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Background Human gut microbiome has an essential role in human health and disease. Although the major dominant microbiota within individuals have been reported, the change of gut microbiome caused by external factors, such as antibiotic use and bowel cleansing, remains unclear. We conducted this study to investigate the change of gut microbiome in overweight male adults after bowel preparation, where none of the participants had been diagnosed with any systemic diseases. Methods A total of 20 overweight, male Taiwanese adults were recruited, and all participants were omnivorous. The participants provided fecal samples and blood samples at three time points: prior to bowel preparation, 7 days after colonoscopy, and 28 days after colonoscopy. The microbiota composition in fecal samples was analyzed using 16S ribosome RNA gene amplicon sequencing. Results Our results demonstrated that the relative abundance of the most dominant bacteria hardly changed from prior to bowel preparation to 28 days after colonoscopy. Using the ratio of Prevotella to the sum of Prevotella and Bacteroides in the fecal samples at baseline, the participants were separated into two groups. The fecal samples of the Type 1 group was Bacteroides-dominant, and that of the Type 2 group was Prevotella-dominant with a noticeable presence Bacteroides. Bulleidia appears more in the Type 1 fecal samples, while Akkermensia appears more in the Type 2 fecal samples. Of each type, the gut microbial diversity differed slightly among the three collection times. Additionally, the Type 2 fecal microbiota was temporarily susceptible to bowel cleansing. Predictive functional analysis of microbial community reveals that their activities for the mineral absorption metabolism and arachidonic acid metabolism differed significantly between the two types. Depending on their fecal type, the variance of triglycerides and C-reactive protein also differed between the two types of participants. Conclusions Depending upon the fecal type, the microbial diversity and the predictive functional modules of microbial community differed significantly after bowel preparation. In addition, blood biochemical markers presented somewhat associated with fecal type. Therefore, our results might provide some insights as to how knowledge of the microbial community could be used to promote health through personalized clinical treatment. Electronic supplementary material The online version of this article (10.1186/s12864-018-5285-6) contains supplementary material, which is available to authorized users.

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Figure S7. Box plots of three inflammation cytokines. (PDF 377â kb)

Figure S2. Principal coordinate analysis (PCoA) based on the UniFrac distance values. (PDF 414â kb)

Figsure S3-S5. Correlation networks for 61 genera at three sample collection times. (PDF 2498â kb)

Table S10. Means of 26 predictive functional modules between the Type 1 and Type 2 fecal samples. (PDF 209â kb)

Figure S1. The differences of microbial diversity between the type 1 and 2 groups. (PDF 331â kb)

Figure S6. Percentage of the number of correlation change between SB and S7; SB and S28. (PDF 232â kb)

Table S3. Descriptive statistics of richness and Shannon diversity index. (PDF 184â kb)

Probiotics modulate immunity and inhibit colon carcinogenesis in experimental models, but these effects largely depend on the bacterial strain, and the precise mechanisms are not well understood. Therefore, we studied the effect of Bifidobacterium longum and/or Lactobacillus gasseri on the development of 1,2-dimethylhydrazine (DMH)-induced colonic precancerous lesions and tumors in mice while delineating the possible mechanisms involved. The results suggest that dietary consumption of probiotics (B. longum and L. gasseri) resulted in a significant inhibition of DMH-induced aberrant crypt foci (ACF) formation in male ICR mice. Long-term (24 weeks) dietary consumption of probiotics resulted in a reduction of colon tumor multiplicity and the size of the tumors. Administration of B. longum and L. gasseri suppressed the rate of colonic mucosa cellular proliferation in a manner correlating with the inhibition of tumor induction by DMH. In addition, the phagocytic activity of peritoneal macrophages was significantly increased in the DMH-treated mice that were fed various doses of B. longum, but not with L. gasseri or combined probiotics (B. longum + L. gasseri). We also found that L. gasseri significantly increased the proliferation of RAW264.7 macrophage cells through an increase in S phase DNA synthesis, which was related to the up-regulation of proliferating cell nuclear antigen (PCNA) and cyclin A. Taken together, these results demonstrate the in vivo chemopreventive efficacy and the immune stimulating mechanisms of dietary probiotics against DMH-induced colonic tumorigenesis.

Free radicals are known to be highly harmful to cellular components, particularly superoxide anion radical (O 2 − ) which is a precursor of the more reactive oxygen species, contributing to various diseases. Although the amount of superoxide anion radicals can be regulated by superoxide dismutase (SOD), the scavenging function of SOD supplied from external sources is difficult to exploit because owing to the restraint of its molecular weight. An alternative approach adopts low-molecular-weight compounds with SOD-like activity. This study screens strains for obtaining molecules with high SOD-like activity, and optimizes the conditions for generating SOD-like metabolites. An Aspergillus phoenicis strain with highly potent of SOD-like antioxidant producing was obtained, and further applied in different lab-scale jars with batch and fed-batch fermentation. The medium composition and culture parameters for the strain with high SOD-like activity were also studied. The SOD-like activity of A. phoenicis was 10 U/mL when cultivated in PDB medium. For more medium investigation, 15% glucose and 2% beef extract were served as carbon and nitrogen sources, respectively, for their benefit of less cost and higher productivity. Response surface methodology (RSM) was then used to determine the optimal growth conditions for A. phoenicis to produce SOD-like activity. The optimal temperature and pH were found to be 30 °C and 5–6, respectively. The SOD-like activity of A. phoenicis in a batch fermentation using a 5 L fermentor was 420 U/mL with a biomass of 5 g/L dry cell weight. With fed-batch cultivation, although the SOD-like activity of A. phoenicis achieves a similar performance with 400 U/mL, the biomass could be observably improved to 21 g/L after fermentation for 96 h.

Asia differs substantially among and within its regions populated by diverse ethnic groups, which maintain their own respective cultures and dietary habits. To address the diversity in their gut microbiota, we characterized the bacterial community in fecal samples obtained from 303 school-age children living in urban or rural regions in five countries spanning temperate and tropical areas of Asia. The microbiota profiled for the 303 subjects were classified into two enterotype-like clusters, each driven by Prevotella (P-type) or Bifidobacterium/Bacteroides (BB-type), respectively. Majority in China, Japan and Taiwan harbored BB-type, whereas those from Indonesia and Khon Kaen in Thailand mainly harbored P-type. The P-type microbiota was characterized by a more conserved bacterial community sharing a greater number of type-specific phylotypes. Predictive metagenomics suggests higher and lower activity of carbohydrate digestion and bile acid biosynthesis, respectively, in P-type subjects, reflecting their high intake of diets rich in resistant starch. Random-forest analysis classified their fecal species community as mirroring location of resident country, suggesting eco-geographical factors shaping gut microbiota. In particular, children living in Japan harbored a less diversified microbiota with high abundance of Bifidobacterium and less number of potentially pathogenic bacteria, which may reflect their living environment and unique diet.

Glucose, peptone and magnesium sulphate were found to be suitable components for the cell growth and glutathione (GSH) production in the yeast strain. Saccharomyces cerevisiae CCRC 21727. The Box–Behnken design and response surface methodology were employed to derive a statistical model to investigate the effects of glucose, peptone and magnesium sulphate concentrations on GSH production. Neural networks were compared with a second-order-polynomial model in predicting the effects of component concentrations on the production of GSH and dry cell weight (DCW). Neural network models can predict cell growth and GSH production more precisely than second-order-response-surface models.

A substrate feeding strategy using an oxystat was first successfully applied to a fed-batch phenylalanine fermentation. The control method allowed the fermentation to be under low dissolved oxygen tension, which was favourable phenylalanine formation, and to be from substrate inhibition during the course of fed-batch operation. The final product concentration was 3 times higher than in a batch culture.

By screening 15,000 mutants, tyrosine auxotrophs T6, T7, and tryptophan auxotrophs P6, P8, were obtained. After primary production test, mutant P6 was chosen for further investigation. Fractional factorial design(FFD) and steepest ascent method(SAM) were used to optimize the medium component Mutant P6 had 17.1 g/l L-phenylalanine production when 0.44 g/l tryptophan was added. When Corynebacterium glutamicum P6 was cultivated in the optimum medium, L-phenylaianine production increased 22% as compared with the parent strain CCRC 18335, and the interference of tryptophan during the purification process was removed.

ThelysC gene encoding aspartokinase of a lysine-hyperproducing mutantBrevibacterium flavum CCRC 18271 was cloned by polymerase chain reaction and its expression in CCRC 18271 was studied. Enzyme assays showed thatB. flavum cells harbouring thelysC gene exhibited 4- to 11-fold higher specific activities of aspartokinase as compared to respective hosts. Introduction of thelysC gene intoB. flavum CCRC 18271 resulted in increased lysine production up to 33% in flask fermentations.

Growth of Pediococcus acidiluctici PO2 and production of associated bacteriocin (pediocin PO2) were demonstrated in whey permeate (WP) supplemented with 0.5–4% yeast extract (YE). Initial pH 6.5 (without PH regulation during fermentation) wag optimal for production of uediocin PO2 in WP containing 2% YE. A pediocin-rich dairy ingredient (PRDI) powder was made of the fermented WP and applied in heat-treated whole milk and pasteurized liquid whole egg. PRDI in-hibited Listeria monocyfogenes in milk. L. monocytogenes was inhib-ited by untreated liquid whole egg and PRDI appeared to contain a factor that offsets the inherent antilisterial action of the egg product.

The aro gene of Corynebacterium glutamucum CCRC 18310 encoding 3-deoxy- D -arabinoheptulosonate-7-phosphate (DAHP) synthase was isolated by complementation of a DAHP synthase-deficient mutant of Escherichia coli AB3257. The specific activity of DAHP synthase was increased four-fold in a C. glutamicum strain harboring the cloned aro gene. The complete nucleotide sequence of the aro gene and 5′ and 3′ flanking regions has been determined. The sequence contained an open reading frame of 368 codons, from which a protein with a molecular mass of 39 340 Da could be predicted. The deduced amino acid sequence shows high identity with the aro gene products of E. coli and Salmonella typhimurium .

Two natural new compounds, pyrroline-2-one ( 1 ) and 2-(2-amino-3-methyl-butyrylamino)-3-(4-hydroxy-phenyl)-propionic acid ( 2 ), together with nine known compounds, iodinin ( 3 ), thymine ( 4 ), N -(2-hydroxy-phenyl)-acetamide ( 5 ), ( Z )-pulchellalactam ( 6 ), uracil ( 7 ), nicotinic acid ( 8 ), nicotiamide ( 9 ); p -nitrophenol ( 10 ) and indole 3-carboxylic acid ( 11 ), all were isolated from the EtOAc extract of the culture broth of a new actinomycete Acrocarpospora sp. strain, FIRDI 001. The structures were elucidated by 1D and 2D NMR spectroscopy and mass spectrometry. Furthermore, the isolated compounds were subjected to evaluate the antimicrobial activity. Compounds 2 , 3 and 10 showed antimicrobial activity. The active metabolite, iodinin existed as a major metabolite in this study. Keywords : Acrocarpospora sp., Actinomycetes, Secondary metabolites, alkaloids, Iodinin, Antimicrobial activity. INTRODUCTION Microorganisms that can survive in diverse environments are of great interest for scientists. The actinomycetes, an order of filamentous bacteria, have proven to be a rich source of secondary metabolites that might be useful for the development of new pharmaceutical agents

Production feedback inhibition both on cell growth and on product formation of phenylalanine fermentation might be alleviated by elevated oxygen supply. Batch fermentations by a high phenylalanine producing strain Corynebacterium glutamicum CCRC 18335 at various initial phenylalanine concentrations (P(0)) ranging from 0 to 20 g/L and different oxygen transfer rate coefficients (K(L)a) ranging from 23 to 76 h(-1) were studied. The fermentation parameters with respect to P(0) were strongly dependent on K(L)a. Cell yield favored higher K(L)a and lower P(0). Product yield with respect to varying phenylalanine concentration was evaluated by the relative oxygen availability (ROA). The optimal ROA for phenylalanine formation was strongly dependent on the product concentration. While P(0) was low, the product inhibition was less significant and the maximum product yield occurred while ROA was at 0.5-0.6. While P(0) was high, the product inhibition was significant and the maximum product yield occurred while ROA was at 0.8-0.9. These results suggest that the product feedback inhibition of phenylalanine fermentation processes can be alleviated by a gradual increase in oxygen supply rate while the increasing product concentration is taken into account. The strategy is demonstrated in a fed-batch culture with elevated oxygen supply. The final phenylalanine concentration was 23.2 g/L, which was 45% better than that of the fed-batch fermentation without elevated oxygen supply. Likewise, the maximum productivity was improved by 42% at 0.37 g/(L x h).

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