Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.

The composition of the intestinal microbiome varies considerably between individuals and is correlated with health 1 . Understanding the extent to which, and how, host genetics contributes to this variation is essential yet has proved to be difficult, as few associations have been replicated, particularly in humans 2 . Here we study the effect of host genotype on the composition of the intestinal microbiota in a large mosaic pig population. We show that, under conditions of exacerbated genetic diversity and environmental uniformity, microbiota composition and the abundance of specific taxa are heritable. We map a quantitative trait locus affecting the abundance of Erysipelotrichaceae species and show that it is caused by a 2.3 kb deletion in the gene encoding N -acetyl-galactosaminyl-transferase that underpins the ABO blood group in humans. We show that this deletion is a ≥3.5-million-year-old trans-species polymorphism under balancing selection. We demonstrate that it decreases the concentrations of N -acetyl-galactosamine in the gut, and thereby reduces the abundance of Erysipelotrichaceae that can import and catabolize N -acetyl-galactosamine. Our results provide very strong evidence for an effect of the host genotype on the abundance of specific bacteria in the intestine combined with insights into the molecular mechanisms that underpin this association. Our data pave the way towards identifying the same effect in rural human populations.

BackgroundThere are growing evidences showing that gut microbiota should play an important role in host appetite and feeding behavior. However, what kind of microbe(s) and how they affect porcine appetite remain unknown.ResultsIn this study, 280 commercial Duroc pigs were raised in a testing station with the circadian feeding behavior records for a continuous period of 30–100 kg. We first analyzed the influences of host gender and genetics in porcine average daily feed intake (ADFI), but no significant effect was observed. We found that the Prevotella-predominant enterotype had a higher ADFI than the Treponema enterotype-like group. Furthermore, 12 out of the 18 OTUs positively associated with the ADFI were annotated to Prevotella, and Prevotella was the hub bacteria in the co-abundance network. These results suggested that Prevotella might be a keystone bacterial taxon for increasing host feed intake. However, some bacteria producing short-chain fatty acids (SCFAs) and lactic acid (e.g. Ruminococcaceae and Lactobacillus) showed negative associations with the ADFI. Predicted function capacity analysis showed that the genes for amino acid biosynthesis had significantly different enrichment between pigs with high and low ADFI.ConclusionsThe present study provided important information on the profound effect of gut microbiota on porcine appetite and feeding behavior. This will profit us to regulate porcine appetite through modulating the gut microbiome in the pig industry.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1364-8) contains supplementary material, which is available to authorized users.

Gut microbiota regulates host metabolism and immunity. The phylogenetic composition of gut microbiota is influenced by diverse factors that include host gender. In this study, the effects of gender on gut microbial composition and its subsequent influence on serum metabolites in pigs were evaluated. The bacterial composition of feces samples was determined by 16S rRNA gene sequencing in 293 pure-bred Duroc pigs (108 gilts and 185 entire boars) and 64 validated pigs from an eight-breed mosaic F 6 population. Twenty-eight F 6 boars were castrated at 80 days of age to evaluate the effects of androgen on gut microbial composition. Untargeted serum metabolite features were determined in 45 boars and 26 gilts by an ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). The study observed an obvious influence of host gender on the gut microbial composition and identified numerous sex-biased bacterial taxa. These included Veillonellaceae, Roseburia , Bulleidia , and Escherichia which showed the higher abundance in boars, and Treponema and Bacteroides which were over-represented in gilts. Castration significantly shifted the fecal microbiota composition of the boars toward that of gilts. The predicted functional pathways of the gut microbiome related to obesity and energy harvest were enriched in gilts, and positively associated with gilt-enriched bacteria. Functional pathways related to peptidases and carbohydrate metabolism were enriched in boars and positively associated with boar-enriched bacteria. Serum metabolites related to androgen and cresol metabolism were identified as sex-biased metabolites. Correlation analysis between serum metabolites and sex-biased bacteria identified that the serum concentration of androgen-related metabolites was positively correlated with Bulleidia and Escherichia , but negatively associated with Treponema , suggesting a significant interaction between gut microbiota and host sex hormone metabolism. These results offer basic knowledge of how host gender and gut microbiota influence host metabolism.

Haloactinospora alba gen. nov., sp. nov., a halophilic filamentous actinomycete of the family Nocardiopsaceae Shu-Kun Tang, 1 3 Xin-Peng Tian, 1,2 3 Xiao-Yang Zhi, 1 A novel halophilic, filamentous, actinomycete strain, designated YIM 90648 T , was isolated from a salt lake in Xinjiang Province, north-west China, and subjected to a polyphasic taxonomic study. Optimal growth occurred at 37 6C, pH 7.0-8.0 and 15 % (w/v) NaCl. The aerial mycelium of strain YIM 90648 T formed long chains of spores at maturity and the spores were cylindrical with smooth surfaces. Spore chains with pseudosporangia at the end were borne on the substrate mycelium and most spores had wrinkled surfaces. Strain YIM 90648 T contained mesodiaminopimelic acid as the diagnostic diamino acid and galactose and ribose as the major wholecell components. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol mannoside. MK-10(H 8 ), MK-11(H 4 ), MK-11(H 6 ) and MK-11(H 8 ) were the predominant menaquinones. The major fatty acids were i-C 16 : 0 and ai-C 17 : 0 . The DNA G+C content was 68 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 90648 T formed a distinct lineage within the family Nocardiopsaceae and showed 16S rRNA gene sequence similarity of 93.3-95.0 % with members of the family Nocardiopsaceae. On the basis of the polyphasic evidence, a novel genus and species, Haloactinospora alba gen. nov., sp. nov., is proposed to accommodate this isolate. The type strain of Haloactinospora alba is YIM 90648 T (5DSM 45015 T 5CCTCC AA 206008 T ).