Biology subjects

Antony, L.

Publications and source records attributed to Antony, L..

4 recordsLinked to original sources

bioRxiv2019

Identifying Clostridioides difficile-inhibiting gut commensals using culturomics, phenotyping, and combinatorial community assembly

A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious level. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota culture collection comprising 1590 isolates belonging to 102 species. Estimated by metagenomic sequencing of fecal samples used for culture, this culture collection represents 50.73% of taxonomic diversity and 70% functional capacity. Using whole genome sequencing we characterized species representatives from this collection, and predicted their phenotypic traits, further characterizing isolates by defining nutrient utilization profile and short chain fatty acid (SCFA) production. When screened using a co-culture assay, 66 species in our culture collection inhibited C. difficile. Several phenotypes, particularly, growth rate, production of SCFAs, and the utilization of mannitol, sorbitol or succinate correlated with C. difficile inhibition. We used a combinatorial community assembly approach to formulate defined bacterial mixes inhibitory to C. difficile. When 256 combinations were tested, we found both species composition and blend size to be important in inhibition. Our results show that the interaction of bacteria with each other in a mix and with other members of gut commensals must be investigated for designing defined bacterial mixes for inhibiting C. difficile in vivo.\n\nIMPORTANCEAntibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, allowing pathogens such as C. difficile to colonize, causing recurrent infection and mortality. Although fecal microbiome transplantation has shown to be an effective treatment for C. difficile infection (CDI), a more desirable approach would be the use of a defined mix of inhibitory gut bacteria. C. difficile-inhibiting species and bacterial combinations we identify herein improve our understanding of the ecological interactions controlling colonization resistance against C. difficile, and could aid the design of defined bacteriotherapy as a non-antibiotic alternative against CDI.

microbiology↗

bioRxiv2019

The Gut Microbiota composition of Feral and Tamworth Pigs determined using High-Throughput Culturomics and Metagenomics Reveals Compositional Variations When Compared to the Commercial Breeds

Bacterial communities in the hindguts of pigs have a profound impact on health and disease. Yet very limited studies have been performed outside intensive swine farms to determine pig gut microbiome composition in natural populations. Feral pigs represent a unique situation where the microbiome structure can be observed outside the realm of modern agriculture. Additionally, Tamworth pigs that freely forage were included to characterize the microbiome structure of this rare breed. In this study, gut microbiome of feral and Tamworth pigs were determined using metagenomics and culturomics. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. In total, 46 distinct species were successfully isolated from 1000 colonies selected. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. Furthermore, the naturally raised Tamworth pig microbiome contained more number of antibiotic resistance genes when compared to feral pig microbiome. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function by assembling simple to complex microbiota communities in bioreactors or germfree animal models.

microbiology↗

bioRxiv2019

Sellimonas caecigallum sp. nov., description and genome sequence of a new member of the Sellimonas genus isolated from the cecum of feral chicken

An obligately anaerobic, non-motile, Gram-positive coccobacillus strain SW451 was isolated from pooled cecum contents of feral chickens. Comparative analysis based on 16s rRNA sequence showed that strain SW451 had 95.24% nucleotide sequence similarity to Sellimonas intestinalis BR31T, the closest species with a valid taxonomy. The genome of SW451 is 2.67 Mbp with 45.23 mol% of G+C content. The major cellular fatty acids were C16: 0, C14: 0 and C16: 0 DMA. Based on taxonogenomic, physiological, and biochemical analysis, the strain SW451 represents a new species of the genus Sellimonas, for which the name Sellimonas caecigallum sp. nov. is proposed. The type strain of Sellimonas caecigallum is SW451 (=DSM 109473T)

microbiology↗

bioRxiv2019

Olsenella lakotia SW165 sp. nov., an acetate producing obligate anaerobe with a GC rich genome

A Gram-positive and obligately anaerobic bacterium was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. The microorganism grew at 37-45{degrees} C and pH 6-7.5. This strain produced acetic acid as the primary metabolic end product. Major fatty acids were C12:0, C14:0, C14:0 DMA and summed feature 1 (C13:1 at 12-13 and C14:0 aldehyde). Phylogenetic analyses based on 16S rRNA gene sequence suggested that strain SW165 belongs to the family Atopobiaceae with the closest relatives being Olsenella profusa DSM 13989T (96.33% similarity), Olsenella umbonate DSM 26220T (96.18%) and Olsenella uli DSM 7084T (96.03%). Genome sequencing revealed a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the highest G+C content among members of the genus Olsenella. Phylogenetic and phenotypic comparison indicated that strain SW165 represents a novel species of the genus Olsenella, for which the name Olsenella lakotia sp. nov. is proposed. The type strain is SW165 (=DSM 107283T).

microbiology↗