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Liu Y, Shu Y, Huang Y, Tan J, Wang F, Tang L, Fang T, Yuan S, Wang L. Microbial Biogeography along the Gastrointestinal Tract of a Wild Chinese Muntjac ( Muntiacus reevesi). Microorganisms 2024; 12:1587. [PMID: 39203429 PMCID: PMC11356339 DOI: 10.3390/microorganisms12081587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 09/03/2024] Open
Abstract
The gut microbiota plays an important role in host nutrient absorption, immune function, and behavioral patterns. Much research on the gut microbiota of wildlife has focused on feces samples, so the microbial composition along the gastrointestinal tract of wildlife is not well reported. To address this gap, we performed high-throughput sequencing of 16s rRNA genes and ITs rRNA genes in the gastrointestinal contents of a wild adult male Chinese muntjac (Muntiacus reevesi) to comparatively analyze the microbial diversity of different gastrointestinal regions. The results showed that the dominant bacterial phyla were Firmicutes (66.19%) and Bacteroidetes (22.7%), while the dominant fungal phyla were Ascomycetes (72.81%). The highest bacterial diversity was found in the stomach, and the highest fungal diversity was found in the cecum. The microbial communities of the large intestine and small intestine were of similar structures, which were distinct from that of the stomach. These results would facilitate the continued exploration of the microbial composition and functional diversity of the gastrointestinal tract of wild Chinese muntjacs and provide a scientific basis for microbial resource conservation of more wildlife.
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Affiliation(s)
- Yuan Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
| | - Yan Shu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
| | - Yuling Huang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
| | - Jinchao Tan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
| | - Fengmei Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
| | - Lin Tang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
| | - Tingting Fang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
| | - Shibin Yuan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
| | - Le Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (Y.L.); (Y.S.); (Y.H.); (J.T.); (F.W.); (L.T.); (T.F.)
- Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control, Nanchong 637009, China
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Johnston SD, Hulse L, Keeley T, Mucci A, Seddon J, Maynard S. The Utility of the Koala Scat: A Scoping Review. BIOLOGY 2024; 13:523. [PMID: 39056716 PMCID: PMC11273466 DOI: 10.3390/biology13070523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/21/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024]
Abstract
The use of samples or scats to provide important ecological, genetic, disease and physiology details on free-range populations is gaining popularity as an alternative non-invasive methodology. Koala populations in SE Queensland and NSW have recently been listed as endangered and continue to face anthropomorphic and stochastic environmental impacts that could potentially lead to their extinction. This scoping review examines the current and potential utility of the koala scat to contribute data relevant to the assessment of koala conservation status and decision making. Although we demonstrate that there is great potential for this methodology in providing details for both individual wild animal and population biology (distribution, abundance, sex ratio, immigration/emigration, genetic diversity, evolutionary significant unit, disease epidemiology, nutrition, reproductive status and stress physiology), the calibre of this information is likely to be a function of the quality of the scat that is sampled.
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Affiliation(s)
- Stephen D. Johnston
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
| | - Lyndal Hulse
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
| | - Tamara Keeley
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
| | - Albano Mucci
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
| | - Jennifer Seddon
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
- Research Division, James Cook University, Townsville 4811, Australia
| | - Sam Maynard
- Saunders Havill Group, Bowen Hills 4006, Australia;
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Kondo K, Suzuki M, Amadaira M, Araki C, Watanabe R, Murakami K, Ochiai S, Ogura T, Hayakawa T. Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas. PeerJ 2024; 12:e17385. [PMID: 38818452 PMCID: PMC11138522 DOI: 10.7717/peerj.17385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Background Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection. Methods Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala's gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection. Results and Discussion This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection. Conclusion We showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas.
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Affiliation(s)
- Kotaro Kondo
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mirei Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mana Amadaira
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Chiharu Araki
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Rie Watanabe
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | | | | | - Tadatoshi Ogura
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
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Jones AL, Pratt CJ, Meili CH, Soo RM, Hugenholtz P, Elshahed MS, Youssef NH. Anaerobic gut fungal communities in marsupial hosts. mBio 2024; 15:e0337023. [PMID: 38259066 PMCID: PMC10865811 DOI: 10.1128/mbio.03370-23] [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: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The anaerobic gut fungi (AGF) inhabit the alimentary tracts of herbivores. In contrast to placental mammals, information regarding the identity, diversity, and community structure of AGF in marsupials is extremely sparse. Here, we characterized AGF communities in 61 fecal samples from 10 marsupial species belonging to four families in the order Diprotodontia: Vombatidae (wombats), Phascolarctidae (koalas), Phalangeridae (possums), and Macropodidae (kangaroos, wallabies, and pademelons). An amplicon-based diversity survey using the D2 region of the large ribosomal subunit as a phylogenetic marker indicated that marsupial AGF communities were dominated by eight genera commonly encountered in placental herbivores (Neocallimastix, Caecomyces, Cyllamyces, Anaeromyces, Orpinomyces, Piromyces, Pecoramyces, and Khoyollomyces). Community structure analysis revealed a high level of stochasticity, and ordination approaches did not reveal a significant role for the animal host, gut type, dietary preferences, or lifestyle in structuring marsupial AGF communities. Marsupial foregut and hindgut communities displayed diversity and community structure patterns comparable to AGF communities typically encountered in placental foregut hosts while exhibiting a higher level of diversity and a distinct community structure compared to placental hindgut communities. Quantification of AGF load using quantitative PCR indicated a significantly smaller load in marsupial hosts compared to their placental counterparts. Isolation efforts were only successful from a single red kangaroo fecal sample and yielded a Khoyollomyces ramosus isolate closely related to strains previously isolated from placental hosts. Our results suggest that AGF communities in marsupials are in low abundance and show little signs of selection based on ecological and evolutionary factors.IMPORTANCEThe AGF are integral part of the microbiome of herbivores. They play a crucial role in breaking down plant biomass in hindgut and foregut fermenters. The majority of research has been conducted on the AGF community in placental mammalian hosts. However, it is important to note that many marsupial mammals are also herbivores and employ a hindgut or foregut fermentation strategy for breaking down plant biomass. So far, very little is known regarding the AGF diversity and community structure in marsupial mammals. To fill this knowledge gap, we conducted an amplicon-based diversity survey targeting AGF in 61 fecal samples from 10 marsupial species. We hypothesize that, given the distinct evolutionary history and alimentary tract architecture, novel and unique AGF communities would be encountered in marsupials. Our results indicate that marsupial AGF communities are highly stochastic, present in relatively low loads, and display community structure patterns comparable to AGF communities typically encountered in placental foregut hosts. Our results indicate that marsupial hosts harbor AGF communities; however, in contrast to the strong pattern of phylosymbiosis typically observed between AGF and placental herbivores, the identity and gut architecture appear to play a minor role in structuring AGF communities in marsupials.
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Affiliation(s)
- Adrienne L. Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Carrie J. Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Rochelle M. Soo
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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McDougall FK, Boardman WS, Speight N, Stephenson T, Funnell O, Smith I, Graham PL, Power ML. Carriage of antibiotic resistance genes to treatments for chlamydial disease in koalas ( Phascolarctos cinereus): A comparison of occurrence before and during catastrophic wildfires. One Health 2023; 17:100652. [PMID: 38024267 PMCID: PMC10665209 DOI: 10.1016/j.onehlt.2023.100652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Growing reports of diverse antibiotic resistance genes in wildlife species around the world symbolises the extent of this global One Health issue. The health of wildlife is threatened by antimicrobial resistance in situations where wildlife species develop disease and require antibiotics. Chlamydial disease is a key threat for koalas in Australia, with infected koalas frequently entering wildlife hospitals and requiring antibiotic therapy, typically with chloramphenicol or doxycycline. This study investigated the occurrence and diversity of target chloramphenicol and doxycycline resistance genes (cat and tet respectively) in koala urogenital and faecal microbiomes. DNA was extracted from 394 urogenital swabs and 91 faecal swabs collected from koalas in mainland Australia and on Kangaroo Island (KI) located 14 km off the mainland, before (n = 145) and during (n = 340) the 2019-2020 wildfires. PCR screening and DNA sequencing determined 9.9% of samples (95%CI: 7.5% to 12.9%) carried cat and/or tet genes, with the highest frequency in fire-affected KI koalas (16.8%) and the lowest in wild KI koalas sampled prior to fires (6.5%). The diversity of cat and tet was greater in fire-affected koalas (seven variants detected), compared to pre-fire koalas (two variants detected). Fire-affected koalas in care that received antibiotics had a significantly higher proportion (p < 0.05) of cat and/or tet genes (37.5%) compared to koalas that did not receive antibiotics (9.8%). Of the cat and/or tet positive mainland koalas, 50.0% were Chlamydia-positive by qPCR test. Chloramphenicol and doxycycline resistance genes in koala microbiomes may contribute to negative treatment outcomes for koalas receiving anti-chlamydial antibiotics. Thus a secondary outcome of wildfires is increased risk of acquisition of cat and tet genes in fire-affected koalas that enter care, potentially exacerbating the already significant threat of chlamydial disease on Australia's koalas. This study highlights the importance of considering impacts to wildlife health within the One Health approach to AMR and identifies a need for greater understanding of AMR ecology in wildlife.
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Affiliation(s)
- Fiona K. McDougall
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Wayne S.J. Boardman
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Tamsyn Stephenson
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Oliver Funnell
- Zoos South Australia, Frome Rd, Adelaide, SA 5001, Australia
| | - Ian Smith
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA 5371, Australia
- Zoos South Australia, Frome Rd, Adelaide, SA 5001, Australia
| | - Petra L. Graham
- School of Mathematical and Physical Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Michelle L. Power
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
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Clough J, Schwab S, Mikac K. Gut Microbiome Profiling of the Endangered Southern Greater Glider ( Petauroides volans) after the 2019-2020 Australian Megafire. Animals (Basel) 2023; 13:3583. [PMID: 38003202 PMCID: PMC10668662 DOI: 10.3390/ani13223583] [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: 10/27/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.
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Affiliation(s)
- Jordyn Clough
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
| | - Sibylle Schwab
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Katarina Mikac
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
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Omaleki L, Blyde D, Hanger J, Loader J, McKay P, Lobo E, Harris LM, Nicolson V, Blackall PJ, Turni C. LONEPINELLA SP. ISOLATED FROM WOUND INFECTIONS OF KOALAS. J Wildl Dis 2023; 59:398-406. [PMID: 37170426 DOI: 10.7589/jwd-d-22-00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/20/2023] [Indexed: 05/13/2023]
Abstract
We describe two cases of wound infections of koalas (Phascolarctos cinereus), one wild and one captive, in which Lonepinella-like organisms were involved. The wild adult koala was captured with bite wound injuries, as part of a koala population management program in Queensland, Australia. In both cases, there was evidence of physical trauma causing the initial wound. The captive koala suffered injury from the cage wire, and the wild koala had injuries suggestive of intermale fighting. Gram-negative bacteria isolated from both cases proved to be challenging to identify using routine diagnostic tests. The wound in the captive koala yielded a pure culture of an organism shown by whole genome sequence (WGS) analysis to be a member of the genus Lonepinella, but not a member of the only formally described species, L. koalarum. The wound of the wild koala yielded a mixed culture of Citrobacter koseri, Enterobacter cloacae and an organism shown by WGS analysis to be Lonepinella, but again not Lonepinella koalarum. Both cases were difficult to treat; the captive koala eventually had to have the phalanges amputated, and the wild koala required removal of the affected claw. The two Lonepinella isolates from these cases have a close relationship to an isolate from a human wound caused by a koala bite and may represent a novel species within the genus Lonepinella. Wound infections in koalas linked to Lonepinella have not been reported previously. Wildlife veterinarians need to be aware of the potential presence of Lonepinella-like organisms when dealing with wound infections in koalas, and the inability of commercial kits and systems to correctly identify the isolates.
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Affiliation(s)
- Lida Omaleki
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - David Blyde
- Sea World Australia, Surfers Paradise, Queensland 4217, Australia
- Dreamworld, Coomera, Queensland 4209, Australia
| | - Jon Hanger
- Endeavour Veterinary Ecology, Toorbul, Queensland, 4510, Australia
| | - Jo Loader
- Endeavour Veterinary Ecology, Toorbul, Queensland, 4510, Australia
| | - Philippa McKay
- Endeavour Veterinary Ecology, Toorbul, Queensland, 4510, Australia
| | - Edina Lobo
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
- Current affiliation: School of Health, Medical and Applied Sciences, Central Queensland University, North Rockhampton, Queensland 4701, Australia
| | | | | | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
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Li Y, Yan Y, Fu H, Jin S, He S, Wang Z, Dong G, Li B, Guo S. Does diet or macronutrients intake drive the structure and function of gut microbiota? Front Microbiol 2023; 14:1126189. [PMID: 36860485 PMCID: PMC9970161 DOI: 10.3389/fmicb.2023.1126189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Shift of ingestive behavior is an important strategy for animals to adapt to change of the environment. We knew that shifts in animal dietary habits lead to changes in the structure of the gut microbiota, but we are not sure about if changes in the composition and function of the gut microbiota respond to changes in the nutrient intake or food items. To investigate how animal feeding strategies affect nutrient intakes and thus alter the composition and digestion function of gut microbiota, we selected a group of wild primate group for the study. We quantified their diet and macronutrients intake in four seasons of a year, and instant fecal samples were analyzed by high-throughput sequencing of 16S rRNA and metagenomics. These results demonstrated that the main reason that causes seasonal shifts of gut microbiota is the macronutrient variation induced by seasonal dietary differences. Gut microbes can help to compensate for insufficient macronutrients intake of the host through microbial metabolic functions. This study contributes to a deeper understanding of the causes of seasonal variation in host-microbial variation in wild primates.
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Affiliation(s)
- Yuhang Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Yujie Yan
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Hengguang Fu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Shiyu Jin
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Shujun He
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Zi Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Guixin Dong
- Guangdong Chimelong Group Co., Ltd., Guangzhou, China,Guangdong South China Rare Wild Animal Species Conservation Center, Zhuhai, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China,Shaanxi Institute of Zoology, Xi’an, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China,Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China,*Correspondence: Songtao Guo,
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Blyton MDJ, Pascoe J, Hynes E, Soo RM, Hugenholtz P, Moore BD. The koala gut microbiome is largely unaffected by host translocation but rather influences host diet. Front Microbiol 2023; 14:1085090. [PMID: 36937253 PMCID: PMC10018171 DOI: 10.3389/fmicb.2023.1085090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/31/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Translocation is a valuable and increasingly used strategy for the management of both threatened and overabundant wildlife populations. However, in some instances the translocated animals fail to thrive. Differences in diet between the source and destination areas may contribute to poor translocation outcomes, which could conceivably be exacerbated if the animals' microbiomes are unsuited to the new diet and cannot adapt. Methods In this study we tracked how the faecal microbiome of a specialist Eucalyptus folivore, the koala (Phascolarctos cinereus), changed over the course of a year after translocation. We assessed microbiome composition by 16S rRNA amplicon sequencing of faecal pellets. Results We found no significant overall changes in the faecal microbiomes of koalas post-translocation (n = 17) in terms of microbial richness, diversity or composition when compared to the faecal microbiomes of koalas from an untranslocated control group (n = 12). This was despite the translocated koalas feeding on a greater variety of Eucalyptus species after translocation. Furthermore, while differences between koalas accounted for half of the microbiome variation, estimated diets at the time of sampling only accounted for 5% of the variation in the koala microbiomes between sampling periods. By contrast, we observed that the composition of koala faecal microbiomes at the time of translocation accounted for 37% of between koala variation in post-translocation diet. We also observed that translocated koalas lost body condition during the first month post-translocation and that the composition of the koalas' initial microbiomes were associated with the magnitude of that change. Discussion These findings suggest that the koala gut microbiome was largely unaffected by dietary change and support previous findings suggesting that the koala gut microbiome influences the tree species chosen for feeding. They further indicate that future research is needed to establish whether the koalas' gut microbiomes are directly influencing their health and condition or whether aspects of the koala gut microbiomes are an indicator of underlying physiological differences or pathologies. Our study provides insights into how animal microbiomes may not always be affected by the extreme upheaval of translocation and highlights that responses may be host species-specific. We also provide recommendations to improve the success of koala translocations in the future.
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Affiliation(s)
- Michaela D. J. Blyton
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, St Lucia, QLD, Australia
- *Correspondence: Michaela D. J. Blyton,
| | - Jack Pascoe
- Conservation Ecology Centre, Cape Otway, VIC, Australia
- School of Ecosystem and Forest Science, University of Melbourne, Parkville, VIC, Australia
| | | | - Rochelle M. Soo
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Ben D. Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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10
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Teklebrhan T, Tan Z, Jonker A. Diet containing sulfur shifted hydrogen metabolism from methanogenesis to alternative sink and influenced fermentation and gut microbial ecosystem of goats. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Condensed and Hydrolyzable Tannins for Reducing Methane and Nitrous Oxide Emissions in Dairy Manure-A Laboratory Incubation Study. Animals (Basel) 2022; 12:ani12202876. [PMID: 36290258 PMCID: PMC9598578 DOI: 10.3390/ani12202876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
The objectives of this study were to (1) examine the effects of plant condensed (CT) and hydrolyzable tannin (HT) extracts on CH4 and N2O emissions; (2) identify the reactions responsible for manure-derived GHG emissions, and (3) examine accompanying microbial community changes in fresh dairy manure. Five treatments were applied in triplicate to the freshly collected dairy manure, including 4% CT, 8% CT, 4% HT, 8% HT (V/V), and control (no tannin addition). Fresh dairy manure was placed into 710 mL glass incubation chambers. In vitro composted dairy manure samples were collected at 0, 24, 48, and 336 h after the start of incubation. Fluxes of N2O and CH4 were measured for 5-min/h for 14 d at a constant ambient incubation temperature of 39 °C. The addition of quebracho CT significantly decreased the CH4 flux rates compared to the tannin-free controls (215.9 mg/m2/h), with peaks of 75.6 and 89.6 mg/m2/h for 4 and 8% CT inclusion rates, respectively. Furthermore, CT significantly reduced cumulative CH4 emission by 68.2 and 57.3% at 4 and 8% CT addition, respectively. The HT treatments failed to affect CH4 reduction. However, both CT and HT reduced (p < 0.001) cumulative and flux rates of N2O emissions. The decrease in CH4 flux with CT was associated with a reduction in the abundance of Bacteroidetes and Proteobacteria.
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12
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Dearing MD, Weinstein SB. Metabolic Enabling and Detoxification by Mammalian Gut Microbes. Annu Rev Microbiol 2022; 76:579-596. [PMID: 35671535 DOI: 10.1146/annurev-micro-111121-085333] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The longstanding interactions between mammals and their symbionts enable thousands of mammal species to consume herbivorous diets. The microbial communities in mammals degrade both plant fiber and toxins. Microbial toxin degradation has been repeatedly documented in domestic ruminants, but similar work in wild mammals is more limited due to constraints on sampling and manipulating the microbial communities in these species. In this review, we briefly describe the toxins commonly encountered in mammalian diets, major classes of biotransformation enzymes in microbes and mammals, and the gut chambers that house symbiotic microbes. We next examine evidence for microbial detoxification in domestic ruminants before providing case studies on microbial toxin degradation in both foregut- and hindgut-fermenting wild mammals. We end by discussing species that may be promising for future investigations, and the advantages and limitations of approaches currently available for studying degradation of toxins by mammalian gut microbes. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- M Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA;
| | - Sara B Weinstein
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA;
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13
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A Peek into the Bacterial Microbiome of the Eurasian Red Squirrel ( Sciurus vulgaris). Animals (Basel) 2022; 12:ani12050666. [PMID: 35268234 PMCID: PMC8909207 DOI: 10.3390/ani12050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 11/18/2022] Open
Abstract
Sciurus vulgaris (the Eurasian red squirrel) is native to Europe and Asia, but due to habitat destruction or fragmentation, interspecific competition, and infectious diseases, especially in European island areas the species finds itself at the brink of extinction. The repopulation of such bare habitats requires healthy squirrel specimens, either translocated from other wild habitats or reintroduced to the wilderness following captive breeding. Captivity, nonetheless, has shown an immense capacity to reshape the structure of wild species’ microbiota, adapting it to the less diverse diet and fewer environmental challenges. Therefore, assessing the differences between “wild” and “captive” microbiota in this species could elucidate if special living conditions are needed in order to augment the survival rate of specimens reintroduced into the wild. Furthermore, the microflora profile of the normal flora of healthy red squirrels raised in captivity could support clinicians in addressing infectious diseases episodes and also raise awareness on the zoonotic risk. Hence, this study aimed at documenting the bacterial species carried by S. vulgaris, disclosing overall similarities and variability patterns of the microbiota identified in individuals from two different living environments. We anticipated that the bacterial community would be less diverse in individuals raised in captivity, owing to their restrictive diet and to unchanging conditions in the enclosure. We also hypothesized that there would be a higher prevalence of zoonotic microorganisms in the captive animals, due to the proximity of humans and of other domestic species. To test this, samples (n = 100) were taken from five body regions of 20 red squirrels, both free-ranging and bred in captivity, processed by classical microbiology techniques, and further identified by biochemical assay (VITEK®2 Compact System). A relatively poor bacterial community, comprising 62 bacterial strains belonging to 18 species and 8 different genera, was identified. Most of these microorganisms were reported for the first time in S. vulgaris. With no discrimination between living environments, the highest prevalence (p < 0.001), was registered in Staphylococcus sciuri (60%; 12/20), followed by Escherichia coli (45%; 9/20) and Bacillus cereus (35%; 7/20). The results suggest unremarkable differences in diversity and richness of the resident aerobic microbiota of S. vulgaris, in relation to the living environment.
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14
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Eisenhofer R, D’Agnese E, Taggart D, Carver S, Penrose B. Microbial biogeography of the wombat gastrointestinal tract. PeerJ 2022; 10:e12982. [PMID: 35228910 PMCID: PMC8881912 DOI: 10.7717/peerj.12982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/01/2022] [Indexed: 01/11/2023] Open
Abstract
Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region-the putative site of primary plant fermentation in wombats-are distinct from the distal colon, and that faecal samples may have limitations in capturing the diversity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account.
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Affiliation(s)
- Raphael Eisenhofer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
| | - Erin D’Agnese
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia,School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America
| | - David Taggart
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, South Australia, Australia,FAUNA Research Alliance, Institute for Land, Water and Society, Kahibah, New South Wales, Australia
| | - Scott Carver
- Department of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Beth Penrose
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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15
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Cabral L, Persinoti GF, Paixão DAA, Martins MP, Morais MAB, Chinaglia M, Domingues MN, Sforca ML, Pirolla RAS, Generoso WC, Santos CA, Maciel LF, Terrapon N, Lombard V, Henrissat B, Murakami MT. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nat Commun 2022; 13:629. [PMID: 35110564 PMCID: PMC8810776 DOI: 10.1038/s41467-022-28310-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy.
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Affiliation(s)
- Lucelia Cabral
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
| | - Douglas A A Paixão
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Marcele P Martins
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
- Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariana A B Morais
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mariana Chinaglia
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
- Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mauricio L Sforca
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Wesley C Generoso
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Clelton A Santos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Lucas F Maciel
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Nicolas Terrapon
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Vincent Lombard
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
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16
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Littleford-Colquhoun BL, Weyrich LS, Hohwieler K, Cristescu R, Frère CH. How microbiomes can help inform conservation: landscape characterisation of gut microbiota helps shed light on additional population structure in a specialist folivore. Anim Microbiome 2022; 4:12. [PMID: 35101152 PMCID: PMC8802476 DOI: 10.1186/s42523-021-00122-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progressive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite this, very little is known about the landscape variability and factors affecting koala gut microbial community dynamics. We used large scale field surveys to evaluate the variation and diversity of koala gut microbiotas and compared these diversity patterns to those detected using a population genetics approach. Scat samples were collected from five locations across South East Queensland with microbiota analysed using 16S rRNA gene amplicon sequencing. RESULTS Across the landscape koala gut microbial profiles showed large variability, with location having a large effect on bacterial community composition and bacterial diversity. Certain bacteria were found to be significantly differentially abundant amongst locations; koalas from Noosa showed a depletion in two bacterial orders (Gastranaerophilales and Bacteroidales) which have been shown to provide beneficial properties to their host. Koala gut microbial patterns were also not found to mirror population genetic patterns, a molecular tool often used to design conservation initiatives. CONCLUSIONS Our data shows that koala gut microbiotas are extremely variable across the landscape, displaying complex micro- and macro- spatial variation. By detecting locations which lack certain bacteria we identified koala populations that may be under threat from future microbial imbalance or dysbiosis. Additionally, the mismatching of gut microbiota and host population genetic patterns exposed important population structure that has previously gone undetected across South East Queensland. Overall, this baseline data highlights the importance of integrating microbiota research into conservation biology in order to guide successful conservation programs such as species translocation and the implementation of faecal inoculations.
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Affiliation(s)
- B. L. Littleford-Colquhoun
- Global Change Ecology, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556 Australia
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912 USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI 02912 USA
| | - L. S. Weyrich
- Department of Anthropology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802 USA
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - K. Hohwieler
- Global Change Ecology, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556 Australia
| | - R. Cristescu
- Global Change Ecology, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556 Australia
| | - C. H. Frère
- Global Change Ecology, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556 Australia
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Blyton MDJ, Soo RM, Hugenholtz P, Moore BD. Characterization of the juvenile koala gut microbiome across wild populations. Environ Microbiol 2022; 24:4209-4219. [PMID: 35018700 DOI: 10.1111/1462-2920.15884] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/21/2021] [Indexed: 11/03/2022]
Abstract
In this study we compared the faecal microbiomes of wild joey koalas (Phascolarctos cinereus) to those of adults, including their mothers, to establish whether gut microbiome maturation and inheritance in the wild is comparable to that seen in captivity. Our findings suggest that joey koala microbiomes slowly shift towards an adult assemblage between 6 and 12 months of age, as the microbiomes of 9-month-old joeys were more similar to those of adults than those of 7-month-olds, but still distinct. At the phylum level, differences between joeys and adults were broadly consistent with those in captivity, with Firmicutes increasing in relative abundance over the joeys' development and Proteobacteria decreasing. Of the fibre-degrading genes that increased in abundance over the development of captive joeys, those involved in hemicellulose and cellulose degradation, but not pectin degradation, were also generally found in higher abundance in adult wild koalas compared to 7-month-olds. Greater maternal inheritance of the faecal microbiome was seen in wild than in captive koalas, presumably due to the more solitary nature of wild koalas. This strong maternal inheritance of the gut microbiome could contribute to the development of localized differences in microbiome composition, population health and diet through spatial clustering of relatives.
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Affiliation(s)
- Michaela D J Blyton
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Rochelle M Soo
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Ben D Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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18
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Furness JB. Comparative and Evolutionary Aspects of the Digestive System and Its Enteric Nervous System Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1383:165-177. [PMID: 36587156 DOI: 10.1007/978-3-031-05843-1_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
All life forms must gain nutrients from the environment and from single cell organisms to mammals a digestive system is present. Components of the digestive system that are recognized in mammals can be seen in the sea squirt that has had its current form for around 500my. Nevertheless, in mammals, the organ system that is most varied is the digestive system, its architecture being related to the dietary niche of each species. Forms include those of foregut or hindgut fermenters, single or multicompartment stomachs and short or capacious large intestines. Dietary niches include nectarivores, folivores, carnivores, etc. The human is exceptional in that, through food preparation (>80% of human consumption is prepared food in modern societies), humans can utilize a wider range of foods than other species. They are cucinivores, food preparers. In direct descendants of simple organisms, such as sponges, there is no ENS, but as the digestive tract becomes more complex, it requires integrated control of the movement and assimilation of its content. This is achieved by the nervous system, notably the enteric nervous system (ENS) and an array of gut hormones. An ENS is first observed in the phylum cnidaria, exemplified by hydra. But hydra has no collections of neurons that could in any way be regarded as a central nervous system. All animals more complex than hydra have an ENS, but not all have a CNS. In mammals, the ENS is extensive and is necessary for control of movement, enteric secretions and local blood flow, and regulation of the gut immune system. In animals with a CNS, the ENS and CNS have reciprocal connections. From hydra to human, an ENS is essential to life.
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Affiliation(s)
- John B Furness
- Digestive Physiology and Nutrition Laboratories, Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia.
- Department of Anatomy & Physiology, University of Melbourne, Parkville, VIC, Australia.
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19
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Blyton MDJ, Soo RM, Hugenholtz P, Moore BD. Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development. Environ Microbiol 2021; 24:475-493. [PMID: 34863030 DOI: 10.1111/1462-2920.15858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/02/2021] [Accepted: 11/20/2021] [Indexed: 11/27/2022]
Abstract
The acquisition and maturation of the gastrointestinal microbiome is a crucial aspect of mammalian development, particularly for specialist herbivores such as the koala (Phascolarctos cinereus). Joey koalas are thought to be inoculated with microorganisms by feeding on specialized maternal faeces (pap). We found that compared to faeces, pap has higher microbial density, higher microbial evenness and a higher proportion of rare taxa, which may facilitate the establishment of those taxa in joey koalas. We show that the microbiomes of captive joey koalas were on average more similar to those of their mothers than to other koalas, indicating strong maternal inheritance of the faecal microbiome, which can lead to intergenerational gut dysbiosis when the mother is ill. Directly after pap feeding, the joey koalas' microbiomes were enriched for milk-associated bacteria including Bacteroides fragilis, suggesting a conserved role for this species across mammalian taxa. The joeys' microbiomes then changed slowly over 5 months to resemble those of adults by 1 year of age. The relative abundance of fibrolytic bacteria and genes involved in the degradation of plant cell walls also increased in the infants over this time, likely in response to an increased proportion of Eucalyptus leaves in their diets.
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Affiliation(s)
- Michaela D J Blyton
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Qld, St Lucia, 4072, Australia
| | - Rochelle M Soo
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Qld, St Lucia, 4072, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Qld, St Lucia, 4072, Australia
| | - Ben D Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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20
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Martínez‐Romero E, Aguirre‐Noyola JL, Bustamante‐Brito R, González‐Román P, Hernández‐Oaxaca D, Higareda‐Alvear V, Montes‐Carreto LM, Martínez‐Romero JC, Rosenblueth M, Servín‐Garcidueñas LE. We and herbivores eat endophytes. Microb Biotechnol 2021; 14:1282-1299. [PMID: 33320440 PMCID: PMC8313258 DOI: 10.1111/1751-7915.13688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Health depends on the diet and a vegetal diet promotes health by providing fibres, vitamins and diverse metabolites. Remarkably, plants may also provide microbes. Fungi and bacteria that reside inside plant tissues (endophytes) seem better protected to survive digestion; thus, we investigated the reported evidence on the endophytic origin of some members of the gut microbiota in animals such as panda, koala, rabbits and tortoises and several herbivore insects. Data examined here showed that some members of the herbivore gut microbiota are common plant microbes, which derived to become stable microbiota in some cases. Endophytes may contribute to plant fibre or antimetabolite degradation and synthesis of metabolites with the plethora of enzymatic activities that they display; some may have practical applications, for example, Lactobacillus plantarum found in the intestinal tract, plants and in fermented food is used as a probiotic that may defend animals against bacterial and viral infections as other endophytic-enteric bacteria do. Clostridium that is an endophyte and a gut bacterium has remarkable capabilities to degrade cellulose by having cellulosomes that may be considered the most efficient nanomachines. Cellulose degradation is a challenge in animal digestion and for biofuel production. Other endophytic-enteric bacteria may have cellulases, pectinases, xylanases, tannases, proteases, nitrogenases and other enzymatic capabilities that may be attractive for biotechnological developments, indeed many endophytes are used to promote plant growth. Here, a cycle of endophytic-enteric-soil-endophytic microbes is proposed which has relevance for health and comprises the fate of animal faeces as natural microbial inoculants for plants that constitute bacterial sources for animal guts.
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Affiliation(s)
| | | | | | - Pilar González‐Román
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
| | | | | | | | | | - Mónica Rosenblueth
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
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21
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Spring S, Premathilake H, Bradway C, Shili C, DeSilva U, Carter S, Pezeshki A. Effect of very low-protein diets supplemented with branched-chain amino acids on energy balance, plasma metabolomics and fecal microbiome of pigs. Sci Rep 2020; 10:15859. [PMID: 32985541 PMCID: PMC7523006 DOI: 10.1038/s41598-020-72816-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/07/2020] [Indexed: 12/31/2022] Open
Abstract
Feeding pigs with very-low protein (VLP) diets while supplemented with limiting amino acids (AA) results in decreased growth. The objective of this study was to determine if supplementing VLP diets with branched-chain AA (BCAA) would reverse the negative effects of these diets on growth and whether this is associated with alterations in energy balance, blood metabolomics and fecal microbiota composition. Twenty-four nursery pigs were weight-matched, individually housed and allotted into following treatments (n = 8/group): control (CON), low protein (LP) and LP supplemented with BCAA (LP + BCAA) for 4 weeks. Relative to CON, pigs fed with LP had lower feed intake (FI) and body weight (BW) throughout the study, but those fed with LP + BCAA improved overall FI computed for 4 weeks, tended to increase the overall average daily gain, delayed the FI and BW depression for ~ 2 weeks and had transiently higher energy expenditure. Feeding pigs with LP + BCAA impacted the phenylalanine and protein metabolism and fatty acids synthesis pathways. Compared to CON, the LP + BCAA group had higher abundance of Paludibacteraceae and Synergistaceae and reduced populations of Streptococcaceae, Oxyphotobacteria_unclassified, Pseudomonadaceae and Shewanellaceae in their feces. Thus, supplementing VLP diets with BCAA temporarily annuls the adverse effects of these diets on growth, which is linked with alterations in energy balance and metabolic and gut microbiome profile.
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Affiliation(s)
- Shelby Spring
- Department of Animal and Food Sciences, Oklahoma State University, 206C Animal Science Building, Stillwater, OK, 74078, USA
| | - Hasitha Premathilake
- Department of Animal and Food Sciences, Oklahoma State University, 206C Animal Science Building, Stillwater, OK, 74078, USA
| | - Chloe Bradway
- Department of Animal and Food Sciences, Oklahoma State University, 206C Animal Science Building, Stillwater, OK, 74078, USA
| | - Cedrick Shili
- Department of Animal and Food Sciences, Oklahoma State University, 206C Animal Science Building, Stillwater, OK, 74078, USA
| | - Udaya DeSilva
- Department of Animal and Food Sciences, Oklahoma State University, 206C Animal Science Building, Stillwater, OK, 74078, USA
| | - Scott Carter
- Department of Animal and Food Sciences, Oklahoma State University, 206C Animal Science Building, Stillwater, OK, 74078, USA
| | - Adel Pezeshki
- Department of Animal and Food Sciences, Oklahoma State University, 206C Animal Science Building, Stillwater, OK, 74078, USA.
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22
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Mesquita EYE, Soares PC, Mello LR, Freire ECB, Lima AR, Giese EG, Branco É. Sloths (Bradypus variegatus) as a polygastric mammal. Microsc Res Tech 2020; 84:79-88. [PMID: 32914926 DOI: 10.1002/jemt.23568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/04/2020] [Accepted: 07/20/2020] [Indexed: 11/07/2022]
Abstract
Fermentative herbivorous animals have peculiar conformations of the digestive system. It is known that B. variegatus obtained the capacity for evolutionary adaptation, due to their ecology and eating habits. However, despite the literature on feeding management for this species, there is a lack of published information regarding its gastric morphology, and such information would support a better understanding on the diet and digestion of these individuals. We found seven gastric compartments, which histologically revealed three distinct patterns: an aglandular keratinized fraction (mechanical stomach) and two glandular fractions, one a mucus secretor and the other one composed of acid secreting cells (chemical stomach). With these evidences we understand that these individuals have gastric resemblance to ruminants, with some inherent peculiarities of this species, including the transit of the bolus.
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Affiliation(s)
- Ellen Y E Mesquita
- Federal Rural University of Amazonia - UFRA Laboratory of Animal Morphology Research, Institute of Animal Health and Production - ISPA, Belém, PA, Brazil.,University of Amazonia, Belém, PA, Brazil
| | - Paola C Soares
- Federal Rural University of Amazonia - UFRA Laboratory of Animal Morphology Research, Institute of Animal Health and Production - ISPA, Belém, PA, Brazil
| | - Luise R Mello
- Federal Rural University of Amazonia - UFRA Laboratory of Animal Morphology Research, Institute of Animal Health and Production - ISPA, Belém, PA, Brazil
| | - Elisa C B Freire
- Federal Rural University of Amazonia - UFRA Laboratory of Animal Morphology Research, Institute of Animal Health and Production - ISPA, Belém, PA, Brazil
| | - Ana R Lima
- Federal Rural University of Amazonia - UFRA Laboratory of Animal Morphology Research, Institute of Animal Health and Production - ISPA, Belém, PA, Brazil
| | - Elane G Giese
- Federal Rural University of Amazonia - UFRA Laboratory of Animal Morphology Research, Institute of Animal Health and Production - ISPA, Belém, PA, Brazil.,Federal Rural University of Amazonia - UFRA Laboratory of Animal Histology and Embryology, Institute of Animal Health and Production - ISPA, Belém, PA, Brazil
| | - Érika Branco
- Federal Rural University of Amazonia - UFRA Laboratory of Animal Morphology Research, Institute of Animal Health and Production - ISPA, Belém, PA, Brazil
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23
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Fan C, Zhang L, Fu H, Liu C, Li W, Cheng Q, Zhang H, Jia S, Zhang Y. Enterotypes of the Gut Microbial Community and Their Response to Plant Secondary Compounds in Plateau Pikas. Microorganisms 2020; 8:microorganisms8091311. [PMID: 32872148 PMCID: PMC7563992 DOI: 10.3390/microorganisms8091311] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
Animal gut microbiomes can be clustered into “enterotypes” characterized by an abundance of signature genera. The characteristic determinants, stability, and resilience of these community clusters remain poorly understood. We used plateau pika (Ochotona curzoniae) as a model and identified three enterotypes by 16S rDNA sequencing. Among the top 15 genera, 13 showed significantly different levels of abundance between the enterotypes combined with different microbial functions and distinct fecal short-chain fatty acids. We monitored changes in the microbial community associated with the transfer of plateau pikas from field to laboratory and observed that feeding them a single diet reduced microbial diversity, resulting in a single enterotype with an altered composition of the dominant bacteria. However, microbial diversity, an abundance of some changed dominant genera, and enterotypes were partially restored after adding swainsonine (a plant secondary compound found in the natural diet of plateau pikas) to the feed. These results provide strong evidence that gut microbial diversity and enterotypes are directly related to specific diet, thereby indicating that the formation of different enterotypes can help animals adapt to complex food conditions. Additionally, natural plant secondary compounds can maintain dominant bacteria and inter-individual differences of gut microbiota and promote the resilience of enterotypes in small herbivorous mammals.
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Affiliation(s)
- Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Haibo Fu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanfa Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence: (S.J.); (Y.Z.)
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- Correspondence: (S.J.); (Y.Z.)
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24
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Chong R, Cheng Y, Hogg CJ, Belov K. Marsupial Gut Microbiome. Front Microbiol 2020; 11:1058. [PMID: 32547513 PMCID: PMC7272691 DOI: 10.3389/fmicb.2020.01058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Threatened species are often housed in captivity, and during this process undergo considerable changes to their gut microbiome. Studying the gut microbiome of captive animals therefore allows identification of dysbiosis and opportunities for improving management practices in captivity and for subsequent translocations. Manipulation of the gut microbiome through methods such as fecal transplant may offer an innovative means of restoring dysbiotic microbiomes in threatened species to provide health benefits. Finally, characterization of the gut microbiome (including the viral components, or virome) provides important baseline health information and may lead to discovery of significant microbial pathogens. Here we summarize our current understanding of microbiomes in Australian marsupial species.
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Affiliation(s)
- Rowena Chong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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25
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Budd K, Gunn JC, Finch T, Klymus K, Sitati N, Eggert LS. Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna ( Loxodonta africana) and forest elephants ( L. cyclotis). Ecol Evol 2020; 10:5637-5650. [PMID: 32607180 PMCID: PMC7319146 DOI: 10.1002/ece3.6305] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/05/2023] Open
Abstract
The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6-5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome composition. Additionally, we examined the influence of habitat types (forest versus savanna) and diet types (crop-raiding versus noncrop-raiding) on the microbiome within L. africana. We found 58 bacterial orders, representing 16 phyla, across all African elephant samples. The most common phyla were Firmicutes, Proteobacteria, and Bacteroidetes. The microbiome of L. africana was dominated by Firmicutes, similar to other hindgut fermenters, while the microbiome of L. cyclotis was dominated by Proteobacteria, similar to more frugivorous species. Alpha diversity did not differ across species, habitat type, or diet, but beta diversity indicated that microbial communities differed significantly among species, diet types, and habitat types. Based on predicted KEGG metabolic pathways, we also found significant differences between species, but not habitat or diet, in amino acid metabolism, energy metabolism, and metabolism of terpenoids and polyketides. Understanding the digestive capabilities of these elephant species could aid in their captive management and ultimately their conservation.
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Affiliation(s)
- Kris Budd
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Joe C. Gunn
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Tabitha Finch
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
- Vermont Genetics NetworkUniversity of VermontBurlingtonVTUSA
| | - Katy Klymus
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
- Columbia Environmental Research CenterUnited States Geological SurveyColumbiaMOUSA
| | - Noah Sitati
- World Wide Fund for NatureDar es SalaamTanzania
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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26
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Siccibacter turicensis from Kangaroo Scats: Possible Implication in Cellulose Digestion. Microorganisms 2020; 8:microorganisms8050635. [PMID: 32349400 PMCID: PMC7284360 DOI: 10.3390/microorganisms8050635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 11/19/2022] Open
Abstract
Microbiota in the kangaroo gut degrade cellulose, contributing to the kangaroo’s energy and survival. In this preliminary study, to discover more about the gut microbes that contribute to the survival of kangaroos, cellulose-degrading bacteria were isolated from kangaroo scats by selection on solidified media containing carboxymethyl cellulose as the main carbon source. One frequently occurring aerobic bacterium was Siccibacter turicensis, a microbe previously isolated in fruit powder and from a patient with angular cheilitis. The whole genome sequence of the kangaroo isolate was obtained using the Illumina MiSeq platform. Its sequence shared 97.98% identity of the S. turicensis Type strain, and the ability of the Type strain to degrade cellulose was confirmed. Analysis of the genomic data focused on the cellulose operon. In addition to genes from the operon, we suggest that a gene following the operon may have an important role in regulating cellulose metabolism by signal transduction. This is the first report of S. turicensis found within microbiota of the animal gut. Because of its frequent presence in the kangaroo gut, we suggest that S. turicensis plays a role in cellulose digestion for kangaroos.
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27
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Krishna SBN, Dubey A, Malla MA, Kothari R, Upadhyay CP, Adam JK, Kumar A. Integrating Microbiome Network: Establishing Linkages Between Plants, Microbes and Human Health. Open Microbiol J 2019. [DOI: 10.2174/1874285801913020330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The trillions of microbes that colonize and live around us govern the health of both plants and animals through a cascade of direct and indirect mechanisms. Understanding of this enormous and largely untapped microbial diversity has been the focus of microbial research from the past few decades or so. Amidst the advancements in sequencing technologies, significant progress has been made to taxonomically and functionally catalogue these microbes and also to establish their exact role in the health and disease state. In comparison to the human microbiome, plants are also surrounded by a vast diversity of microbes that form complex ecological communities that affect plant growth and health through collective metabolic activities and interactions. This plant microbiome has a substantial influence on human health and environment via its passage through the nasal route and digestive tract and is responsible for changing our gut microbiome. This review primarily focused on the advances and challenges in microbiome research at the interface of plant and human, and role of microbiome at different compartments of the body’s ecosystems along with their correlation to health and diseases. This review also highlighted the potential therapies in modulating the gut microbiota and technologies for studying the microbiome.
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28
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Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala. Anim Microbiome 2019; 1:6. [PMID: 33499955 PMCID: PMC7803123 DOI: 10.1186/s42523-019-0008-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
Background Differences between individuals in their gastrointestinal microbiomes can lead to variation in their ability to persist on particular diets. Koalas are dietary specialists, feeding almost exclusively on Eucalyptus foliage but many individuals will not feed on particular Eucalyptus species that are adequate food for other individuals, even when facing starvation. We undertook a faecal inoculation experiment to test whether a koala’s gastrointestinal (GI) microbiome influences their diet. Wild-caught koalas that initially fed on the preferred manna gum (Eucalyptus viminalis) were brought into captivity and orally inoculated with encapsulated material derived from faeces from koalas feeding on either the less preferred messmate (E. obliqua; treatment) or manna gum (control). Results The gastrointestinal microbiomes of wild koalas feeding primarily on manna gum were distinct from those feeding primarily on messmate. We found that the gastrointestinal microbiomes of koalas were unresponsive to dietary changes because the control koalas’ GI microbiomes did not change even when the nocturnal koalas were fed exclusively on messmate overnight. We showed that faecal inoculations can assist the GI microbiomes of koalas to change as the treatment koalas’ GI microbiomes became more similar to those of wild koalas feeding on messmate. There was no overall difference between the control and treatment koalas in the quantity of messmate they consumed. However, the greater the change in the koalas’ GI microbiomes, the more messmate they consumed after the inoculations had established. Conclusions The results suggest that dietary changes can only lead to changes in the GI microbiomes of koalas if the appropriate microbial species are present, and/or that the koala gastrointestinal microbiome influences diet selection. Electronic supplementary material The online version of this article (10.1186/s42523-019-0008-0) contains supplementary material, which is available to authorized users.
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29
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Speight KN, Houston-Francis M, Mohammadi-Dehcheshmeh M, Ebrahimie E, Saputra S, Trott DJ. Oxalate-degrading bacteria, including Oxalobacter formigenes, colonise the gastrointestinal tract of healthy koalas (Phascolarctos cinereus) and those with oxalate nephrosis. Aust Vet J 2019; 97:166-170. [PMID: 31025325 DOI: 10.1111/avj.12799] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/17/2019] [Accepted: 02/21/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND Koalas in the Mount Lofty Ranges, South Australia, have a high prevalence of oxalate nephrosis, or calcium oxalate kidney crystals. Gastrointestinal tract oxalate-degrading bacteria, particularly Oxalobacter formigenes, have been identified in other animal species and humans, and their absence or low abundance is postulated to increase the risk of renal oxalate diseases. This study aimed to identify oxalate-degrading bacteria in the gastrointestinal tract of koalas and determine their association with oxalate nephrosis. METHODS Caecal and faecal samples were collected at necropsy from 22 Mount Lofty Ranges koalas that had been euthanased on welfare grounds, with 8 koalas found to have oxalate nephrosis by renal histopathology. Samples were analysed by PCR for the oxc gene, which encodes oxalyl-CoA decarboxylase, and also by Illumina sequencing of the V3-V4 region of the bacterial 16S rRNA gene. RESULTS The oxc gene was detected in 100% of koala samples, regardless of oxalate nephrosis status. Oxalobacter formigenes was detected in all but one faecal sample, with no difference in abundance between koalas affected and unaffected by oxalate nephrosis. Other species of known oxalate-degrading bacteria were infrequently detected. CONCLUSION This is the first study to identify Oxalobacter and other oxalate-degrading bacterial species in koalas, but an association with oxalate nephrosis and absence or low abundance of Oxalobacter was not found. This suggests other mechanisms underlie the risk of oxalate nephrosis in koalas.
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Affiliation(s)
- K N Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - M Houston-Francis
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - M Mohammadi-Dehcheshmeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - E Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia.,School of Medicine, The University of Adelaide, SA, Australia
| | - S Saputra
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - D J Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
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30
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Brice KL, Trivedi P, Jeffries TC, Blyton MDJ, Mitchell C, Singh BK, Moore BD. The Koala ( Phascolarctos cinereus) faecal microbiome differs with diet in a wild population. PeerJ 2019; 7:e6534. [PMID: 30972242 PMCID: PMC6448554 DOI: 10.7717/peerj.6534] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/28/2019] [Indexed: 12/25/2022] Open
Abstract
Background The diet of the koala (Phascolarctos cinereus) is comprised almost exclusively of foliage from the genus Eucalyptus (family Myrtaceae). Eucalyptus produces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist, and although dietary specialisation is rare in mammalian herbivores, it has been found elsewhere to promote a highly-conserved but low-diversity gut microbiome. The gut microbes of dietary specialists have been found sometimes to enhance tolerance of dietary PSMs, facilitating competition-free access to food. Although the koala and its gut microbes have evolved together to utilise a low nutrient, potentially toxic diet, their gut microbiome has not previously been assessed in conjunction with diet quality. Thus, linking the two may provide new insights in to the ability of the koala to extract nutrients and detoxify their potentially toxic diet. Method The 16S rRNA gene was used to characterise the composition and diversity of faecal bacterial communities from a wild koala population (n = 32) comprising individuals that predominately eat either one of two different food species, one the strongly preferred and relatively nutritious species Eucalyptus viminalis, the other comprising the less preferred and less digestible species Eucalyptus obliqua. Results Alpha diversity indices indicated consistently and significantly lower diversity and richness in koalas eating E. viminalis. Assessment of beta diversity using both weighted and unweighted UniFrac matrices indicated that diet was a strong driver of both microbial community structure, and of microbial presence/absence across the combined koala population and when assessed independently. Further, principal coordinates analysis based on both the weighted and unweighted UniFrac matrices for the combined and separated populations, also revealed a separation linked to diet. During our analysis of the OTU tables we also detected a strong association between microbial community composition and host diet. We found that the phyla Bacteroidetes and Firmicutes were co-dominant in all faecal microbiomes, with Cyanobacteria also co-dominant in some individuals; however, the E. viminalis diet produced communities dominated by the genera Parabacteroides and/or Bacteroides, whereas the E. obliqua-associated diets were dominated by unidentified genera from the family Ruminococcaceae. Discussion We show that diet differences, even those caused by differential consumption of the foliage of two species from the same plant genus, can profoundly affect the gut microbiome of a specialist folivorous mammal, even amongst individuals in the same population. We identify key microbiota associated with each diet type and predict functions within the microbial community based on 80 previously identified Parabacteroides and Ruminococcaceae genomes.
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Affiliation(s)
- Kylie L Brice
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Bioagricultural Sciences & Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Pankaj Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Bioagricultural Sciences & Pest Management, Colorado State University, Fort Collins, CO, United States of America.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Michaela D J Blyton
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Christopher Mitchell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Ben D Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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Ren L, Holzknecht RA, Holzknecht ZE, Kotzé SH, Bowles DE, Lin SS, McKenney EA, Parker W. A mole rat's gut microbiota suggests selective influence of diet on microbial niche space and evolution. Exp Biol Med (Maywood) 2019; 244:471-483. [PMID: 30760029 DOI: 10.1177/1535370219828703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
IMPACT STATEMENT The composition of the microbiota is of critical importance for health and disease, and is receiving increased scientific and medical scrutiny. Of particular interest is the role of changing diets as a function of agriculture and, perhaps to an even greater extent, modern food processing. To probe the connection between diet and the gut's microbial community, the microbiota from a mole rat, a rodent with a relatively unusual diet, was analyzed in detail, and the microbes found were compared with previously identified organisms. The results show evidence of an adaptive radiation of some microbial clades, but relative stability in others. This suggests that the microbiota, like the genome, carries with it housekeeping components as well as other components which can evolve rapidly when the environment changes. This study provides a very broad view of the niche space in the gut and how factors such as diet might influence that niche space.
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Affiliation(s)
- Linda Ren
- 1 Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Robert A Holzknecht
- 1 Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Zoie E Holzknecht
- 1 Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Sanet H Kotzé
- 2 Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town 8000, South Africa
| | - Dawn E Bowles
- 1 Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Shu S Lin
- 1 Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Erin A McKenney
- 3 Department of Biology, Duke University, Durham, NC 27710, USA
| | - William Parker
- 1 Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
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32
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Wei F, Wu Q, Hu Y, Huang G, Nie Y, Yan L. Conservation metagenomics: a new branch of conservation biology. SCIENCE CHINA-LIFE SCIENCES 2018; 62:168-178. [PMID: 30588567 DOI: 10.1007/s11427-018-9423-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/06/2018] [Indexed: 12/11/2022]
Abstract
Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.
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Affiliation(s)
- Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yonggang Nie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Li Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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Phillips S, Robbins A, Loader J, Hanger J, Booth R, Jelocnik M, Polkinghorne A, Timms P. Chlamydia pecorum gastrointestinal tract infection associations with urogenital tract infections in the koala (Phascolarctos cinereus). PLoS One 2018; 13:e0206471. [PMID: 30383822 PMCID: PMC6211709 DOI: 10.1371/journal.pone.0206471] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 10/12/2018] [Indexed: 11/21/2022] Open
Abstract
Background Chlamydia infects multiple sites within hosts, including the gastrointestinal tract (GIT). In certain hosts, gastrointestinal infection is linked to treatment avoidance and self-infection at disease susceptible sites. GIT C. pecorum has been detected in livestock and koalas, however GIT prevalence rates within the koala are yet to be established. Methods Paired conjunctival, urogenital and rectal samples from 33 koalas were screened for C. pecorum and C. pecorum plasmid using 16S rRNA and CDS5-specific quantitative PCR assays, respectively. Amplicon sequencing of 359 bp ompA fragment was used to identify site-specific genotypes. Results The overall C. pecorum prevalence collectively (healthy and clinically diseased koalas) was 51.5%, 57.6% and 42.4% in urogenital, conjunctival and gastrointestinal sites, respectively. Concurrent urogenital and rectal Chlamydia was identified in 14 koalas, with no cases of GIT only Chlamydia shedding. The ompA genotype G dominated the GIT positive samples, and genotypes A and E’ were dominant in urogenital tract (UGT) positive samples. Increases in C. pecorum plasmid per C. pecorum load (detected by PCR) showed clustering in the clinically diseased koala group (as assessed by scatter plot analysis). There was also a low correlation between plasmid positivity and C. pecorum infected animals at any site, with a prevalence of 47% UGT, 36% rectum and 40% faecal pellet. Conclusions GIT C. pecorum PCR positivity suggests that koala GIT C. pecorum infections are common and occur regularly in animals with concurrent genital tract infections. GIT dominant genotypes were identified and do not appear to be related to plasmid positivity. Preliminary results indicated a possible association between C. pecorum plasmid load and clinical UGT disease.
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Affiliation(s)
- Samuel Phillips
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
- * E-mail:
| | - Amy Robbins
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Australia
| | - Joanne Loader
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Australia
| | | | | | - Martina Jelocnik
- Animal Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
| | - Adam Polkinghorne
- Animal Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
| | - Peter Timms
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, The University of the Sunshine Coast, Queensland, Australia
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34
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McKenney EA, Maslanka M, Rodrigo A, Yoder AD. Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes. MICROBIAL ECOLOGY 2018; 76:272-284. [PMID: 29188302 DOI: 10.1007/s00248-017-1114-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/20/2017] [Indexed: 05/25/2023]
Abstract
Bamboo specialization is one of the most extreme examples of convergent herbivory, yet it is unclear how this specific high-fiber diet might selectively shape the composition of the gut microbiome compared to host phylogeny. To address these questions, we used deep sequencing to investigate the nature and comparative impact of phylogenetic and dietary selection for specific gut microbial membership in three bamboo specialists-the bamboo lemur (Hapalemur griseus, Primates: Lemuridae), giant panda (Ailuropoda melanoleuca, Carnivora: Ursidae), and red panda (Ailurus fulgens, Carnivora: Musteloideadae), as well as two phylogenetic controls-the ringtail lemur (Lemur catta) and the Asian black bear (Ursus thibetanus). We detected significantly higher Shannon diversity in the bamboo lemur (10.029) compared to both the giant panda (8.256; p = 0.0001936) and the red panda (6.484; p = 0.0000029). We also detected significantly enriched bacterial taxa that distinguished each species. Our results complement previous work in finding that phylogeny predominantly governs high-level microbiome community structure. However, we also find that 48 low-abundance OTUs are shared among bamboo specialists, compared to only 8 OTUs shared by the bamboo lemur and its sister species, the ringtail lemur (Lemur catta, a generalist). Our results suggest that deep sequencing is necessary to detect low-abundance bacterial OTUs, which may be specifically adapted to a high-fiber diet. These findings provide a more comprehensive framework for understanding the evolution and ecology of the microbiome as well as the host.
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Affiliation(s)
- Erin A McKenney
- Department of Biology, Duke University, Durham, NC, USA.
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.
| | - Michael Maslanka
- Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC, USA
| | - Allen Rodrigo
- Department of Biology, Duke University, Durham, NC, USA
- Australia National University, Canberra, Australia
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
- Duke Lemur Center, Duke University, Durham, NC, USA
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35
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Legione AR, Amery-Gale J, Lynch M, Haynes L, Gilkerson JR, Sansom FM, Devlin JM. Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without 'wet bottom'. PLoS One 2018; 13:e0194881. [PMID: 29579080 PMCID: PMC5868818 DOI: 10.1371/journal.pone.0194881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
Koalas (Phascolarctos cinereus) are iconic Australian marsupials currently threatened by several processes, including infectious diseases and ecological disruption. Infection with Chlamydia pecorum, is considered a key driver of population decline. The clinical sign of 'wet bottom', a staining of the rump associated with urinary incontinence, is often caused by chlamydial urinary tract infections. However, wet bottom has been recorded in koalas free of C. pecorum, suggesting other causative agents in those individuals. We used 16S rRNA diversity profiling to investigate the microbiome of the urogenital tract of ten female koalas in order to identify potential causative agents of wet bottom, other than C. pecorum. Five urogenital samples were processed from koalas presenting with wet bottom and five were clinically normal. All koalas were negative for C. pecorum infection. We detected thirteen phyla across the ten samples, with Firmicutes occurring at the highest relative abundance (77.6%). The order Lactobacillales, within the Firmicutes, comprised 70.3% of the reads from all samples. After normalising reads using DESeq2 and testing for significant differences (P < 0.05), there were 25 operational taxonomic units (OTUs) more commonly found in one group over the other. The families Aerococcaceae and Tissierellaceae both had four significantly differentially abundant OTUs. These four Tissierellaceae OTUs were all significantly more abundant in koalas with wet bottom. This study provides the foundation for future investigations of causes of koala wet bottom, other than C. pecorum infection. This is of clinical relevance as wet bottom is often assumed to be caused by C. pecorum and treated accordingly. Our research highlights that other organisms may be causing wet bottom, and these potential aetiological agents need to be further investigated to fully address the problems this species faces.
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Affiliation(s)
- Alistair R. Legione
- Asia Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
| | - Jemima Amery-Gale
- Asia Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael Lynch
- Veterinary Department, Melbourne Zoo, Parkville, Victoria, Australia
| | - Leesa Haynes
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - James R. Gilkerson
- Centre for Equine Infectious Diseases, The University of Melbourne, Parkville, Victoria, Australia
| | - Fiona M. Sansom
- Asia Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Joanne M. Devlin
- Asia Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
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36
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Dahlhausen KE, Doroud L, Firl AJ, Polkinghorne A, Eisen JA. Characterization of shifts of koala ( Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment. PeerJ 2018; 6:e4452. [PMID: 29576947 PMCID: PMC5853612 DOI: 10.7717/peerj.4452] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 02/14/2018] [Indexed: 01/01/2023] Open
Abstract
Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydia infections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala’s health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities.
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Affiliation(s)
| | - Ladan Doroud
- Department of Computer Science, University of California, Davis, CA, United States of America
| | - Alana J Firl
- Genome Center, University of California, Davis, CA, United States of America
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, United States of America
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37
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Kohl KD, Dearing MD, Bordenstein SR. Microbial communities exhibit host species distinguishability and phylosymbiosis along the length of the gastrointestinal tract. Mol Ecol 2017; 27:1874-1883. [PMID: 29230893 DOI: 10.1111/mec.14460] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023]
Abstract
Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates, it has only been investigated using samples from faeces or the distal colon. Here, we collected the contents of five gut regions from seven rodent species and inventoried the bacterial communities by sequencing the 16S rRNA gene. We investigated how community structures varied across gut regions and whether the pattern of phylosymbiosis was present along the length of the gut. Gut communities varied by host species and gut region, with Oscillospira and Ruminococcus being more abundant in the stomach and hindgut regions. Gut microbial communities were highly distinguishable by host species across all gut regions, with the strength of the discrimination increasing along the length of the gut. Last, the pattern of phylosymbiosis was found in all five gut regions, as well as faeces. Aspects of the gut environment, such as oxygen levels, production of antimicrobials or other factors, may shift microbial communities across gut regions. However, regardless of these differences, host species maintain distinguishable, phylosymbiotic assemblages of microbes that may have functional impacts for the host.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
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38
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Zeng Y, Zeng D, Ni X, Zhu H, Jian P, Zhou Y, Xu S, Lin Y, Li Y, Yin Z, Pan K, Jing B. Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity. AMB Express 2017; 7:75. [PMID: 28378284 PMCID: PMC5380569 DOI: 10.1186/s13568-017-0378-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/28/2017] [Indexed: 11/10/2022] Open
Abstract
Chinese Mongolian sheep are an important ruminant raised for wool and meat production. However, little is known about the microbiota of the gastrointestinal tract (GIT) of Chinese Mongolian sheep. To increase our understanding of the microbial community composition in the GIT of Chinese Mongolian sheep, microbiota of five sheep is investigate for the first time using the Illumina MiSeq platform. High microbial diversity was obtained from the GIT, and the microbiota exhibited a higher biodiversity in the stomach and large intestine than in the small intestine. Firmicutes (44.62%), Bacteroidetes (38.49%), and Proteobacteria (4.11%) were the three most abundant phyla present in the GIT of the sheep. The present study also revealed the core genera of Prevotella, Bacteroides, Ruminococcus, Oscillospira, Treponema, and Desulfovibrio in the GIT. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States indicated that the metabolic pathway related to carbohydrate metabolism was the richest in the sheep GIT. In addition, a series of metabolic pathways related to plant secondary metabolism was most abundant in the stomach and large intestine than in the small intestine. Overall, the present study provides insight into the microbial community composition in GIT of the Chinese Mongolian sheep which is highly diverse and needs to be studied further to exploit the complex interactions with the host.
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39
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Shiffman ME, Soo RM, Dennis PG, Morrison M, Tyson GW, Hugenholtz P. Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ 2017; 5:e4075. [PMID: 29177117 PMCID: PMC5697889 DOI: 10.7717/peerj.4075] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/31/2017] [Indexed: 01/09/2023] Open
Abstract
The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attributable to dietary specialization. Several populations discriminated between the koala and wombat fecal communities, most notably S24-7 and Synergistaceae in the koala, and Christensenellaceae and RF39 in the wombat. As expected for herbivores, both communities contained the genes necessary for lignocellulose degradation and urea recycling partitioned and redundantly encoded across multiple populations. Secondary metabolism was overrepresented in the koala fecal samples, consistent with the need to process Eucalyptus secondary metabolites. The Synergistaceae population encodes multiple pathways potentially relevant to Eucalyptus compound metabolism, and is predicted to be a key player in detoxification of the koala's diet. Notably, characterized microbial isolates from the koala gut appear to be minor constituents of this habitat, and the metagenomes provide the opportunity for genome-directed isolation of more representative populations. Metagenomic analysis of other obligate and facultative Eucalyptus folivores will reveal whether putatively detoxifying bacteria identified in the koala are shared across these marsupials.
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Affiliation(s)
- Miriam E. Shiffman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Rochelle M. Soo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Paul G. Dennis
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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40
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O’ Donnell MM, Harris HMB, Ross RP, O'Toole PW. Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals. Microbiologyopen 2017; 6:e00509. [PMID: 28834331 PMCID: PMC5635170 DOI: 10.1002/mbo3.509] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/21/2022] Open
Abstract
In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.
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Affiliation(s)
- Michelle M. O’ Donnell
- Food Biosciences DepartmentTeagasc Food Research CentreCorkIreland
- Department of MicrobiologyUniversity College CorkCorkIreland
| | | | - R. Paul Ross
- Food Biosciences DepartmentTeagasc Food Research CentreCorkIreland
- Department of MicrobiologyUniversity College CorkCorkIreland
| | - Paul W. O'Toole
- Department of MicrobiologyUniversity College CorkCorkIreland
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41
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Peel E, Cheng Y, Djordjevic JT, Kuhn M, Sorrell T, Belov K. Marsupial and monotreme cathelicidins display antimicrobial activity, including against methicillin-resistant Staphylococcus aureus. MICROBIOLOGY-SGM 2017; 163:1457-1465. [PMID: 28949902 DOI: 10.1099/mic.0.000536] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
With the growing demand for new antibiotics to combat increasing multi-drug resistance, a family of antimicrobial peptides known as cathelicidins has emerged as potential candidates. Expansions in cathelicidin-encoding genes in marsupials and monotremes are of specific interest as the peptides they encode have evolved to protect immunologically naive young in the harsh conditions of the pouch and burrow. Our previous work demonstrated that some marsupial and monotreme cathelicidins have broad-spectrum antibacterial activity and kill resistant bacteria, but the activity of many cathelicidins is unknown. To investigate associations between peptide antimicrobial activity and physiochemical properties, we tested 15 cathelicidin mature peptides from tammar wallaby, grey short-tailed opossum, platypus and echidna for antimicrobial activity against a range of bacterial and fungal clinical isolates. One opossum cathelicidin ModoCath4, tammar wallaby MaeuCath7 and echidna Taac-CATH1 had broad-spectrum antibacterial activity and killed methicillin-resistant Staphylococcus aureus. However, antimicrobial activity was reduced in the presence of serum or whole blood, and non-specific toxicity was observed at high concentrations. The active peptides were highly charged, potentially increasing binding to microbial surfaces, and contained amphipathic helical structures, which may facilitate membrane permeabilisation. Peptide sequence homology, net charge, amphipathicity and alpha helical content did not correlate with antimicrobial activity. However active peptides contained a significantly higher percentage of cationic residues than inactive ones, which may be used to predict active peptides in future work. Along with previous studies, our results indicate that marsupial and monotreme cathelicidins show potential for development as novel therapeutics to combat increasing antimicrobial resistance.
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Affiliation(s)
- Emma Peel
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia.,UQ Genomics Initiative, The University of Queensland, St Lucia, QLD, Australia
| | - Julianne T Djordjevic
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead, NSW, Australia
| | - Michael Kuhn
- Zoetis, Veterinary Medicine Research and Development, Kalamazoo, Michigan, USA
| | - Tania Sorrell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead, NSW, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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42
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Vidgen ME, Hanger J, Timms P. Microbiota composition of the koala (Phascolarctos cinereus) ocular and urogenital sites, and their association with Chlamydia infection and disease. Sci Rep 2017; 7:5239. [PMID: 28701755 PMCID: PMC5507983 DOI: 10.1038/s41598-017-05454-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/24/2017] [Indexed: 12/14/2022] Open
Abstract
Disease caused by Chlamydia pecorum is characterised by ocular and urogenital infections that can lead to blindness and infertility in koalas. However, koalas that are infected with C. pecorum do not always progress to disease. In other host systems, the influence of the microbiota has been implicated in either accelerating or preventing infections progressing to disease. This study investigates the contribution of koala urogenital and ocular microbiota to Chlamydia infection and disease in a free ranging koala population. Using univariate and multivariate analysis, it was found that reproductive status in females and sexual maturation in males, were defining features in the koala urogenital microbiota. Changes in the urogenital microbiota of koalas is correlated with infection by the common pathogen, C. pecorum. The correlation of microbiota composition and C. pecorum infection is suggestive of members of the microbiota being involved in the acceleration or prevention of infections progressing to disease. The analysis also suggests that multiple microbes are likely to be associated with this process of disease progression, rather than a single organism. While other Chlamydia-like organisms were also detected, they are unlikely to contribute to chlamydial disease as they are rare members of the urogenital and ocular microbiota communities.
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Affiliation(s)
- Miranda E Vidgen
- University of the Sunshine Coast, Faculty of Science, Health, Education & Engineering, Centre for Animal Health Innovation, Locked Bag 4, Maroochydore, Qld 4558, Australia
| | - Jonathan Hanger
- Endeavour Veterinary Ecology Pty Ltd., 1695 Pumicestone Rd., Toorbul, Qld 4510, Australia
| | - Peter Timms
- University of the Sunshine Coast, Faculty of Science, Health, Education & Engineering, Centre for Animal Health Innovation, Locked Bag 4, Maroochydore, Qld 4558, Australia.
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Xiao M, Yang J, Feng Y, Zhu Y, Chai X, Wang Y. Metaproteomic strategies and applications for gut microbial research. Appl Microbiol Biotechnol 2017; 101:3077-3088. [PMID: 28293710 DOI: 10.1007/s00253-017-8215-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/28/2017] [Accepted: 03/04/2017] [Indexed: 01/16/2023]
Abstract
The human intestine hosts various complex microbial communities that are closely associated with multiple health and disease processes. Determining the composition and function of these microbial communities is critical to unveil disease mechanisms and promote human health. Recently, meta-omic strategies have been developed that use high-throughput techniques to provide a wealth of information, thus accelerating the study of gut microbes. Metaproteomics is a newly emerged analytical approach that aims to identify proteins on a large scale in complex environmental microbial communities (e.g., the gut microbiota). This review introduces the recent analytical strategies and applications of metaproteomics, with a focus on advances in gut microbiota research, including a discussion of the limitations and challenges of these approaches.
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Affiliation(s)
- Mingming Xiao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Junjun Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yuxin Feng
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yan Zhu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Xin Chai
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yuefei Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China. .,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
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Hernández-Gómez O, Kimble SJA, Briggler JT, Williams RN. Characterization of the Cutaneous Bacterial Communities of Two Giant Salamander Subspecies. MICROBIAL ECOLOGY 2017; 73:445-454. [PMID: 27677893 DOI: 10.1007/s00248-016-0859-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/09/2016] [Indexed: 05/21/2023]
Abstract
Pathogens currently threaten the existence of many amphibian species. In efforts to combat global declines, researchers have characterized the amphibian cutaneous microbiome as a resource for disease management. Characterization of microbial communities has become useful in studying the links between organismal health and the host microbiome. Hellbender salamanders (Cryptobranchus alleganiensis) provide an ideal system to explore the cutaneous microbiome as this species requires extensive conservation management across its range. In addition, the Ozark hellbender subspecies (Cryptobranchus alleganiensis bishopi) exhibits chronic wounds hypothesized to be caused by bacterial infections, whereas the eastern hellbender (Cryptobranchus alleganiensis alleganiensis) does not. We assessed the cutaneous bacterial microbiome of both subspecies at two locations in the state of Missouri, USA. Through 16S rRNA gene-based amplicon sequencing, we detected more than 1000 distinct operational taxonomic units (OTUs) in the cutaneous and environmental bacterial microbiome. Phylogenetic and abundance-based dissimilarity matrices identified differences in the bacterial communities between the two subspecies, but only the abundance-based dissimilarity matrix identified differences between wounds and healthy skin on Ozark hellbenders. The higher abundance of OTUs on Ozark wounds suggests that commensal bacteria present on the skin and environment may be opportunistically colonizing the wounds. This brief exploration of the hellbender cutaneous bacterial microbiome provides foundational support for future studies seeking to understand the hellbender cutaneous bacterial microbiome and the role of the bacterial microbiota on chronic wounds of Ozark hellbenders.
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Affiliation(s)
- Obed Hernández-Gómez
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN, 47907, USA.
| | - Steven J A Kimble
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN, 47907, USA
| | - Jeffrey T Briggler
- Missouri Department of Conservation, 2901 W. Truman Blvd, Jefferson City, MO, 65109, USA
| | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN, 47907, USA
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Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis). PLoS One 2016; 11:e0156457. [PMID: 27227334 PMCID: PMC4881982 DOI: 10.1371/journal.pone.0156457] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/13/2016] [Indexed: 11/19/2022] Open
Abstract
The North American Beaver (Castor canadensis) is the second largest living rodent and an iconic symbol of Canada. The beaver is a semi-aquatic browser whose diet consists of lignocellulose from a variety of plants. The beaver is a hindgut fermenter and has an enlarged ceacum that houses a complex microbiome. There have been few studies examining the microbial diversity in gastrointestinal tract of hindgut fermenting herbivores. To examine the bacterial and archaeal communities inhabiting the gastrointestinal tract of the beaver, the microbiome of the ceacum and feaces was examined using culture-independent methods. DNA from the microbial community of the ceacum and feaces of 4 adult beavers was extracted, and the16S rRNA gene was sequenced using either bacterial or archaeal specific primers. A total of 1447 and 1435 unique bacterial OTUs were sequenced from the ceacum and feaces, respectively. On average, the majority of OTUs within the ceacum were classified as Bacteroidetes (49.2%) and Firmicutes (47.6%). The feaces was also dominated by OTUs from Bacteroidetes (36.8%) and Firmicutes (58.9%). The composition of bacterial community was not significantly different among animals. The composition of the ceacal and feacal microbiome differed, but this difference is due to changes in the abundance of closely related OTUs, not because of major differences in the taxonomic composition of the communities. Within these communities, known degraders of lignocellulose were identified. In contrast, to the bacterial microbiome, the archaeal community was dominated by a single species of methanogen, Methanosphaera stadtmanae. The data presented here provide the first insight into the microbial community within the hindgut of the beaver.
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Cheng Y, Fox S, Pemberton D, Hogg C, Papenfuss AT, Belov K. The Tasmanian devil microbiome-implications for conservation and management. MICROBIOME 2015; 3:76. [PMID: 26689946 PMCID: PMC4687321 DOI: 10.1186/s40168-015-0143-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/08/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Tasmanian devil, the world's largest carnivorous marsupial, is at risk of extinction due to devil facial tumour disease (DFTD), a fatal contagious cancer. The Save the Tasmanian Devil Program has established an insurance population, which currently holds over 600 devils in captive facilities across Australia. Microbes are known to play a crucial role in the health and well-being of humans and other animals, and increasing evidence suggests that changes in the microbiota can influence various aspects of host physiology and development. To improve our understanding of devils and facilitate management and conservation of the species, we characterised the microbiome of wild devils and investigated differences in the composition of microbial community between captive and wild individuals. RESULTS A total of 1,223,550 bacterial 16S ribosomal RNA (rRNA) sequences were generated via Roche 454 sequencing from 56 samples, including 17 gut, 15 skin, 18 pouch and 6 oral samples. The devil's gut microbiome was dominated by Firmicutes and showed a high Firmicutes-to-Bacteroidetes ratio, which appears to be a common feature of many carnivorous mammals. Metabolisms of carbohydrates, amino acids, energy, cofactors and vitamins, nucleotides and lipids were predicted as the most prominent metabolic pathways that the devil's gut flora contributed to. The microbiota inside the female's pouch outside lactation was highly similar to that of the skin, both co-dominated by Firmicutes and Proteobacteria. The oral microbiome had similar proportions of Proteobacteria, Bacteroidetes, Firmicutes and Fusobacteria. CONCLUSIONS Compositional differences were observed in all four types of microbiota between devils from captive and wild populations. Certain captive devils had significantly lower levels of gut bacterial diversity than wild individuals, and the two groups differed in the proportion of gut bacteria accounting for the metabolism of glycan, amino acids and cofactors and vitamins. Further studies are underway to investigate whether alterations in the microbiome of captive devils can have impacts on their ability to adapt and survive following re-introduction to the wild.
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Affiliation(s)
- Yuanyuan Cheng
- Faculty of Veterinary Science, RMC Gunn Building, University of Sydney, Sydney, New South Wales, 2006, Australia.
| | - Samantha Fox
- Department of Primary Industries, Parks, Water and Environment, 134 Macquarie Street, Hobart, Tasmania, 7000, Australia.
| | - David Pemberton
- Department of Primary Industries, Parks, Water and Environment, 134 Macquarie Street, Hobart, Tasmania, 7000, Australia.
| | - Carolyn Hogg
- Zoo and Aquarium Association, Mosman, New South Wales, 2088, Australia.
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia.
| | - Katherine Belov
- Faculty of Veterinary Science, RMC Gunn Building, University of Sydney, Sydney, New South Wales, 2006, Australia.
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Dill-McFarland KA, Weimer PJ, Pauli JN, Peery MZ, Suen G. Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths. Environ Microbiol 2015; 18:1391-402. [DOI: 10.1111/1462-2920.13022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 01/03/2023]
Affiliation(s)
| | - Paul J. Weimer
- Department of Bacteriology; University of Wisconsin-Madison; Madison WI 53706 USA
- US Department of Agriculture; Agricultural Research Service; Madison WI 53706 USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Garret Suen
- Department of Bacteriology; University of Wisconsin-Madison; Madison WI 53706 USA
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Variation in koala microbiomes within and between individuals: effect of body region and captivity status. Sci Rep 2015; 5:10189. [PMID: 25960327 PMCID: PMC4426690 DOI: 10.1038/srep10189] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/25/2015] [Indexed: 12/24/2022] Open
Abstract
Metagenomic analysis of 16S ribosomal RNA has been used to profile microbial communities at high resolution, and to examine their association with host diet or diseases. We examined the oral and gut microbiome composition of two captive koalas to determine whether bacterial communities are unusual in this species, given that their diet consists almost exclusively of Eucalyptus leaves. Despite a highly specialized diet, koala oral and gut microbiomes were similar in composition to the microbiomes from the same body regions of other mammals. Rectal swabs contained all of the diversity present in faecal samples, along with additional taxa, suggesting that faecal bacterial communities may merely subsample the gut bacterial diversity. Furthermore, the faecal microbiomes of the captive koalas were similar to those reported for wild koalas, suggesting that captivity may not compromise koala microbial health. Since koalas frequently suffer from ocular diseases caused by Chlamydia infection, we also examined the eye microbiome composition of two captive koalas, establishing the healthy baseline for this body part. The eye microbial community was very diverse, similar to other mammalian ocular microbiomes but with an unusually high representation of bacteria from the family Phyllobacteriaceae.
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Furness JB, Cottrell JJ, Bravo DM. COMPARATIVE GUT PHYSIOLOGY SYMPOSIUM: Comparative physiology of digestion1. J Anim Sci 2015; 93:485-91. [DOI: 10.2527/jas.2014-8481] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Bacteria and methanogens differ along the gastrointestinal tract of Chinese roe deer (Capreolus pygargus). PLoS One 2014; 9:e114513. [PMID: 25490208 PMCID: PMC4260832 DOI: 10.1371/journal.pone.0114513] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 11/10/2014] [Indexed: 02/01/2023] Open
Abstract
The current study provides the insight into the bacteria in the gastrointestinal tract (GIT) and methanogens presented in the rumen and cecum of the Chinese roe deer (Capreolus pygargus). The ruminal, ileal, cecal, and colonic contents, as well as feces, were obtained from each of the three, free-range, roe deer ingesting natural pasture after euthanasia. For the bacterial community, a total of 697,031 high-quality 16S rRNA gene sequences were generated using high-throughput sequencing, and assigned to 2,223 core operational taxonomic units (OTUs) (12 bacterial phyla and 87 genera). The phyla Firmicutes (51.2%) and Bacteroidetes (39.4%) were the dominant bacteria in the GIT of roe deer. However, the bacterial community in the rumen was significantly (P<0.01) different from the other sampled regions along the GIT. Secondly, Prevotella spp., Anaerovibrio spp., and unidentified bacteria within the families Veillonellaceae and Paraprevotellaceae were more abundant in the rumen than in the other regions. Unidentified bacteria within the family Enterobacteriaceae, Succinivibrio spp., and Desulfovibrio spp. were more predominant in the colon than in other regions. Unidentified bacteria within the family Ruminococcaceae, and Bacteroides spp. were more prevalent in the ileum, cecum and fecal pellets. For methanogens in the rumen and cecum, a total of 375,647 high quality 16S rRNA gene sequences were obtained and assigned to 113 core OTUs. Methanobrevibacter millerae was the dominant species accounting for 77.3±7.4 (S.E) % and 68.9±4.4 (S.E) % of total sequences in the rumen and cecum of roe deer, respectively. However, the abundance of Methanobrevibacter smithii was higher in the rumen than in the cecum (P = 0.004). These results revealed that there was intra variation in the bacterial community composition across the GIT of roe deer, and also showed that the methanogen community in the rumen differed from that in the cecum.
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