Large bowel preparation may cause a substantial change in the gut microbiota and metabolites. Here, we included a bowel prep group and a no-procedure control group and evaluated the effects of bowel prep on the stability of the gut microbiome and metabolome as well as on recovery. Gut microbiota and metabolome compositions were analyzed by 16S rRNA sequencing and capillary electrophoresis time-of-flight mass spectrometry, respectively. Analysis of coefficients at the genus and species level and weighted UniFrac distance showed that, compared with controls, microbiota composition was significantly reduced immediately after the prep but not at 14 days after it. For the gut metabolome profiles, correlation coefficients between before and immediately after the prep were significantly lower than those between before and 14 days after prep and were not significantly different compared with those for between-subject differences. Thirty-two metabolites were significantly changed before and immediately after the prep, but these metabolites recovered within 14 days. In conclusion, bowel preparation has a profound effect on the gut microbiome and metabolome, but the overall composition recovers to baseline within 14 days. To properly conduct studies of the human gut microbiome and metabolome, fecal sampling should be avoided immediately after bowel prep.

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In order to clarify the taxonomic position of serotypes 20, 22 and 26 of Streptococcus suis, biochemical and molecular genetic studies were performed on isolates (SUT-7, SUT-286 T , SUT-319, SUT-328 and SUT-380) reacted with specific antisera of serotypes 20, 22 or 26 from the saliva of healthy pigs as well as reference strains of serotypes 20, 22 and 26. Comparative recN gene sequencing showed high genetic relatedness among our isolates, but marked differences from the type strain S. suis NCTC 10234 T , i.e. 74.8-75.7 % sequence similarity. The genomic relatedness between the isolates and other strains of species of the genus Streptococcus, including S. suis, was calculated using the average nucleotide identity values of whole genome sequences, which indicated that serotypes 20, 22 and 26 should be removed taxonomically from S. suis and treated as a novel genomic species. Comparative sequence analysis revealed 99.0-100 % sequence similarities for the 16S rRNA genes between the reference strains of serotypes 20, 22 and 26, and our isolates. Isolate STU-286 T had relatively high 16S rRNA gene sequence similarity with S. suis NCTC 10234 T (98.8 %). SUT-286 T could be distinguished from S. suis and other closely related species of the genus Streptococcus using biochemical tests. Due to its phylogenetic and phenotypic similarities to S. suis we propose naming the novel species Streptococcus parasuis sp. nov., with SUT-286 T (5JCM 30273 T 5DSM 29126 T ) as the type strain.Streptococcus suis is a major pathogen of swine and has also been isolated from a variety of animals such as ruminants, cats, dogs, deer and horses (Staats et al., 1997). Moreover, human S. suis infection is considered to be one of the most important emerging zoonotic diseases in Asian countries (Gottschalk et al., 2010). On the basis of their polysaccharide capsular antigens, a total of 33 serotypes (types 1-31, 33 and type 1/2) of S. suis have been described elsewhere (Gottschalk et al., 1989(Gottschalk et al., , 1991Higgins et al., 1995), in which serotype 2 was most frequently associated with disease in both pigs and humans (Gottschalk et al., 2007). Genetic relatedness among S. suis serotypes has been described previously by several investigators. However, a phylogenetic analysis based on 16S rRNA gene and chaperonin-60 gene sequences comparison (Chatellier et al., 1998; Brousseau et al., 2001) indicated a marked genetic discrepancy between serotypes 20, 22, 26 and 33 and other serotypes of S. suis. Moreover, our previous study (Tien et al. 2013) suggested that the reference strains of serotypes 20, 22, 26 and 33 should be removed taxonomically from S. suis. This was based on DNA-DNA relatedness 3Present address:

It is generally difficult to specify the sources of infection by which domestic animals may acquire pathogens. Through 16S rRNA gene amplicon sequencing, we compared the composition of microbiota in the saliva, vaginal mucus, and feces of pigs, and in swabs of feeder troughs and water dispensers collected from pig farms in Vietnam. The composition of the microbiota differed between samples in each sample group. Streptococcus , Actinobacillus , Moraxella , and Rothia were the most abundant genera and significantly discriminative in saliva samples, regardless of the plasticity and changeability of the composition of microbiota in saliva. Moreover, species assignment of the genus Streptococcus revealed that Streptococcus suis was exceptional in the salivary microbiota, due to being most abundant among the streptococcal species and sharing estimated proportions of 5.7%–9.4% of the total bacteria in saliva. Thus, pig oral microbiota showed unique characteristics in which the major species was the pig pathogen. On the other hand, β-diversity analysis showed that the microbiota in saliva was distinct from those in the others. From the above results, pig saliva was shown to be the major natural habitat of S . suis , and is suggested to be the most probable source of S . suis infection.

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