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Wildlife Microbiology 2.0

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A special issue of Microorganisms (ISSN 2076-2607).

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 41489

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Special Issue Editors

Dr. Kazunari Ushida

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Guest Editor

Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan
Interests: antimicrobials; antibiotic resistance; nutrition; microbial molecular biology; environmental microbiology; biotechnology; wildlife microbiology; fiber digestion
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Monica A. Sundset

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Guest Editor

Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
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 Issues, Collections and Topics in MDPI journals

Prof. Dr. Richard Kock

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Guest Editor

The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
Interests: wildlife diseases and epidemiology; food systems and environment; wildlife livestock interface and emerging diseases; mass mortality diseases particularly morbilliviruses which are a food security issue and wildlife conservation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Our recent Special Issue on "Wildlife Microbiology" (https://0-www-mdpi-com.brum.beds.ac.uk/journal/microorganisms/special_issues/wildlife_microbiology) includes papers on the gut microbiota of the marsupial carnivorous Australian quoll, the fecal bacterial community and potential zoonotic bacteria of muskoxen in Greenland and Norway, the cecal microbiome in wild Japanese rock ptarmigans, bacterial isolates from captive and wild mountain gorillas in Uganda, the effect of season and diet on fiber digestion and ruminal bacterial community structure in muskoxen in Alaska, shifting gut microbiomes in captive-reared endangered voles, and adaptations to a frugivore/folivore diet in gorillas, chimpanzees, and wild forest elephants.

Research on the effect of host-associated microbiomes on animal health through their impact on digestion, the immune system, development, and behavior is accumulating. These host-associated communities can be disrupted by anthropogenic factors such as those that effect phenology (vegetation, life cycles, land-use, and climate), infectious diseases, and environmental contamination. Seasonal and dietary factors are also well-known to affect these communities. The need for microbiome research in an ecological context is widely recognized as it applies to wildlife conservation, and the biodiversity of the host-associated microbiota must be included as an essential component of wildlife management practices (Trevelline et al. 2019 https://royalsocietypublishing.org/doi/full/10.1098/rspb.2018.2448 ).

In this new Special Issue, we are happy to welcome more manuscripts on wildlife microbiology, including the symbiotic gut microflora and bacterial pathogens in wildlife, and how these are affected by both natural and anthropogenic factors in their environment. There is a particular interest in commensal and opportunistic pathogens and how the relationship between host and parasite is influenced by intrinsic and extrinsic factors.

This Special Issue welcomes:

(1) Studies that include isolation, cultivation, identification, and function of host-associated microbes and pathogens from wildlife;

(2) Molecular ecological approaches, which characterize the microbiome (symbiotic, normal flora or pathogens) inside or on wildlife in relation to function and health;

(3) Wildlife microbiome studies in an ecological and/or physiological context are especially welcomed.

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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Related Special Issue

Wildlife Microbiology in Microorganisms (7 articles)

Published Papers (14 papers)

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Editorial

Jump to: Research, Other

3 pages, 189 KiB

Open AccessEditorial

Special Issue: Wildlife Microbiology

by Kazunari Ushida, Richard Kock and Monica A. Sundset

Microorganisms 2021, 9(9), 1968; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091968 - 16 Sep 2021

Cited by 1 | Viewed by 2177

Abstract

Research on the effect of symbiotic microbes on the health of the host through their impact on digestion, the immune system, development, and behavior is accumulating [...] Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

Research

Jump to: Editorial, Other

8 pages, 627 KiB

Open AccessArticle

Plasmodium matutinum Causing Avian Malaria in Lovebirds (Agapornis roseicollis) Hosted in an Italian Zoo

by Cristiano Cocumelli, Manuela Iurescia, Elena Lavinia Diaconu, Valentina Galietta, Caterina Raso, Carmela Buccella, Fiorentino Stravino, Francesco Grande, Letizia Fiorucci, Claudio De Liberato, Andrea Caprioli and Antonio Battisti

Microorganisms 2021, 9(7), 1356; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071356 - 23 Jun 2021

Cited by 9 | Viewed by 2436

Abstract

Avian malaria is a worldwide distributed, vector-born disease of birds caused by parasites of the order Haemosporida. There is a lack of knowledge about the presence and pathogenetic role of Haemosporida in Psittacidae. Here we report a case of avian malaria infection in lovebirds (Agapornis roseicollis), with the genetic characterization of the Plasmodium species involved. The birds were hosted in a zoo located in Italy, where avian malaria cases in African penguins (Spheniscus demersus) were already reported. Animals (n = 11) were submitted for necropsy after sudden death and were subjected to further analyses including histopathology, bacteriology, and PCR for the research of haemosporidians. Clinical history, gross lesions and histopathological observation of schizonts, together with positive PCR results for Plasmodium spp., demonstrated that avian malaria was the cause of death for one animal and the possible cause of death for the other nine. The sequences obtained were compared using BLAST and analyzed for similarity to sequences available at the MalAvi database. Genetic analyses demonstrated a 100% nucleotide identity to Plasmodium matutinum LINN1 for all the obtained sequences. To our knowledge, this is the first report describing avian malaria in lovebirds. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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14 pages, 3178 KiB

Open AccessArticle

Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean

by Anne A. M. J. Becker, KC Hill and Patrick Butaye

Microorganisms 2021, 9(3), 465; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9030465 - 24 Feb 2021

Cited by 7 | Viewed by 3416

Abstract

Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5^TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator’s impact throughout the Caribbean. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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14 pages, 1016 KiB

Open AccessArticle

Antimicrobial Activity of Lactococcus lactis subsp. lactis Isolated from a Stranded Cuvier’s Beaked Whale (Ziphius cavirostris) against Gram-Positive and -Negative Bacteria

by Akihiko Suzuki and Miwa Suzuki

Microorganisms 2021, 9(2), 243; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020243 - 25 Jan 2021

Cited by 8 | Viewed by 2738

Abstract

In the present study, we isolated and characterized Lactococcus lactis (L. lactis) subsp. lactis from a female Cuvier’s beaked whale (Ziphius cavirostris) stranded in Shizuoka, Japan. Only five isolates (CBW1-5), grown on Lactobacilli de Man Rogosa Sharpe (MRS) agar plates prepared using 50% artificial seawater, were positive in L. lactis species-specific primer PCR. Their 16S rRNA sequences were highly similar to those of L. lactis subsp. lactis JCM 5805^T. The Gram reaction, motility, gas production from glucose, catalase production, and growth conditions were consistent with those of the type strain. Additionally, carbohydrate utilization of the strains was consistent with previously reported marine organism-derived strains. The pH-neutralized cell-free culture supernatant of strain CBW2 inhibited the growth of Bacillus subtilis subsp. subtilis ATCC 6051 and Vibrio alginolyticus ATCC 17749, whereas protease treatment eliminated or diminished its inhibitory activity. The strain possesses a precursor of the nisin structural gene (nisA), which showed 100% homology with nisin Z, and nisin biosynthesis-related genes (nisB, nisC, nisT, nisP, nisF, nisI, and nisRK), suggesting that the strain produces a nisin-like substance. This study provides fundamental information on whale-derived L. lactis subsp. lactis which may be useful for reducing the carriage of B. subtilis subsp. subtilis and V. alginolyticus. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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11 pages, 1435 KiB

Open AccessArticle

The Oral Bacterial Community in Melanophryniscus admirabilis (Admirable Red-Belly Toads): Implications for Conservation

by Michele Bertoni Mann, Janira Prichula, Ícaro Maia Santos de Castro, Juliana Mello Severo, Michelle Abadie, Thayná Mendes De Freitas Lima, Valentina Caorsi, Márcio Borges-Martins, Jeverson Frazzon and Ana Paula Guedes Frazzon

Microorganisms 2021, 9(2), 220; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020220 - 22 Jan 2021

Cited by 4 | Viewed by 3103

Abstract

Melanophryniscus admirabilis (admirable red-belly toad) is a microendemic and critically endangered species found exclusively along 700 m of the Forqueta River, in a fragment of the Atlantic Forest of southern Brazil. One of the greatest concerns regarding the conservation of this species is the extensive use of pesticides in areas surrounding their natural habitat. In recent years, the adaptation and persistence of animal species in human-impacted environments have been associated with microbiota. Therefore, the present study aimed to characterize the oral bacterial community of wild M. admirabilis and to address the question of how this community might contribute to this toad’s adaptation in the anthropogenic environment as well as its general metabolic capabilities. A total of 11 oral samples collected from wild M. admirabilis were characterized and analyzed via high-throughput sequencing. Fragments of the 16S rRNA variable region 4 (V4) were amplified, and sequencing was conducted using an Ion Personal Genome Machine (PGM) System with 316 chips. A total of 181,350 sequences were obtained, resulting in 16 phyla, 34 classes, 39 orders, and 77 families. Proteobacteria dominated (53%) the oral microbiota of toads, followed by Firmicutes (18%), Bacteroidetes (17%), and Actinobacteria (5%). No significant differences in microbial community profile from among the samples were reported, which suggests that the low dietary diversity observed in this population may directly influence the bacterial composition. Inferences of microbiome function were performed using PICRUSt2 software. Important pathways (e.g., xenobiotic degradation pathways for pesticides and aromatic phenolic compounds) were detected, which suggests that the bacterial communities may serve important roles in M. admirabilis health and survival in the anthropogenic environment. Overall, our results have important implications for the conservation and management of this microendemic and critically endangered species. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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14 pages, 479 KiB

Open AccessArticle

Study on Bacteria Isolates and Antimicrobial Resistance in Wildlife in Sicily, Southern Italy

by Delia Gambino, Domenico Vicari, Maria Vitale, Giorgia Schirò, Francesco Mira, Maria La Giglia, Alessandra Riccardi, Antonino Gentile, Susanna Giardina, Anna Carrozzo, Valentina Cumbo, Antonio Lastra and Valeria Gargano

Microorganisms 2021, 9(1), 203; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010203 - 19 Jan 2021

Cited by 17 | Viewed by 4057

Abstract

Wild environments and wildlife can be reservoirs of pathogens and antibiotic resistance. Various studies have reported the presence of zoonotic bacteria, resistant strains, and genetic elements that determine antibiotic resistance in wild animals, especially near urban centers or agricultural and zootechnical activities. The purpose of this study was the analysis, by cultural and molecular methods, of bacteria isolated from wild animals in Sicily, Italy, regarding their susceptibility profile to antibiotics and the presence of antibiotic resistance genes. Bacteriological analyses were conducted on 368 wild animals, leading to the isolation of 222 bacterial strains identified by biochemical tests and 16S rRNA sequencing. The most isolated species was Escherichia coli, followed by Clostridium perfringens and Citrobacter freundii. Antibiograms and the determination of resistance genes showed a reduced spread of bacteria carrying antibiotic resistance among wild animals in Sicily. However, since several wild animals are becoming increasingly close to residential areas, it is important to monitor their health status and to perform microbiological analyses following a One Health approach. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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12 pages, 560 KiB

Open AccessArticle

Phylogenetic Relationships within the Nematode Subfamily Phascolostrongylinae (Nematoda: Strongyloidea) from Australian Macropodid and Vombatid Marsupials

by Tanapan Sukee, Ian Beveridge, Ahmad Jawad Sabir and Abdul Jabbar

Microorganisms 2021, 9(1), 9; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010009 - 22 Dec 2020

Cited by 5 | Viewed by 1792

Abstract

The strongyloid nematode subfamily Phascolostrongylinae comprises parasites of the large intestine and stomach of Australian macropods and wombats. In this study, we tested the phylogenetic relationships among the genera of the Phascolostrongylinae using the first and second internal transcribed spacers of the nuclear ribosomal DNA. Monophyly was encountered in the tribe Phascolostrongylinea comprising two genera, Phascolostrongylus and Oesophagostomoides, found exclusively in the large intestine of wombats. The tribe Hypodontinea, represented by the genera Hypodontus and Macropicola from the ileum and large intestine of macropods, was also found to be monophyletic. The tribe Macropostrongyloidinea, comprising the genera Macropostrongyloides and Paramacropostrongylus, was paraphyletic with the species occurring in the stomach grouping separately from those found in the large intestines of their hosts. However, Macropostrongyloidesdissimilis from the stomach of the swamp wallaby and Paramacropostrongylus toraliformis from the large intestine of the eastern grey kangaroo were distinct from their respective congeners. This study provided strong support for the generic composition of the tribe Phascolostrongylinea. The unexpected finding of M. dissimilis and P. toraliformis being distantly related to their respective congeners suggests a requirement for future taxonomic revision that may warrant separation of these species at the generic level. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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16 pages, 1257 KiB

Open AccessArticle

The Bacterial Microbiome in the Small Intestine of Hooded Seals (Cystophora cristata)

by Mario Acquarone, Alejandro Salgado-Flores and Monica Alterskjær Sundset

Microorganisms 2020, 8(11), 1664; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111664 - 27 Oct 2020

Cited by 5 | Viewed by 2724

Abstract

Arctic hooded seals (Cystophora cristata) are monogastric carnivores that go through extreme fasting and re-feeding in early life. They are born isolated on sea ice; suckle high-fat milk for four days and may then fast for up to one month before they start hunting and feeding on small prey (fish and crustaceans). Previous studies of the gut microbiota in pinnipeds have focused on the large intestine, while little data exist on the small intestinal microbiota. In this study, the bacterial microbiome in the proximal and distal small intestine of four captive two-year old seals (two males and two females) fed herring (Clupea harengus) was sampled post-mortem and characterized using 16S rRNA metabarcoding from the V1–V3 hypervariable region of the 16S ribosomal RNA (rRNA) genes. The seals were originally born in the wild and taken into human care at the end of the suckling period. Molecular-based analysis using Illumina Hiseq resulted in 569,910 16S rRNA sequences from the four seals (both sampling sites together). Taxonomical classification applying a naive Bayesian algorithm gave 412 Operational Taxonomic Units (OTUs). Firmicutes was the major phylum across samples (Proximal (P): 90.5% of total sequences, on average; Distal (D): 94.5%), followed by Actinobacteria (P: 7%; D: 0.3%) and Proteobacteria (P: 1.7%; D: 1.9%). Bacterial spp. belonging to the Clostridium (P: 54.1%; D: 41.6%) and SMB53 (P: 15.3%; D: 21.5%) constituted the major genera in both the proximal and distal small intestine. Furthermore, comparison with hindgut and fecal samples from geographically diverse marine mammals highlighted similarities in the microbiome between our seals and those sharing similar aquatic environments. This study has provided a first reliable glimpse of the bacterial microbiota in the small intestine microbiome of hooded seals. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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11 pages, 618 KiB

Open AccessArticle

Mycobacterium bovis Infection in Red Foxes in Four Animal Tuberculosis Endemic Areas in France

by Céline Richomme, Edouard Réveillaud, Jean-Louis Moyen, Perrine Sabatier, Krystel De Cruz, Lorraine Michelet and Maria Laura Boschiroli

Microorganisms 2020, 8(7), 1070; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8071070 - 17 Jul 2020

Cited by 15 | Viewed by 2408

Abstract

In France, animal tuberculosis (TB) due to Mycobacterium bovis (M. bovis) affects a multi-host community that include cattle and wildlife species such as wild boars (Sus scrofa), badgers (Meles meles), or wild deer (Cervus elaphus, Capreolus capreolus). The involvement of foxes in the epidemiology of TB is fairly described in countries facing multispecies concerns. After the discovery of grouped cases of TB in foxes in a French TB endemic region, a study was implemented in the core of four TB endemic areas in Dordogne, Charente, Landes (departments of Nouvelle-Aquitaine region), and Côte-d’Or (Burgundy-Franche-Comté region). No infected fox was found in Côte-d’Or (n = 146), where in parallel TB in cattle and other wild species became sparse in the last years. In contrast, in Dordogne, Charente, and Landes, 13 (n = 184), 9 (n = 98) and 7 (n = 140) foxes were found infected by M. bovis, respectively, corresponding to 7.1% (CI_95% 3.8–11.8%), 9.2% (4.3–16.7%) and 5.0% (CI_95% 2.0–10.0%) prevalence rates, respectively. These infection rates are comparable with those observed in badgers and wild boar in these same three areas (ranging from 9 to 13.2% and 4.3 to 17.9%, respectively), where the number of cattle outbreaks has increased in the last 10-15 years. In each area, the genotypes of foxes’ M. bovis isolates were the same as those in local cattle and other wildlife species. None of the infected foxes presented TB-like gross lesions. M. bovis was found in the mesenteric lymph nodes of 28 foxes (68%). For the 12 foxes where retropharyngeal and respiratory lymph nodes were analyzed separately, M. bovis was present in the respiratory lymph nodes of eight individuals. With regard to excretion, appropriate samples were available for 12 infected foxes from Dordogne. M. bovis DNA was detected in the feces of five of these animals, four of which were infected in the mesenteric lymph nodes. Combined with the knowledge on the biology and ecology of foxes, the results of this study suggest that in areas where infection in cattle is still active in France, foxes might play a role of spillover host in the epidemiology of M. bovis. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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21 pages, 2162 KiB

Open AccessArticle

Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome

by André C. Pereira, Victor Bandeira, Carlos Fonseca and Mónica V. Cunha

Microorganisms 2020, 8(6), 808; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8060808 - 27 May 2020

Cited by 3 | Viewed by 2409

Abstract

Recently, we unveiled taxonomical and functional differences in Egyptian mongoose (Herpestes ichneumon) gut microbiota across sex and age classes by microbial profiling. In this study, we generate, through culturomics, extended baseline information on the culturable bacterial and fungal microbiome of the species using the same specimens as models. Firstly, this strategy enabled us to explore cultivable microbial community differences across sexes and to ascertain the influence exerted by biological and environmental contexts of each host in its microbiota signature. Secondly, it permitted us to compare the culturomics and microbial profiling approaches and their ability to provide information on mongoose gut microbiota. In agreement with microbial profiling, culturomics showed that the core gut cultivable microbiota of the mongoose is dominated by Firmicutes and, as previously found, is able to distinguish sex- and age class-specific genera. Additional information could be obtained by culturomics, with six new genera unveiled. Richness indices and the Shannon index were concordant between culture-dependent and culture-independent approaches, highlighting significantly higher values when using microbial profiling. However, the Simpson index underlined higher values for the culturomics-generated data. These contrasting results were due to a differential influence of dominant and rare taxa on those indices. Beta diversity analyses of culturable microbiota showed similarities between adults and juveniles, but not in the data series originated from microbial profiling. Additionally, whereas the microbial profiling indicated that there were several bioenvironmental features related to the bacterial gut microbiota of the Egyptian mongoose, a clear association between microbiota and bioenvironmental features could not be established through culturomics. The discrepancies found between the data generated by the two methodologies and the underlying inferences, both in terms of β-diversity and role of bioenvironmental features, confirm that culture-independent, sequence-based methods have a higher ability to assess, at a fine scale, the influence of abiotic and biotic factors on the microbial community composition of mongoose’ gut. However, when used in a complementary perspective, this knowledge can be expanded by culturomics. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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19 pages, 1871 KiB

Open AccessArticle

Egyptian Mongoose (Herpestes ichneumon) Gut Microbiota: Taxonomical and Functional Differences across Sex and Age Classes

by André C. Pereira, Victor Bandeira, Carlos Fonseca and Mónica V. Cunha

Microorganisms 2020, 8(3), 392; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8030392 - 11 Mar 2020

Cited by 10 | Viewed by 4847

Abstract

The Egyptian mongoose (Herpestes ichneumon) is a medium-size carnivore that, in Europe, is restricted to Iberia. The bio-ecology of this species remains to be elucidated in several dimensions, including gut microbiota that is nowadays recognized as a fundamental component of mammals. In this work, we investigated the gut microbiota of this herpestid by single-molecule real-time sequencing of twenty paired male (n = 10) and female (n = 10) intestinal samples. This culture-independent approach enabled microbial profiling based on 16S rDNA and investigation of taxonomical and functional features. The core gut microbiome of the adult subpopulation was dominated by Firmicutes, Fusobacteria, Actinobacteria, and Proteobacteria. Eight genera were uniquely found in adults and five in non-adults. When comparing gut bacterial communities across sex, four genera were exclusive of females and six uniquely found in males. Despite these compositional distinctions, alpha- and beta-diversity analyses showed no statistically significant differences across sex or between adult and non-adult specimens. However, when function was inferred, males presented a significantly higher abundance of amino acid and citrate cycle metabolic pathways, compared to the significant overrepresentation in females of galactose metabolic pathways. Additionally, adults exhibited a significantly higher abundance of cationic antimicrobial peptide resistance pathways, while non-adults bared a significant overrepresentation of two-component systems associated with antibiotic synthesis, flagellin and biofilm production, and chemotaxis control. This study adds new insights into the mongoose bio-ecology palette, highlighting taxonomical and functional microbiome dissimilarities across sex and age classes, possibly related to primary production resources and life-history traits that impact on behavior and diet. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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13 pages, 724 KiB

Open AccessArticle

Detection of Wood Mice (Apodemus sylvaticus) Carrying Non-Tuberculous Mycobacteria Able to Infect Cattle and Interfere with the Diagnosis of Bovine Tuberculosis

by Lucía Varela-Castro, Olalla Torrontegi, Iker A. Sevilla and Marta Barral

Microorganisms 2020, 8(3), 374; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8030374 - 06 Mar 2020

Cited by 5 | Viewed by 2602

Abstract

Mycobacterial infections caused by the Mycobacterium tuberculosis complex (MTC) and non-tuberculous mycobacteria (NTM) are of great medical and veterinary relevance. The aim of this research was to study whether small mammals play a role in the epidemiology of mycobacterioses. Four samplings of 100 traps were performed in each of three cattle farms with previous history of tuberculosis or NTM between 2017 and 2018. A total of 108 animals belonging to seven species were trapped, classified, and necropsied, and tissues were submitted to microbiological and molecular methods for mycobacteria identification. The wood mouse (Apodemus sylvaticus) was the most abundant species (87%). No MTC was detected but six different NTM were identified (M. intracellulare, M. avium subsp. paratuberculosis, M. gordonae, M. celatum, M. fortuitum, and a not determined Mycobacterium sp.), showing a prevalence of 6.5%. No significant association was found between mycobacteria prevalence and the analyzed factors. Although a role in the epidemiology of MTC could not be attributed to small mammals, A. sylvaticus carries NTM that could be pathogenic or interfere with the diagnosis of tuberculosis. According to our results, there is a risk of NTM transmission at the wildlife–livestock interface through potential indirect contacts between small mammals and cattle. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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15 pages, 1399 KiB

Open AccessArticle

Characterization of ESBL-Producing Enterobacteria from Fruit Bats in an Unprotected Area of Makokou, Gabon

by Pierre Philippe Mbehang Nguema, Richard Onanga, Guy Roger Ndong Atome, Jean Constant Obague Mbeang, Arsène Mabika Mabika, Moussa Yaro, Manon Lounnas, Yann Dumont, Zaidi Fatma Zohra, Sylvain Godreuil and François Bretagnolle

Microorganisms 2020, 8(1), 138; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010138 - 19 Jan 2020

Cited by 22 | Viewed by 3934 | Correction

Abstract

In Gabon, terrestrial mammals of protected areas have been identified as a possible source of antibiotic-resistant bacteria. Some studies on antibiotic resistance in bats have already been carried out. The main goal of our study was to detect extended-spectrum beta-lactamases (ESBLs) that are produced by enterobacteria from bats in the Makokou region in Gabon. Sixty-eight fecal samples were obtained from 68 bats caught in the forests located 1 km from the little town of Makokou. After culture and isolation, 66 Gram-negative bacterial colonies were obtained. The double-disk diffusion test confirmed the presence of ESBLs in six (20.69%) Escherichia coli isolates, four (13.79%) Klebsiella pneumoniae isolates, and one (3.45%) Enterobacter cloacae isolate. The analysis based on the nucleotide sequences of the ESBL resistance genes showed that all cefotaximase-Munichs (CTX-Ms) were CTX-M-15 and that all sulfhydryl variables (SHVs) were SHV-11: 41.67% CTX-M-15-producing E. coli, 16.67% CTX-M-15+SHV-11-producing E. coli, 8.33% CTX-M-15-producing K. pneumoniae, 25% CTX-M-15+SHV-11-producing K. pneumoniae, and 8.33% CTX-M-15-produced E. cloacae. This study shows for the first time the presence of multiresistant ESBL-producing enterobacteria in fruit bats in Makokou. Full article

(This article belongs to the Special Issue Wildlife Microbiology 2.0)

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