Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-17

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

31719139

DOI Digital object identifier for electronic documents.

https://doi.org/10.1128/msystems.00438-19

URI

https://pubmed.ncbi.nlm.nih.gov/31719139/

Authors

Gupta A, Dhakan DB, Maji A, Saxena R, P K VP, Mahajan S, Pulikkan J, Kurian J, Gomez AM, Scaria J, Amato KR, Sharma AK, Sharma VK

Journal

mSystems

Year

2019

Keywords:

Flavonifractor plautii, biomarkers, colorectal cancer, gut microbiome

Recently, dysbiosis in the human gut microbiome and shifts in the relative abundances of several bacterial species have been recognized as important factors in colorectal cancer (CRC). However, these studies have been carried out mainly in developed countries where CRC has a high incidence, and it is unclear whether the host-microbiome relationships deduced from these studies can be generalized to the global population. To test if the documented associations between the microbiome and CRC are conserved in a distinct context, we performed metagenomic and metabolomic association studies on fecal samples from 30 CRC patients and 30 healthy controls from two different locations in India, followed by a comparison of CRC data available from other populations. We confirmed the association of Bacteroides and other bacterial taxa with CRC that have been previously reported in other studies. However, the association of CRC with Flavonifractor plautii in Indian patients emerged as a novel finding. The plausible role of F. plautii appears to be linked with the degradation of beneficial anticarcinogenic flavonoids, which was also found to be significantly correlated with the enzymes and modules involved in flavonoid degradation within Indian CRC samples. Thus, we hypothesize that the degradation of beneficial flavonoids might be playing a role in cancer progression within this Indian cohort. We also identified 20 potential microbial taxonomic markers and 33 potential microbial gene markers that discriminate the Indian CRC from healthy microbiomes with high accuracy based on machine learning approaches.IMPORTANCE This study provides novel insights on the CRC-associated microbiome of a unique cohort in India, reveals the potential role of a new bacterium in CRC, and identifies cohort-specific biomarkers, which can potentially be used in noninvasive diagnosis of CRC. The study gains additional significance, as India is among the countries with a very low incidence of CRC, and the diet and lifestyle in India have been associated with a distinct gut microbiome in healthy Indians compared to other global populations. Thus, in this study, we hypothesize a unique relationship between CRC and the gut microbiome in an Indian population.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-18

Curated date: 2023/03/18

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Subjects

Location of subjects: India

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Colorectal carcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy control

Group 1 name Corresponds to the case (exposed) group for case-control studies: Colorectal cancer patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Indians who are colorectial cancer patients

Group 0 sample size Number of subjects in the control (unexposed) group: 30

Group 1 sample size Number of subjects in the case (exposed) group: 30

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Recent use of antibiotics.

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Signature 3

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-18

Curated date: 2023/03/27

Curator: Atrayees

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Source: Text, Figure 2, Table S3

Description: Species observed to be significantly associated with CRC or healthy samples.

Abundance in Group 1: increased abundance in

NCBI	Quality Control	Links
Akkermansia muciniphila
Bacteroides eggerthii
Campylobacter hominis
Citrobacter koseri
Enterococcus gallinarum
Gemella morbillorum
Klebsiella oxytoca
Limosilactobacillus vaginalis
Methanobrevibacter smithii
Odoribacter splanchnicus
Parasutterella excrementihominis
Porphyromonas uenonis
Prevotella bivia
Roseburia inulinivorans
Streptococcus oralis
Streptococcus sanguinis
Bacteroides clarus
Bacteroides fragilis
Bacteroides intestinalis
Escherichia coli
Flavonifractor plautii
Parabacteroides distasonis
Parvimonas micra
Streptococcus parasanguinis
Veillonella parvula
Peptostreptococcus stomatis

Revision editor(s): Atrayees, Claregrieve1, WikiWorks

Signature 4

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-18

Curated date: 2023/03/27

Curator: Atrayees

Revision editor(s): Atrayees, Claregrieve1, WikiWorks

Source: Text, Figure 2, Table S3

Description: Species observed to be significantly associated with CRC or healthy samples

Abundance in Group 1: decreased abundance in

NCBI	Quality Control	Links
Acidaminococcus fermentans
Alistipes putredinis
Anaerobutyricum hallii
Bacteroides caccae
Bacteroides uniformis
Bifidobacterium adolescentis
Bifidobacterium dentium
Eshraghiella crossota
Comamonas testosteroni
Coprococcus comes
Dorea longicatena
Eggerthella lenta
Eubacterium ventriosum
Fusobacterium varium
Haemophilus pittmaniae
Lactobacillus amylovorus
Mitsuokella multacida
Segatella copri
Roseburia intestinalis
Streptococcus infantis
Treponema succinifaciens
[Clostridium] leptum
Faecalibacterium prausnitzii
Ligilactobacillus ruminis
Megasphaera elsdenii
Agathobacter rectalis

Revision editor(s): Atrayees, Claregrieve1, WikiWorks