Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome

Johny, Tina Kollannoor; Puthusseri, Rinu Madhu; Bhat, Sarita G.

doi:10.1007/s00203-021-02675-y

Cited by 17 publications

(7 citation statements)

References 63 publications

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“…Many of these predicted virulence factors may have as main purpose to facilitate longterm interactions with other organisms or to collaborate with Shewanella's survival and adaptation to different habitats (i.e., in aquatic niches or within a host). In this regard, metagenomic studies have shown the relevant abundance of members of the Shewanella genus in fish gut and invertebrates, which may vary under different conditions (Parris et al, 2016;Tepaamorndech et al, 2020;Jia et al, 2022;Johny et al, 2022). Moreover, these bacteria were also detected in the gastric and colorectal mucosal microbiomes of healthy and sick patients (Angelakis et al, 2016;Yang et al, 2022), showing an unexpected incidence.…”

Section: Discussionmentioning

confidence: 99%

Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Cerbino

Traglia²,

Nuñez³

et al. 2023

Front. Microbiol.

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Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.

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Section: Discussionmentioning

confidence: 99%

Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Cerbino

Traglia²,

Nuñez³

et al. 2023

Front. Microbiol.

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“…establishing levels of co-authorship between authors with their affiliations and their collaborators, using VOSviewer and Pajek [76,77].…”

Section: Results Of the Number Of Trail Tourism Publications From 199...mentioning

confidence: 99%

“…In order to identify a core concentration of journals where authors engage in deep path tourism discussion, Lotka’s law [ 71 , 72 ] was used. To estimate the concentration of authors and distinguish the set of prolific authors [ 73 , 74 ], following a meta-analytic scientometric approach [ 75 ] of production, impact and relatedness that relationally focused on establishing levels of co-authorship between authors with their affiliations and their collaborators, using VOSviewer and Pajek [ 76 , 77 ].…”

Section: Methodsmentioning

confidence: 99%

Scientometric Analysis of Hiking Tourism and Its Relevance for Wellbeing and Knowledge Management

Acevedo-Duque

Llanos-Herrera

García-Salirrosas

et al. 2022

IJERPH

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Hiking is a sports activity that takes place in the natural environment. From the point of view of well-being, it is an aerobic activity that prevents and improves cardiovascular diseases. According to data provided by the United Nations, within the framework of the International Year of Mountains, mountain tourism represents around 15% to 20% of total world tourism revenue. This approach aims to critically analyze the scientific production on trail tourism (HT) with contributions from authors from around the world from 1991 to 2022, in order to respond to the connection between this research, knowledge management and the sustainable development of the industry. Key knowledge contributions are examined using a scientometric approach as a method (spatial, production, impact, and relational) based on registry data stored in the Web of Science (JCR and ESCI). Regarding the results, there has been an increase in scientific production in the last decade, which is manifested in the quality of the publications.

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“…Additionally, high‐throughput sequencing is a powerful tool to perform functional annotations on microbial communities. Sequences obtained using metagenomics or transcriptomics are annotated against several nucleotide and protein databases, including NCBI non‐redundant protein sequence (NR), NCBI non‐redundant nucleotide sequence (NT), Swiss‐Prot, InterPro, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) or Cluster of Orthologous Groups of proteins (COG) 91,92 . Moreover, sequence annotation for the prediction and identification of antimicrobial peptides database has been performed to search for specific antimicrobial compounds in the gut microbiome of fish 93 …”

Section: The Gastrointestinal System Of Fish and Their Microbiotamentioning

confidence: 99%

Fish disease and intestinal microbiota: A close and indivisible relationship

Félix

Garibay-Valdez

Vargas‐Albores

et al. 2022

Reviews in Aquaculture

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The gut microbiota is currently one of the most studied 'organs' in animals, and fish are no exception. A complex diversity of microbes, including bacteria, archaea, yeast and fungus, constitute the gut microbiota, creating a complex interaction with their host and accomplishing multiple beneficial functions, such as food digestion, nutrient absorption, immune system, endocrine and stress response. The microbiotapathogen interaction protects the host by mounting colonization resistance, competing for nutrients and space. Changes in the balance of the microbiota community could affect their structure and homeostasis, inducing dysbiosis. In addition, invading pathogens can induce dysbiosis by evading the host's defence barriers, acquiring nutrients from the fish host, using metabolites produced by the microbiota and producing toxins. In this regard, understanding the interactions within the fish gut microbiota is essential to prevent pathogen establishment in the host. Hence, this review describes the close and indivisible relationships and interactions between gut microbiota and pathogens that could lead to dysbiosis and disease.

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Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome

Cited by 17 publications

References 63 publications

Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Scientometric Analysis of Hiking Tourism and Its Relevance for Wellbeing and Knowledge Management

Fish disease and intestinal microbiota: A close and indivisible relationship

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