Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome

Tyagi, Anuj; Singh, Balwinder; Thammegowda, Naveen K Billekallu; Singh, Niraj Kumar

doi:10.1007/s00203-018-1615-y

Cited by 71 publications

(39 citation statements)

References 38 publications

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“…The extended-spectrum β-lactamase (ESBL) was found to be predominantly associated with Klebsiella pneumoniae present in the gut of Tor putitora. Similar to this study, genes encoding extended spectrum betalactamase (TEM, CTX-M-1) and multidrug resistance proteins (mdtA, mdtB, mdtC) were also found in the gut microbiome of freshwater Indian carp [19].…”

Section: Discussionsupporting

confidence: 85%

Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health

Khurana

Singh

et al. 2020

BMC Microbiol

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Background: Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome. Results: The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens. Conclusions: Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.

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Section: Discussionsupporting

confidence: 85%

Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health

Khurana

Singh

et al. 2020

BMC Microbiol

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“…These limitations can be mitigated by the use of shotgun metagenomics, which offers enhanced detection of bacterial species, a better estimation of diversity, and a more in-depth insight into the functional composition of microbiomes (Llewellyn et al, 2014;Romero et al, 2014;Ghanbari et al, 2015;Merrifield and Rodiles, 2015;Colston and Jackson, 2016;Ranjan et al, 2016;Tarnecki et al, 2017). Despite these advantages, however, only a handful of studies has used metagenomics approaches to investigate the intestinal microbiome in fish, and the existing studies are all limited in their number of samples investigated, their community characterization at the lower taxonomical levels (i.e., species) or geographical sampling range, with a focus on Pacific aquaculture species (Xing et al, 2013;Xia et al, 2014;Hennersdorf et al, 2016;Tyagi et al, 2019). Nevertheless, there exist no studies that use metagenomic shotgun sequencing to characterize the geographical structure and community complexity in the intestinal microbiome of wild fish.…”

Section: Introductionmentioning

confidence: 99%

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Riiser

Haverkamp

Varadharajan

et al. 2019

Environmental Microbiology

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Summary Atlantic cod (Gadus morhua) is an ecologically important species with a wide‐spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine‐scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway–located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.

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“…Calves could have acquired drug resistant bacteria and resistant genes from their mothers during birth, from the waste milk used as feed [26,27] or from the environment [8,28], including cross-contamination through farm workers and feeding equipment [29]. Studies have found AMR genes in animals raised without antimicrobials as well [30,31].…”

Section: Discussionmentioning

confidence: 99%

Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and function of dairy calves

Foditsch

Pereira

Siler

et al. 2019

Preprint

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16The increasing concerns with antimicrobial resistance highlights the need for studies 17 evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new 18 sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal 19 microbiome composition and function, with a focus on functions related to antimicrobial 20 resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the 21 farm before enrollment, were randomly allocated to one of three study groups: control (no 22 treatment), enrofloxacin, or tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 23 days after enrollment, and DNA extraction and sample preparation and sequencing was conducted. 2 24 The effect of antibiotic treatment on each taxon and functional level by time (including Day 0 as 25 a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had 26 higher abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides 27when compared to other treatment groups. The SEED database was used for functional analyses, 28 which showed that calves in the enrofloxacin group started with a higher abundance of "Resistance 29 to antibiotics and toxic compounds" function on Day 0, however an increase in antibiotic resistance 30 genes after treatment with enrofloxacin was not observed. "Resistance to Fluoroquinolones" and 31 "Erythromycin resistance", of relevance given the study groups, were not statistically different in 32 abundance between treatment groups. "Resistance to fluoroquinolones" increased during the study 33 period regardless of treatment group. Despite small differences over the first weeks between 34 treatment groups, at Day 112 the microbiota composition and functional profile was similar among 35 all study groups. These findings show that metaphylaxis treatment of dairy calves with either 36 enrofloxacin or tulathromycin have minimal impacts on the microbial composition and functional 37 microbiota of dairy calves over time. 38 39 40 42 45and resistance genes are present even in places that were never inhabited by humans [3,4] and in 46 wild animals [5]. However, the use of antibiotics in human and animal medicine, as well as in plant 3 47 agriculture and animal production systems, has resulted in an acceleration in the selection and 48 spread of antimicrobial resistance [1,6]. Antimicrobial resistant enteric bacteria can be transmitted 49 from livestock to humans through the fecal-oral route, or contamination in the food chain and 50 environment [1,7,8]. Together with prevention of disease and infectious agent transmission, the 51 prudent use of antibiotics is extremely important to preserve treatment effectiveness and decrease 52 the dissemination of resistant bacteria. 53Antimicrobials may be used to control and prevent the spread of the disease in production 54 animals at high risk of developing a bacterial infectious disease. This practice is referred to as 55 metaph...

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Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome

Cited by 71 publications

References 38 publications

Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health

Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and function of dairy calves

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