Saponins from Clematis mandshurica Rupr. regulates gut microbiota and its metabolites during alleviation of collagen-induced arthritis in rats.

Gut microbiota and their metabolites (short-chain fatty acids, SCFAs) are associated with the pathogenesis of rheumatoid arthritis (RA). Total Clematis triterpenoid saponins (CTSs) prepared from Clematis mandshurica Rupr. possess therapeutic benefits for arthritic diseases. However, the poor pharmacokinetic properties of CTSs have obstructed the translation of these natural agents to drugs. Here, we examined the effects of CTSs on arthritis symptoms, gut microbiota and SCFAs in rats with collagen-induced arthritis (CIA). Our results showed that the arthritis index scores of CIA rats treated with CTSs were significantly lower than those of the model group. Most importantly, CTSs moderated gut microbial dysbiosis and significantly downregulated the total SCFA concentration in CIA rats. Compared to the control group, CTSs treatment have no significant side effects on the gut microbiota and SCFA metabolism in normal rats. Two differential analyses (LEfSe and DESeq2) were combined to study the details of the changes in gut microbiome, and twenty-four marker taxa at the genus level were identified via a comparison among control, model and CIA rats treated with high doses of CTSs. In particular, the mostly significantly increased gram-negative (G-) and decreased gram-positive (G+) genera in CIA rats were well restored by CTSs. The observed SCFA concentrations demonstrated that CTSs tend to maintain the balance of the gut microbiota. The data presented herein suggest that CTSs could ameliorate arthritis-associated gut microbial dysbiosis and may be potential adjuvant drugs that could provide relief from the gastrointestinal damage caused as a side effect of commonly used drugs.

Archaeal diversity in acid mine drainage from Dabaoshan Mine, China.

Three acid mine drainage (AMD) samples collected from Dabaoshan Mine (Guangdong Province, China) were studied. In addition to physicochemical analyses, the diversity and community structures of the archaeal communities in these samples were described at the genetic level by amplified ribosomal DNA restriction analysis (ARDRA). Nine different ARDRA patterns were obtained from 146 clones and were studied as operational taxonomic units (OTUs), which were re-amplified and sequenced. Sequence data and phylogenetic analysis showed that most of the clones belonged to the Thermoplasmatales, and that archaea belonging to the Sulfolobales were absent. Only 1 OTU attributed to Ferroplasma was found and was observed to be abundant in all 3 samples. Eight OTUs were related to 2 new undefined groups in the Thermoplasmatales. Of the 8 OTUs, the clones in 2 similar units were isolated from samples collected from an abandoned sulfide mine (Huelva, Spain) and those in 5 similar units were isolated from samples collected from a closed copper mine (Tonglushan, China). These diversities were characterized by the reciprocal of Simpson's index (1/D) and correlated with the concentrations of ferrous ions and toxic ions in the AMD samples. The high temperature of the sampling sites was one of the factors that could explain why archaea belonging to the Thermoplasmatales were abundant in the analyzed AMD samples while those belonging to the Sulfolobales were absent.

[Isolation, identification and field control efficacy of an endophytic strain against tobacco bacterial wilt (Ralstonia solanacarum)].

In this paper, an endophytic strain B-001 against tobacco bacterial wilt (Ralstonia solanacarum) was isolated from the stem of healthy tobacco in R. solanacarum-infected fields, which had a stronger inhibitory effect on some kinds of gram-positive bacteria, gram-negative bacteria, and pathogenic fungi. This strain belonged to Bacillus, and its 16S rDNA after PCR and sequencing had an accession of GenBank being DQ444283. The 16S rDNA phylogenetic tree was constructed with MEGA3, and compared with the published 16S rDNA sequences of relative bacteria species. B-001 had a 99.2% sequence similarity with Bacillus subtilis (DQ415893). According to the morphological, physiological and biochemical characteristics, and based on phylogenetic analysis, B-001 was identified as a strain of B. subtilis. Field experiments in Guiyang and Ningxiang counties of Hunan Province showed that in 2005 and 2006, the control efficacy of B-001 on R. solanacarum ranged from 40.03% to 78. 14%, better than that of Streptomycini.

[The community and structure of nitrogen-fixing microorganism in Sanjiangyuan natural reserve].

Research on the diversity of microorganism community in natural environment has been concerned hot spot using the newly molecular biotechnology in the world now. To understand the composition and structure of nitrogen-fixing bacteria communities in the Qingzang plateau, the molecular diversity and phylogenetic of nifH genes of Sangjiangyuan natural reserve were examined by using the PCR-RFLP based cloning approach. The 3 samples were come from different sites and different plant types, and their biogeochemical parameters were diverse. DNA was directly extracted from the soil microorganism and amplified the nifH gene fragment using PCR by the primers of nifH-34F 5'-AAAGG(C/T)GG(A/T) ATCGG(C/T)AA(A/G) TCCACCAC-3' and nifH-491R 5'-TFGTT(G/C)GC(G/C)GC(A/G)TACAT(G/C)GCCATCAT-3'. For the nifH gene segment, diverse PCR products were characterized by cloning, restriction fragment length polymorphism (RFLP) analysis and sequencing. A total of 233 clones and 99 operational taxonomic units (OTUs) which were digested the clones by the restriction enzymes MspI and RsaI were obtained from all samples. YS-1 had 63 clones and 24 OTUs, ZD-1 had 75 clones and 28 OTUs, and NQ-1 had 95 clones and 47 OTUs, respectively. They were found 1-2 significant domain groups of clones and shared 4 OTUs in all samples. A wide range of sequence divergence was observed in the 26 nifH clones that were sequenced from all samples. Sequence comparison showed that the nifH clones were 66% to 98% similar. The phylogenetic tree was constructed by the Clustal W and Mega software. 26 sequences could be subdivided into 4 clusters in the phylogenetic tree, and some of them had the closely similar to Proteobacteria, but The majority of the clones were not closely related to any known cultivated nitrogen-fixing bacteria, Therefore, most of them are unique and may represent novel sequences of nitrogen-fixing bacteria.

[Molecular diversity and phylogenetic analysis of nitrogen-fixing (nifH) genes in alp prairie soil of Sanjiangyuan natural reserve].

Research on the diversity of microorganism community in natural environment has been concerned hot spot using the newly molecular biotechnology in the world now. This was the first description of the molecular diversity and phylogenetic analysis of nitrogen-fixing (nifH) genes in alp prairie soil of Sanjiangyuan natural reserve. DNA was directly extracted from the soil microorganism and amplified the nifH gene fragment using PCR by the primers of nifH-34F 5'-AAAGG(C/T)GG(A/T) ATCGG(C/T)AA(A/G) TCCACCAC-3' and nifH-491R 5'-TYGTT(G/C)GC(G/C)GC(A/G)TACAT(G/C)G CCATCAT-3'. For the gene fragment, diverse PCR products were characterized by cloning, restriction fragment length polymorphism (RFLP) analysis and sequencing. 143 clones and 35 different RFLP patterns were received in two samples by the restriction enzymes MspI and RsaI digested. ZD sample had 82 clones and 21 different RFLP patterns, and YS sample had 61 clones and 19 different RFLP patterns. There were shared 5 RFLP patterns in two samples. The analysis result found a significant dominant group of clones occurring in both samples which account for 29.3% and 32.8%, respectively, and several minor groups were also detected. 21 clones were sequenced, and their levels of nucleotide identity were from 71% to 98%. None of the sequenced nifH gene was completely identical to any deposited in the data banks, and therefore each of them belong to a noncharacterized bacterium. Finally, the phylogenetic tree was constructed by the Clustal W and Mega software. 21 sequences can be subdivided into 4 clusters in the phylogenetic tree, and most of them had the closely similar toalpha- , beta-, and gamma-Proteobacteria . The significant dominant group in YS sample and ZD sample had the closely related with Rhodobacter sphaeroides and Delftia tsuruhatensis, respectively. The YS-nifH-11 was the only sequence which had highly similar to Cyanobacteria .