Multivariate Analysis in Microbiome Description: Correlation of Human Gut Protein Degraders, Metabolites, and Predicted Metabolic Functions

Abstract

Protein catabolism by intestinal bacteria is infamous for releasing many harmful compounds, negatively affecting the health status, both locally and systemically. In a previous study, we enriched in protein degraders the fecal microbiota of five subjects, utilizing a medium containing protein and peptides as sole fermentable substrates and we monitored their evolution by 16S rRNA gene profiling. In the present study, we fused the microbiome data and the data obtained by the analysis of the volatile organic compounds (VOCs) in the headspace of the cultures. Then, we utilized ANOVA simultaneous component analysis (ASCA) to establish a relationship between metabolites and bacteria. In particular, ASCA allowed to separately assess the effect of subject, time, inoculum concentration, and their binary interactions on both microbiome and volatilome data. All the ASCA submodels pointed out a consistent association between indole and Escherichia–Shigella, and the relationship of butyric, 3-methyl butanoic, and benzenepropanoic acids with some bacterial taxa that were major determinants of cultures at 6 h, such as Lachnoclostridiaceae (Lachnoclostridium), Clostridiaceae (Clostridium sensu stricto), and Sutterellaceae (Sutterella and Parasutterella). The metagenome reconstruction with PICRUSt2 and its functional annotation indicated that enrichment in a protein-based medium affected the richness and diversity of functional profiles, in the face of a decrease of richness and evenness of the microbial community. Linear discriminant analysis (LDA) effect size indicated a positive differential abundance (p < 0.05) for the modules of amino acid catabolism that may be at the basis of the changes of VOC profile. In particular, predicted genes encoding functions belonging to the superpathways of ornithine, arginine, and putrescine transformation to GABA and eventually to succinyl-CoA, of methionine degradation, and various routes of breakdown of aromatic compounds yielding succinyl-CoA or acetyl-CoA became significantly more abundant in the metagenome of the bacterial community.

Integrative analysis of gut microbiota and fecal metabolites in metabolic associated fatty liver disease patients

“…However, the discovery and confirmation of the specific role relationship and related mechanisms require further follow-up research. For multi-omics data obtained through designed experiments, the ANOVA simultaneous component analysis (ASCA) and the group-wise ANOVA-simultaneous component analysis (GASCA) were considered to have certain advantages for analyzing the variations ascribable to the main experimental factors and their interactions ( Saccenti et al, 2018 ; Raimondi et al, 2021 ).…”

β-Glucuronidase Pattern Predicted From Gut Metagenomes Indicates Potentially Diversified Pharmacomicrobiomics

“…Humans and their colon microbiota evolved together, establishing a close symbiotic interrelationship, fruitful for both. The gut microbiota is implicated in a number of biological processes such as resistance to colonization ( Ruan et al, 2020 ), immune system modulation ( Saldana-Morales et al, 2021 ), synthesis of essential vitamins and nutrients ( Oliphant and Allen-Vercoe, 2019 ), and breakdown of undigested polysaccharides and proteins ( El Kaoutari et al, 2013 ; Huang et al, 2017 ; Raimondi et al, 2021 ). Furthermore, it encodes a broad diversity of enzymes capable of processing foreign compounds (e.g., phytochemicals, environmental pollutants, pharmaceuticals, and other xenobiotics) and their endogenous metabolites, adding significant chemical diversity and modifying lifetimes, bioavailability, and biological activity ( Rossi et al, 2013 ; Koppel et al, 2017 ).…”

Tropical postbiotics alleviate the disorders in the gut microbiota and kidney damage induced by ochratoxin A exposure

“…Simultaneously, there is evidence that Alistipes had the most putrefactive pathways among gut bacteria, capable of generating harmful metabolites including ammonia, H 2 S, cresol, and phenol. 35,36…”

“…Simultaneously, there is evidence that Alistipes had the most putrefactive pathways among gut bacteria, capable of generating harmful metabolites including ammonia, H 2 S, cresol, and phenol. 35,36 In addition to this, an annotation of virulence factors within the intestinal microbiota was carried out (Fig. 6).…”