Application of culturomics to characterize diverse anaerobic bacteria from the gastrointestinal tract of broiler chickens in relation to environmental reservoirs

Abstract

Characterization of the microbiota of chickens is of current interest. The goals of the current study were to apply anaerobic isolation methods to comprehensively isolate and identify bacteria from the gastrointestinal tract of chickens and their environment. Bacterial communities within the drinking water were dominated by Escherichia, whereas communities in litter were more representative of the cecum. The crop and small intestine (jejunum and ileum) were dominated by Lactobacillus and Enterococcus spp., and the cecum was dominated by Proteus spp. The collection of bacteria isolated was dominated by Enterococcus spp., Escherichia/Shigella spp., Lactobacillus spp., and Proteus spp.; however, many rare taxa were observed. These included members of the Clostridiales and Clostridium spp., which were commonly isolated from the ileum and cecum. Bacteria isolated by enrichment and direct plating differed. The selective de Man–Rogosa–Sharpe agar was commonly associated with the isolation of Lactobacillus spp. and yielded the lowest diversity of all methods utilized. Increased diversity and frequency of Clostridium spp. was observed in enrichments of blood and mucus or by plating on Columbia agar supplemented with 10% blood and gentamicin. The bacteria isolated from this study provide source material for genomic and functional studies in chicken hosts.

Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine

“…77) was used. All media were reduced before use (77). Media were prepared without the addition of cysteine and were autoclaved for 5 min.…”

Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping

“…The pioneering work of Venter and his team during the large-scale Sorcerer II expedition have yielded a wealth of insights into the genetic information on diverse marine microorganisms . Meanwhile, the rise of culturomics, i.e., the systematic isolation of multiple isolates by assaying numerous culture conditions, , has shown to be a valuable tool for the discovery of novel clinical and environmental isolates . The high number of isolates obtained from such methods requires fast, robust, and cost-effective identification techniques that lend themselves to high-throughput isolation approaches.…”

“… 19 Meanwhile, the rise of culturomics, i.e., the systematic isolation of multiple isolates by assaying numerous culture conditions, 20 , 21 has shown to be a valuable tool for the discovery of novel clinical and environmental isolates. 22 The high number of isolates obtained from such methods requires fast, robust, and cost-effective identification techniques that lend themselves to high-throughput isolation approaches. The analysis of specific gene sequences or even the whole genome sequence can be further used for taxonomic classification.…”

Decoding the intestinal microbiota repertoire of sow and weaned pigs using culturomic and metagenomic approaches

“…As the limitations of metagenomics have been revealed and the importance of culturomics has emerged, a wide range of culture-dependent analyses of intestinal microbiota and studies on optimal culture methods for gut microbiota are being conducted [10,[12][13][14][15]. However, most of the studies focused exclusively on the analysis of human gut microbiota, and studies on culturomics of fecal microbiota of livestock animals are extremely rare [16,17].…”