Kingsley Anukam
Professor/Researcher; Nnamdi Azikiwe University, Nigeria
Kingsley C Anukam is a research scientist in human microbiome and biotherapeutics with over 20 years experience. He shares his time between Canada and Nigeria as research professor at Nnamdi Azikiwe University where he assists in the training and supervision of post graduate students working in the area of probiotics, fermented foods, human microbiome, infectious diseases, laboratory diagnostics, human genomics and forensic DNA analysis. He had his graduate education in Nigeria and post doctorate training in Dr. Gregor Reid’s Lab at Lawson Health Research Institute and Department of Microbiology and Immunology, Western University, London, Ontario, Canada. He has over 80 scientific research publications in peer-reviewed journals and listed among first 10 most cited researcher at Nnamdi Azikiwe University by Google Scholar. He was the first to sequence the full genome of Lactobacillus pentosus KCA1, the first human vaginal isolate (https://doi.org/10.1371/journal.pone.0059239) and has sequenced, deposited in NCBI over 10 Lactic acid bacteria of African origin.
Abstract
Overweight is becoming increasingly a burden to individuals due to changes in lifestyle. The objectives are to determine and compare the gut microbiota compositions of lean and overweight women in South East Nigeria and second to predict the bacterial metabolic functional genes in the two cohorts.
Forty-six (46) adult healthy Nigerian women comprising of 23 lean and overweight subjects provided stool samples. Bacteria DNA was extracted, 16S rRNA V4 region was amplified, purified and sequencing done in a pair-end set-up on the Illumina NextSeq 500 rendering 2 x 150 bp. EzBiocloud Microbiome Taxonomic Profile (MTP) pipeline was employed for alpha and beta diversity estimation using PKSSU4.0 version database and Open reference UCLUST_MC2 for OTUs picking at 97% cut-off. Sequences were pre-screened using QIIME-UCLUST algorithms for at least 97% identity to ribosomal sequences from the RNA databases. Alpha-diversity was calculated for species richness by Abundance Coverage Estimate (ACE), while diversity indexes were calculated by Shannon. Principle coordinate analysis (PCoA) with Bray-Curtis divergence distance metrices were used to evaluate beta diversity between lean and overweight samples. Linear discriminant analysis (LDA) effect size was used to identify significant differences in the OTU relative abundance. PICRUSt was used to predict the metabolic functions from the 16S rRNA gene dataset.
The alpha-diversity ACE (P=0.767) and Shannon index (P=0.621) were not significant. However, Bray-Curtis beta diversity distance matrices delineated the OTUs at Species level. Taxonomic profiles at phyla indicates lean and overweight subjects had Firmicutes (46.16% vs 50.26%), Bacteroidetes (26.16% vs 28.11%), Proteobacteria (23.49 % vs 18.35%), Actinobacteria (1.37% vs 2.11%), Verrucomicrobia (1.76) vs 0.0%). At the genera level Bacteroides (24.73% vs 23.79%), followed by Faecalibacterium (14.43% vs 11.99%), Escherichia (12.49 vs 8.83%), Roseburia (5.96% vs 7.39%), Comamonas (3.41% vs 0.0%), Blautia (2.76% vs 3.5%), Ruminococcus_g2 (2.39% vs 1.85%), Akkermansia (1.75% vs 0.0%), Stenotrophomonas (1.56% vs 0.0%), Subdoligranulum (1.56% vs 2.52%), Oscillibacter (1.54% vs 0.0%), Rummeliibacillus (1.51% vs 0.0%) and others.
Taxonomic biomarkers with leanness include Akkermansia muciniphila, Bacteroides vulgatus, and Clostridium clostridioforme. Overweight was associated with Campylobacter pinnipediorum, Desulfovibrio piger and Lactobacillus fermentum. Some bacterial metabolic functional genes were upregulated in lean and overweight subjects