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Vaasjo E, Stothart MR, Black SR, Poissant J, Whiteside DP. The impact of management on the fecal microbiome of endangered greater sage-grouse ( Centrocercus urophasianus) in a zoo-based conservation program. CONSERVATION PHYSIOLOGY 2024; 12:coae052. [PMID: 39113731 PMCID: PMC11304599 DOI: 10.1093/conphys/coae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/09/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
Greater sage-grouse (Centrocercus urophasianus) are a critically endangered species in Canada with fewer than 140 individuals remaining on native habitats in southern Alberta and Saskatchewan. In 2014, the Wilder Institute/Calgary Zoo initiated North America's only zoo-based conservation breeding program for this species to bolster declining wild populations through conservation reintroductions. Within the managed population of sage-grouse, morbidity and mortality have primarily been associated with intestinal bacterial infections. As a preliminary study to assess the gastrointestinal health of this species in managed care, the fecal bacterial microbiome of adult and juvenile captive sage-grouse was characterized with 16S rRNA sequencing. The composition of the microbiome at the phylum level in greater sage-grouse is consistent with previous studies of the avian microbiome, with Bacillota as the most abundant phyla, and Actinomycetota, Bacteroidota and Pseudomonadota also being highly abundant. Antibiotic use and sex did not have a significant impact on the diversity or composition of the microbiome, but the management of juvenile sage-grouse did influence the development of the microbiome. Juveniles that were raised outdoors under maternal care developed a microbiome much more similar to adults when compared to chicks that were incubated and hand-raised. The local environment and parental care appear to be important factors influencing the diversity and composition of the gastrointestinal microbiome in this species.
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Affiliation(s)
- Emma Vaasjo
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
| | - Mason R Stothart
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
| | - Sandra R Black
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
| | - Douglas P Whiteside
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Animal Health Department, Wilder Institute/Calgary Zoo, 1300 Zoo Rd NE, Calgary, AB T2E 7V6, Canada
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2
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Bean TG, Chadwick EA, Herrero-Villar M, Mateo R, Naidoo V, Rattner BA. Do Pharmaceuticals in the Environment Pose a Risk to Wildlife? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:595-610. [PMID: 36398854 DOI: 10.1002/etc.5528] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/29/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The vast majority of knowledge related to the question "To what extent do pharmaceuticals in the environment pose a risk to wildlife?" stems from the Asian vulture crisis (>99% decline of some species of Old World vultures on the Indian subcontinent related to the veterinary use of the nonsteroidal anti-inflammatory drug [NSAID] diclofenac). The hazard of diclofenac and other NSAIDs (carprofen, flunixin, ketoprofen, nimesulide, phenylbutazone) to vultures and other avian species has since been demonstrated; indeed, only meloxicam and tolfenamic acid have been found to be vulture-safe. Since diclofenac was approved for veterinary use in Spain and Italy in 2013 (home to ~95% of vultures in Europe), the risk of NSAIDs to vultures in these countries has become one of the principal concerns related to pharmaceuticals and wildlife. Many of the other bodies of work on pharmaceutical exposure, hazard and risk to wildlife also relate to adverse effects in birds (e.g., poisoning of scavenging birds in North America and Europe from animal carcasses containing pentobarbital, secondary and even tertiary poisoning of birds exposed to pesticides used in veterinary medicine as cattle dips, migratory birds as a vector for the transfer of antimicrobial and antifungal resistance). Although there is some research related to endocrine disruption in reptiles and potential exposure of aerial insectivores, there remain numerous knowledge gaps for risk posed by pharmaceuticals to amphibians, reptiles, and mammals. Developing noninvasive sampling techniques and new approach methodologies (e.g., genomic, in vitro, in silico, in ovo) is important if we are to bridge the current knowledge gaps without extensive vertebrate testing. Environ Toxicol Chem 2024;43:595-610. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
| | | | - Marta Herrero-Villar
- Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Castilla-La-Mancha, Spain
| | - Rafael Mateo
- Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Castilla-La-Mancha, Spain
| | - Vinny Naidoo
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Barnett A Rattner
- Eastern Ecological Science Center at the Patuxent Research Refuge, US Geological Survey, Laurel, Maryland, USA
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3
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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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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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Dallas JW, Warne RW. Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation. MICROBIAL ECOLOGY 2023; 85:820-838. [PMID: 35316343 DOI: 10.1007/s00248-022-01991-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.
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Affiliation(s)
- Jason W Dallas
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
| | - Robin W Warne
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
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Eisenhofer R, Brice KL, Blyton MDJ, Bevins SE, Leigh K, Singh BK, Helgen KM, Hough I, Daniels CB, Speight N, Moore BD. Individuality and stability of the koala ( Phascolarctos cinereus) faecal microbiota through time. PeerJ 2023; 11:e14598. [PMID: 36710873 PMCID: PMC9879153 DOI: 10.7717/peerj.14598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/29/2022] [Indexed: 01/24/2023] Open
Abstract
Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
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Affiliation(s)
- Raphael Eisenhofer
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kylie L. Brice
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Michaela DJ Blyton
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, Brisbane, Queensland, Australia
| | - Scott E. Bevins
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Kellie Leigh
- Science for Wildlife Ltd, Sydney, New South Wales, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia,Global Centre for Land Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Kristofer M. Helgen
- Australian Museum Research Institute, Sydney, New South Wales, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, New South Wales, Australia,Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Ian Hough
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Christopher B. Daniels
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ben D. Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
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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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Abstract
In mammals, the composition of the gut microbiota is associated with host phylogenetic history, and host-lineage specific microbiota have been shown, in some cases, to contribute to fitness-related traits of their hosts. However, in primates, captivity can disrupt the native microbiota through a process of humanization in which captive hosts acquire gut microbiota constituents found in humans. Despite the potential importance of this process for the health of captive hosts, the degree to which captivity humanizes the gut microbiota of other mammalian taxa has not been explored. Here, we analyzed hundreds of published gut microbiota profiles generated from wild and captive hosts spanning seven mammalian families to investigate the extent of humanization of the gut microbiota in captivity across the mammalian phylogeny. Comparisons of these hosts revealed compositional convergence between captive mammal and human gut microbiota in the majority of mammalian families examined. This convergence was driven by a diversity of microbial lineages, including members of the Archaea, Clostridium, and Bacteroides. However, the gut microbiota of two families—Giraffidae and Bovidae—were remarkably robust to humanization in captivity, showing no evidence of gut microbiota acquisition from humans relative to their wild confamiliars. These results demonstrate that humanization of the gut microbiota is widespread in captive mammals, but that certain mammalian lineages are resistant to colonization by human-associated gut bacteria.
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Affiliation(s)
- Brian K Trevelline
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, United States.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
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9
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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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10
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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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Ren G, Fan X, Teng C, Li Y, Everaert N, Blecker C. The Beneficial Effect of Coarse Cereals on Chronic Diseases through Regulating Gut Microbiota. Foods 2021; 10:foods10112891. [PMID: 34829172 PMCID: PMC8620804 DOI: 10.3390/foods10112891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/20/2022] Open
Abstract
In recent years, chronic diseases including obesity, diabetes, cancer, cardiovascular, and neurodegenerative disorders have been the leading causes of incapacity and death globally. Increasing evidence suggests that improvements of lifestyle habits and diet is the most commonly adopted strategy for the prevention of chronic disorders. Moreover, many dietary compounds have revealed health-promoting benefits beyond their nutritional effects. It is worth noting that diet plays an important role in shaping the intestinal microbiota. Coarse cereals constitute important sources of nutrients for the gut microbiota and contribute to a healthy gut microbiome. Furthermore, the gut microbiota converts coarse cereals into functional substances and mediates the interaction between the host and these components. In this study, we summarize the recent findings concerning functional components of cereal grains and their potential chemopreventive activity via modulating the gut microbiota.
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Affiliation(s)
- Guixing Ren
- College of Pharmacy and Biological Engineering, Chengdu University, No. 1 Shilling Road, Chenglo Avenue, Longquan District, Chengdu 610106, China;
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (X.F.); (C.T.)
- Correspondence: ; Tel.: +86-10-6211-5596; Fax: +86-10-6215-6596
| | - Xin Fan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (X.F.); (C.T.)
- Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (N.E.); (C.B.)
| | - Cong Teng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (X.F.); (C.T.)
| | - Yajie Li
- College of Pharmacy and Biological Engineering, Chengdu University, No. 1 Shilling Road, Chenglo Avenue, Longquan District, Chengdu 610106, China;
| | - Nadia Everaert
- Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (N.E.); (C.B.)
| | - Christophe Blecker
- Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (N.E.); (C.B.)
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12
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Abstract
Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.
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13
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Didion EM, Sabree ZL, Kenyon L, Nine G, Hagan RW, Osman S, Benoit JB. Microbiome reduction prevents lipid accumulation during early diapause in the northern house mosquito, Culex pipiens pipiens. JOURNAL OF INSECT PHYSIOLOGY 2021; 134:104295. [PMID: 34411585 PMCID: PMC8530159 DOI: 10.1016/j.jinsphys.2021.104295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/09/2021] [Accepted: 08/09/2021] [Indexed: 05/05/2023]
Abstract
The mosquito microbiome is critical to multiple facets of their biology, including larval development and disease transmission. For mosquitoes that reside in temperate regions, periods of diapause are critical to overwintering survival, but how the microbiome impacts this state is unknown. In this study, we compared the midgut microbial communities of diapausing and non-diapausing Culex pipiens and assessed how a reduced midgut microbiome influences diapause preparation. High community variability was found within and between non-diapausing and diapausing individuals, but no specific diapause-based microbiome was noted. Emergence of adult, diapausing mosquitoes under sterile conditions generated low bacterial load (LBL) lines with nearly a 1000-fold reduction in bacteria levels. This reduction in bacterial content resulted in significantly lower survival of diapausing females after two weeks, indicating acquisition of the microbiome in adult females is critical for survival throughout diapause. LBL diapausing females had high carbohydrate levels, but did not accumulate lipid reserves, suggesting an inability to process ingested sugars necessary for diapause-associated lipid accumulation. Expression patterns of select genes associated with mosquito lipid metabolism during diapause showed no significant differences between LBL and control lines, suggesting transcriptional changes may not underlie impaired lipid accumulation. Overall, a diverse, adult-acquired microbiome is critical for diapause in C. pipiens to process sugar reserves and accumulate lipids that are necessary to survive prolonged overwintering.
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Affiliation(s)
- Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States.
| | - Zakee L Sabree
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, United States
| | - Laura Kenyon
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, United States
| | - Gabriela Nine
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Richard W Hagan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Sema Osman
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, United States
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States.
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14
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MOLECULAR IDENTIFICATION OF MEMBERS OF THE FAMILY PASTEURELLACEAE FROM THE ORAL CAVITY OF KOALAS ( PHASCOLARCTOS CINEREUS) AND THEIR RELATIONSHIP WITH ISOLATES FROM KOALA BITE WOUNDS IN HUMANS. J Zoo Wildl Med 2021; 51:771-779. [PMID: 33480557 DOI: 10.1638/2020-0041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2020] [Indexed: 11/21/2022] Open
Abstract
A total of 22 Pasteurellaceae isolates obtained from the oral cavity of koalas (Phascolarctos cinereus) at different wildlife centers in Australia were investigated using amplification and sequencing of two housekeeping genes, rpoA and recN. The available sequences from the Lonepinella koalarum type strain (ACM3666T) and the recent isolates of Lonepinella-like bacteria obtained from human infected wounds associated with koala bites were also included. Phylogenetic analysis was performed on the concatenated rpoA-recN genes and genome relatedness was calculated based on the recN sequences. The oral cavity isolates, the koala bite wound isolates, and L. koalarum ACM3666T resulted in four clusters (Clusters 1-4). Clusters 1-3 were clearly not members of the genus Lonepinella. Cluster 1 was closely related to the genus Fredericksenia, and Clusters 2 and 3 appeared to be novel genera. Cluster 4 consisted of three subclusters: Cluster 4a with one koala bite wound isolate and L. koalarum ACM3666T, Cluster 4b with three oral cavity isolates and two Lonepinella-like wound isolates, and Cluster 4c with three nearly identical oral cavity isolates that may represent a different species within the genus Lonepinella. The rich Pasteurellaceae population, including potential novel taxa in the oral cavity of koalas supports an important role of these highly adapted microorganisms in the physiology of koalas. Moreover, the pathogenic potential of Lonepinella-like species is an important consideration when investigating infected koala bites in humans.
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15
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Eisenhofer R, Helgen KM, Taggart D. Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons). Anim Microbiome 2021; 3:4. [PMID: 33499985 PMCID: PMC7934541 DOI: 10.1186/s42523-020-00068-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Herbivorous mammals co-opt microbes to derive energy and nutrients from diets that are recalcitrant to host enzymes. Recent research has found that captive management-an important conservation tool for many species-can alter the gut microbiota of mammals. Such changes could negatively impact the ability of herbivorous mammals to derive energy from their native diets, and ultimately reduce host fitness. To date, nothing is known of how captivity influences the gut microbiota of the Southern Hairy-nosed Wombat (SHNW), a large herbivorous marsupial that inhabits South Australia. Here, using 16S rRNA gene sequencing, we characterized the faecal microbiota of SHNWs in captivity and from three wild populations, two from degraded habitats and one from an intact native grass habitat. RESULTS We found that captive SHNWs had gut microbiota that were compositionally different and less diverse compared to wild SHNWs. There were major differences in gut microbiota community membership between captive and wild animals, both in statistically significant changes in relative abundance of microbes, and in the presence/absence of microbes. We also observed differences in microbial composition between wild populations, with the largest difference associated with native vs. degraded habitat. CONCLUSIONS These results suggest that captivity has a major impact on the gut microbiota of SHNWs, and that different wild populations harbour distinct microbial compositions. Such findings warrant further work to determine what impacts these changes have on the fitness of SHNWs, and whether they could be manipulated to improve future management of the species.
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Affiliation(s)
- Raphael Eisenhofer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. .,Australian Research Council Centre for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia.
| | - Kristofer M Helgen
- Australian Museum Research Institute, 1 William St, Sydney, New South Wales, Australia.,Australian Research Council Centre for Australian Biodiversity and Heritage, University of New South Wales, Sydney, New South Wales, Australia
| | - David Taggart
- School of Animal and Veterinary Sciences (Waite), University of Adelaide, Adelaide, South Australia, Australia.,FAUNA Research Alliance, PO Box 5092, Kahibah, NSW, 2290, Australia
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16
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Zhu L, Li J, Wei C, Luo T, Deng Z, Fan Y, Zheng L. A polysaccharide from Fagopyrum esculentum Moench bee pollen alleviates microbiota dysbiosis to improve intestinal barrier function in antibiotic-treated mice. Food Funct 2020; 11:10519-10533. [PMID: 33179663 DOI: 10.1039/d0fo01948h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Antibiotics are the most commonly used clinical drugs for anti-infection, but they can also destroy normal microorganisms and cause intestinal barrier dysfunction. To elucidate the effects and mechanism of a water-soluble polysaccharide from Fagopyrum esculentum Moench bee pollen (WFPP) on intestinal barrier integrity in antibiotic-treated mice, BALB/c mice were exposed to a broad-spectrum antibiotic (ceftriaxone) or not (control), and were administered low-, medium- and high-dose WFFP (100 mg kg-1, 200 mg kg-1 and 400 mg kg-1, respectively) daily by oral gavage for 3 weeks. Mice treated with ceftriaxone displayed symptoms of growth retardation, atrophy of immune organs including thymus and spleen, increased gut permeability, and intestinal barrier damage, which were restored after intervention with WFFP at different doses. Moreover, the beneficial effects of WFFP were closely associated with enhanced intestinal sIgA secretion and reduced inflammatory response. Furthermore 16S rDNA gene sequencing revealed that WFPP elevated microbial diversity and richness and changed the community structure, therefore, alleviating microbiota dysbiosis caused by ceftriaxone. Interestingly, WFPP could modulate the abundance of sIgA secretion-related bacteria (e.g. Proteobacteria) and inflammation-related bacteria (e.g. Enterococcus). Therefore, WFPP can relieve antibiotic-induced microbiota dysbiosis to improve intestinal barrier integrity by increasing intestinal sIgA secretion and inhibiting inflammation.
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Affiliation(s)
- Liuying Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, Jiangxi, P. R. China.
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17
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Dahlhausen KE, Jospin G, Coil DA, Eisen JA, Wilkins LG. Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PeerJ 2020; 8:e10177. [PMID: 33150080 PMCID: PMC7583611 DOI: 10.7717/peerj.10177] [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: 03/27/2020] [Accepted: 09/22/2020] [Indexed: 11/23/2022] Open
Abstract
Koalas (Phascolarctos cinereus) are highly specialized herbivorous marsupials that feed almost exclusively on Eucalyptus leaves, which are known to contain varying concentrations of many different toxic chemical compounds. The literature suggests that Lonepinella koalarum, a bacterium in the Pasteurellaceae family, can break down some of these toxic chemical compounds. Furthermore, in a previous study, we identified L. koalarum as the most predictive taxon of koala survival during antibiotic treatment. Therefore, we believe that this bacterium may be important for koala health. Here, we isolated a strain of L. koalarum from a healthy koala female and sequenced its genome using a combination of short-read and long-read sequencing. We placed the genome assembly into a phylogenetic tree based on 120 genome markers using the Genome Taxonomy Database (GTDB), which currently does not include any L. koalarum assemblies. Our genome assembly fell in the middle of a group of Haemophilus, Pasteurella and Basfia species. According to average nucleotide identity and a 16S rRNA gene tree, the closest relative of our isolate is L. koalarum strain Y17189. Then, we annotated the gene sequences and compared them to 55 closely related, publicly available genomes. Several genes that are known to be involved in carbohydrate metabolism could exclusively be found in L. koalarum relative to the other taxa in the pangenome, including glycoside hydrolase families GH2, GH31, GH32, GH43 and GH77. Among the predicted genes of L. koalarum were 79 candidates putatively involved in the degradation of plant secondary metabolites. Additionally, several genes coding for amino acid variants were found that had been shown to confer antibiotic resistance in other bacterial species against pulvomycin, beta-lactam antibiotics and the antibiotic efflux pump KpnH. In summary, this genetic characterization allows us to build hypotheses to explore the potentially beneficial role that L. koalarum might play in the koala intestinal microbiome. Characterizing and understanding beneficial symbionts at the whole genome level is important for the development of anti- and probiotic treatments for koalas, a highly threatened species due to habitat loss, wildfires, and high prevalence of Chlamydia infections.
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Affiliation(s)
| | - Guillaume Jospin
- Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA
| | - David A. Coil
- Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA
| | - Jonathan A. Eisen
- Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA
| | - Laetitia G.E. Wilkins
- Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA
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18
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Gupta SK, Fotedar R, Foysal MJ, Priyam M, Siddik MAB, Chaklader MR, Dao TTT, Howieson J. Impact of varied combinatorial mixture of non-fishmeal ingredients on growth, metabolism, immunity and gut microbiota of Lates calcarifer (Bloch, 1790) fry. Sci Rep 2020; 10:17091. [PMID: 33051467 PMCID: PMC7555901 DOI: 10.1038/s41598-020-72726-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/19/2020] [Indexed: 01/09/2023] Open
Abstract
The search for suitable fish meal replacements in aqua-diets is a salient agenda in the constant effort of making aquaculture practices more sustainable. In this study, we tested four customised diets composed by systematic inclusion of pre-selected fish meal substitutes, lupin kernel meal, BSF meal, TH and PBM on growth, metabolism, cytokine profile, gut morphology and microbiota of juvenile Lates calcarifer. Five isoproteic and isoenergetic diets were prepared viz. FM100 as a control (without fish meal substitute), while FM75, FM50, FM25 and FM0 indicates replacement of fish meal (FM) at 25%, 50%, 75%, and 100%, respectively by a mixture of four different pre-selected non-fish meal (NFM) ingredients. Fish fed FM100, FM75, FM50, FM25 exhibited consistent growth and haematological response, while the fish fed no fishmeal (FM0) showed significant decline in final body weight (FBW) and specific growth rate (SGR). The poor growth performance was correlated with a decrease in villous width, microvilli height and goblet cells density. A significant shift in abundance profile of Psychrobacter in the gut microbial profile of fish fed FM50 was noticed compared to fish fed FM100. The results of qRT-PCR showed up-regulated expression of innate immune responsive genes in the FM50 group. The adverse impacts on growth performance and gut health of fish fed FM0 suggest that the complete substitution of fishmeal is not advisable and the inclusion range of these alternatives should be decided for a species only after examining their effect on maximal physiological performance.
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Affiliation(s)
- Sanjay K Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India.
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Manisha Priyam
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Muhammad A B Siddik
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, 8602, Bangladesh
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Thi Thanh Thuy Dao
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Janet Howieson
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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19
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Kobayashi A, Tsuchida S, Hattori T, Ogata K, Ueda A, Yamada T, Murata K, Nakamura H, Ushida K. Metabolomic LC-MS/MS analyses and meta 16S rRNA gene analyses on cecal feces of Japanese rock ptarmigans reveal fundamental differences between semi-wild and captive raised individuals. J Vet Med Sci 2020; 82:1165-1172. [PMID: 32581149 PMCID: PMC7468055 DOI: 10.1292/jvms.20-0003] [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] [Indexed: 12/15/2022] Open
Abstract
Ex situ conservation of Japanese rock ptarmigans began in 2015 with the aim of reintroducing artificially raised birds into their original habitat. However, the current raising method in captivity seems insufficient in terms of the survivability of artificially raised birds in natural conditions. Feeding management is one potential reason for such insufficiency. In this study, we performed a comprehensive analysis of the hydrophilic metabolites by LC-MS/MS for the cecal feces of Japanese rock ptarmigans under in situ and ex situ conservation to reveal their gut chemical environment. We also analyzed the developmental processes of cecal microbiomes both in situ semi-wild and ex situ captive individuals. Metabolites of nucleic acid were rich in the in situ individuals, and free amino acids were rich in the ex situ individuals. The differences in the microbiome composition between in situ and ex situ individuals were also pronounced; major genera of in situ individuals were not detected or few in ex situ individuals. The alpha diversity of the cecal microbiome of semi-wild chicks at 1 week of age was almost the same as that of their hens, while it was very low in captive individuals. Sub-therapeutic use of oxytetracycline, a diet rich in protein and energy, and isolation from adult birds are considered to be causes for these great differences in gut chemical and microbiological environment between in situ and ex situ individuals.
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Affiliation(s)
| | - Sayaka Tsuchida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.,Chubu University, Academy of Emerging Sciences, Kasugai 487-8501, Japan
| | | | | | - Atsushi Ueda
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | | | - Koichi Murata
- Faculty of Bioresource Sciences, Nihon University, Kanagawa 252-0800, Japan
| | - Hiroshi Nakamura
- General Foundation Hiroshi Nakamura International Institute for Ornithology, Nagano 380-0934, Japan
| | - Kazunari Ushida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.,Chubu University, Academy of Emerging Sciences, Kasugai 487-8501, Japan
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20
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Vaccination of koalas during antibiotic treatment for Chlamydia-induced cystitis induces an improved antibody response to Chlamydia pecorum. Sci Rep 2020; 10:10152. [PMID: 32576914 PMCID: PMC7311432 DOI: 10.1038/s41598-020-67208-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022] Open
Abstract
Chlamydia infection and disease are endemic in free-ranging koalas. Antibiotics remain the front line treatment for Chlamydia in koalas, despite their rates of treatment failure and adverse gut dysbiosis outcomes. A Chlamydia vaccine for koalas has shown promise for replacing antibiotic treatment in mild ocular Chlamydia disease. In more severe disease presentations that require antibiotic intervention, the effect of vaccinating during antibiotic use is not currently known. This study investigated whether a productive immune response could be induced by vaccinating koalas during antibiotic treatment for Chlamydia-induced cystitis. Plasma IgG antibody levels against the C. pecorum major outer membrane protein (MOMP) dropped during antibiotic treatment in both vaccinated and unvaccinated koalas. Post-treatment, IgG levels recovered. The IgG antibodies from naturally-infected, vaccinated koalas recognised a greater proportion of the MOMP protein compared to their naturally-infected, unvaccinated counterparts. Furthermore, peripheral blood mononuclear cell gene expression revealed an up-regulation in genes related to neutrophil degranulation in vaccinated koalas during the first month post-vaccination. These findings show that vaccination of koalas while they are being treated with antibiotics for cystitis can result in the generation of a productive immune response, in the form of increased and expanded IgG production and host response through neutrophil degranulation.
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21
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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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22
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Schmidlin PR. Periodontal Therapy of the Future—Many Challenges and Opportunities. FRONTIERS IN DENTAL MEDICINE 2020. [DOI: 10.3389/fdmed.2020.00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Waugh CA, Timms P. A proposed roadmap for the control of infections in wildlife using Chlamydia vaccine development in koalas Phascolarctos cinereus as a template. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Courtney A. Waugh
- C. Waugh ✉ , Faculty of Bioscience and Aquaculture, Nord Univ., Steinkjer, Norway
| | - Peter Timms
- P. Timms, Univ. of the Sunshine Coast, Sippy Downs, Queensland, Australia
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24
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Siddik MAB, Chaklader MR, Foysal MJ, Howieson J, Fotedar R, Gupta SK. Influence of fish protein hydrolysate produced from industrial residues on antioxidant activity, cytokine expression and gut microbial communities in juvenile barramundi Lates calcarifer. FISH & SHELLFISH IMMUNOLOGY 2020; 97:465-473. [PMID: 31866445 DOI: 10.1016/j.fsi.2019.12.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/19/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
The present study investigated the supplemental effects of tuna hydrolysate (TH) in poultry by-product meal (PBM) and dietary fishmeal (FM) diets on antioxidant enzymatic activities, gut microbial communities and expression of cytokine genes in the distal intestine of juvenile barramundi, Lates calcarifer. Fish were fed with fermented (FPBM + TH) as well as non-fermented PBM (PBM + TH) and FM (FMBD + TH) diets with 10% TH supplementation for 10 weeks. A basal diet prepared without TH supplementation served as control. The results showed that the activity of glutathione peroxidase was significantly higher in FPBM + TH than the control, while the malondialdehyde and catalase activities were unchanged. FPBM + TH diet significantly (P < 0.05) upregulated the pro-inflammatory cytokines including IL-1β and TNF-α while considerable downregulation (P < 0.05) was observed in the mRNA expression levels of anti-inflammatory cytokine, IL-10 in the distal intestine of fish. The 16SrRNA analysis using V3-V4 region evidenced the ability of FPBM + TH to modulate the distal intestinal gut microbiome, augmenting the richness of Firmicutes and Fusobacteriaat at phylum level and Bacillus, Lactococcus and Cetobacterium at genus level. All these results have shown that fermented PBM with TH supplementation could improve the antioxidant capacity and inflammatory responses of juvenile barramundi while influencing the microbial communities at both phylum and genera levels.
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Affiliation(s)
- Muhammad A B Siddik
- School of Molecular and Life Sciences, Curtin University, 1 Turner Avenue, Bentley, WA, 6102, Australia; Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, 8602, Bangladesh.
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, 1 Turner Avenue, Bentley, WA, 6102, Australia
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, 1 Turner Avenue, Bentley, WA, 6102, Australia; Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Janet Howieson
- School of Molecular and Life Sciences, Curtin University, 1 Turner Avenue, Bentley, WA, 6102, Australia
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, 1 Turner Avenue, Bentley, WA, 6102, Australia
| | - Sanjay K Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jhankhand, India
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Foysal MJ, Momtaz F, Robiul Kawser AQM, Chaklader MR, Siddik MAB, Lamichhane B, Tay ACY, Rahman MM, Fotedar R. Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh. J Appl Microbiol 2019; 126:1879-1890. [PMID: 30888695 DOI: 10.1111/jam.14257] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/22/2019] [Accepted: 03/10/2019] [Indexed: 12/11/2022]
Abstract
AIMS This study conducted bacterial community, virulence and antibiogram profiling inside the hindgut and skin of freshly caught hilsa fish and those sold at markets. METHODS AND RESULTS The results of 16S rRNA-based high-throughput sequencing showed a higher number of bacterial genera in marketed fish samples than in fresh fish samples. The total operational taxonomic units, genus counts and diversity index were significantly higher (P > 0·05) in marketed fish, which also had abundant pathogenic bacterial groups. Skin samples had a lower profusion of pathogenic bacteria than gut samples. A total of 52 bacterial isolates from nine species were identified in this study, of which 25 were from a Chittagong market and 22 were from a Dhaka market, whereas only five were from fresh hilsa. The polymerase chain reaction amplification of 12 species-specific virulence genes in the 52 isolates, namely, aer, hly, chxA, toxB, rtxC, sfa, uge, norB, trx, toxA, ipaH, sigA and coa, indicated a high number of positive samples containing Vibrio cholerae, Aeromonas spp., Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus. Antibiogram profiling of these bacteria against 10 commercial antibiotics showed high-resistance patterns of the isolates against sulfamethoxazole, kanamycin, neomycin, ampicillin and tetracycline. CONCLUSION The results reveal the spread of multidrug-resistant bacteria in hilsa fish marketed for human consumption in Bangladesh. SIGNIFICANCE AND IMPACT OF THE STUDY This study highlights the risk of spreading environmentally and clinically pathogenic bacteria in fish sold for human consumption in Bangladesh. Such bacteria come from aquatic pollution and poor handling, storage and transportation practices that may predispose fish to major outbreaks of infectious and waterborne diseases.
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Affiliation(s)
- M J Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - F Momtaz
- Department of Microbiology, Chittagong University, Chittagong, Bangladesh
| | - A Q M Robiul Kawser
- Department of Aquaculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - M R Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - M A B Siddik
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - B Lamichhane
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - A C Y Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - M M Rahman
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - R Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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Trevelline BK, Fontaine SS, Hartup BK, Kohl KD. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc Biol Sci 2019; 286:20182448. [PMID: 30963956 PMCID: PMC6364583 DOI: 10.1098/rspb.2018.2448] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022] Open
Abstract
The central aim of conservation biology is to understand and mitigate the effects of human activities on biodiversity. To successfully achieve this objective, researchers must take an interdisciplinary approach that fully considers the effects, both direct and indirect, of anthropogenic disturbances on wildlife physiology and health. A recent surge in research has revealed that host-associated microbiota-the archaeal, bacterial, fungal and viral communities residing on and inside organisms-profoundly influence animal health, and that these microbial communities can be drastically altered by anthropogenic activities. Therefore, conservation practitioners should consider the disruption of host-associated microbial diversity as a serious threat to wildlife populations. Despite the tremendous potential for microbiome research to improve conservation outcomes, few efforts have been made to truly integrate these fields. In this review, we call for the microbial renaissance of conservation biology, where biodiversity of host-associated microbiota is recognized as an essential component of wildlife management practices. Using evidence from the existing literature, we will examine the known effects of anthropogenic activities on the diversity of host-associated microbial communities and integrate approaches for maintaining microbial diversity to successfully achieve conservation objectives.
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Affiliation(s)
- Brian K. Trevelline
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samantha S. Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Barry K. Hartup
- Department of Conservation Medicine, International Crane Foundation, Baraboo, WI, USA
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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Nyari S, Booth R, Quigley BL, Waugh CA, Timms P. Therapeutic effect of a Chlamydia pecorum recombinant major outer membrane protein vaccine on ocular disease in koalas (Phascolarctos cinereus). PLoS One 2019; 14:e0210245. [PMID: 30615687 PMCID: PMC6322743 DOI: 10.1371/journal.pone.0210245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 12/19/2018] [Indexed: 12/29/2022] Open
Abstract
Chlamydia pecorum is responsible for causing ocular infection and disease which can lead to blindness in koalas (Phascolarctos cinereus). Antibiotics are the current treatment for chlamydial infection and disease in koalas, however, they can be detrimental for the koala’s gastrointestinal tract microbiota and in severe cases, can lead to dysbiosis and death. In this study, we evaluated the therapeutic effects provided by a recombinant chlamydial major outer membrane protein (MOMP) vaccine on ocular disease in koalas. Koalas with ocular disease (unilateral or bilateral) were vaccinated and assessed for six weeks, evaluating any changes to the conjunctival tissue and discharge. Samples were collected pre- and post-vaccination to evaluate both humoral and cell-mediated immune responses. We further assessed the infecting C. pecorum genotype, host MHC class II alleles and presence of koala retrovirus type (KoRV-B). Our results clearly showed an improvement in the clinical ocular disease state of all seven koalas, post-vaccination. We observed increases in ocular mucosal IgA antibodies to whole C. pecorum elementary bodies, post-vaccination. We found that systemic cell-mediated immune responses to interferon-γ, interleukin-6 and interleukin-17A were not significantly predictive of ocular disease in koalas. Interestingly, one koala did not have as positive a clinical response (in one eye primarily) and this koala was infected with a C. pecorum genotype (E’) that was not used as part of the vaccine formula (MOMP genotypes A, F and G). The predominant MHC class II alleles identified were DAb*19, DAb*21 and DBb*05, with no two koalas identified with the same genetic sequence. Additionally, KoRV-B, which is associated with chlamydial disease outcome, was identified in two (29%) ocular diseased koalas, which still produced vaccine-induced immune responses and clinical ocular improvements post-vaccination. Our findings show promise for the use of a recombinant chlamydial MOMP vaccine for the therapeutic treatment of ocular disease in koalas.
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Affiliation(s)
- Sharon Nyari
- University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Rosemary Booth
- Australia Zoo Wildlife Hospital, Beerwah, Queensland, Australia
| | - Bonnie L. Quigley
- University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Courtney A. Waugh
- University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Peter Timms
- University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- * E-mail:
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