Mining bacterial NGS data vastly expands the complete genomes of temperate phages.

Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to their lysogenicity, curbing their identification and characterization. Existing bioinformatics tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. This study proposes a novel computational temperate phage detection method (TemPhD) mining both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data. Applying the method to the available dataset resulted in 192 326 complete temperate phage genomes with different host species, expanding the existing number of complete temperate phage genomes by more than 100-fold. The wet-lab experiments demonstrated that TemPhD can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites, outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the microbial evolution by (i) cross-infecting different bacterial host species; (ii) transferring antibiotic resistance and virulence genes and (iii) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensively complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.

Dietary butyrate suppresses inflammation through modulating gut microbiota in high-fat diet-fed mice.

Butyrate, a key metabolite fermented by gut microbiota mainly from undigested carbohydrates such as dietary fibers is widely used as feed additive. However, mechanisms of its contributions in maintaining host health are relatively poorly revealed. The aim of this study was to investigate how butyrate impacts gut microbiota and immunity response in high-fat diet-fed mice. Gut microbial analysis exhibited that butyrate intervention increased short-chain fatty acids (SCFAs)-producing bacteria and decreased pathogenic bacteria, such as endotoxin-secreting bacteria. Our result also demonstrated that butyrate intervention enhanced fecal SCFAs concentrations, and inhibited endotoxin levels in feces and serum. Correlation analysis indicated positive relation between endotoxin level and Desulfovibrionaceae abundance. Furthermore, butyrate intervention inhibited expressions of IL-1ß, IL-6 and MCP1/CCL2 in liver, as well as TLR4 in adipose tissue. Apart from inhibiting expressions of proinflammatory cytokines, butyrate exerted anti-inflammation effect through selectively modulating gut microbiota, such as increasing SCFAs-producing bacteria and decreasing endotoxin-secreting bacteria, as well as via regulating levels of microbiota-dependent metabolites and components, such as SCFAs and endotoxin.

Effects of phycocyanin in modulating the intestinal microbiota of mice.

The health-promoting effects of phycocyanin (PC) have become widely accepted over the last two decades. In this study, we investigated the effects of different doses of PC in modulating the intestinal microbiota and the intestinal barrier in mice. Six-week-old male C57BL/6 mice were treated with PC for 28 days. Fecal samples were collected before and after PC intervention, and the microbiota were analyzed by 16S rRNA high-throughput sequencing. Bacterial abundance and diversity increased after PC intervention. Saccharolytic bacteria of the families Lachnospiraceae and Ruminococcaceae, which can produce butyric acid, increased after PC treatment. The family Rikenellaceae, which contains hydrogen-producing bacteria, also increased after PC intervention. The PC treatment reduced intestinal permeability and increased the intestinal barrier function, as demonstrated by hematoxylin-eosin staining and reduced serum lipopolysaccharide levels. The modulating effects on the intestinal microbiota were more favorable in the low-dose PC group.

Effect of lactulose intervention on gut microbiota and short chain fatty acid composition of C57BL/6J mice.

Gut microbiota have strong connections with health. Lactulose has been shown to regulate gut microbiota and benefit host health. In this study, the effect of short-term (3 week) intervention of lactulose on gut microbiota was investigated. Gut microbiota were detected from mouse feces by 16S rRNA high-throughput sequencing, and short chain fatty acids (SCFAs) were detected by gas chromatography-mass spectrometry (GC-MS). Lactulose intervention enhanced the α-diversity of the gut microbiota; increased the abundance of hydrogen-producing bacteria Prevotellaceae and Rikenellaceae, probiotics Bifidobacteriaceae and Lactobacillaceae, and mucin-degrading bacteria Akkermansia and Helicobacter; decreased the abundance of harmful bacteria Desulfovibrionaceae and branched-chain SCFAs (BCFAs). These results suggest that lactulose intervention effectively increased the diversity and improved the structure of the intestinal microbiota, which may be beneficial for host health.

Inulin with different degrees of polymerization modulates composition of intestinal microbiota in mice.

The study aimed to analyze the global influences of dietary inulin with different degrees of polymerization (DP) on intestinal microbial communities. Six-week-old male C57BL/6J mice were treated with fructo-oligosaccharides and inulin for 6 weeks. Fecal samples were obtained at time point 0 and 6th week. 16S rRNA sequence analysis was used to measure intestinal microbiota performed on the Illumina MiSeq platform. Influences of dietary inulin on intestinal microbiota were more complex effects than bifidogenic effects, relative abundance of butyrate-producing bacteria increased after interventions. Akkermansia muciniphila, belonging to mucin-degrading species, became a dominant species in Verrucomicrobia phylum after treatment with fructo-oligosaccharides and inulin. Modulation effects of intestinal microbiota were positively correlated with DP. Lower DP interventions exhibited better effects than higher DP treatment on stimulation of probiotics. We hypothesized that Akkermansia muciniphila played an important role on maintaining balance between mucin and short chain fatty acids.