levels (measured as AOC or BDOC), stagnation, flushing of pipes and cleaning of storage tank sediments, and corrosion control. Pressure management and distribution system integrity are also important to the microbial quality of water but are related more to the intrusion of contaminants into the distribution system rather than directly related to microbial growth. Summarizing the identified risk from drinking water, the availability and quality of disinfection data for treatment, and guidelines or standards for control showed that adequate information is best available for management of L. pneumophila. For L. pneumophila, the risk for this organism has been clearly established from drinking water, cases have increased worldwide, and it is one of the most identified causes of drinking water outbreaks. Water management best practices (e.g., maintenance of a disinfectant residual throughout the distribution system, flushing and cleaning of sediments in pipelines and storage tanks, among others) have been shown to be effective for control of L. pneumophila in water supplies. In addition, there are well documented management guidelines available for the control of the organism in drinking water distribution systems. By comparison, management of risks for Mycobacteria from water are less clear than for L. pneumophila. Treatment of M. avium is difficult due to its resistance to disinfection, the tendency to form clumps, and attachment to surfaces in biofilms. Additionally, there are no guidelines for management of M. avium in drinking water, and one risk assessment study suggested a low risk of infection. The role of tap water in the transmission of the other opportunistic pathogens is less clear and, in many cases, actions to manage L. pneumophila (e.g., maintenance of a disinfectant residual, flushing, cleaning of storage tanks, etc.) will also be beneficial in helping to manage these organisms as well. Full article
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14 pages, 2114 KB  
Article
A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants
by Haozhe Zhao, Mingfei Yang, Xiang Fan, Qian Gui, Hao Yi, Yigang Tong and Wei Xiao
Viruses 2024, 16(4), 535; https://doi.org/10.3390/v16040535 - 29 Mar 2024
Cited by 5 | Viewed by 3003
Abstract
The concentration of viruses in sewage sludge is significantly higher (10–1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well [...] Read more.
The concentration of viruses in sewage sludge is significantly higher (10–1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)
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15 pages, 311 KB  
Article
Microbiological and Toxicological Investigations on Bivalve Molluscs Farmed in Sicily
by Annamaria Castello, Vincenzina Alio, Gaetano Cammilleri, Sonia Sciortino, Andrea Macaluso, Vincenzo Ferrantelli, Sonia Dall’Ara, Fiorella Pino, Irene Servadei, Giuseppa Oliveri and Antonella Costa
Foods 2024, 13(4), 552; https://doi.org/10.3390/foods13040552 - 11 Feb 2024
Cited by 2 | Viewed by 2750
Abstract
Bivalves can concentrate biological and chemical pollutants, causing foodborne outbreaks whose occurrence is increasing, due to climatic and anthropic factors that are difficult to reverse, hence the need for improved surveillance. This study aimed to evaluate the hygienic qualities of bivalves sampled along [...] Read more.
Bivalves can concentrate biological and chemical pollutants, causing foodborne outbreaks whose occurrence is increasing, due to climatic and anthropic factors that are difficult to reverse, hence the need for improved surveillance. This study aimed to evaluate the hygienic qualities of bivalves sampled along the production and distribution chain in Sicily and collect useful data for consumer safety. Bacteriological and molecular analyses were performed on 254 samples of bivalves for the detection of enteropathogenic Vibrio, Arcobacter spp., Aeromonas spp., Salmonella spp., and beta-glucuronidase-positive Escherichia coli. A total of 96 out of 254 samples, collected in the production areas, were processed for algal biotoxins and heavy metals detection. Bacterial and algal contaminations were also assessed for 21 samples of water from aquaculture implants. Vibrio spp., Arcobacter spp., Aeromonas hydrophila, Salmonella spp., and Escherichia coli were detected in 106/254, 79/254, 12/254, 16/254, and 95/254 molluscs, respectively. A total of 10/96 bivalves tested positive for algal biotoxins, and metals were under the legal limit. V. alginolyticus, A. butzleri, and E. coli were detected in 5, 3, and 3 water samples, respectively. Alexandrium minutum, Dinophysis acuminata, Lingulodinium polyedra, and Pseudonitzschia spp. were detected in water samples collected with the biotoxin-containing molluscs. Traces of yessotoxins were detected in molluscs from water samples containing the corresponding producing algae. Despite the strict regulation by the European Commission over shellfish supply chain monitoring, our analyses highlighted the need for efficiency improvement. Full article
(This article belongs to the Special Issue Contaminants in Seafood: Prevention, Control, and Detection)
14 pages, 1987 KB  
Article
Host–Microbiome Interactions in a Changing Sea: The Gill Microbiome of an Invasive Oyster under Drastic Temperature Changes
by Yahala Rina Dor-Roterman, Yehuda Benayahu, Leah Reshef and Uri Gophna
Microorganisms 2024, 12(1), 197; https://doi.org/10.3390/microorganisms12010197 - 18 Jan 2024
Cited by 4 | Viewed by 1955
Abstract
The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to host health. Spondylus spinosus is an invasive Lessepsian oyster in the Eastern Mediterranean Sea that has become highly abundant while constantly expanding its range northwestward. Using 16S rRNA [...] Read more.
The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to host health. Spondylus spinosus is an invasive Lessepsian oyster in the Eastern Mediterranean Sea that has become highly abundant while constantly expanding its range northwestward. Using 16S rRNA gene amplicon sequencing, we examined how temperature affects S. spinosus oysters and their gill microbiota in a series of experiments: exposing them to the current annual seawater temperature range, to the colder temperature of the Western Mediterranean Sea, and to the elevated temperature as predicted under global warming scenarios. The bacterial genus Endozoicomonas dominated the communities of the S. spinosus, mainly upon exposure to winter-like (16 °C) temperatures. Exposure to the elevated seawater temperature resulted in a significant change in the bacterial communities, while the oysters maintained normal functioning, suggesting that the oyster may survive a seawater warming scenario. Exposure to 11 °C led to the health deterioration of the oysters, the emergence of opportunistic pathogens, such as Arcobacter, Vibrio, Colwelliaceae, and Pseudoalteromonas, and a decline in the relative abundance of Endozoicomonas, suggesting that S. spinosus might not survive Western Mediterranean Sea winters. Both the host and its gill bacteria are thus greatly affected by temperature, which could consequently restrict the range of expansion of this and other invasive oysters. Full article
(This article belongs to the Section Gut Microbiota)
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