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Yi S, Song H, Kim WH, Lee S, Guk JH, Woo J, Cho S. Dynamics of microbiota and antimicrobial resistance in on-farm dairy processing plants using metagenomic and culture-dependent approaches. Int J Food Microbiol 2024; 417:110704. [PMID: 38640816 DOI: 10.1016/j.ijfoodmicro.2024.110704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
On-farm dairy processing plants, which are situated close to farms and larger dairy processing facilities, face unique challenges in maintaining environmental hygiene. This can impact various stages of dairy processing. These plants operate on smaller scales and use Low-Temperature-Long-Time (LTLT) pasteurization, making them more susceptible to microbial contamination through direct and indirect contact. Antimicrobial-resistant bacteria found on dairy farms pose risks to human health by potentially transferring resistance via dairy products. Our study aimed to investigate microbial distribution and antimicrobial resistance at four key stages: the farm, pre-pasteurization, post-pasteurization, and processing environments. We assessed microbial distribution by quantifying indicator bacteria and conducting metagenomic analysis. Antimicrobial resistance was examined by identifying resistance phenotypes and detecting resistance genes in bacterial isolates and metagenomes. Our results showed that the indicator bacteria were detected at all stages of on-farm dairy processing. We observed a significant reduction in aerobic microbes and coliforms post-pasteurization. However, contamination of the final dairy products increased, suggesting potential cross-contamination during post-pasteurization. Metagenomic analysis revealed that Pseudomonas, a representative psychrotrophic bacterium, was predominant in both the farm (24.1 %) and pre-pasteurization (65.9 %) stages, indicating microbial transfer from the farms to the processing plants. Post-pasteurization, Pseudomonas and other psychrotrophs like Acinetobacter and Enterobacteriaceae remained dominant. Core microbiota analysis identified 74 genera in total, including 13 psychrotrophic bacteria, across all stages. Of the 59 strains isolated from these plants, 49 were psychrotrophic. Antimicrobial resistance analysis showed that 74.6 % (44/59) of isolates were resistant to at least one antibiotic, with cefoxitin-, ampicillin-, amoxicillin-, and ticarcillin-resistant bacteria present at all stages. Identical antimicrobial resistance patterns were observed in isolates from serial stages of the same farm and season, suggesting bacterial transmission across stages. Additionally, 27.1 % (16/59) of isolates carried plasmid-mediated resistance genes, which were also detected in the metagenomes of non-isolated samples, indicating potential antimicrobial resistance gene transmission and their presence in uncultured bacteria. These findings reveal the persistence of antimicrobial-resistant psychrotrophic bacteria in on-farm dairy processing plants, which pose potential health risks via dairy consumption. Our study underscores the importance of both culture-dependent and culture-independent methods to fully understand their distribution and impact.
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Affiliation(s)
- Saehah Yi
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Hyokeun Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Woo-Hyun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Soomin Lee
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Jae-Ho Guk
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - JungHa Woo
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea.
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Dorn-In S, Daldrup E, Mang S, Esteban-Cuesta I, Gareis M, Schwaiger K. Viable Campylobacter jejuni on Eggshells and Its Potential to Cross-contaminate Egg White and Yolk When Using a Manual Separation Technique, Determined by Culture and Propidium Monoazide (PMA) qPCR. J Food Prot 2024; 87:100246. [PMID: 38369191 DOI: 10.1016/j.jfp.2024.100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/07/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Manual separation of egg yolk from egg white using the eggshell is common practice in private households. For this, the egg is cracked and both components are separated by passing the egg yolk back and forth between the two halves of the eggshell, allowing the egg white to drip down while the egg yolk remains in the shell. During this process, the egg content naturally gets in contact with the outside of the eggshell, which might lead to a cross-contamination with its microorganisms, thus was correspondingly assessed in this study. Campylobacter jejuni is one of the most important zoonotic pathogens that can be found on eggshells. Therefore, this bacterium was used to artificially contaminate the eggshells (n = 22) with concentrations of 3.1 ± 0.6 log10 cfu/g. After separating the egg yolk from the egg white, cross-contamination was determined using culture and qPCR. Altogether, cross-contaminations with C. jejuni were found in 15 egg white (68%) and in three egg yolk (14%) samples. Afterward, 90 eggs from 30 egg packs from different producers in and around Munich (Germany) were obtained for field study purposes. To address the problem of culturing due to a possible viable but nonculturable (VBNC) status of C. jejuni, a method to differentiate viable and dead C. jejuni on eggshell using 10 µM propidium monoazide (PMA) and qPCR was developed. As a result, seven egg packs (23%) were positive for C. jejuni. Of these, only one (3%) was contaminated with viable cells, but still in a concentration of 3.3 log10 cells/g shell. According to these results and considering that eggshells might also be naturally contaminated with other pathogens, the authors recommend avoiding the manual separation technique of egg white and yolk by the eggshell. Especially if raw egg white or yolk is used for preparation of not sufficiently heated foods, where contaminating pathogens are not inactivated during processing, this technique might be a safety hazard for the consumer.
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Affiliation(s)
- Samart Dorn-In
- Unit of Food Hygiene and Technology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Eva Daldrup
- Chair of Food Safety and Analytics, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Schoenleutnerstr. 8, 85764 Oberschleissheim, Germany
| | - Sirkka Mang
- Chair of Food Safety and Analytics, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Schoenleutnerstr. 8, 85764 Oberschleissheim, Germany
| | - Irene Esteban-Cuesta
- Chair of Food Safety and Analytics, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Schoenleutnerstr. 8, 85764 Oberschleissheim, Germany
| | - Manfred Gareis
- Chair of Food Safety and Analytics, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Schoenleutnerstr. 8, 85764 Oberschleissheim, Germany
| | - Karin Schwaiger
- Unit of Food Hygiene and Technology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
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Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024; 22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024] Open
Abstract
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.
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Affiliation(s)
- Chankyung Kim
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Graduate Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Cancer and Inflammation, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Graduate Program in Geriatric and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
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Jang J, Hwang S, Oh AR, Park S, Yaseen U, Kim JG, Park S, Jung Y, Cha JY. Fructose malabsorption in ChREBP-deficient mice disrupts the small intestine immune microenvironment and leads to diarrhea-dominant bowel habit changes. Inflamm Res 2023; 72:769-782. [PMID: 36813915 DOI: 10.1007/s00011-023-01707-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND The mechanism by which incompletely absorbed fructose causes gastrointestinal symptoms is not fully understood. In this study, we investigated the immunological mechanisms of bowel habit changes associated with fructose malabsorption by examining Chrebp-knockout mice exhibiting defective fructose absorption. METHODS Mice were fed a high-fructose diet (HFrD), and stool parameters were monitored. The gene expression in the small intestine was analyzed by RNA sequencing. Intestinal immune responses were assessed. The microbiota composition was determined by 16S rRNA profiling. Antibiotics were used to assess the relevance of microbes for HFrD-induced bowel habit changes. RESULTS Chrebp-knockout (KO) mice fed HFrD showed diarrhea. Small-intestine samples from HFrD-fed Chrebp-KO mice revealed differentially expressed genes involved in the immune pathways, including IgA production. The number of IgA-producing cells in the small intestine decreased in HFrD-fed Chrebp-KO mice. These mice showed signs of increased intestinal permeability. Chrebp-KO mice fed a control diet showed intestinal bacterial imbalance, which the HFrD exaggerated. Bacterial reduction improved diarrhea-associated stool parameters and restored the decreased IgA synthesis induced in HFrD-fed Chrebp-KO mice. CONCLUSIONS The collective data indicate that gut microbiome imbalance and disrupting homeostatic intestinal immune responses account for the development of gastrointestinal symptoms induced by fructose malabsorption.
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Affiliation(s)
- Jinsun Jang
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science and Technology, Gachon University, Inchon, Korea
| | - Soonjae Hwang
- Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, 155 Gaetbeol-ro, Yeonsu-gu, Inchon, 21999, Korea
| | - Ah-Reum Oh
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science and Technology, Gachon University, Inchon, Korea.,Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, 22212, Korea
| | - Sohyeon Park
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science and Technology, Gachon University, Inchon, Korea
| | - Uzma Yaseen
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science and Technology, Gachon University, Inchon, Korea
| | - Jae Gon Kim
- Department of Microbiology, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, 155 Gaetbeol-ro, Yeonsu-gu, Inchon, 21999, Korea
| | - Sangbin Park
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science and Technology, Gachon University, Inchon, Korea
| | - YunJae Jung
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science and Technology, Gachon University, Inchon, Korea. .,Department of Microbiology, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, 155 Gaetbeol-ro, Yeonsu-gu, Inchon, 21999, Korea.
| | - Ji-Young Cha
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science and Technology, Gachon University, Inchon, Korea. .,Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, 155 Gaetbeol-ro, Yeonsu-gu, Inchon, 21999, Korea. .,Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, 22212, Korea.
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Wei D, Li Y, Che M, Li C, Wu Q, Sun C. Melatonin relieves hepatic lipid dysmetabolism caused by aging via modifying the secondary bile acid pattern of gut microbes. Cell Mol Life Sci 2022; 79:527. [PMID: 36151409 DOI: 10.1007/s00018-022-04412-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/17/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
It has been reported that aging-generated gut microecosystem may promote host hepatic lipid dysmetabolism through shaping the pattern of secondary bile acids (BAs). Then as an oral drug, melatonin (Mel)-mediated beneficial efforts on the communication between gut microbiota and aging host are still not clearly. Here, we show that aging significantly shapes the pattern of gut microbiota and BAs, whereas Mel treatment reverses these phenotypes (P < 0.05), which is identified to depend on the existence of gut microbiota. Mechanistically, aging-triggered high-level expression of ileac farnesoid X receptor (FXR) is significantly decreased through Mel-mediated inhibition on Campylobacter jejuni (C. jejuni)-induced deconjugation of tauroursodeoxycholic acid (TUDCA) and glycoursodeoxycholic acid (GUDCA) (P < 0.05). The aging-induced high-level of serum taurine chenodeoxycholic acid (TCDCA) activate trimethylamine-N-oxide (TMAO)-triggered activating transcriptional factor 4 (ATF4) signaling via hepatic FXR, which further regulates hepatic BAs metabolism, whereas TUDCA inhibits aging-triggered high-level of hepatic ATF4. Overall, Mel reduces C. jejuni-mediated deconjugation of TUDCA to inhibit aging-triggered high-level expression of hepatic FXR, which further decreases hepatic TMAO production, to relieve hepatic lipid dysmetabolism.
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Affiliation(s)
- Dongqin Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yizhou Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Meng Che
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chaowei Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qiong Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chao Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Abstract
The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.
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Liu Z, Wang K, Zhang Y, Xia L, Zhao L, Guo C, Liu X, Qin L, Hao Z. High Prevalence and Diversity Characteristics of blaNDM, mcr, and blaESBLs Harboring Multidrug-Resistant Escherichia coli From Chicken, Pig, and Cattle in China. Front Cell Infect Microbiol 2022; 11:755545. [PMID: 35198455 PMCID: PMC8859839 DOI: 10.3389/fcimb.2021.755545] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022] Open
Abstract
The objective of this study was to understand the diversity characteristics of ESBL-producing Escherichia coli (ESBL-EC) in chicken, pig, and cattle. A high prevalence of ESBL-EC (260/344) was observed in all food animals with prevalence rates of 78.6% (110/140) for chicken, 70.7% (58/82) for cattle, and 75.4% (92/122) for swine. However, the resistance rates presented significant differences in different animal origin ESBL-EC, where resistance to CTX, GEN, IMP, NEO, and OFL was the highest in chicken ESBL-EC, then in cattle, and the lowest in swine. Seriously, most ESBL-EC harbor multidrug resistance to antibiotics (MDR, ≥3 antibiotic categories), and the MDR rates of ESBL-EC were the highest in chicken (98.18%), followed by swine (93.48%), and the lowest in cow (58.62%), while the same trend also was observed in MDR of ≥5 antibiotic categories. This high prevalence and resistance can be partly interpreted by the high carriage rates of the β-lactamases CTX-M (n = 89), OXA (n = 59), SHV (n = 7), and TEM (n = 259). A significant difference of β-lactamase genes also presented in different animal species isolates, where the chicken origin ESBL-EC possessed higher carriage rates of almost all genes tested than cattle and swine. Notably, eight chicken origin ESBL-EC carried transferable plasmid-mediated blaNDM-1 or blaNDM-5, especially, of which four ESBL-EC also contained the colistin resistance gene mcr-1, as confirmed by genomic analysis. More interestingly, two deletion events with a 500-bp deletion in ΔISAba125 and a 180-bp deletion in dsbC were observed in three blaNDM-5 IncX3 plasmids, which, as far as we know, is the first discovery. This showed the instability and horizontal transfer of blaNDM genetic context, suggesting that blaNDM is evolving to “pack light” to facilitate rapid and stable horizontal transfer. Sequence types (STs) and PFGE showed diversity patterns. The most prevalent STs were ST48 (n = 5), ST189 (n = 5), ST206 (n = 4), ST6396 (n = 3), ST10 (n = 3), and ST155 (n = 3), where ST48 ESBL-EC originated from three food animal species. The STs of all blaNDM-positive ESBL-EC were attributed to three STs, namely, ST6396 (n = 2), ST206 (n = 2), and ST189 (n = 4), where ST189 was also the unique type for four mcr-1-carrying ESBL-EC. In conclusion, we suggest that the three animal species ESBL-EC show similar high prevalence, diversity in isolate lineages, and significant discrepancies in antibiotic resistance and resistance genes. This suggests that monitoring and anti-infection of different food animal origin ESBL-EC need different designs, which deserves more attention and further surveillance.
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Affiliation(s)
- Zhihai Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Microbiology and Immunology, College of Husbandry and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ke Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China
- College of Veterinary Medicine, Xinjiang Agricultural University, Wulumuqi, China
- Department of Instruments, Autobio Labtec Instruments Co., Ltd, Zhengzhou, China
| | - Yaru Zhang
- Academy of Poultry Industry Research, The New Hope Liuhe Co., Ltd., Qingdao, China
| | - Lining Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Wulumuqi, China
| | - Li Zhao
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China
| | - Changmei Guo
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China
- College of Veterinary Medicine, Xinjiang Agricultural University, Wulumuqi, China
| | - Xudong Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China
| | - Liting Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhihui Hao
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- *Correspondence: Zhihui Hao,
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Fu S, Yang Q, Sheng Y, Wang Q, Wu J, Qiu Z, Lan R, Wang Y, Liu Y. Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off. WATER RESEARCH 2022; 209:117941. [PMID: 34920315 DOI: 10.1016/j.watres.2021.117941] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/13/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Early detection of emerging and life-threatening pathogens circulating in complex environments is urgently required to combat infectious diseases. This study proposed a public health risk assessment workflow with three stages, pathogen screening, pathogen genotyping, and risk assessment. In stage one, pathogens were screened with metagenomic sequencing, microfluidic chip, and qPCR. In stage two, pathogens were isolated and genotyped with multi-locus sequence typing (MLST) or conventional PCR. Finally, virulence genes from metagenomic data were assessed for pathogenicity. Two regions (Donggang and Zhanjiang) with potential public health concerns were selected for evaluation, each of which comprised of one urban and one farming wastewater sampling location. Overall, metagenomic sequencing reflected the variation in the relative abundance of medically important bacteria. Over 90 bacterial pathogens were monitored in the metagenomic dataset, of which 56 species harbored virulence genes. In Donggang, a pathogenic Acinetobacter sp. reached high abundances in 2018 and 2020, whereas all pathogenic Vibrio spp. peaked in October 2019. In Zhanjiang, A. baumanni, and other Enterobacteriaceae species were abundantly present in 2019 and 2020, whereas Aeromonas and Vibrio spp. peaked in November-2017. Forty species were subsequently isolated and subtyped by MLST, half of which were prevalent genotypes in clinical data. Additionally, we identified the African Swine Fever Virus (ASFV) in water samples collected in 2017, ahead of the first reported ASFV outbreak in 2018 in China. RNA viruses like Hepatitis A virus (HAV) and Enterovirus 71 (EV71) were also detected, with concentrations peaking in April 2020 and April 2018, respectively. The dynamics of HAV and EV71 were consistent with local epidemic trends. Finally, based on the virulence gene profiles, our study identified the risk level in wastewater of two cities. This workflow illustrates the potential for an early warning of local epidemics, which helps to prioritize the preparedness for specific pathogens locally.
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Affiliation(s)
- Songzhe Fu
- College of Marine Science and Environment, Dalian Ocean University, Dalian, China; Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, Dalian 116023, China.
| | - Qian Yang
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Gent 9000, Belgium
| | - Yijian Sheng
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Qingyao Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian, China; Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, Dalian 116023, China
| | - Junmin Wu
- College of Marine Science and Environment, Dalian Ocean University, Dalian, China; Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, Dalian 116023, China
| | - Zhiguang Qiu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Yongjie Wang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Ying Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 150791, China
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Bacteriophage-Mediated Modulation of Bacterial Competition during Selective Enrichment of Campylobacter. Microbiol Spectr 2021; 9:e0170321. [PMID: 34908437 PMCID: PMC8672905 DOI: 10.1128/spectrum.01703-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Selective media using antimicrobial supplements generate unique microbial ecology to facilitate bacterial isolation. However, antibiotic-resistant bacteria indigenous to samples can interfere with the isolation process using selective media. Recent studies showed that extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is highly prevalent on retail raw chicken and compromises the efficacy of Campylobacter isolation because ESBL-producing E. coli are resistant to antimicrobial supplements in Campylobacter-selective media and outgrows Campylobacter. The objective of this study was to improve Campylobacter isolation by inhibiting the growth of ESBL-producing E. coli using bacteriophages (phages). The supplementation of Campylobacter-selective media with E. coli phages reduced the level of ESBL-producing E. coli during the enrichment step. When E. coli phages were combined with the antimicrobial supplements of Campylobacter-selective media, antimicrobial synergy was observed, particularly with rifampicin, an antibiotic used in Preston medium. Although the same materials (i.e., phages and selective media) were used, the sequence of combining the materials markedly influenced the inhibition of ESBL-producing E. coli and the isolation of Campylobacter. These findings indicated that the modulation of microbial competition at the enrichment step was critical to the successful isolation of fastidious bacteria and that phages can be utilized to facilitate the selective enrichment of target bacteria by inhibiting their competitive bacteria. IMPORTANCE Phages are promising antimicrobial alternatives. In this study, we first demonstrated that phages can be used to facilitate selective isolation of fastidious bacteria that are prone to be outgrown by bacterial competitors during isolation. The effectiveness of a phage-based isolation method was primarily dependent on the antimicrobial synergy between phages and antibiotics used in selective media. The same approach could be applied to the development of isolation methods for other fastidious bacteria.
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Zhou Q, Lan F, Li X, Yan W, Sun C, Li J, Yang N, Wen C. The Spatial and Temporal Characterization of Gut Microbiota in Broilers. Front Vet Sci 2021; 8:712226. [PMID: 34527716 PMCID: PMC8435590 DOI: 10.3389/fvets.2021.712226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023] Open
Abstract
The gut microbiota of chickens plays an important role in host physiology. However, the colonization and prevalence of gut microbiota have not been well-characterized. Here, we performed 16S rRNA gene sequencing on the duodenal, cecal and fecal microbiota of broilers at 1, 7, 21, and 35 days of age and characterized the dynamic succession of microbiota across the intestinal tract. Our results showed that Firmicutes was the most abundant phylum detected in each gut site at various ages, while the microbial diversity and composition varied among the duodenum, cecum, and feces at different ages. The microbial diversity and complexity of the cecal microbiota increased with age, gradually achieving stability at 21 days of age. As a specific genus in the cecum, Clostridium_sensu_stricto_1 accounted for 83.50% of the total abundance at 1 day of age, but its relative abundance diminished with age. Regarding the feces, the highest alpha diversity was observed at 1 day of age, significantly separated from the alpha diversity of other ages. In addition, no significant differences were observed in the alpha diversity of duodenal samples among 7, 21, and 35 days of age. The predominant bacterium, Lactobacillus, was relatively low (0.68–6.04%) in the intestinal tract of 1-day-old chicks, whereas its abundance increased substantially at 7 days of age and was higher in the duodenum and feces. Escherichia-Shigella, another predominant bacterium in the chicken intestinal tract, was also found to be highly abundant in fecal samples, and the age-associated dynamic trend coincided with that of Lactobacillus. In addition, several genera, including Blautia, Ruminiclostridium_5, Ruminococcaceae_UCG-014, and [Ruminococcus]_torques_group, which are related to the production of short-chain fatty acids, were identified as biomarker bacteria of the cecum after 21 days of age. These findings shed direct light on the temporal and spatial dynamics of intestinal microbiota and provide new opportunities for the improvement of poultry health and production.
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Affiliation(s)
- Qianqian Zhou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Fangren Lan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Xiaochang Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Wei Yan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Chaoliang Wen
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
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11
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Um HN, Baek JO, Park S, Lee EH, Jang J, Park WJ, Roh JY, Jung Y. Small intestinal immune-environmental changes induced by oral tolerance inhibit experimental atopic dermatitis. Cell Death Dis 2021; 12:243. [PMID: 33664229 PMCID: PMC7933185 DOI: 10.1038/s41419-021-03534-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
Atopic dermatitis is a chronic skin inflammatory disease mediated by Th2-type immune responses. Although intestinal immune responses have been shown to play a critical role in the development or prevention of atopic dermatitis, the precise influence of intestinal immunity on atopic dermatitis is incompletely understood. We show here that orally tolerized mice are protected from experimental atopic dermatitis induced by sensitization and epicutaneous (EC) challenge to ovalbumin. Although the expression of Th2-type cytokines in the small intestine of orally tolerized and EC-challenged mice did not change significantly, these mice showed decreased inflammatory responses in the small intestine with restoration of microbial change elicited by the EC challenge. Interestingly, an increase in small intestinal eosinophils was observed with the EC challenge, which was also inhibited by oral tolerance. The role of small intestinal eosinophils and microbiota in the pathogenesis of experimental atopic dermatitis was further substantiated by decreased inflammatory mediators in the small intestine and attenuated Th2-type inflammation in the skin of eosinophil-deficient and microbiota-ablated mice with EC challenges. Based on these data, we propose that the bidirectional interaction between the skin and the intestine has a role in the pathogenesis of atopic dermatitis and that modulation of the intestinal microenvironments could be a therapeutic approach to atopic dermatitis.
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MESH Headings
- Administration, Oral
- Animals
- Bacteria/immunology
- Claudin-4/genetics
- Claudin-4/metabolism
- Cytokines/genetics
- Cytokines/metabolism
- Dermatitis, Atopic/immunology
- Dermatitis, Atopic/metabolism
- Dermatitis, Atopic/microbiology
- Dermatitis, Atopic/prevention & control
- Desensitization, Immunologic
- Disease Models, Animal
- Dysbiosis
- Female
- Gastrointestinal Microbiome
- Host-Pathogen Interactions
- Immune Tolerance
- Intestine, Small/immunology
- Intestine, Small/metabolism
- Intestine, Small/microbiology
- Leukocytes/immunology
- Leukocytes/metabolism
- Mice, Inbred BALB C
- Ovalbumin/administration & dosage
- Skin/immunology
- Skin/metabolism
- Mice
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Affiliation(s)
- Han-Na Um
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science & Technology, Gachon University, Incheon, 21999, South Korea
| | - Jin-Ok Baek
- Department of Dermatology, Gachon Gil Medical Center, College of Medicine, Gachon University, Incheon, 21565, Korea
| | - Sohyeon Park
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science & Technology, Gachon University, Incheon, 21999, South Korea
| | - Eun-Hui Lee
- Department of Microbiology, College of Medicine, Gachon University, Incheon, 21999, Korea
| | - Jinsun Jang
- Department of Dermatology, Gachon Gil Medical Center, College of Medicine, Gachon University, Incheon, 21565, Korea
- Department of Microbiology, College of Medicine, Gachon University, Incheon, 21999, Korea
| | - Woo-Jae Park
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science & Technology, Gachon University, Incheon, 21999, South Korea
- Department of Biochemistry, College of Medicine, Gachon University, Incheon, 21999, Korea
| | - Joo-Young Roh
- Department of Dermatology, Gachon Gil Medical Center, College of Medicine, Gachon University, Incheon, 21565, Korea.
| | - YunJae Jung
- Department of Health Science and Technology, Gachon Advanced Institute for Health Science & Technology, Gachon University, Incheon, 21999, South Korea.
- Department of Microbiology, College of Medicine, Gachon University, Incheon, 21999, Korea.
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12
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Patuzzi I, Orsini M, Cibin V, Petrin S, Mastrorilli E, Tiengo A, Gobbo F, Catania S, Barco L, Ricci A, Losasso C. The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time. Microorganisms 2021; 9:221. [PMID: 33499060 PMCID: PMC7911313 DOI: 10.3390/microorganisms9020221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022] Open
Abstract
Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.
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Affiliation(s)
- Ilaria Patuzzi
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Massimiliano Orsini
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Veronica Cibin
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Sara Petrin
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Eleonora Mastrorilli
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Alessia Tiengo
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Federica Gobbo
- Avian Pathology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (F.G.); (S.C.)
| | - Salvatore Catania
- Avian Pathology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (F.G.); (S.C.)
| | - Lisa Barco
- Experimental Microbiology Department, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy;
| | - Antonia Ricci
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Carmen Losasso
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
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13
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Nafarrate I, Lasagabaster A, Sevillano E, Mateo E. Prevalence, molecular typing and antimicrobial susceptibility of Campylobacter spp. isolates in northern Spain. J Appl Microbiol 2020; 130:1368-1379. [PMID: 32886839 DOI: 10.1111/jam.14842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/08/2020] [Accepted: 08/27/2020] [Indexed: 11/29/2022]
Abstract
AIM To analyse the prevalence, genetic diversity and antimicrobial susceptibility of Campylobacter spp. in northern Spain. METHODS AND RESULTS Campylobacter was isolated from 139 samples of broiler meat and faecal dropping of broiler and swine with a prevalence of 35·4, 62 and 42·8%, respectively. Campylobacter jejuni (n = 55) and Campylobacter coli (n = 31) were identified by multiplex-PCR in meat, faeces and human clinical samples while Campylobacter fetus (n = 3) was exclusively detected in the latter. Fingerprinting by flaA-RFLP and PFGE revealed 68 different genotypes from the 89 isolates with a Biodiversity Simpson's index of 0·98. The 86·5% of the isolates were resistant to ciprofloxacin, 85·4% to tetracycline and 49·4% to erythromycin; only three genotypes were susceptible to the three antimicrobial drugs. Multidrug resistance was detected in the 40·7% of the isolates. CONCLUSIONS Campylobacter remains prevalent in northern Spain with a high biodiversity degree. About 93·3% of the isolates were resistant to one or more drugs. SIGNIFICANCE AND IMPACT OF THE STUDY Although different measures are taken to control Campylobacter, the detection of isolates resistant to the drugs used in the treatment of campylobacteriosis is still high, including different species and genotypes. This evidences the need of additional strategies against this pathogen.
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Affiliation(s)
- I Nafarrate
- AZTI, Food Research, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Bizkaia, Derio (Bizkaia), Spain
| | - A Lasagabaster
- AZTI, Food Research, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Bizkaia, Derio (Bizkaia), Spain
| | - E Sevillano
- Department of Immunology, Microbiology and Parasitology, UFI 11/25, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - E Mateo
- Department of Immunology, Microbiology and Parasitology, UFI 11/25, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Bilbao, Spain
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14
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Mei R, Nobu MK, Liu WT. Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:173-184. [PMID: 31965729 DOI: 10.1111/1758-2229.12821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/24/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Degradation of amino acids is an important process in methanogenic environments. Early studies in the 1980s focused on isolated clostridia species to study the degradation behaviours. However, it is now well-recognized that isolated species may not represent those with important roles in situ. This study conducted a continuous enrichment experiment with focus on the comparison of the microbial communities after short-term enrichment (SE) and long-term enrichment (LE). Individual amino acids were used as the substrate, and two different anaerobic digester sludge were used as the inoculum. Based on 16S rRNA and 16S rRNA gene, a clear community shift was observed during a time course of 18 months. The SE communities were dominated by microbial populations such as an uncultured Bacteroidales that was different from known fermenters. In the LE communities, known amino acids fermenters were consistently observed with high abundance, including Peptoclostridium acidaminophilum, Acidaminobacter hydrogenoformans and Propionivibrio pelophilus. The community structures could be classified into four types depending on the diversity of fermenters and syntrophs. A culturability index was developed to compare the SE and LE community and revealed that long-term enrichment tended to select microbial populations closely related to species that has been cultivated whereas larger fractions of the inoculum and SE communities remained uncultured.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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15
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Kim J, Guk JH, Mun SH, An JU, Kim W, Lee S, Song H, Seong JK, Suh JG, Cho S. The Wild Mouse ( Micromys minutus): Reservoir of a Novel Campylobacter jejuni Strain. Front Microbiol 2020; 10:3066. [PMID: 31993041 PMCID: PMC6971111 DOI: 10.3389/fmicb.2019.03066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/19/2019] [Indexed: 11/25/2022] Open
Abstract
Campylobacter jejuni is one of the most common zoonotic pathogens worldwide. Although the main sources of human C. jejuni infection are livestock, wildlife can also affect C. jejuni transmission in humans. However, it remains unclear whether wild mice harbor C. jejuni and are involved in the "environment-wildlife-livestock-human" transmission cycle of C. jejuni in humans. Here, we characterized C. jejuni from wild mice and identified genetic traces of wild mouse-derived C. jejuni in other hosts using a traditional approach, along with comparative genomics. We captured 115 wild mice (49 Mus musculus and 66 Micromys minutus) without any clinical symptoms from 22 sesame fields in Korea over 2 years. Among them, M. minutus were typically caught in remote areas of human houses and C. jejuni was solely isolated from M. minutus (42/66, 63.6%). We identified a single clone (MLST ST-8388) in all 42 C. jejuni isolates, which had not been previously reported, and all isolates had the same virulence/survival-factor profile, except for the plasmid-mediated virB11 gene. No isolates exhibited antibiotic resistance, either in phenotypic and genetic terms. Comparative-genomic analysis and MST revealed that C. jejuni derived from M. minutus (strain SCJK2) was not genetically related to those derived from other sources (registered in the NCBI genome database and PubMLST database). Therefore, we hypothesize that C. jejuni from M. minutus is a normal component of the gut flora following adaptation to the gastro-intestinal tract. Furthermore, M. minutus-derived C. jejuni had different ancestral lineages from those derived from other sources, and there was a low chance of C. jejuni transmission from M. minutus to humans/livestock because of their habitat. In conclusion, M. minutus may be a potential reservoir for a novel C. jejuni, which is genetically different from those of other sources, but may not be involved in the transmission of C. jejuni to other hosts, including humans and livestock. This study could form the basis for further studies focused on understanding the transmission cycle of C. jejuni, as well as other zoonotic pathogens originating from wild mice.
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Affiliation(s)
- Junhyung Kim
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Jae-Ho Guk
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Seung-Hyun Mun
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Jae-Uk An
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Woohyun Kim
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Soomin Lee
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Hyokeun Song
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Je Kyung Seong
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Jun Gyo Suh
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Seongbeom Cho
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
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16
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Huang H, Raymond P, Grenier C, Fahey J. Development and improvement of a colony blot immunoassay for the detection of thermotolerant Campylobacter species. J Microbiol Methods 2020. [DOI: 10.1016/bs.mim.2019.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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17
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Kim J, Guk JH, Mun SH, An JU, Song H, Kim J, Ryu S, Jeon B, Cho S. Correction to: Metagenomic analysis of isolation methods of a targeted microbe, Campylobacter jejuni, from chicken feces with high microbial contamination. MICROBIOME 2019; 7:81. [PMID: 31153386 PMCID: PMC6545208 DOI: 10.1186/s40168-019-0700-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Following publication of the original article [1], the authors reported an error in Fig. 2. The correct figure is shown below.
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Affiliation(s)
- Junhyung Kim
- Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jae-Ho Guk
- Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Seung-Hyun Mun
- Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jae-Uk An
- Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hyokeun Song
- Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jinshil Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Byeonghwa Jeon
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Seongbeom Cho
- Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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