Metagenomic characterization of the culturable bacterial community structure of Tapuy, a Philippine indigenous rice wine, reveals significant presence of potential probiotic bacteria

Background@#Tapuy is an indigenous fermented rice wine produced in the Northern areas of the Philippines. Fermented foods and drinks have gained interest due to their associated health benefits, attributable to probiotic bacteria in the food items. However, pathogenic bacteria may also be present in fermented food and pose health risks, signifying a need for standardization. Currently, there is limited knowledge on the bacterial content of tapuy. @*Objectives@#This study aimed to characterize the bacterial diversity and community structure of culturable bacteria in traditionally fermented tapuy samples, to perform standardization of tapuy fermentation, and to compare the bacterial diversity and community structure of culturable bacteria in laboratory fermented tapuy with that of the traditional samples. @*Methods@#Tapuy samples were obtained from four municipalities in Benguet, Philippines. Laboratory fermentation of tapuy was performed simultaneously with the fermentation in the sampling site using a standardized protocol. Samples were plated on de Man, Rogosa, and Sharpe (MRS) agar and NA, and the colonies were harvested for DNA extraction. DNA samples were sent for 16S rDNA metagenomic sequencing. Results. Metagenomic analysis revealed the presence of many bacterial species that were previously unreported in tapuy. Traditional tapuy samples were composed primarily of members of the genera Bacillus and Lactobacillus in varying proportions. Potential probiotic bacteria were abundant in Kapangan (97.42%) and Sablan (99.89%) field samples. B. wiedmannii was present in all samples and was identified as a harmful species. Laboratory fermentation increased the abundance of potential probiotic bacteria in Itogon and La Trinidad samples (differences of 75.36% and 78.36%, respectively). It decreased the quantity of B. wiedmannii in La Trinidad (a difference of 97.1%). Laboratory fermented samples generally exhibited higher bacterial diversity and species richness compared to field samples. @*Conclusions@#Traditionally fermented tapuy samples contained a significant proportion of potential probiotic bacteria belonging to the genera Bacillus and Lactobacillus. Laboratory fermented samples were found to have higher bacterial diversity and richness compared to field samples. The significant presence of potential probiotic bacteria suggests that tapuy is a good candidate for development into functional food and a good source of likely probiotic species that could be explored for health applications. The presence of harmful bacteria suggests the need for possible standardization of fermentation practices.

Effects of Comamonas testosteroni on PAHs degradation and bacterial community structure in Leymus chinensis rhizosphere soil / 生物工程学报

To investigate the degradation of polycyclic aromatic hydrocarbons (PAHs) and the changes of rhizosphere microorganisms in the rhizosphere soil of Leymus chinensis during the remediation of PAHs contaminated soil by Comamonas testosteroni (C.t)-assisted Leymus chinensis, we evaluated the removal of PAHs in the rhizosphere of Leymus chinensis using gas chromatography-mass spectrometry (GC-MS), analyzed the bacterial community and the diversity in Leymus chinensis rhizosphere soil by high-throughput sequencing technology, characterized the correlation among PAHs degradation and bacterial community components performing redundancy analysis (RDA) and network analysis, and predicted PAHs degradation potential via PICRUSt software in this paper. The degradation of PAHs in the rhizosphere of Leymus chinensis was promoted, the abundance and diversity of bacteria and the correlation among bacteria and PAHs were changed, and the degradation potential of PAHs in Leymus chinensis rhizosphere soil was enhanced in the later stage of phytoremediation (60-120 d) due to the incorporation of C.t. The accelerated degradation of three PAHs (Nap, Phe, BaP) was accompanied by the differ abundance and correlation of Proteobacteria (Sphingomonas, MND1, Nordella), Actinomycetes (Rubrobacter, Gaiella), Acidobacteria (RB41) and Bacteroides (Flavobacterium) affected by C.t. The results provide new insight into the microorganism choices for microbial assisted plant remediation of soil PAHs and the mechanisms of enhanced PAHs degradation via the combination of Comamonas testosteroni engineering bacteria and plants.

Analysis of bacteria distribution characteristics in different layers of agarwood based on Hiseq sequencing / 中国中药杂志

To explore the diversity of bacterial community structure between different layers of agarwood, Hiseq(high-throughput sequencing) was used to analyze the bacterial community structure of samples from different layers of agarwood. Our results showed that 1 150 096 optimized sequences and 9 690 OTUs were obtained from 15 samples of 5 layers of agarwood, which belonged to 28 bacterial phyla, 61 classes, 110 orders, 212 families and 384 genera. Further analysis revealed that the normal layer(NL) had the lowest bacterial species richness and the smallest number of OTUs. And the total number of OTUs of the agarwood layer(AL) and NL was zero, which was quite different.At the same time, there were significant differences in bacterial community structure and species diversity between NL and the other four layers. While there were some common dominant bacterial genera in both transition layer(TL) and NL. The similarity of bacterial distribution in 4 non-NL layers was relatively high, which had four common genera, such as Acidibacter, Bradyrhizobium, Acidothemus and Sphingomonas. While Acidibacter, Bradyrhizobium and Acidothemus were the dominant bacterial genus of DA and AL, and all of these layers contained volatile oil. In addition, the Bradyrhizobium was the most abundant in agarwood layer. Our results showed that bacterial community diversity and abundance were decreasing from DL to AL, and different layers showed significant differences in bacterial enrichment. It provided the clues to investigate how bacteria participate in the formation of agarwood.

Changes in Cold and Hot Syndrome and Gastrointestinal Bacterial Community Structure in Mice by Intervention with Food of Different Nature / 中国结合医学杂志

OBJECTIVE@#To reveal the effect of foods with different natures on cold or hot syndrome and gastrointestinal bacterial community structure in mice.@*METHODS@#Forty-five 6-week-old male ICR Kunming mice of clean grade were divided into 5 groups, 9 per group, including the control (CK), hot nature herbs (HM), Hong Qu glutinous rice wine (RW), tea rice wine (TW), and cold nature herbs (CM) groups. Distilled water or corresponding herbs were administered to mice (0.01 mL/g body weight) in the 5 groups by gastric infusion respectively, once daily for 28 d. Appearance, behavior, and serum biochemical indicators, including 5-hydroxytryptamine (5-HT), thyroid stimulating hormone (TSH), noradrenaline (NE), cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), the hot nature index, as well as the gastrointestinal bacterial community structure were analyzed in all groups after treatment.@*RESULTS@#After supplementation for 28 d, CM and TW mice showed different degrees of cold syndrome, and HM and RW mice showed different degrees of hot syndrome. Compared with the HM and RW mice, the TSH, NE, cAMP levels and hot nature indices in the CM and TW mice were significantly decreased and 5-HT and cGMP levels were significantly increased (P<0.05). There was no obvious change in appearance or behavior in CK mice. Results of clustering analysis showed that the gastrointestinal bacterial community structures were highly similar in TW and CM mice as well as in RW and HM mice, and that they were from the same branch, respectively, when the distance was 0.02. The key microbes associated with cold syndrome were Lachnospiraceae uncultured, Lactococcus, etc., and the key microbes associated with hot syndrome were S24-7 norank, Ruminococcaceae uncultured, etc. CONCLUSION: The interventions with different nature foods could change cold or hot syndrome in mice, leading to changes in gastrointestinal bacterial community structure.

Effects of biocontrol strain BZJN1 and streptoprofen on physicochemical properties and bacteria structure of rhizosphere soil of Atractylodes macrocephala / 中国中药杂志

Soil microorganisms are one of the important biological indictors of soil quality and can reflct the comprehensive ecological environment characteristics of the soil. The research of soil microbial diversity is the key to know the ecological functions and balance with soil. In this paper, high-throughput sequencing on PCR-amplified 16 S rRNA gene V3-V4 fragments was used to determine the bacterial diversity in rhizosphere soil of A. macrocephala under the treatment with BZJN1 or streptoprofen. The results showed that there were no significant differences of the bacteria in A. macrocephala rhizosphere soil of the streptoprofen treatment group and the biocontrol BZJN1 treatment group. All the soil bacteria was classified into 25 categories,67 classes, 108 orders, 167 families and 271 generas, except some unidentified bacteria. Proteobacteria(30.7%-34.8%) was the dominant phylum, of which Alphaproteobacteria(16.8%-18.5%) was the dominant subgroup. Compared with the control group, the relative abundance of multiple phylums bacteria in the rhizosphere soil of A. macrocephala was significantly changed in the streptoprofen treatment group and the biocontrol BZJN1 treatment group. In addition, RDA analysis showed that there was connection with different environmental factors and microbial communities. The abundance of the three genera in the rhizosphere soil of A. macrocephala was significantly positively correlated with Invertase, Urease and AP. PICRUSt function prediction results showed that BZNJ1 could enhance some bacterial functions and promote the plant growth. Biocontrol is a new type of green and safety control pest method. BZNJ1 significantly enhances some bacterial functions on the basis of effectively preventing root rot of A. macrocephala and promoting plant growth, and has no significant effect on the soil bacterial community structure. All the results can provide theoretical support for popularization of BZNJ1.

The community structure of intestinal bacteria from cirrhosis patients and its influence factors / 中华消化内镜杂志

Objective To investigate the community structure of intestinal bacteria from patients with cirrhosis and its influencing factors. Methods From 2016 to 2017, 24 patients with liver cirrhosis ( the LC group) and 23 healthy family members of patients ( the HC group) were enrolled at the First Hospital of Lanzhou University. A comparative analysis of the community structure of intestinal bacteria was performed using 16S rRNA gene sequencing in LC and HC groups. Combined with LEfSe analysis and NMDS analysis, the differential markers were screened and the factors affecting the intestinal community structure of subjects were studied. Results The dominant six phylum of bacteria in intestines in LC and HC groups included Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria and Tenericumes. However, in the LC sample, Firmicutes was significantly reduced, while Bacteroides was significantly increased. The diversity of intestinal bacteria was significantly reduced, and the Firmicutes/Bacteroides ratio was significantly decreased, suggesting a variation of the community structure in intestinal bacteria of cirrhosis patients. The LEfSe result indicated that the abundance of Enterococcus, Lactobacillales, Bacilli, and Bacteroidetes showed a significant difference in the LC sample, which may be used as potential marked bacterial groups for cirrhosis. The NMDS analysis revealed a positive relationship between the concentration of Cd and Pb and the abundance of intestinal bacteria in the LC sample. Conclusion The community structure of intestinal bacteria from patients with cirrhosis has changed. Enterococcus, Lactobacillales, Bacilli, and Bacteroidetes are potential marked bacterial groups. The concentration of Cd and Pb in the intestinal tract of cirrhosis patients may interact with the abundance and structure of bacteria, and further affect the occurrence and development of cirrhosis.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China

Abstract In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.