Larkinella bovis sp. nov., isolated from fermented bovine products, and emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006

Anandham, Rangasamy; Kwon, Soon-Wo; Weon, Hang-Yeon; Kim, Soojin; Kim, Yiseul; Gandhi, Pandiyan Indira; Kim, Yong Ki; Jee, Hyeong Jin

doi:10.1099/ijs.0.020453-0

Cited by 20 publications

(2 citation statements)

References 14 publications

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“…At the genus and clade level, these increases of common taxa may represent an overall increase in bacterial load in ESCA, or may be linked to tissue and microenvironment differences between the cohorts. On the other hand, members of the small genus Larkinella (class Cytophagales ), which have been isolated from diverse environments, principally soil [ 51 – 55 ], were identified by one study in bladder cancer, reporting an association between Larkinella and recurrence [ 56 ].…”

Section: Resultsmentioning

confidence: 99%

Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

Schäffer,

Li,

Elbasir

et al. 2023

ISME Communications

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Local microbiome shifts are implicated in the development and progression of gastrointestinal cancers, and in particular, esophageal carcinoma (ESCA), which is among the most aggressive malignancies. Short-read RNA sequencing (RNAseq) is currently the leading technology to study gene expression changes in cancer. However, using RNAseq to study microbial gene expression is challenging. Here, we establish a new tool to efficiently detect viral and bacterial expression in human tissues through RNAseq. This approach employs a neural network to predict reads of likely microbial origin, which are targeted for assembly into longer contigs, improving identification of microbial species and genes. This approach is applied to perform a systematic comparison of bacterial expression in ESCA and healthy esophagi. We uncover bacterial genera that are over or underabundant in ESCA vs healthy esophagi both before and after correction for possible covariates, including patient metadata. However, we find that bacterial taxonomies are not significantly associated with clinical outcomes. Strikingly, in contrast, dozens of microbial proteins were significantly associated with poor patient outcomes and in particular, proteins that perform mitochondrial functions and iron-sulfur coordination. We further demonstrate associations between these microbial proteins and dysregulated host pathways in ESCA patients. Overall, these results suggest possible influences of bacteria on the development of ESCA and uncover new prognostic biomarkers based on microbial genes. In addition, this study provides a framework for the analysis of other human malignancies whose development may be driven by pathogens.

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Section: Resultsmentioning

confidence: 99%

Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

Schäffer,

Li,

Elbasir

et al. 2023

ISME Communications

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“…The family Cytophagaceae in the phylum Bacteroidetes comprises 26 genera at the time of writing (http://www.bacterio.net/). Members of the family Cytophagaceae frequently have rod- or ring-shaped cells (Anandham et al , 2011; Kulichevskaya et al , 2009) or form multicellular filaments in broth medium (Filippini et al , 2011; Finster et al , 2009; Weon et al , 2008). Their colonies are usually pigmented with yellow, orange, pink or red owing to carotenoids, flexirubin-type pigments, or both (Nakagawa, 2011).…”

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confidence: 99%

Nibrella saemangeumensis gen. nov., sp. nov. and Nibrella viscosa sp. nov., novel members of the family Cytophagaceae, isolated from seawater

Kang

Chun

Choi

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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Two strains, designated GCR0103T and GYR3121T, were isolated from seawater of the Saemangeum Embankment in Jeollabuk-do, Korea. The cells of the two strains were Gram-reaction-negative and non-motile, and formed multicellular filaments. The colonies of the two strains were pink-pigmented and able to grow at 15–37 °C (optimum 25 °C) on R2A and NA medium. Strains GCR0103T and GYR3121T grew at pH 6.5–10 (optimum pH 7.5) and pH 5.5–9.5 (optimum pH 7.5), and within NaCl ranges of 0–0.4 % and 0–1 %, respectively. The polar lipid profiles of the two strains contained phosphatidylethanolamine, five unknown aminolipids, an unknown phospholipid and four or five unknown lipids. The DNA G+C contents of strains GCR0103T and GYR3121T were 56.0 and 54.5 mol%, respectively. The respiratory quinone detected in both strains was MK-7. The 16S rRNA gene sequence similarity between GCR0103T and GYR3121T was 95.5 %. The 16S rRNA gene sequence similarities of the two strains to closely related reference strains were less than 89 %. Phylogenetic analysis based on 16S rRNA genes showed that GCR0103T and GYR3121T formed a distinct phyletic line in the family Cytophagaceae . On the basis of the phenotypic, chemotaxonomic and phylogenetic properties, strains GCR0103T and GYR3121T represent two novel species in a new genus within the family Cytophagaceae , for which the names Nibrella saemangeumensis gen. nov., sp. nov. and Nibrella viscosa sp. nov. are proposed. The type strain of Nibrella saemangeumensis is GCR0103T ( = KACC 16453T = JCM 17927T) and the type strain of Nibrella viscosa is GYR3121T ( = KACC 16447T = JCM 17925T).

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Larkinella punicea sp. nov., isolated from manganese mine soil

et al. 2020

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Larkinella bovis sp. nov., isolated from fermented bovine products, and emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006

Abstract: Larkinella bovis sp. nov., isolated from fermented bovine products, and emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006

Cited by 20 publications

References 14 publications

Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

Nibrella saemangeumensis gen. nov., sp. nov. and Nibrella viscosa sp. nov., novel members of the family Cytophagaceae, isolated from seawater

Larkinella punicea sp. nov., isolated from manganese mine soil

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