Title : Studies on alteration of gut microbial composition with probiotics administration in health and disease using metagenomic analysis
Background and objectives: Functional foods, including probiotics, have attracted increased attention in many countries. Probiotics are live microorganisms that when ingested in sufficient quantities, confer health benefits. The gut microbiome, an immensely diverse and dynamic niche of the human body, is a critical determinant of human health and disease, and a key regulator of host physiology. But it is not clearly known to what extent the ingested probiotics effect the composition and functionality of the gut microbiota. Here, the study expands the understanding of probiotic food benefits by metagenomic analysis of 16S rRNA gene marker from human gut microbiome.
Methods: MiSeq single-end fastq sequences of 16S rRNA bacterial genes were fetched using SRA (https://www.ncbi.nlm.nih.gov/sra), pertaining to 25 gut samples (5 datasets) in health and disease including Type 2 diabetes melltitus (T2DM), Prader Willi Syndrome (PWS), and obesity. The sequences were imported to QIIME2 (https://qiime2.org) in Miniconda-3, and subjected to demultiplexing, quality control with Dada2 algorithm, phylogenetic analysis, and taxonomic classification using GREENGENES. The OTU abundance were attached with their corresponding taxonomy to generate the biom file. The downstream statistical analysis and data visualization were carried out using MicrobiomeAnalyst (https://www.microbiomeanalyst.ca). Community profiling was achieved with alpha-, beta diversity, and core microbiome analysis; clustering analysis with heatmap to compare abundance of different taxonomic levels, dendrogram, correlation analysis, pattern search; differential abundance analysis with univariate statistics, and marker-gene survey with metagenomeSeq. The PICRUSt was used for prediction of the functional potential and pathway analysis of the microbiota from 16S output (https://www.microbiomeanalyst.ca).
Results: Healthy omnivorous individuals exhibited greater level of alpha-diversity than healthy vegetarians, without probiotic supplementation. Probiotic intervention, in obesity exerted higher diversity compared to T2DM followed by PWS; OTU diversity in T2DM was greater than non-diabetics. Probiotic ingestion in healthy individuals was associated with lowest diversity. Species richness was more evenly distributed after probiotic administration in obesity, diabetes, and health. Beta diversity revealed similar variance in bacterial diversity with formation of three clusters consisting of healthy individuals without probiotic administration, obesity and PWS both with probiotic intervention. Firmicutes (46.0%), Bacteroidetes (45%), Proteobacteria (4%) and Actinobacteria (5%) were observed in all the samples. Univariate analysis indicated significant abundance of Clostridiales in T2DM with probiotic administration comprising two OTUs (2626509, 290018), and Coriobacteriales (OTU: 276120), among healthy vegeterians without probiotic consumption. The significantly expressed KEGG pathways were metabolism of carbohydrate, amino acids, energy, lipid, nucleotide, and xenobiotics; biosynthesis of secondary metabolites and glycan; xenobiotics biodegradation.
Conclusions: Post probiotic treatment among T2DM, PWS, and obese individuals expressed Lachnospiraceae as the dominant family known to be involved in the production of SCFAs compared to healthy individuals dominated with Ruminococcaceae known to be more abundant in a stable gut microbiota during probiotic treatment. Bacteroidetes, which is highly relevant in dysbiosis and disease, was significantly reduced with probiotic administration in T2DM, PWS, obese, and was eliminated from otherwise healthy individuals. Enterobacteriaceae, responsible for causing nosocomial and community-acquired infections, were completely removed from healthy individuals with probiotic intervention, while supression of Enterobacteriaceae was comparitively more effective in T2DM than PWS and obesity. There was an abundance of beneficial bacteria Bifidobacterium breve with probiotic intake more in PWS compared to healthy, T2DM and obese people.
What will audience learn from your presentation?
- The present study revealed the association of probiotic administration with gut microbiome effecting bacterial diversity, community structure, functional enrichment and metabolic potentiality specific in health and certain diseases.
- Modification of gut microbiota composition by probiotic administration might be a promising therapeutic approach to treat many disorders.