Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population

Minh, Chau Nguyen Ngoc; Hong, Chau Tran Thi; Nguyen, To Nguyen Thi; Pike, Lindsay J.; Zellmer, Caroline; Duc, Trung Pham; Tran, Tuan Anh; Thanh, Tuyen Ha; Van, Minh Pham; Thwaites, Guy; Rabaa, Maia A.; Hall, Lindsay J.; Baker, Stephen

doi:10.1128/spectrum.00526-21

Cited by 13 publications

(7 citation statements)

References 84 publications

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“…Similarly, using arbitrarily primed PCR, Komiya and colleagues showed that identical F. nucleatum strains were isolated from 6/14 paired gut tissue-saliva samples 45 , but WGS was not conducted to verify the exact genetic differences. The populations of Fusobacterium colonising the oral cavity and gut were heterogeneous within some individuals, even at the subspecies level, which mirrors the diversity observed previously for gut commensals such as Bifidobacterium 46 . Chronic infections with Helicobacter pylori at the stomach, which increases the risk of gastric cancer, usually result in extensive clonal propagations detected by WGS within each patient, though isolates were collected in a single timepoint 47 .…”

Section: Discussionsupporting

confidence: 78%

Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients

Tran

Thu

Nguyen³

et al. 2022

npj Biofilms Microbiomes

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Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite its significance in the promotion of CRC, genomic studies of Fusobacterium is limited. We enrolled 43 Vietnamese CRC patients and 25 participants with non-cancerous colorectal polyps to study the colonic microbiomes and genomic diversity of Fusobacterium in this population, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome analysis. Oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour microbiomes. We obtained 53 Fusobacterium genomes, representing 26 strains, from the saliva, tumour and non-tumour tissues of six CRC patients. Isolates from the gut belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of Fusobacterium periodonticum. The Fusobacterium population within each individual was distinct and in some cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within four individuals, tumour-associated Fusobacterium were clonal to those isolated from non-tumour tissues. Genes encoding major virulence factors (Fap2 and RadD) showed evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.

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Section: Discussionsupporting

confidence: 78%

Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients

Tran

Thu

Nguyen³

et al. 2022

npj Biofilms Microbiomes

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“…Furthermore, our approach allows for delineation of bacteria from tumour and non-tumour sites, which is inaccessible by faecal metagenomes. The populations of Fusobacterium colonizing the oral cavity and gut mucosa were heterogeneous within each individual, even at the subspecies level, which mirrors the diversity observed previously for gut commensals such as Bifidobacterium species [47]. Though this study did not provide evidence of genetic relatedness between oral and gut Fusobacterium isolates, this likely point to the high diversity of Fusobacterium in the oral niche [48].…”

Section: Discussionsupporting

confidence: 71%

Mucosal microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients

Tran

Thu

Nguyen³

et al. 2022

Preprint

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Perturbations in the gut microbiome have been linked to the promotion and prognosis of colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite the increasing health burden inflicted by CRC in low- and middle-income countries like Vietnam, the CRC-specific microbiome in these populations remains underexplored. Here we conducted a study in Vietnam to enrol 43 CRC patients (cases) and 25 patients with non-cancerous colorectal polyps (controls) between December 2018 and January 2020. Our study investigated the mucosal microbiome signature and genomic diversity of Fusobacterium in Vietnamese CRC patients, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome sequencing. We found that several oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour mucosa, and these two bacteria were also more enriched in tumours of advanced CRC stages (III-IV). We obtained 53 Fusobacterium genomes from the saliva, tumour and non-tumour mucosa of six CRC patients. Isolates from the gut mucosa belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of F. periodonticum. The Fusobacterium population within each individual was distinct and in many cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within each individual, tumour-associated Fusobacterium were clonal to those isolated from non-tumour mucosa, but distantly related to those isolated from saliva. Genes encoding major virulence factors (Fap2 and RadD) showed variability in length and evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.

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“…Representatives of these genera are known to be early and long-term persistent colonizers of infant intestine that can, in some settings, promote inflammatory response (53). By contrast, several inflammation-reducing representatives of the Bifidobacterium genus, from the early human milk oligosaccharide-metabolizer B. longum to the later complex carbohydrate relying B. pseudocatenulatum (54), commonly associated with weaning to solid food in early age, also showed high relative importance. The involvement of most important taxa in different aspects of inflammatory response resonates with previous findings that associate chronic inflammation with changes to neural responses in some types of stimuli (55).…”

Section: Discussionmentioning

confidence: 99%

Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children

Bonham,

Fahur Bottino,

McCann

et al. 2023

Sci. Adv.

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Emerging evidence implicates gut microbial metabolism in neurodevelopmental disorders, but its influence on typical neurodevelopment has not been explored in detail. We investigated the relationship between the microbiome and neuroanatomy and cognition of 381 healthy children, demonstrating that differences in microbial taxa and genes are associated with overall cognitive function and the size of brain regions. Using a combination of statistical and machine learning models, we showed that species including Alistipes obesi , Blautia wexlerae , and Ruminococcus gnavus were enriched or depleted in children with higher cognitive function scores. Microbial metabolism of short-chain fatty acids was also associated with cognitive function. In addition, machine models were able to predict the volume of brain regions from microbial profiles, and taxa that were important in predicting cognitive function were also important for predicting individual brain regions and specific subscales of cognitive function. These findings provide potential biomarkers of neurocognitive development and may enable development of targets for early detection and intervention.

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Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population

Abstract: Bifidobacterium pseudocatenulatum is a beneficial member of the human gut microbiota. The organism can modulate inflammation and has probiotic potential, but its characteristics are largely strain dependent and associated with distinct genomic and biochemical features.

Cited by 13 publications

References 84 publications

Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients

Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients

Mucosal microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients

Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children

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