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Park I, Nam H, Lee Y, Wickramasuriya SS, Smith AH, Rehberger TG, Lillehoj HS. The effect of gut microbiota-derived carnosine on mucosal integrity and immunity in broiler chickens challenged with Eimeria maxima. Poult Sci 2024; 103:103837. [PMID: 38848630 PMCID: PMC11214313 DOI: 10.1016/j.psj.2024.103837] [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: 03/11/2024] [Revised: 04/22/2024] [Accepted: 05/04/2024] [Indexed: 06/09/2024] Open
Abstract
In the first study, an in vitro culture system was developed to investigate the effects of carnosine on macrophage proinflammatory cytokine response using an established chicken macrophage cell line (CMC), gut integrity using a chicken intestinal epithelial cell line (IEC), muscle differentiation in quail muscle cells (QMCs) and primary chicken embryonic muscle cells (PMCs), and direct anti-parasitic effect against Eimeria maxima sporozoites. Cells to be tested were seeded in 24-well plates and treated with carnosine at 4 different concentrations (0.1, 1.0, and 10.0 µg). After 18 h of incubation, cells were harvested to measure gene expression of proinflammatory cytokines in CMC, tight junction (TJ) proteins in IECs, and muscle cell growth markers in QMCs and PMCs. In vivo trials were conducted to investigate the effect of dietary carnosine on disease parameters in broiler chickens challenged with E. maxima. One hundred and twenty male broiler chickens (0-day-old) were allocated into 4 treatment groups: 1) basal diet without infection (NC), 2) basal diet with E. maxima infection (PC), 3) carnosine at 10.0 mg/kg feed with PC (HCS), and 4) carnosine at 1.0 mg/kg feed with PC (LCS). All groups except NC were orally infected with E. maxima on d 14. Jejunal samples were collected for lesion scoring and jejunum gut tissues were used for transcriptomic analysis of cytokines and TJ proteins. In vitro, carnosine treatment significantly decreased IL-1β gene expression in CMC following LPS stimulation. In vivo feeding studies showed that dietary carnosine increased BW and ADG of chickens in E. maxima-infected groups and reduced the jejunal lesion score and fecal oocyst shedding in HCS group. Jejunal IL-1β, IL-8, and IFN-γ expression were suppressed in the HCS group compared to PC. The expression levels of claudin-1 and occludin in IECs were also increased in HCS following carnosine treatment. In conclusion, these findings highlight the beneficial effects of dietary carnosine supplementation on intestinal immune responses and gut barrier function in broiler chickens exposed to E. maxima infection.
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Affiliation(s)
- Inkyung Park
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, MD 20705, USA
| | - Hyoyoun Nam
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, MD 20705, USA
| | - Youngsub Lee
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, MD 20705, USA
| | - Samiru S Wickramasuriya
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, MD 20705, USA
| | | | | | - Hyun S Lillehoj
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, MD 20705, USA.
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Durán-Viseras A, Lindner BG, Hatt JK, Lai A, Wallace R, Ginn O, Brown J, Konstantinidis KT. Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170772. [PMID: 38346660 DOI: 10.1016/j.scitotenv.2024.170772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla 41012, Spain; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amanda Lai
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Robert Wallace
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Olivia Ginn
- Chemical, Materials and Biomedical Engineering Department and Institute for Bioinformatics, University of Georgia, Athens, GA 30601, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Rosch MEG, Rehner J, Schmartz GP, Manier SK, Becker U, Müller R, Meyer MR, Keller A, Becker SL, Keller V. Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept. ONE HEALTH OUTLOOK 2024; 6:4. [PMID: 38549118 PMCID: PMC10979557 DOI: 10.1186/s42522-024-00100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND Different production systems of livestock animals influence various factors, including the gut microbiota. METHODS We investigated whether changing the conditions from barns to free-range chicken farming impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment. RESULTS Over the six time points, 12 taxa-mostly lactobacilli-changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken. CONCLUSION Our data indicate that the gut microbiota can undergo alterations over time in response to changes in production systems. These changes subsequently exert an influence on the metabolites found in the eggs. The preliminary results of our proof-of-concept study motivate larger scale observations with more individual chicken and longer observation periods.
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Affiliation(s)
- Michael E G Rosch
- Medical Doctor program Human Medicine, Saarland University/ Saarland University Medical Center, 66123/66421, Saarbrücken/Homburg, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg/Saar, Germany
| | - Georges P Schmartz
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Sascha K Manier
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Center for Molecular Signaling (PZMS), 66421, Homburg/Saar, Germany
| | - Uta Becker
- MIP Pharma GmbH, 66386, Sankt Ingbert, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Center for Molecular Signaling (PZMS), 66421, Homburg/Saar, Germany
| | - Andreas Keller
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg/Saar, Germany
| | - Verena Keller
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
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Zhang M, Yu A, Wu H, Xiong X, Li J, Chen L. Lactobacillus acidophilus and Bacillus subtilis significantly change the growth performance, serum immunity and cecal microbiota of Cherry Valley ducks during the fattening period. Anim Sci J 2024; 95:e13946. [PMID: 38651265 DOI: 10.1111/asj.13946] [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: 03/13/2023] [Revised: 02/16/2024] [Accepted: 03/10/2024] [Indexed: 04/25/2024]
Abstract
This study explored the effects of a Bacillus subtilis and Lactobacillus acidophilus mixture containing the co-fermented products of the two probiotics on growth performance, serum immunity and cecal microbiota of Cherry Valley ducks. This study included 480 one-day-old Cherry Valley ducks divided into four feeding groups: basal diet (control group) and basal diet supplemented with 300, 500, or 700 mg/kg of the probiotic powder; the ducks were raised for 42 days. Compared with the control group, body weight on day 42 and the average daily gain on days 15-42 significantly increased (p < 0.05), and the feed conversion rate significantly decreased (p < 0.05) in the experimental groups. Furthermore, the serum immunoglobulin (Ig) A, IgG, IgM, and interleukin (IL)-4 levels increased significantly (p < 0.05), and IL-1β, IL-2, and tumor necrosis factor-α decreased significantly (p < 0.05) in the experimental groups. Finally, Sellimonas, Prevotellaceae NK3B31 group, Lachnospiraceae NK4A136 group and Butyricoccus played an important role in the cecal microbiota of the experimental group. Thus, the probiotic powder has impacts on the growth performance, serum immunity and cecal microbiota of Cherry Valley Ducks.
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Affiliation(s)
- Menghui Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Anan Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Hongzhi Wu
- Chinese Academy of Tropical Agricultural Sciences Tropical Crops Genetic Resources Insititute, Haikou, China
| | - Xiaolan Xiong
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Jianhui Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
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Xu F, Wu H, Xie J, Zeng T, Hao L, Xu W, Lu L. The Effects of Fermented Feed on the Growth Performance, Antioxidant Activity, Immune Function, Intestinal Digestive Enzyme Activity, Morphology, and Microflora of Yellow-Feather Chickens. Animals (Basel) 2023; 13:3545. [PMID: 38003161 PMCID: PMC10668758 DOI: 10.3390/ani13223545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
This experiment was conducted to investigate the effects of fermented feed on growth performance, antioxidant activity, immune function, intestinal digestive enzyme activity, morphology, and microflora of yellow-feather chickens. A total of 240 one-day-old female yellow-feathered (Hexi dwarf) chickens were randomly divided into two treatment groups, with six replicates per group and 20 chickens per replicate. The control group (CK) received a basal diet, whereas the experimental group was fed a basal diet of +2.00% fermented feed (FJ). The trial lasted for 22 days. Compared with the CK, (1) the growth performance was not affected (p > 0.05); (2) immunoglobin a, immunoglobin g, immunoglobin m, interleukin-1β, and interleukin-6 were affected (p < 0.05); (3) liver superoxide dismutase, glutathione peroxidase, and catalase were higher (p < 0.05); (4) trypsin activity in the duodenum and cecal Shannon index were increased (p < 0.05); (5) the relative abundance of Actinobacteriota in cecum was increased (p < 0.05); (6) the abundance of dominant microflora of Bacteroides as well as Clostridia UCG-014_norank were increased (p < 0.05). In summary, the fermented feed improved the growth performance, antioxidant activity, immune function, intestinal digestive enzyme activity, morphology, and microflora of yellow-feather chickens.
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Affiliation(s)
- Fei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310002, China
- Junan Agriculture and Rural Bureau, Linyi 276600, China
| | - Hongzhi Wu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jiajun Xie
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310002, China
- Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310002, China
| | - Lijian Hao
- Junan Agriculture and Rural Bureau, Linyi 276600, China
| | - Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310002, China
- Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310002, China
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310002, China
- Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310002, China
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Gao H, Jiang F, Zhang J, Chi X, Song P, Li B, Cai Z, Zhang T. Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang). Integr Zool 2023; 18:1089-1104. [PMID: 37231976 DOI: 10.1111/1749-4877.12726] [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] [Indexed: 05/27/2023]
Abstract
Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.
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Affiliation(s)
- Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Jingjie Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiangwen Chi
- Department of Student Affairs, Qinghai University, Xining, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Lee STM. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Anim Microbiome 2023; 5:35. [PMID: 37461084 DOI: 10.1186/s42523-023-00256-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. RESULTS We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.
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Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
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Cisek AA, Dolka B, Bąk I, Cukrowska B. Microorganisms Involved in Hydrogen Sink in the Gastrointestinal Tract of Chickens. Int J Mol Sci 2023; 24:ijms24076674. [PMID: 37047647 PMCID: PMC10095559 DOI: 10.3390/ijms24076674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Hydrogen sink is a beneficial process, which has never been properly examined in chickens. Therefore, the aim of this study was to assess the quantity and quality of microbiota involved in hydrogen uptake with the use of real-time PCR and metagenome sequencing. Analyses were carried out in 50 free-range chickens, 50 commercial broilers, and 54 experimental chickens isolated from external factors. The median values of acetogens, methanogens, sulfate-reducing bacteria (SRB), and [NiFe]-hydrogenase utilizers measured in the cecum were approx. 7.6, 0, 0, and 3.2 log10/gram of wet weight, respectively. For the excreta samples, these values were 5.9, 4.8, 4, and 3 log10/gram of wet weight, respectively. Our results showed that the acetogens were dominant over the other tested groups of hydrogen consumers. The quantities of methanogens, SRB, and the [NiFe]-hydrogenase utilizers were dependent on the overall rearing conditions, being the result of diet, environment, agrotechnical measures, and other factors combined. By sequencing of the 16S rRNA gene, archaea of the genus Methanomassiliicoccus (Candidatus Methanomassiliicoccus) were discovered in chickens for the first time. This study provides some indication that in chickens, acetogenesis may be the main metabolic pathway responsible for hydrogen sink.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Beata Dolka
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, St. Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Iwona Bąk
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, St. Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Bożena Cukrowska
- Department of Pathology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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Zhao W, Huang Y, Cui N, Wang R, Xiao Z, Su X. Glucose oxidase as an alternative to antibiotic growth promoters improves the immunity function, antioxidative status, and cecal microbiota environment in white-feathered broilers. Front Microbiol 2023; 14:1100465. [PMID: 36937262 PMCID: PMC10020722 DOI: 10.3389/fmicb.2023.1100465] [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: 11/16/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
This study aimed to demonstrate the effects of glucose oxidase (GOD) on broilers as a potential antibiotic substitute. A total of four hundred twenty 1-day-old male Cobb500 broilers were randomly assigned into five dietary treatments, each with six replicates (12 chicks per replicate). The treatments included two control groups (a basal diet and a basal diet with 50 mg/kg aureomycin) and three GOD-additive groups involving three different concentrations of GOD. Analysis after the t-test showed that, on day 21, the feed:gain ratio significantly decreased in the 1,200 U/kg GOD-supplied group (GOD1200) compared to the antibiotic group (Ant). The same effect was also observed in GOD1200 during days 22-42 and in the 600 U/kg GOD-supplied group (GOD600) when compared to the control group (Ctr). The serum tests indicated that, on day 21, the TGF-β cytokine was significantly decreased in both GOD600 and GOD1200 when compared with Ctr. A decrease in malondialdehyde and an increase in superoxide dismutase in GOD1200 were observed, which is similar to the effects seen in Ant. On day 42, the D-lactate and glutathione peroxidase activity changed remarkably in GOD1200 and surpassed Ant. Furthermore, GOD upregulated the expression of the jejunal barrier genes (MUC-2 and ZO-1) in two phases relative to Ctr. In the aureomycin-supplied group, the secretory immunoglobulin A significantly decreased in the jejunum at 42 days. Changes in microbial genera were also discovered in the cecum by sequencing 16S rRNA genes at 42 days. The biomarkers for GOD supplementation were identified as Colidextribacter, Oscillibacter, Flavonifractor, Oscillospira, and Shuttleworthia. Except for Shuttleworthia, all the abovementioned genera were n-butyrate producers known for imparting their various benefits to broilers. The PICRUSt prediction of microbial communities revealed 11 pathways that were enriched in both the control and GOD-supplied groups. GOD1200 accounted for an increased number of metabolic pathways, demonstrating their potential in aiding nutrient absorption and digestion. In conclusion, a diet containing GOD can be beneficial to broiler health, particularly at a GOD concentration of 1,200 U/kg. The improved feed conversion ratio, immunity, antioxidative capacity, and intestinal condition demonstrated that GOD could be a valuable alternative to antibiotics in broiler breeding.
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Affiliation(s)
| | | | | | | | | | - Xiaoou Su
- Key Laboratory of Agro-Product Quality and Safety of the Ministry of Agriculture, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
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Albright S, Louca S. Trait biases in microbial reference genomes. Sci Data 2023; 10:84. [PMID: 36759614 PMCID: PMC9911409 DOI: 10.1038/s41597-023-01994-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA. .,Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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11
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Adjei-Mensah B, Koranteng AAA, Hamidu JA, Tona K. Antibacterial activities of garlic ( Allium sativum) in broiler and laying hens production. WORLD POULTRY SCI J 2023. [DOI: 10.1080/00439339.2023.2164236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- B. Adjei-Mensah
- Centre d’Excellence Régional sur les Sciences Aviaires, Université of Lomé, Lomé, Togo
| | - A. A. A. Koranteng
- Centre d’Excellence Régional sur les Sciences Aviaires, Université of Lomé, Lomé, Togo
| | - J. A. Hamidu
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - K. Tona
- Centre d’Excellence Régional sur les Sciences Aviaires, Université of Lomé, Lomé, Togo
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12
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Zhang Y, Jiang F, Yang B, Wang S, Wang H, Wang A, Xu D, Fan W. Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads. Gigascience 2022; 11:6833030. [PMID: 36399059 PMCID: PMC9673493 DOI: 10.1093/gigascience/giac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/27/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Background Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads. Results We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the “RNA complete” criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella, and Enterococcus, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes. Conclusions HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host–microbiota interaction studies, thereby contributing to the sustainable development of poultry resources.
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Affiliation(s)
- Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
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13
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Montso PK, Mnisi CM, Ayangbenro AS. Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal. Front Microbiol 2022; 13:1009945. [PMID: 36338038 PMCID: PMC9630332 DOI: 10.3389/fmicb.2022.1009945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
The caecum of a chicken harbors complex microbial communities that play vital roles in feed digestion, nutrient absorption, and bird health. Understanding the caecal microbial communities could help improve feed utilization efficiency and chicken product quality and, ultimately, deliver sustainable poultry production systems. Thus, this study assessed the caecal microbial communities and their functional diversity and metabolic pathways in broilers reared on diets containing different levels of marama (Tylosema esculentum) bean meal (MBM). A total of 350, day-old male Ross 308 broiler chicks were randomly allocated to five dietary treatments formulated as follows: a soybean-based standard broiler diet (Con_BC); Con_BC in which soybean products were substituted with 7 (M7_BC), 14 (M14_BC), 21 (M21_BC), and 28% (M28_BC) MBM. The dietary treatments were distributed to 35 replicate pens (10 birds each). After 42 days of feeding, the birds were slaughtered and thereafter caecal samples were collected from each replicate pen. Subsequently, the samples were pooled per treatment group for metagenomics sequence analysis. The results revealed that the bacteria domain (99.11%), with Bacteroides, Firmicutes and Proteobacteria being the most prominent phyla (48.28, 47.52, and 4.86%, respectively). Out of 846 genera obtained, the most abundant genera were Bacteroides, Clostridium, Alistipes, Faecalibacterium, Ruminococcus, Eubacterium, and Parabacterioides. At the genus level, the alpha-diversity showed significant (p < 0.05) difference across all treatment groups. Based on the SEED subsystem, 28 functional categories that include carbohydrates (14.65%), clustering-based subsystems (13.01%), protein metabolism (10.12%) were obtained. The KO analysis revealed 183 endogenous pathways, with 100 functional pathways associated with the metabolism category. Moreover, 15 pathways associated with carbohydrates were observed. The glycolysis/gluconeogenesis, galactose metabolism, pyruvate metabolism (15.32, 12.63, and 11.93%) were the most abundant pathways. Moreover, glycoside hydrolases (GH1, GH5, and GH13) were the most prominent carbohydrates-active enzymes. Therefore, results presented in this study suggest that dietary MB meal can improve microbial communities and their functional and metabolic pathways, which may help increase poultry production.
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Affiliation(s)
- Peter Kotsoana Montso
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- *Correspondence: Peter Kotsoana Montso,
| | - Caven Mguvane Mnisi
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- Department of Animal Science, School of Agricultural Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ayansina Segun Ayangbenro
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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14
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Smith MM, Melrose J. Xylan Prebiotics and the Gut Microbiome Promote Health and Wellbeing: Potential Novel Roles for Pentosan Polysulfate. Pharmaceuticals (Basel) 2022; 15:ph15091151. [PMID: 36145372 PMCID: PMC9503530 DOI: 10.3390/ph15091151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/17/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022] Open
Abstract
This narrative review highlights the complexities of the gut microbiome and health-promoting properties of prebiotic xylans metabolized by the gut microbiome. In animal husbandry, prebiotic xylans aid in the maintenance of a healthy gut microbiome. This prevents the colonization of the gut by pathogenic organisms obviating the need for dietary antibiotic supplementation, a practice which has been used to maintain animal productivity but which has led to the emergence of antibiotic resistant bacteria that are passed up the food chain to humans. Seaweed xylan-based animal foodstuffs have been developed to eliminate ruminant green-house gas emissions by gut methanogens in ruminant animals, contributing to atmospheric pollution. Biotransformation of pentosan polysulfate by the gut microbiome converts this semi-synthetic sulfated disease-modifying anti-osteoarthritic heparinoid drug to a prebiotic metabolite that promotes gut health, further extending the therapeutic profile and utility of this therapeutic molecule. Xylans are prominent dietary cereal components of the human diet which travel through the gastrointestinal tract as non-digested dietary fibre since the human genome does not contain xylanolytic enzymes. The gut microbiota however digest xylans as a food source. Xylo-oligosaccharides generated in this digestive process have prebiotic health-promoting properties. Engineered commensal probiotic bacteria also have been developed which have been engineered to produce growth factors and other bioactive factors. A xylan protein induction system controls the secretion of these compounds by the commensal bacteria which can promote gut health or, if these prebiotic compounds are transported by the vagal nervous system, may also regulate the health of linked organ systems via the gut–brain, gut–lung and gut–stomach axes. Dietary xylans are thus emerging therapeutic compounds warranting further study in novel disease prevention protocols.
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Affiliation(s)
- Margaret M. Smith
- Raymond Purves Laboratory of Bone and Joint Research, Kolling Institute of Medical Research, Faculty of Health and Science, University of Sydney at Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
| | - James Melrose
- Raymond Purves Laboratory of Bone and Joint Research, Kolling Institute of Medical Research, Faculty of Health and Science, University of Sydney at Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Sydney Medical School, Northern Campus, University of Sydney at Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
- Correspondence:
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15
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Xu Y, Huang Y, Guo L, Zhang S, Wu R, Fang X, Xu H, Nie Q. Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens. Front Microbiol 2022; 13:930289. [PMID: 36160245 PMCID: PMC9490229 DOI: 10.3389/fmicb.2022.930289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022] Open
Abstract
Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China.
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Affiliation(s)
- Yibin Xu
- Lingnan Guangdong Laboratory of Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Yulin Huang
- Lingnan Guangdong Laboratory of Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Lijin Guo
- Lingnan Guangdong Laboratory of Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Siyu Zhang
- Lingnan Guangdong Laboratory of Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Ruiquan Wu
- Lingnan Guangdong Laboratory of Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Xiang Fang
- Lingnan Guangdong Laboratory of Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Haiping Xu
- Lingnan Guangdong Laboratory of Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
- *Correspondence: Haiping Xu,
| | - Qinghua Nie
- Lingnan Guangdong Laboratory of Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
- Qinghua Nie,
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16
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Zhang T, Li M, Shi T, Yan Y, Niyazbekova Z, Wang X, Li Z, Jiang Y. Transmission of the gut microbiome in cohousing goats and pigs. Front Microbiol 2022; 13:948617. [PMID: 36160207 PMCID: PMC9490217 DOI: 10.3389/fmicb.2022.948617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Social interaction facilitates the horizontal transmission of the microbiota between different individuals. However, little is known about the level of microbiota transmission in different livestock animals and different digestive tracts. The Hainan black goat and Wuzhishan pig are typical tropical local breeds on Hainan Island in China. Thus, we sampled and analyzed the gut microbiome in Hainan black goats (cecum and rumen) and Wuzhishan pigs (cecum) to study horizontal transmission by rearing them in the same pen (six goats and six pigs) or separate pens (nine goats and nine pigs). De novo assembly and binning recovered 3,262 strain-level and 2,488 species-level metagenome-assembled genomes (MAGs) using ∼1.3 Tb sequencing data. Of these MAGs, 1,856 MAGs were identified as novel strain. Compared with goats living in separate pens, social interaction in the same pen promotes community homogeneity in the rumen microbiome (P < 0.05) and the cecum microbiome (P < 0.05), respectively. Notably, approximately 7.08% (231/3262) of the gut microbial population could transmit during cohousing, 12 strains only in inter-species transmission, versus 190 strains only in intra-species transmission, and 10 strains only in foregut and hindgut transmission. In addition, the social contact group has high transmitted strain abundance, which is correlated with community composition. This study provided a new insight into the influence of social interaction on the animal gut microbiota.
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Affiliation(s)
- Tingting Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Mao Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Tao Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yueyang Yan
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zhannur Niyazbekova
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Zongjun Li,
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- *Correspondence: Yu Jiang,
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Dehau T, Ducatelle R, Immerseel FV, Goossens E. Omics technologies in poultry health and productivity - part 1: current use in poultry research. Avian Pathol 2022; 51:407-417. [PMID: 35675291 DOI: 10.1080/03079457.2022.2086447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.
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Affiliation(s)
- Tessa Dehau
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evy Goossens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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18
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Zhou H, Guo Y, Liu Z, Wu H, Zhao J, Cao Z, Zhang H, Shang H. Comfrey polysaccharides modulate the gut microbiota and its metabolites SCFAs and affect the production performance of laying hens. Int J Biol Macromol 2022; 215:45-56. [PMID: 35718145 DOI: 10.1016/j.ijbiomac.2022.06.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/17/2022] [Accepted: 06/11/2022] [Indexed: 12/24/2022]
Abstract
Effects of dietary supplementation of comfrey polysaccharides (CPs) on production performance, egg quality, and microbial composition of cecum in laying hens were evaluated. A total of 240 laying hens were allocated into 4 groups with 6 replicates per group. The laying hens were fed diets containing CPs at levels of 0, 0.5, 1.0, and 1.5 %, respectively. The results showed that the egg production rate increased by 5.97 %, the egg mass improved by 6.71 %, and the feed conversion rate reduced by 5.43 % in the 1.0 % supplementation group of CPs compared with those in the control group. The digestibility of ash, crude fat, and phosphorus was notably improved by the addition of CPs at 1.0 % (P < 0.05). The relative abundances of Bacteroidetes at the phylum level, Bacteroidaceae, Rikenellaceae, and Prevotellaceae at the family level were increased by CPs (P < 0.05). The relative abundances of Bacteroides, Megamonas, Rikenellaceae_RC9_gut_group, [Ruminococcus]_torques_group, Methanobrevibacter, Desulfovibrio, Romboutsia, Alistipes, and Intestinimonas at the genus level were increased by CPs (P < 0.05). Dietary supplementation of CPs could enhance the production performance of laying hens, which might be related to the improvement of nutrient digestibility and microbial community modulations in the cecum. Therefore, CPs have potential application value as prebiotics in laying hens.
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Affiliation(s)
- Haizhu Zhou
- College of Forestry and Pratacultural Science, Jilin Agricultural University, Changchun 130118, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yang Guo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Zhenhua Liu
- The Third Affiliated Clinical Hospital of Changchun University of Chinese Medicine, Changchun 130000, China
| | - Hongxin Wu
- Institute of Grassland Research, CAAS, Hohhot 010010, China
| | - Jiangchao Zhao
- Department of Animal Science, University of Arkansas, Fayetteville 72701, USA
| | - Zihang Cao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Hexiang Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Hongmei Shang
- College of Forestry and Pratacultural Science, Jilin Agricultural University, Changchun 130118, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; Jilin Provincial Key Lab of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun 130118, China.
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Danladi Y, Loh TC, Foo HL, Akit H, Md Tamrin NA, Mohammad Naeem A. Impact of Feeding Postbiotics and Paraprobiotics Produced From Lactiplantibacillus plantarum on Colon Mucosa Microbiota in Broiler Chickens. Front Vet Sci 2022; 9:859284. [PMID: 35425828 PMCID: PMC9001976 DOI: 10.3389/fvets.2022.859284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
This study was conducted to evaluate the impact of feeding postbiotics and paraprobiotics produced from Lactiplantibacillus plantarum on colon mucosa microbiota in broiler chickens. In this study, 336 one-day-old COBB 500 chicks were randomly allotted to eight treatment groups and replicated six times with seven birds per replicate. The treatment included T1 (Negative control) = Basal diet, T2 (Positive control) = Basal diet + 0.01% oxytetracycline, T3 = Basal diet + 0.2% postbiotic TL1, T4 = Basal diet + 0.2% postbiotic RS5, T5 = Basal diet + 0.2% paraprobiotic RG11, T6 = Basal diet + 0.2% postbiotic RI11, T7 = Basal diet + 0.2% paraprobiotic RG14, and T8 = Basal diet + 0.2% paraprobiotic RI11. There were reported changes in the bacterial community using 16S rRNA sequencing of the colon mucosa. The results of the sequencing of 16S rRNA genes in the colon mucosa samples indicated that compared to birds fed the negative control diet, birds fed paraprobiotic RI11 diets were recorded to have a lower relative abundance of Proteobacteria, while those fed the positive control were recorded to have a higher proportion of Firmicutes. Also, lower Enterococcus was reported in paraprobiotic RI11, while the most abundant genus was Bacteroides in postbiotic TL1. This study revealed that supplementation of postbiotics and paraprobiotics in the diets of broilers demonstrated positive effects on the microbiota by supporting the increase of beneficial microbes like the Firmicutes while decreasing harmful microbes like the Proteobacteria. Therefore, this study has provided knowledge on the modification of chicken mucosa microbiota through the feeding of postbiotics and paraprobiotics.
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Affiliation(s)
- Yohanna Danladi
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | - Teck Chwen Loh
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang, Malaysia
- *Correspondence: Teck Chwen Loh
| | - Hooi Ling Foo
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Hooi Ling Foo
| | - Henny Akit
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nur Aida Md Tamrin
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | - Azizi Mohammad Naeem
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
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20
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Dittoe DK, Olson EG, Ricke SC. IMPACT OF THE GASTROINTESTINAL MICROBIOME AND FERMENTATION METABOLITES ON BROILER PERFORMANCE. Poult Sci 2022; 101:101786. [PMID: 35346496 PMCID: PMC9079343 DOI: 10.1016/j.psj.2022.101786] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 01/04/2023] Open
Affiliation(s)
- Dana K Dittoe
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Elena G Olson
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Steven C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA.
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21
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Glendinning L, Chintoan-Uta C, Stevens MP, Watson M. Effect of cecal microbiota transplantation between different broiler breeds on the chick flora in the first week of life. Poult Sci 2021; 101:101624. [PMID: 34936955 PMCID: PMC8704443 DOI: 10.1016/j.psj.2021.101624] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/30/2022] Open
Abstract
The cecal microbiota plays numerous roles in chicken health and nutrition. Where such microbiota differs between lines exhibiting distinct phenotypes, microbiota transplantation offers scope to dissect the role of gut microbial communities in those traits. However, the composition and stability of transplants over time is relatively ill-defined and varying levels of success have been reported. In this study, we transplanted cecal contents from adult Roslin broilers into chicks from a different broiler line. Within <12 h posthatch, Ross 308 chicks received an oral gavage of cecal contents (n = 26) or a PBS control (n = 24). Cecal contents samples were collected postmortem from birds on d 1, 2, 3, 4, and 7 posthatch. DNA was extracted from these samples and the transplant inoculum and the V4 region of the 16S rRNA gene was amplified and sequenced. The cecal microbiota of chickens receiving the microbiota transplant was significantly different in composition and significantly richer and more diverse, in comparison to control birds. At the final timepoint (d 7), of the 150 Operational Taxonomic Units (OTUs) that were >0.1% abundant (average) in the donor sample, 137 were detected in the treated group (75 were >0.1% abundant (average)) while only 88 were detected in the control group (29 were >0.1% abundant (average)). Our data therefore suggests that stable transplantation of the cecal microbiota between lines is achievable using the methods described in this paper.
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Affiliation(s)
- Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom.
| | - Cosmin Chintoan-Uta
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Mark P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
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22
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Feng Y, Wang Y, Zhu B, Gao GF, Guo Y, Hu Y. Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes. Commun Biol 2021; 4:1305. [PMID: 34795385 PMCID: PMC8602611 DOI: 10.1038/s42003-021-02827-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Gut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes. Feng et al. include genome recovery and data analysis of large number of chicken gut metagenomic datasets which significantly expands the reference genomes available from the chicken gut microbial communities, and catalog the genes prevalent in the gut systems. They further depict the countryspecific chicken gut antibiotic resistomes and the effects of geography and host species on the gut resistome.
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Affiliation(s)
- Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Yanan Wang
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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