Bacteroides caecicola sp. nov. and Bacteroides gallinaceum sp. nov., isolated from the caecum of an Indonesian chicken.

Six strains of anaerobic bacteria, C13EG70T, C13EG118, C13EG186T, C13GAMG5, C13GAMG28 and C13GAMG40, were isolated from the caecum of a healthy chicken bred in Bogor, Indonesia. Phylogenetic analysis showed the isolates were separated into two groups. Group I (C13EG70T and C13EG118) showed nearly identical 16S rRNA gene sequences (99.9 % sequence similarity). Group II (C13EG186T, C13GAMG5, C13GAMG28 and C13GAMG40) showed nearly identical 16S rRNA gene sequences (>99.4 % sequence similarity). The isolates showed low 16S rRNA gene sequence similarities to recognized species of the genus Bacteroides. High gene sequence similarities were found between type strains (C13EG70T and C13EG186T) and Bacteroides salanitronis JCM 13657T (87.9, 91.5 %, respectively). Physiological, biochemical and genotypic characteristics demonstrated that these strains could be separated from the type strain of B. salanitronis. It is concluded that Group I and Group II represent novel species. Two novel species of the genus Bacteroides are proposed as Bacteroides caecicola sp. nov. (type strain C13EG70T = LIPI12-4-Ck732T = JSAT12-4-Ck732T = InaCC B449T = NBRC 110958T) and Bacteroides gallinaceum sp. nov. (type strain C13EG186T = LIPI12-4-Ck844T = JSAT12-4-Ck884T = InaCC B451T = NBRC 110963T).

Bacteroides caecigallinarum sp. nov., isolated from caecum of an Indonesian chicken.

Three strains of anaerobic Gram-stain-negative, short to longer rod-shaped bacteria isolated from the caecum of chicken in Indonesia were studied using a polyphasic taxonomic approach. These strains belonged to the genus Bacteroides, based on sequence analysis of 16S rRNA and hsp60 (groEL) genes, with similarities of 93.2-94.1 and 89.8-90.8 %, respectively, to the closest recognized species, Bacteroides coprocola JCM 17929T. Sugar fermentation and enzyme characteristics, cellular fatty acid profiles, menaquinone profiles and metabolic end products were also investigated. Furthermore, DNA-DNA hybridization studies confirmed that the three novel strains are different from the closest related species. The strains were also found to be distinct from each other on the basis of ribotype profiles. The DNA G+C contents of the three strains were 41.1-41.8 mol%. Based on phenotypic and phylogenetic characteristics, a novel species, Bacteroides caecigallinarum sp. nov., is proposed (type strain C13EG111T = LIPI12-4-Ck773T = JSAT12-4-Ck773T = InaCC B455T = NBRC 110959T).

Marine-Derived Streptomyces sennicomposti GMY01 with Anti-Plasmodial and Anticancer Activities: Genome Analysis, In Vitro Bioassay, Metabolite Profiling, and Molecular Docking.

To discover novel antimalarial and anticancer compounds, we carried out a genome analysis, bioassay, metabolite profiling, and molecular docking of marine sediment actinobacteria strain GMY01. The whole-genome sequence analysis revealed that Streptomyces sp. GMY01 (7.9 Mbp) is most similar to Streptomyces sennicomposti strain RCPT1-4T with an average nucleotide identity (ANI) and ANI based on BLAST+ (ANIb) values of 98.09 and 97.33% (>95%). An in vitro bioassay of the GMY01 bioactive on Plasmodium falciparum FCR3, cervical carcinoma of HeLa cell and lung carcinoma of HTB cells exhibited moderate activity (IC50 value of 46.06; 27.31 and 33.75 µg/mL) with low toxicity on Vero cells as a normal cell (IC50 value of 823.3 µg/mL). Metabolite profiling by LC-MS/MS analysis revealed that the active fraction of GMY01 contained carbohydrate-based compounds, C17H29NO14 (471.15880 Da) as a major compound (97.50%) and mannotriose (C18H32O16; 504.16903 Da, 1.96%) as a minor compound. Molecular docking analysis showed that mannotriose has a binding affinity on glutathione reductase (GR) and glutathione-S-transferase (GST) of P. falciparum and on autophagy proteins (mTORC1 and mTORC2) of cancer cells. Streptomyces sennicomposti GMY01 is a potential bacterium producing carbohydrate-based bioactive compounds with anti-plasmodial and anticancer activities and with low toxicity to normal cells.

Analysis of the Antibacterial Activity and the Total Phenolic and Flavonoid Contents of the Moringa oleifera Leaf Extract as an Antimicrobial Agent against Pseudomonas aeruginosa.

Pseudomonas aeruginosa is a bacterium that causes metal deterioration by forming biofilms on metal surfaces. This work was carried out to analyze the antibacterial activity and the phenolic and flavonoid contents of the Moringa oleifera leaf extract against Pseudomonas aeruginosa. M. oleifera leaves were extracted in a methanol solution at different concentrations. The M. oleifera leaf extract yields were 12.84%, 18.96%, and 19.64% for the 100%, 75%, and 50% methanol ratios, respectively. Extracts of M. oleifera leaves had a minimum inhibiting concentration (MIC) of approximately 6144 µg/mL against P. aeruginosa for a ratio of 100% methanol. In addition, no antibacterial activity was found for the 75% and 50% methanol ratios. The total phenolic levels were 16.26%, 12.73%, and 12.33% for the 100%, 75%, and 50% methanol solvent ratios, respectively. The total amounts of flavonoids were 23.32%, 3.40%, and 0.64% for the 100%, 75%, and 50% methanol solvents, respectively. The chemical structure of M. oleifera consists of kaemferol-3-O-rutinoside, quercimeritrin, kaempferol-3-O-ß-D-glucopyranoside, stearidonic acid, trichosanic acid, pyrophaeophorbide A, and stigmastan-3,6-dione. The concentration of the solvent is essential in the extraction of plant constituents. Different concentrations indicate differences in antibacterial activity, phenolic and flavonoid contents, and chemical structure.

Draft Genome Sequence of the Marine-Derived, Anticancer Compound-Producing Bacterium Streptomyces sp. Strain GMY01.

The marine Streptomyces sp. strain GMY01 was isolated from Indonesian marine sediment. Genome mining analysis revealed that GMY01 has 28 biosynthetic gene clusters, dominated by genes encoding nonribosomal peptide synthetase and polyketide synthase.

Diversity and distribution of culturable lactic acid bacterial species in Indonesian Sayur Asin.

BACKGROUND AND OBJECTIVES: Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia. MATERIALS AND METHODS: Four Sayur Asin samples (fermentation liquor and fermented mustard) were collected at harvesting times (3-7 days after fermentation) from two traditional manufactures in Tulung Agung (TA) and Kediri (KDR), East Java provinces, Indonesia. LAB strains were isolated by using MRS agar method supplemented with 1% CaCO 3 and characterized morphologically. Identification of the strains was performed basedon 16S rDNA analysis and the phylogenetic tree was drawn to understand the phylogenetic relationship of the collected strains. RESULTS: Different profiles were detected in total count of the plates, salinity and pH of fermenting liquor of Sayur Asin in TA and KDR provinces. A total of 172 LAB isolates were successfully isolated and identified based on their 16S rDNA sequences. Phylogenetic analysis of 27 representative LAB strains from Sayur Asin showed that these strains belonged to 5 distinct species namely Lactobacilus farciminis (N=32), L. fermentum (N=4), L. namurensis (N=15), L. plantarum (N=118) and L. parafarraginis (N=1). Strains D5-S-2013 and B4-S-2013 showed a close phylogenetic relationship with L. composti and L. paralimentarius, respectively where as the sequence had slightly lower similarity of lower than 99%, suggesting that they may be classified into novel species and need further investigation due to exhibition of significant differences in their nucleotide sequences. Lactobacillus plantarum was found being dominant in all sayur asin samples. CONCLUSION: Lactobacilli were recognized as the major group of lactic acid bacteria in Sayur Asin including 5 known and 2 novel candidate species. The distribution of LAB species was associated with the manufactures where Sayur Asin is produced.

Synbiotic promotion of epithelial proliferation by orally ingested encapsulated Bifidobacterium breve and raffinose in the small intestine of rats.

We evaluated the effects of Bifidobacterium breve JCM1192(T )and/or raffinose on epithelial proliferation in the rat small and large intestines. WKAH/Hkm Slc rats (4 wk old) were fed a control diet, a diet supplemented with either encapsulated B. breve (30 g/kg diet, 1.5 x 10(7) colony-forming unit/g capsule) or raffinose (30 g/kg diet), or a diet supplemented with both encapsulated B. breve and raffinose, for 3 wk. Epithelial proliferation in the small intestine, as assessed by bromodeoxyuridine immunohistochemistry, was increased only in the B. breve plus raffinose-fed group. We determined the number of bifidobacteria in cecal contents using fluorescence in situ hybridization and confirmed the presence of ingested B. breve only in the B. breve plus raffinose-fed group. This suggests that the ingested B. breve cells used raffinose and were activated in the small intestine, where they subsequently influenced epithelial proliferation. In conclusion, we found a prominent synbiotic effect of encapsulated B. breve in combination with raffinose on epithelial proliferation in rat small intestine but not in large intestine. To our knowledge, this is the first report of a synbiotic that affects epithelial proliferation.

Population dynamics of Bifidobacterium species in human feces during raffinose administration monitored by fluorescence in situ hybridization-flow cytometry.

The population dynamics of bifidobacteria in human feces during raffinose administration were investigated at the species level by using fluorescence in situ hybridization (FISH) coupled with flow cytometry (FCM) analysis. Although double-staining FISH-FCM using both fluorescein isothiocyanate (FITC) and indodicarbocyanine (Cy5) as labeling dyes for fecal samples has been reported, the analysis was interfered with by strong autofluorescence at the FITC fluorescence region because of the presence of autofluorescence particles/debris in the fecal samples. We circumvented this problem by using only Cy5 fluorescent dye in the FISH-FCM analysis. Thirteen subjects received 2 g of raffinose twice a day for 4 weeks. Fecal samples were collected, and the bifidobacterial populations were monitored using the established FISH-FCM method. The results showed an increase in bifidobacteria from about 12.5% of total bacteria in the prefeeding period to about 28.7 and 37.2% after the 2-week and 4-week feeding periods, respectively. Bifidobacterium adolescentis, the Bifidobacterium catenulatum group, and Bifidobacterium longum were the major species, in that order, at the prefeeding period, and these bacteria were found to increase nearly in parallel during the raffinose administration. During the feeding periods, indigenous bifidobacterial populations became more diverse, such that minor species in human adults, such as Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium dentium, and Bifidobacterium angulatum, proliferated. Four weeks after raffinose administration was stopped, the proportion of each major bifidobacterial species, as well as that of total bifidobacteria, returned to approximately the original values for the prefeeding period, whereas that of each minor species appeared to differ considerably from its original value. To the best of our knowledge, these results provide the first clear demonstration of the population dynamics of indigenous bifidobacteria at the species level in response to raffinose administration.

Modulation of rat cecal microbiota by administration of raffinose and encapsulated Bifidobacterium breve.

To investigate the effects of administration of raffinose and encapsulated Bifidobacterium breve JCM 1192T cells on the rat cecal microbiota, in a preclinical synbiotic study groups of male WKAH/Hkm Slc rats were fed for 3 weeks with four different test diets: basal diet (group BD), basal diet supplemented with raffinose (group RAF), basal diet supplemented with encapsulated B. breve (group CB), and basal diet supplemented with both raffinose and encapsulated B. breve (group RCB). The bacterial populations in cecal samples were determined by fluorescence in situ hybridization (FISH) and terminal restriction fragment length polymorphism (T-RFLP). B. breve cells were detected only in the RCB group and accounted for about 6.3% of the total cells as determined by FISH analysis. B. breve was also detected only in the RCB group by T-RFLP analysis. This was in contrast to the CB group, in which no B. breve signals were detected by either FISH or T-RFLP. Increases in the sizes of the populations of Bifidobacterium animalis, a Bifidobacterium indigenous to the rat, were observed in the RAF and RCB groups. Principal-component analysis of T-RFLP results revealed significant alterations in the bacterial populations of rats in the RAF and RCB groups; the population in the CB group was similar to that in the control group (group BD). To the best of our knowledge, these results provide the first clear picture of the changes in the rat cecal microbiota in response to synbiotic administration.