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.

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 mucindegrading 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. K E Y W O R D S16S rRNA high-throughput sequencing, gut microbiota, prebiotic, probiotics, short chain fatty acids 2 of 8 | ZHAI et Al. enzymes in the intestine, but is metabolized by gut microbiota to short chain fatty acids (SCFAs) in the ileum (Guerra-Ordaz et al., 2014).Lactulose can change the composition of the gut microbiota. For example, Vanhoutte et al. (2006), reported a significant increase in Bifidobacterium adolescentis following lactulose intake. Tuohy et al. (2002) showed that Bifidobacterium spp. were increased, whereas Clostridia and Lactobacilli were decreased after lactulose treatment in humans.SCFAs are main metabolites of gut microbiota, and are divided into straight-chain SCFAs and branched-chain SCFAs (BCFAs). Straightchain SCFAs are mainly produced by microbial fermentation of unabsorbed dietary carbohydrates in the gut. Lactate and succinate can also be metabolized to straight-chain SCFAs, including acetate, propionate, and butyrate (Hasebe et al., 2016;Verbeke et al., 2015). Straight-chain SCFAs have a range of beneficial effects, including regulation of the colonic and intracellular environment (Wong et al. 2006), and modulation of cell proliferation and gene expression. In addition, straightchain SCFAs are able to improve immune function, glucose regulation, and prevent obesity (Polyviou et al., 2016). In contrast, BCFAs are always derived from catabolism of branched-chain amino acids (Zheng et al., 2013), and are major markers of protein fermentation, which is likely to be detrimental to the host (Yang & Rose, 2015).Although some studies have assessed the effects of lactulose on gut microbiota, the gel-or PCR-based methods used limit our ability to evaluate the full extent of the impact of lactulose on the gut microbiotic community. In this study, 16S rRNA high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS) were used to evaluate effect of lactulose on gut microbiota and their metabolites in mice. | MATERIAL S AND ME THODS | Animals and experiment designSix-week-old male C57BL/6J mice were...

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 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-1β, 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.

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.

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.

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 the lysogenicity of these phages, which curb the identification and characterization of temperate phages. Existing in silico tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. In this study, by a novel computational method mining both the integrated active prophages and their spontaneously induced forms (temperate phages), we obtained 192,326 complete temperate phage genomes from bacterial next-generation sequencing (NGS) data, hence expanded the existing number of complete temperate phage genomes by more than 100-fold. The reliability of our method was validated by wet-lab experiments. The experiments demonstrated that our method can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites (attP and attB sites), outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the evolution of microbes by 1) cross-infecting different bacterial host species; 2) transferring antibiotic resistance and virulence genes; and 3) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensive complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.