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Faleiros CA, Nunes AT, Gonçalves OS, Alexandre PA, Poleti MD, Mattos EC, Perna-Junior F, Rodrigues PHM, Fukumasu H. Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle. Sci Rep 2024; 14:13056. [PMID: 38844487 PMCID: PMC11156634 DOI: 10.1038/s41598-024-63951-7] [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: 12/13/2023] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
Metagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.
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Affiliation(s)
- Camila A Faleiros
- Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Alanne T Nunes
- Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Osiel S Gonçalves
- Department of Microbiology, Institute of Biotechnology Applied to Agriculture (BIOAGRO), Federal University of Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Pâmela A Alexandre
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Brisbane, QLD, Australia
| | - Mirele D Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Elisângela C Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Flavio Perna-Junior
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo (FMVZ-USP), Pirassununga, São Paulo, 13635-900, Brazil
| | - Paulo H Mazza Rodrigues
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo (FMVZ-USP), Pirassununga, São Paulo, 13635-900, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of São Paulo, Pirassununga, SP, 13635-900, Brazil.
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Dillon L, Dimonaco NJ, Creevey CJ. Accessory genes define species-specific routes to antibiotic resistance. Life Sci Alliance 2024; 7:e202302420. [PMID: 38228374 DOI: 10.26508/lsa.202302420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
A deeper understanding of the relationship between the antimicrobial resistance (AMR) gene carriage and phenotype is necessary to develop effective response strategies against this global burden. AMR phenotype is often a result of multi-gene interactions; therefore, we need approaches that go beyond current simple AMR gene identification tools. Machine-learning (ML) methods may meet this challenge and allow the development of rapid computational approaches for AMR phenotype classification. To examine this, we applied multiple ML techniques to 16,950 bacterial genomes across 28 genera, with corresponding MICs for 23 antibiotics with the aim of training models to accurately determine the AMR phenotype from sequenced genomes. This resulted in a >1.5-fold increase in AMR phenotype prediction accuracy over AMR gene identification alone. Furthermore, we revealed 528 unique (often species-specific) genomic routes to antibiotic resistance, including genes not previously linked to the AMR phenotype. Our study demonstrates the utility of ML in predicting AMR phenotypes across diverse clinically relevant organisms and antibiotics. This research proposes a rapid computational method to support laboratory-based identification of the AMR phenotype in pathogens.
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Affiliation(s)
- Lucy Dillon
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Nicholas J Dimonaco
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
- https://ror.org/02fa3aq29 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- https://ror.org/02fa3aq29 Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
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Lee C, Zaheer R, Munns K, Holman DB, Van Domselaar G, Zovoilis A, McAllister TA. Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome. Microorganisms 2023; 11:2982. [PMID: 38138126 PMCID: PMC10745953 DOI: 10.3390/microorganisms11122982] [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: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.
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Affiliation(s)
- Catrione Lee
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
| | - Krysty Munns
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 6000 C and E Trail, Lacombe, AB T4L 1W1, Canada;
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Government of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada;
| | - Athanasios Zovoilis
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
| | - Tim A. McAllister
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
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Diaz GR, Gaire TN, Ferm P, Case L, Caixeta LS, Goldsmith TJ, Armstrong J, Noyes NR. Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves. Anim Microbiome 2023; 5:61. [PMID: 38041127 PMCID: PMC10691087 DOI: 10.1186/s42523-023-00284-2] [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: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described. RESULTS Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance. CONCLUSIONS Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.
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Affiliation(s)
- Gerardo R Diaz
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tara N Gaire
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter Ferm
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lacey Case
- North Central Research and Outreach Center, Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luciano S Caixeta
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Timothy J Goldsmith
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joe Armstrong
- Agricultural and Natural Resource Systems, University of Minnesota Extension, University of Minnesota, St. Paul, MN, 55108, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
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Yan M, Pratama AA, Somasundaram S, Li Z, Jiang Y, Sullivan MB, Yu Z. Interrogating the viral dark matter of the rumen ecosystem with a global virome database. Nat Commun 2023; 14:5254. [PMID: 37644066 PMCID: PMC10465536 DOI: 10.1038/s41467-023-41075-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen microbiome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top-down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.
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Affiliation(s)
- Ming Yan
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Akbar Adjie Pratama
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Sripoorna Somasundaram
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Matthew B Sullivan
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
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Yu S, Li L, Zhao H, Liu M, Jiang L, Zhao Y. Citrus flavonoid extracts alter the profiling of rumen antibiotic resistance genes and virulence factors of dairy cows. Front Microbiol 2023; 14:1201262. [PMID: 37362928 PMCID: PMC10289158 DOI: 10.3389/fmicb.2023.1201262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Citrus flavonoid extracts (CFE) have the potential to reduce rumen inflammation, improve ruminal function, and enhance production performance in ruminants. Our previous studies have investigated the effects of CFE on the structure and function of rumen microbiota in dairy cows. However, it remains unclear whether CFE affects the prevalence of antibiotic resistance genes (ARG) and virulence factors genes (VFG) in the rumen. Therefore, metagenomics was used to identify the rumen ARG and VFG in lactating dairy cows fed with CFE diets. The results showed that CFE significantly reduced the levels of Multidrug and Antiphagocytosis in the rumen (p < 0.05) and increased the levels of Tetracycline, Iron uptake system, and Magnesium uptake system (p < 0.05). Furthermore, the changes were found to have associations with the phylum Lentisphaerae. It was concluded that CFE could be utilized as a natural plant product to regulate virulence factors and antibiotic resistance of rumen microbiota, thereby improving rumen homeostasis and the health of dairy cows.
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Affiliation(s)
- Shiqiang Yu
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Liuxue Li
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Huiying Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ming Liu
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Linshu Jiang
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yuchao Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
- Beijing Beinong Enterprise Management Co., Ltd., Beijing, China
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Kluyveromyces marxianus Ameliorates High-Fat-Diet-Induced Kidney Injury by Affecting Gut Microbiota and TLR4/NF-κB Pathway in a Mouse Model. Cell Microbiol 2023. [DOI: 10.1155/2023/2822094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Objectives. The effects of Kluyveromyces marxianus on high-fat diet- (HFD-) induced kidney injury (KI) were explored. Methods. HFD-induced KI model was established using male C57BL/6 mice and treated with K. marxianus JLU-1016 and acid-resistant (AR) strain JLU-1016A. Glucose tolerance was evaluated via an oral glucose tolerance test (OGTT). KI was measured using Hematoxylin and Eosin (H&E) staining and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) analysis. The chemical indexes were analyzed, including lipid profiles, inflammatory cytokines, and creatinine. The levels of Toll-like receptor 4 (TLR4)/nuclear factor kappa B (NF-κB) or phospho-NF-κB p65 (Ser536) and alpha inhibitor of NF-κB (IκBα) were measured using qPCR and Western blot. The gut microbiota was sequenced using high-throughput sequencing. Results. HFD induction increased OGTT value, KI severity, oxidative stress, inflammatory cytokines, oxidative stress, apoptotic rate, creatinine levels, and the expression of TLR4/NF-κB, phospho-NF-κB p65 (Ser536), and IκBα deteriorated lipid profiles (
) and reduced gut microbiota abundance. K. marxianus treatment ameliorated HFD-induced metabolic disorders and reversed these parameters (
). Compared with the control, HFD induction increased the proportion of Firmicutes but reduced the proportion of Bacteroidetes and Lactobacillus. K. marxianus JLU-1016 and AR strain JLU-1016A treatments improved gut microbiota by reducing the proportion of Firmicutes and increasing the proportion of Bacteroidetes and Lactobacillus in the KI model (
). Helicobacter has been identified with many infectious diseases and was increased after HFD induction and inhibited after K. marxianus JLU-1016 and AR strain JLU-1016A treatments. The strain JLU-1016A exhibited better results possibly with acid-tolerance properties to pass through an acidic environment of the stomach. Conclusions. K. marxianus may have a beneficial effect on KI by improving gut microbiota and inhibiting TLR4/NF-κB pathway activation.
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