Special Issue "Wildlife Microbiology"

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (31 December 2018)

Special Issue Editors

Guest Editor
Dr. Kazunari Ushida

Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo Sakyo-ku, Kyoto 606–8522, Japan
Website | E-Mail
Guest Editor
Prof. Dr. Monica A. Sundset

Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
Website | E-Mail
Interests: Symbiotic Microbial Digestion; Comparative Digestive Physiology; Dietary Specialization; Molecular Microbial Ecology and Function in the Gut; Plant-Herbivore Interactions; Anti-nutrients; Methanogenesis and Methane Emissions

Special Issue Information

Dear Colleagues,

Intestinal microbiota is now well recognized as an important part of the host (Qin et al. 2010. Nature 464, 59-65). The size and diversity of the “cumulative genomes” are far bigger than host one, in fact its functionality is comparable to organs like the liver. “Dysbiosis” may relate to various refractory diseases. Wild animals in natural habitats rely on natural food, which often contain toxic and/or anti-nutritional compounds that elicit feed aversion. Wild animals, at least in part, rely on their gut microbiota to decompose such harmful compounds. These host-beneficial gut microbes can be considered as an essential component of the host.  

Intestinal bacteriology was once conducted only by culture-dependent classical approach (Holdeman et al. 1972, Mitsuoka 1981) before the “Molecular era”. After the introduction of PCR technology, the composition of microbiota has been analyzed using molecular ecological approaches with a tremendous increase in the degree of integration since then. Culture-dependent technology requires a high skill of basic bacteriology, but culture-independent technology does not. In this circumstance, researchers who have an access to the fecal specimens can now realize the study of intestinal microbiology. Recently-developed so-called Next Generation Sequencing (NGS) technology promotes many commercial services, which increases the number of papers focusing on intestinal microbiology of any kind of research subject.

In the case of wild animals, several attempts have been made to isolate intestinal bacteria from captured individuals. However, wild animals in a natural habitat have rarely been subjected to this type of microbiological study, due to the tremendous difficulty in culturing by the lack of access to appropriate microbiological tools at the laboratory level in field conditions. Although the amounts of data are increasing due to the culture-independent approach, the functionality of “essential microbes for the host” could not be easily revealed by phylogenetic analysis of 16S rRNA molecules. Studies on isolated bacteria should be conducted for such purposes. However, even with such limitations, culture-independent SSU rRNA phylogenetic approaches provide characterization of gut microbiome of particular host animals and a comparative point of view among the host species may be interesting to reveal the adaptation gut bacteria and co-evolution of gut bacteria with host.

This Special Issue welcomes:

(1) Isolation approaches, which reveal co-evolution and health beneficial characteristics of gut bacteria for host wild animals. Zoo animals often lose these essential bacteria. (2) Molecular ecological approaches, which characterize the gut microbiome of the host. Comparative studies on animal hosts (at the genus or species level of host) will be most welcome, because such comparisons characterize the relationships between gut microbiome and particular host animals.

This Special Issue focuses on:

(1) Technical elaboration to isolate gut bacteria from wild animals in natural habitats.

(2) Essential gut microbes, which characterize the host animal in terms of defense against harmful compounds, better food utilization, etc.

(3) Culture-independent molecular approaches to gut microbiome of wildlife in natural conditions. Comparative studies are most welcome.

Dr. Kazunari Ushida
Prof. Dr. Monica A. Sundset
Guest Editors

Manuscript Submission Information

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Published Papers (7 papers)

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Research

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Open AccessArticle Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior
Microorganisms 2019, 7(4), 99; https://doi.org/10.3390/microorganisms7040099
Received: 29 December 2018 / Revised: 1 April 2019 / Accepted: 1 April 2019 / Published: 4 April 2019
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Abstract
Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility [...] Read more.
Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle Conservation Implications of Shifting Gut Microbiomes in Captive-Reared Endangered Voles Intended for Reintroduction into the Wild
Microorganisms 2018, 6(3), 94; https://doi.org/10.3390/microorganisms6030094
Received: 30 June 2018 / Revised: 5 September 2018 / Accepted: 11 September 2018 / Published: 12 September 2018
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Abstract
The Amargosa vole is a highly endangered rodent endemic to a small stretch of the Amargosa River basin in Inyo County, California. It specializes on a single, nutritionally marginal food source in nature. As part of a conservation effort to preserve the species, [...] Read more.
The Amargosa vole is a highly endangered rodent endemic to a small stretch of the Amargosa River basin in Inyo County, California. It specializes on a single, nutritionally marginal food source in nature. As part of a conservation effort to preserve the species, a captive breeding population was established to serve as an insurance colony and a source of individuals to release into the wild as restored habitat becomes available. The colony has successfully been maintained on commercial diets for multiple generations, but there are concerns that colony animals could lose gut microbes necessary to digest a wild diet. We analyzed feces from colony-reared and recently captured wild-born voles on various diets, and foregut contents from colony and wild voles. Unexpectedly, fecal microbial composition did not greatly differ despite drastically different diets and differences observed were mostly in low-abundance microbes. In contrast, colony vole foregut microbiomes were dominated by Allobaculum sp. while wild foreguts were dominated by Lactobacillus sp. If these bacterial community differences result in beneficial functional differences in digestion, then captive-reared Amargosa voles should be prepared prior to release into the wild to minimize or eliminate those differences to maximize their chance of success. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle Influence of Season and Diet on Fiber Digestion and Bacterial Community Structure in the Rumen of Muskoxen (Ovibos moschatus)
Microorganisms 2018, 6(3), 89; https://doi.org/10.3390/microorganisms6030089
Received: 28 June 2018 / Revised: 8 August 2018 / Accepted: 14 August 2018 / Published: 20 August 2018
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Abstract
We studied the relationship between fiber digestion and the composition of the bacterial community in the rumen of muskoxen at the start and the end of the annual window of plant growth from spring to fall. Eight ruminally cannulated castrated males were fed [...] Read more.
We studied the relationship between fiber digestion and the composition of the bacterial community in the rumen of muskoxen at the start and the end of the annual window of plant growth from spring to fall. Eight ruminally cannulated castrated males were fed brome hay or triticale straw (69.6% vs. 84.6% neutral detergent fiber, respectively) that were similar in fiber content to the sedges consumed by wild muskoxen (64.5 to 71.7% neutral detergent fiber). Muskoxen digested fiber from both forages faster and to a greater extent when straw rather than hay was consumed. Fiber digestion was therefore inducible by diet 4 in each season. We used 16S rRNA sequences from ruminal contents to study how season and diet affected the bacterial community and how the latter related to fiber digestion. We found that Bacteroidetes and Firmicutes accounted for 90% of the sequences at the level of Phylum, which is typical for the mammal gut microbiome. Using partial least square regressions, it was found that between 48% and 72% of the variation in fiber digestion was associated with 36–43 genera of bacteria. The main fibrolytic bacteria typical of domestic ruminants were generally not among the most important bacteria associated with fiber digestion in muskoxen. This reveals that muskoxen rely upon on a large suite of bacterial genera that are largely distinct from those used by other ruminants to digest the cell walls of plants that vary widely in both abundance and nutritional quality through the year. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle Characteristics of Gorilla-Specific Lactobacillus Isolated from Captive and Wild Gorillas
Microorganisms 2018, 6(3), 86; https://doi.org/10.3390/microorganisms6030086
Received: 30 June 2018 / Revised: 11 August 2018 / Accepted: 14 August 2018 / Published: 14 August 2018
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Abstract
Lactic acid bacteria (LAB) reside in a wide range of mammals, such as autochthonous intestinal bacteria. In this paper, we present the phenotypic and phylogenetic characteristics of gorilla-specific LAB. Lactobacillus gorillae—previously isolated from the wild and captive western lowland gorillas (Gorilla [...] Read more.
Lactic acid bacteria (LAB) reside in a wide range of mammals, such as autochthonous intestinal bacteria. In this paper, we present the phenotypic and phylogenetic characteristics of gorilla-specific LAB. Lactobacillus gorillae—previously isolated from the wild and captive western lowland gorillas (Gorilla gorilla gorilla)—were successfully isolated from wild mountain gorillas (Gorilla gorilla beringei) in addition to other captive and wild western lowland gorillas. The strains from wild gorillas could ferment D-xylose, arbutine, cellobiose, and trehalose better than those from captive gorillas. By contrast, tolerance to NaCl was higher in isolates from captive gorillas than in those from wild gorillas. This tendency may have been induced by regular foods in zoos, which contain sufficient amount of salts but less amount of indigestible fiber and plant secondary metabolites compared to foods in the wild. All strains of L. gorillae showed inhibitory activities to enteric pathogenic bacteria; however, the activity was significantly higher for strains from wild gorillas than for those from captive gorillas. This may have been induced by the captive condition with routine veterinary intervention. Since L. gorillae can grow in the gastrointestinal tract of gorillas in captivity, the strains from wild mountain gorillas are potential probiotics for gorillas under captive conditions. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle Cecal Microbiome Analyses on Wild Japanese Rock Ptarmigans (Lagopus muta japonica) Reveals High Level of Coexistence of Lactic Acid Bacteria and Lactate-Utilizing Bacteria
Microorganisms 2018, 6(3), 77; https://doi.org/10.3390/microorganisms6030077
Received: 26 June 2018 / Revised: 23 July 2018 / Accepted: 25 July 2018 / Published: 28 July 2018
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Abstract
Preservation of indigenous gastrointestinal microbiota is critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we compared the cecal microbial composition of wild living Japanese rock ptarmigans (Lagopus muta japonica) in different locations of [...] Read more.
Preservation of indigenous gastrointestinal microbiota is critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we compared the cecal microbial composition of wild living Japanese rock ptarmigans (Lagopus muta japonica) in different locations of Japanese mountains, and the dominant cecal microbial structure of wild Japanese rock ptarmigans is elucidated. Coriobacteraceae and Lachnospraceae were the two dominant bacterial families in all samples analyzed. At the genus level, 10 genera Olsenella, Actinomyces, Megasphaera, Slackia, Cloacibacillus, Bifidobacterium,Escherichia,Dialister, Megamonas, and Bilophila were dominant. These results reveal the high level of coexistence of lactic acid bacteria (Olsenella and Bifidobacterium) and lactate-utilizing bacteria (Megasphaera). This coexistence should be taken into account for the successful breeding of captive Japanese rock ptarmigans in the national conservation program. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway
Microorganisms 2018, 6(3), 76; https://doi.org/10.3390/microorganisms6030076
Received: 31 May 2018 / Revised: 11 July 2018 / Accepted: 19 July 2018 / Published: 25 July 2018
Cited by 1 | PDF Full-text (2418 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Muskoxen (Ovibos moschatus) are ruminants adapted to a high-fibre diet. There is increasing interest in the role that gut microbes play in the digestion and utilization of these specialized diets but only limited data available on the gut microbiome of high-Arctic [...] Read more.
Muskoxen (Ovibos moschatus) are ruminants adapted to a high-fibre diet. There is increasing interest in the role that gut microbes play in the digestion and utilization of these specialized diets but only limited data available on the gut microbiome of high-Arctic animals. In this study, we metabarcoded the 16S rRNA region of faecal samples from muskoxen of Northeast Greenland, Northwest Greenland and Norway, and quantified the effects of physiological and temporal factors on bacterial composition. We found significant effects of body mass, year of sampling and location on the gut bacterial communities of North East Greenland muskoxen. These effects were however dwarfed by the effects of location, emphasizing the importance of the local ecology on the gut bacterial community. Habitat alterations and rising temperatures may therefore have a considerable impact on muskoxen health and reproductive success. Moreover, muskoxen are hunted and consumed in Greenland, Canada and Alaska; therefore, this study also screened for potential zoonoses of food safety interest. A total of 13 potentially zoonotic genera were identified, including the genera Erysipelothrix and Yersinia implicated in recent mass die-offs of the muskoxen themselves. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessBrief Report Cloacal and Ocular Microbiota of the Endangered Australian Northern Quoll
Microorganisms 2018, 6(3), 68; https://doi.org/10.3390/microorganisms6030068
Received: 30 May 2018 / Revised: 4 July 2018 / Accepted: 10 July 2018 / Published: 12 July 2018
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Abstract
The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a [...] Read more.
The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a role in their health. This study provides an initial characterization of the cloacal microbiota of the northern quoll, as well as other marsupials including possums and kangaroos which were opportunistically sampled. The northern quoll cloaca microbiota was dominated by Enterococcus and Lactobacillus and had a relatively high proportion of members of the Proteobacteria phylum, which has been observed in other carnivorous marsupials. The diversity and structure of the microbiota was not influenced by presence of Chlamydiales which are intracellular bacteria and potential pathogens. The microbiota of the other marsupials was quite varied, which may be related to their health status. Characterization of the northern quoll microbiota will help to better understand the biology of this endangered animal. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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