A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

Abstract

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.

Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria

“…The 10 habitats with the highest prevalence are shown for each isolate. The number of MAGs matching the genome of the corresponding isolate (MASH distance of <0.05) out of a total of 52,605 MAGs ( 20 , 24 , 93 – 103 ) is also indicated.…”

“…Now, combining cultivation and sequencing offers unique opportunities to study gut microbes ( 18 , 19 ). In comparison to numerous studies that have investigated the gut microbiota of mice and humans ( 20 , 21 ), work on domestic animals other than cows and pigs ( 22 – 24 ) is scarce.…”

Weaning age and its effect on the development of the swine gut microbiome and resistome

“…Several short-chain fatty acid-producing bacterial species were prevalent among those that were more relatively abundant in pigs that had been weaned. These included Anaerovibrio slackiae [16][17][18][19][20][21] . Short-chain fatty acidproduction occurs mostly in the lower gastrointestinal tract of pigs as a result of bacterial fermentation of undigested carbohydrates 22 .…”

Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility

“…were predominant SRB in piglet gut 32 . Recently, a new species Desulfovibrio porci isolated from pig faeces was described under a large cultivation project, called ‘Pig intestinal bacterial collection’ 33 . Desulfovibrio are often found in human and animal gut 34 , where they can utilise hydrogen, produced by fermentation 20 .…”

“…The occurrence of Desulfovibrio sp. in pig intestines 33 suggests that this transfer could have occurred already in the gut and was followed by dissemination of a drug-resistant Desulfovibrio strain in the environment.…”