Identifying Gut Microbiota Associated With Colorectal Cancer Using a Zero-Inflated Lognormal Model

Ai, Dongmei; Pan, Hongfei; Li, Xiaoxin; Gao, Yingxin; Liu, Gang; Li, Xia

doi:10.3389/fmicb.2019.00826

Cited by 129 publications

(105 citation statements)

References 56 publications

(58 reference statements)

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“…Samples were clustered based on the relative abundances of differentially abundant species with false discovery rate (FDR) ≤ 0.2. Clustering and plotting were performed with STAMP (statistical analysis of taxonomic and functional profiles) [16] increase in microbial diversity [26,27], contrary to what is observed in other cancers such as those of the colon [28].…”

Section: Discussionmentioning

confidence: 99%

Tongue microbiome of smokeless tobacco users

et al. 2020

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Background: The possibility that smokeless tobacco may contribute to oral carcinogenesis by influencing the oral microbiome has not been explored. This preliminary cross-sectional study sought to assess the effect of using shammah, a form of smokeless tobacco prevalent in Arabia, on the tongue microbiome. Tongue scarping samples were obtained from 29 shammah users (SU; 27.34 ± 6.9 years) and 23 shammah non-users (SNU; 27.7 ± 7.19 years) and analyzed with 16S rRNA gene sequencing (V1-V3). Species-level taxonomy assignment of the high-quality, merged reads was obtained using a previously described BLASTn-based algorithm. Downstream analyses were performed with QIIME, LEfSe, and R. Results: A total of 178 species, belonging to 62 genera and 8 phyla were identified. Genera Streptococcus, Leptotrichia, Actinomyces, Veillonella, Haemophilus, Prevotella and Neisseria accounted for more than 60% of the average microbiome. There were no differences between the two groups in species richness and alpha-diversity, but PCoA showed significant separation (P = 0.015, ANOSIM). LEfSe analysis identified 22 species to be differentially abundant between the SU and SNU. However, only 7 species maintained a false discovery rate of ≤0.2 and could cluster the two groups separately: Rothia mucilaginosa, Streptococcus sp. oral taxon 66, Actinomyces meyeri, Streptococcus vestibularis Streptococcus sanguinis and a potentially novel Veillonella species in association with SU, and Oribacterium asaccharolyticum with SNU. Conclusion: These preliminary results indicate that shammah use induces tongue microbiome changes including enrichment of several species with high acetaldehyde production potential, which warrants further investigation.

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Section: Discussionmentioning

confidence: 99%

Tongue microbiome of smokeless tobacco users

et al. 2020

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“…Among the three bacteria with altered abundance in the gut microbiota in TMEV infection, the physiological and pathogenic roles of Dorea and Marvinbryantia genera are largely unknown. On the other hand, the genus Coprococcus is a component of human fecal microbiota (69,70), and their increased abundance was observed in patients with neuromyelitis optica (NMO), but not in MS, compared with healthy controls (71,72). NMO is an inflammatory demyelinating disease, in which autoantibody against the water channel protein aquoaporin-4 has been associated with pathogenesis.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics Analysis of Gut Microbiota and CNS Transcriptome in Virus-Induced Acute Myelitis and Chronic Inflammatory Demyelination; Potential Association of Distinct Bacteria With CNS IgA Upregulation

et al. 2020

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Virus infections have been associated with acute and chronic inflammatory central nervous system (CNS) diseases, e.g., acute flaccid myelitis (AFM) and multiple sclerosis (MS), where animal models support the pathogenic roles of viruses. In the spinal cord, Theiler's murine encephalomyelitis virus (TMEV) induces an AFM-like disease with gray matter inflammation during the acute phase, 1 week post infection (p.i.), and an MS-like disease with white matter inflammation during the chronic phase, 1 month p.i. Although gut microbiota has been proposed to affect immune responses contributing to pathological conditions in remote organs, including the brain pathophysiology, its precise role in neuroinflammatory diseases is unclear. We infected SJL/J mice with TMEV; harvested feces and spinal cords on days 4 (before onset), 7 (acute phase), and 35 (chronic phase) p.i.; and examined fecal microbiota by 16S rRNA sequencing and CNS transcriptome by RNA sequencing. Although TMEV infection neither decreased microbial diversity nor changed overall microbiome patterns, it increased abundance of individual bacterial genera Marvinbryantia on days 7 and 35 p.i. and Coprococcus on day 35 p.i., whose pattern-matching with CNS transcriptome showed strong correlations: Marvinbryantia with eight T-cell receptor (TCR) genes on day 7 and with seven immunoglobulin (Ig) genes on day 35 p.i.; and Coprococcus with gene expressions of not only TCRs and IgG/IgA, but also major histocompatibility complex (MHC) and complements. The high gene expression of IgA, a component of mucosal immunity, in the CNS was unexpected. However, we observed substantial IgA positive cells and deposition in the CNS, as well as a strong correlation between CNS IgA gene expression Omura et al. Microbiome in MS Viral Model and serum anti-TMEV IgA titers. Here, changes in a small number of distinct gut bacteria, but not overall gut microbiota, could affect acute and chronic immune responses, causing AFM-and MS-like lesions in the CNS. Alternatively, activated immune responses would alter the composition of gut microbiota.

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“…; depletion of the butyryl-CoA transferase in CRC subjects have also been reported. 136,143 Among Eubacterium spp., E. rectale, E. hallii and E. ventriosum are reported to be significantly reduced in abundance in the gut of individuals with CRC 136,[143][144][145] (Table 2). E. ventriosum has been proposed as biomarker for low risk of CRC, with significant enrichment in healthy individuals compared to CRC patients in diverse populations.…”

Section: Butyrate-mediated Contribution Of Eubacterium Spp In Inhibimentioning

confidence: 99%

Gut microbes from the phylogenetically diverse genusEubacteriumand their various contributions to gut health

et al. 2020

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Over the last two decades our understanding of the gut microbiota and its contribution to health and disease has been transformed. Among a new 'generation' of potentially beneficial microbes to have been recognized are members of the genus Eubacterium, who form a part of the core human gut microbiome. The genus consists of phylogenetically, and quite frequently phenotypically, diverse species, making Eubacterium a taxonomically unique and challenging genus. Several members of the genus produce butyrate, which plays a critical role in energy homeostasis, colonic motility, immunomodulation and suppression of inflammation in the gut. Eubacterium spp. also carry out bile acid and cholesterol transformations in the gut, thereby contributing to their homeostasis. Gut dysbiosis and a consequently modified representation of Eubacterium spp. in the gut, have been linked with various human disease states. This review provides an overview of Eubacterium species from a phylogenetic perspective, describes how they alter with diet and age and summarizes its association with the human gut and various health conditions.

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Identifying Gut Microbiota Associated With Colorectal Cancer Using a Zero-Inflated Lognormal Model

Cited by 129 publications

References 56 publications

Tongue microbiome of smokeless tobacco users

Tongue microbiome of smokeless tobacco users

Bioinformatics Analysis of Gut Microbiota and CNS Transcriptome in Virus-Induced Acute Myelitis and Chronic Inflammatory Demyelination; Potential Association of Distinct Bacteria With CNS IgA Upregulation

Gut microbes from the phylogenetically diverse genusEubacteriumand their various contributions to gut health

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