Environment-Related Genes Analysis of Limosilactobacillus fermentum Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution

Abstract

Limosilactobacillus fermentum is ubiquitous in traditional fermented vegetables, meat products, and the human gut. It is regarded as a “generally recognized as safe” organism by the US Food and Drug Administration. So far, the genetic features and evolutionary strategies of L. fermentum from the human gut and food remain unknown. In this study, comparative genomic analysis of 224 L. fermentum strains isolated from food and human gut (164 L. fermentum strains isolated from human gut was sequenced in our lab) was performed to access genetic diversity and explore genomic features associated with environment. A total of 20,505 gene families were contained by 224 L. fermentum strains and these strains separated mainly into six clades in phylogenetic tree connected with their origin. Food source L. fermentum strains carried more carbohydrate active enzyme genes (belonging to glycosyltransferase family 2, glycoside hydrolase family 43_11, and glycoside hydrolase family 68) compared with that of human gut and L. fermentum derived from food showed higher ability to degrade xylulose and ribose. Moreover, the number of genes encoding otr(A), tetA(46), lmrB, poxtA, and efrB were more abundant in food source L. fermentum, which was consistent with the number of CRISPR spacers and prophages in L. fermentum of food source. This study provides new insight into the adaption of L. fermentum to the food and intestinal tract of humans, suggesting that the genomic evolution of L. fermentum was to some extent driven by environmental stress.

Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers

“…Furthermore, two genes involved in the CRISPR-Cas system, including cas2 and cas9 , were found to be gained by the badger group and affected by positive selection. Spacers are small fragments of foreign DNA incorporated into CRISPR loci to confer adaptive immunity to the host [ 43 ]. In total, 412 spacer sequences were obtained from all CRISPR loci of the 24 strains, and 0–89 spacers were identified in each isolate.…”

“…Five major CAZymes (AAs, GHs, GTs, CEs, and CBMs) were annotated in the 24 strains. GHs and GTs were the most abundant gene families in L. salivarius , with GT2, GT4, GH13, and CBM50 being the largest families, which is consistent with the results in other Lactobacillus species [ 43 ]. The diet of the host is a key evolutionary force that shapes the gut microbiota and influences the evolutionary trend of gut symbionts [ 53 ].…”

Strain-specific effect of Limosilactobacillus fermentum with distinct genetic lineages on loperamide-induced constipation in mice: attributing effects to certain genes

“…Detailed information on these strains and genomes can be found in our previous article. 28 Orthologous genes were analyzed using OrthoMCL1.4 and a phylogenetic analysis was conducted using the maximum likelihood method based on core genes.…”