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Dallas JW, Warne RW. Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation. Microb Ecol 2023; 85:820-838. [PMID: 35316343 DOI: 10.1007/s00248-022-01991-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.
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Affiliation(s)
- Jason W Dallas
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
| | - Robin W Warne
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
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2
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Chen PC, Lin MS, Lin TC, Kang TW, Ruan JW. The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling. Bioinform Biol Insights 2023; 17:11779322231166229. [PMID: 37077899 PMCID: PMC10108413 DOI: 10.1177/11779322231166229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/11/2023] [Indexed: 04/21/2023] Open
Abstract
Antibiotic treatment has been shown to cause gut microbiota dysbiosis. However, lacking critical features defining gut microbiota dysbiosis makes it challenging to prevent. By co-occurrence network analysis, we found that despite short antibiotic courses eliminating certain microbial taxa, the Akkermansia genus played the role of a high-centrality hub to maintain microbiota homeostasis. When the antibiotic courses continued, the elimination of Akkermansia induced a significant microbiota remodeling of the gut microbiota networks. Based on this finding, we found that under long-term antibiotic stress, the gut microbiota was rearranged into a stable network with a significantly lower Akkermansiaceae/Lachnospiraceae (A/L) ratio and no microbial hub. By functional prediction analysis, we confirmed that the gut microbiota with a low A/L ratio also had enhanced mobile elements and biofilm-formation functions that may be associated with antibiotic resistance. This study identified A/L ratio as an indicator of antibiotic-induced dysbiosis. This work reveals that besides the abundance of specific probiotics, the hierarchical structure also critically impacts the microbiome function. Co-occurrence analysis may help better monitor the microbiome dynamics than only comparing the differentially abundant bacteria between samples.
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Affiliation(s)
- Pei-Chen Chen
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan
| | - Ming-Shian Lin
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi
| | - Tien-Ching Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan
| | - Ting-Wei Kang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan
| | - Jhen-Wei Ruan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan
- Jhen-Wei Ruan, Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, No. 1, University Road, Tainan 701.
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3
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West AG, Digby A, Lear G, Taylor MW, Bromley M, Buckley E, Chatterton J, Cox MP, Cramer RA, Crane J, Dearden PK, Eason D, Fisher MC, Gago S, Gartrell B, Gemmell NJ, Glare TR, Guhlin J, Howard J, Lacap-Bugler D, Le Lec M, Lin XX, Lofgren L, Mackay J, Meis J, Morelli KA, Perrott J, Petterson M, Quinones-Mateu M, Rhodes J, Roberts J, Stajich J, Taylor MW, Tebbutt SJ, Truter-Meyer A, Uddstrom L, Urban L, van Rhijn N, Vercoe D, Vesely E, Weir BS, West AG, Winter DJ, Yeung J, Taylor MW. Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter. Anim Microbiome 2022; 4:55. [PMID: 36175950 PMCID: PMC9523977 DOI: 10.1186/s42523-022-00204-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/29/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The critically endangered kākāpō is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a low-diversity microbiota that is often dominated by Escherichia-Shigella bacteria. Given the importance of associated microbial communities to animal health, and increasing appreciation of their potential relevance to threatened species conservation, we sought to better understand the development of this unusual gut microbiota profile. To this end, we conducted a longitudinal analysis of faecal material collected from kākāpō chicks during the 2019 breeding season, in addition to associated nest litter material. RESULTS Using an experimental approach rarely seen in studies of threatened species microbiota, we evaluated the impact of a regular conservation practice on the developing kākāpō microbiota, namely the removal of faecal material from nests. Artificially removing chick faeces from nests had negligible impact on bacterial community diversity for either chicks or nests (p > 0.05). However, the gut microbiota did change significantly over time as chick age increased (p < 0.01), with an increasing relative abundance of Escherichia-Shigella coli over the study period and similar observations for the associated nest litter microbiota (p < 0.01). Supplementary feeding substantially altered gut bacterial diversity of kākāpō chicks (p < 0.01), characterised by a significant increase in Lactobacillus bacteria. CONCLUSIONS Overall, chick age and hand rearing conditions had the most marked impact on faecal bacterial communities. Similarly, the surrounding nest litter microbiota changed significantly over time since a kākāpō chick was first placed in the nest, though we found no evidence that removal of faecal material influenced the bacterial communities of either litter or faecal samples. Taken together, these observations will inform ongoing conservation and management of this most enigmatic of bird species.
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Affiliation(s)
- Annie G. West
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Andrew Digby
- Department of Conservation, Kākāpō Recovery Team, PO Box 743, Invercargill, New Zealand
| | - Gavin Lear
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Kākāpō Recovery Team
- Department of Conservation, Kākāpō Recovery Team, PO Box 743, Invercargill, New Zealand
| | | | - Michael W. Taylor
- grid.9654.e0000 0004 0372 3343School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
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4
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Gaio D, DeMaere MZ, Anantanawat K, Eamens GJ, Falconer L, Chapman TA, Djordjevic S, Darling AE. Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig. PLoS One 2022; 17:e0270372. [PMID: 35749534 PMCID: PMC9232140 DOI: 10.1371/journal.pone.0270372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.
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Affiliation(s)
- Daniela Gaio
- iThree Institute, University of Technology Sydney, Ultimo, Australia
- * E-mail:
| | | | - Kay Anantanawat
- iThree Institute, University of Technology Sydney, Ultimo, Australia
| | - Graeme J. Eamens
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Linda Falconer
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Steven Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, Australia
| | - Aaron E. Darling
- iThree Institute, University of Technology Sydney, Ultimo, Australia
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5
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Bornbusch SL, Harris RL, Grebe NM, Roche K, Dimac-Stohl K, Drea CM. Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts. Anim Microbiome 2021; 3:65. [PMID: 34598739 PMCID: PMC8485508 DOI: 10.1186/s42523-021-00126-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 09/19/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases. RESULTS Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups. CONCLUSIONS Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.
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Affiliation(s)
| | - Rachel L. Harris
- Department of Evolutionary Anthropology, Duke University, Durham, USA
| | - Nicholas M. Grebe
- Department of Evolutionary Anthropology, Duke University, Durham, USA
| | - Kimberly Roche
- Program in Computational Biology & Bioinformatics, Duke University, Durham, USA
| | | | - Christine M. Drea
- Department of Evolutionary Anthropology, Duke University, Durham, USA
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Campbell TP, Sun X, Patel VH, Sanz C, Morgan D, Dantas G. The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography. ISME J 2020; 14:1584-1599. [PMID: 32203121 DOI: 10.1038/s41396-020-0634-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/25/2022]
Abstract
The gut microbiome can vary across differences in host lifestyle, geography, and host species. By comparing closely related host species across varying lifestyles and geography, we can evaluate the relative contributions of these factors in structuring the composition and functions of the microbiome. Here we show that the gut microbial taxa, microbial gene family composition, and resistomes of great apes and humans are more related by host lifestyle than geography. We show that captive chimpanzees and gorillas are enriched for microbial genera commonly found in non-Westernized humans. Captive ape microbiomes also had up to ~34-fold higher abundance and up to ~5-fold higher richness of all antibiotic resistance genes compared with wild apes. Through functional metagenomics, we identified a number of novel antibiotic resistance genes, including a gene conferring resistance to colistin, an antibiotic of last resort. Finally, by comparing our study cohorts to human and ape gut microbiomes from a diverse range of environments and lifestyles, we find that the influence of host lifestyle is robust to various geographic locations.
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Affiliation(s)
- Tayte P Campbell
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Vishal H Patel
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Crickette Sanz
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Congo Program, Wildlife Conservation Society, Brazzaville, Republic of Congo
| | - David Morgan
- Lincoln Park Zoo, Lester E. Fisher Center, Chicago, IL, 60614, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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7
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Allan N, Knotts TA, Pesapane R, Ramsey JJ, Castle S, Clifford D, Foley J. Conservation Implications of Shifting Gut Microbiomes in Captive-Reared Endangered Voles Intended for Reintroduction into the Wild. Microorganisms 2018; 6:microorganisms6030094. [PMID: 30213049 PMCID: PMC6165168 DOI: 10.3390/microorganisms6030094] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 12/16/2022] Open
Abstract
The Amargosa vole is a highly endangered rodent endemic to a small stretch of the Amargosa River basin in Inyo County, California. It specializes on a single, nutritionally marginal food source in nature. As part of a conservation effort to preserve the species, a captive breeding population was established to serve as an insurance colony and a source of individuals to release into the wild as restored habitat becomes available. The colony has successfully been maintained on commercial diets for multiple generations, but there are concerns that colony animals could lose gut microbes necessary to digest a wild diet. We analyzed feces from colony-reared and recently captured wild-born voles on various diets, and foregut contents from colony and wild voles. Unexpectedly, fecal microbial composition did not greatly differ despite drastically different diets and differences observed were mostly in low-abundance microbes. In contrast, colony vole foregut microbiomes were dominated by Allobaculum sp. while wild foreguts were dominated by Lactobacillus sp. If these bacterial community differences result in beneficial functional differences in digestion, then captive-reared Amargosa voles should be prepared prior to release into the wild to minimize or eliminate those differences to maximize their chance of success.
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Affiliation(s)
- Nora Allan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
- Wildlife Investigations Lab, California Department of Fish and Wildlife, 1701 Nimbus Road, Rancho Cordova, CA 95670, USA.
| | - Trina A Knotts
- Department of Molecular Biosciences, University of California, Davis, CA 95616, USA.
| | - Risa Pesapane
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
| | - Jon J Ramsey
- Department of Molecular Biosciences, University of California, Davis, CA 95616, USA.
| | - Stephanie Castle
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
- Wildlife Investigations Lab, California Department of Fish and Wildlife, 1701 Nimbus Road, Rancho Cordova, CA 95670, USA.
| | - Deana Clifford
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
- Wildlife Investigations Lab, California Department of Fish and Wildlife, 1701 Nimbus Road, Rancho Cordova, CA 95670, USA.
| | - Janet Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
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Vlčková K, Pafčo B, Petrželková KJ, Modrý D, Todd A, Yeoman CJ, Torralba M, Wilson BA, Stumpf RM, White BA, Nelson KE, Leigh SR, Gomez A. Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas. Front Microbiol 2018; 9:1202. [PMID: 29963018 PMCID: PMC6013710 DOI: 10.3389/fmicb.2018.01202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Relationships between gastrointestinal parasites (GIPs) and the gastrointestinal microbiome (GIM) are widely discussed topics across mammalian species due to their possible impact on the host's health. GIPs may change the environment determining alterations in GIM composition. We evaluated the associations between GIP infections and fecal microbiome composition in two habituated and two unhabituated groups of wild western lowland gorillas (Gorilla g. gorilla) from Dzanga Sangha Protected Areas, Central African Republic. We examined 43 fecal samples for GIPs and quantified strongylid nematodes. We characterized fecal microbiome composition through 454 pyrosequencing of the V1-V3 region of the bacterial 16S rRNA gene. Entamoeba spp. infections were associated with significant differences in abundances of bacterial taxa that likely play important roles in nutrition and metabolism for the host, besides being characteristic members of the gorilla gut microbiome. We did not observe any relationships between relative abundances of several bacterial taxa and strongylid egg counts. Based on our findings, we suggest that there is a significant relationship between fecal microbiome and Entamoeba infection in wild gorillas. This study contributes to the overall knowledge about factors involved in modulating GIM communities in great apes.
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Affiliation(s)
- Klára Vlčková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Barbora Pafčo
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia.,Liberec Zoo, Liberec, Czechia.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - David Modrý
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia.,Central European Institute for Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Angelique Todd
- WWF, Dzanga Sangha Protected Areas, Bangui, Central African Republic
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, United States
| | | | - Brenda A Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Rebecca M Stumpf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Bryan A White
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Karen E Nelson
- J. Craig Venter Institute, Rockville, MD, United States.,J. Craig Venter Institute, La Jolla, CA, United States
| | - Steven R Leigh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Anthropology, University of Colorado at Boulder, Boulder, CO, United States
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St Paul, MN, United States
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Ganda EK, Bisinotto RS, Lima SF, Kronauer K, Decter DH, Oikonomou G, Schukken YH, Bicalho RC. Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin. Sci Rep 2016; 6:37565. [PMID: 27874095 DOI: 10.1038/srep37565] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/01/2016] [Indexed: 01/09/2023] Open
Abstract
Antimicrobial usage in food animals has a direct impact on human health, and approximately 80% of the antibiotics prescribed in the dairy industry are used to treat bovine mastitis. Here we provide a longitudinal description of the changes in the microbiome of milk that are associated with mastitis and antimicrobial therapy. Next-generation sequencing, 16 S rRNA gene quantitative real-time PCR, and aerobic culturing were applied to assess the effect of disease and antibiotic therapy on the milk microbiome. Cows diagnosed with clinical mastitis associated with Gram-negative pathogens or negative aerobic culture were randomly allocated into 5 days of Ceftiofur intramammary treatment or remained as untreated controls. Serial milk samples were collected from the affected quarter and the ipsilateral healthy quarter of the same animal. Milk from the mastitic quarter had a higher bacterial load and reduced microbial diversity compared to healthy milk. Resolution of the disease was accompanied by increases in diversity indexes and a decrease in pathogen relative abundance. Escherichia coli-associated mastitic milk samples had a remarkably distinct bacterial profile, dominated by Enterobacteriaceae, when compared to healthy milk. However, no differences were observed in culture-negative mastitis samples when compared to healthy milk. Antimicrobial treatment had no significant effect on clinical cure, bacteriological cure, pathogen clearance rate or bacterial load.
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