Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food

Zhang, Jiachao; Wang, Xiaoru; Huo, Dongxue; Li, Wu; Hu, Qisong; Xu, Chang; Liu, Sixin; Li, Congfa

doi:10.1038/srep32524

Cited by 75 publications

(50 citation statements)

References 33 publications

(37 reference statements)

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“…Then, the effective tags were classified as an operational taxonomic unit (OTU) with a 97% threshold [59]. We pick a representative sequence for each OTU and the taxonomy of each OTU representative sequence was assigned and annotated using the Ribosomal Database Project (RDP) classifier with a minimum bootstrap threshold of 80% [60]. The heat-map visualization with hierarchical clustering of the top 20 most abundant genera was generated using R-package, gplots (version 3.3.1), and color-coded by row z-scores [61].…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut (Arachis hypogaea L.) Cultivars

Zhang

Dai

et al. 2020

IJMS

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Background: Exposure of seeds to high salinity can cause reduced germination and poor seedling establishment. Improving the salt tolerance of peanut (Arachis hypogaea L.) seeds during germination is an important breeding goal of the peanut industry. Bacterial communities in the spermosphere soils may be of special importance to seed germination under salt stress, whereas extant results in oilseed crop peanut are scarce. Methods: Here, bacterial communities colonizing peanut seeds with salt stress were characterized using 16S rRNA gene sequencing. Results: Peanut spermosphere was composed of four dominant genera: Bacillus, Massilia, Pseudarthrobacter, and Sphingomonas. Comparisons of bacterial community structure revealed that the beneficial bacteria (Bacillus), which can produce specific phosphatases to sequentially mineralize organic phosphorus into inorganic phosphorus, occurred in relatively higher abundance in salt-treated spermosphere soils. Further soil enzyme activity assays showed that phosphatase activity increased in salt-treated spermosphere soils, which may be associated with the shift of Bacillus. Conclusion: This study will form the foundation for future improvement of salt tolerance of peanuts at the seed germination stage via modification of the soil microbes.

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Section: Bioinformatics Analysismentioning

confidence: 99%

Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut (Arachis hypogaea L.) Cultivars

Zhang

Dai

et al. 2020

IJMS

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“…The bioinformatics analysis protocols were described in our previous research (Zhang et al, 2016). Briefly, the sequence data from different samples were separated based on the barcode sequences.…”

Section: Bioinformatics Analysis Of the Sequence Datamentioning

confidence: 99%

Bacterial diversity in goat milk from the Guanzhong area of China

Zhang

Wang

Lei

et al. 2017

Journal of Dairy Science

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In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator. Functional genes and their likely metabolic pathways were predicted, which demonstrated that the functional genes present in the bacteria in goat milk were enriched in pathways for amino acid metabolism and carbohydrate metabolism, which represented 11.93 and 11.23% of functional genes, respectively. Physicochemical properties such as pH, protein, fat, and AA levels were also determined and correlations made with microbial diversity. We detected a significant difference in the content of lactose and 6 AA, which were higher in Saanen milk than in Guanzhong milk, and positively correlated with microbial carbohydrate metabolism and AA metabolism. Lactococcus, Lactobacillus, Bifidobacterium, Enterococcus, and Streptococcus, which are lactose-utilizing genera, were more abundant in Saanen milk than in Guanzhong milk. Higher levels of lactose in Saanen goat milk may explain its greater microbial diversity. We also demonstrated that most of the AA metabolism-related bacterial genera (e.g., Massilia, Bacteroides, Lysobacter) were enriched in Saanen goat milk. In this research, both probiotic and pathogenic bacteria were identified in goat milk, which provided the microbial information necessary to direct the utilization of beneficial microbial resources and prevent the development of harmful organisms in goat milk.

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“…The commercial metagenomic DNA extraction kit of QIAamp1 DNA Stool Mini Kit (Qiagen, Hilden, Germany) coupled with bead-beating was used for DNA extraction from the faecal samples to guarantee the integrity, purity, and concentration of the DNA [24]. The quality of metagenomic DNA was evaluated using 0.8% agarose gel electrophoresis.…”

Section: Metagenomic Dna Extractionmentioning

confidence: 99%

“…The V3-V4 regions of the 16S rRNA genes were amplified using PCR assays [25,26]. A set of 6-nucleotide barcodes was added to the universal forward primer 338F (5 0 -ACTCCTACGG GAGGCAGCA-3 0 ) and the reverse primer 806R (5 0 -GGACTACHVGGGTWTCTAAT-3 0 ), which was targeted at domain bacteria [24]. PCR amplification was achieved following the methods of Wu et al [27].…”

Section: Amplification V3-v4 Regions Of 16s Rrna Gene and High-througmentioning

confidence: 99%

The distal intestinal microbiome of hybrids of Hainan black goats and Saanen goats

et al. 2020

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Intestinal microbiota performed numerous important functions during digestion. The first filial generation (F1) hybrids of Hainan black goats and Saanen goats had different traits, black goats (BG) and white goats (WG), which also brought different production performance. We explored the difference of gut microbiota between black goats and white goats that both belonged to the first filial generation (F1) hybrids. In general, the alpha diversity of the black goat group was significantly higher than the white goat group. The species richness had no significant difference, while the species evenness of BG was higher than WG. Bacteroides, Oscillospira, Alistipes, Ruminococcus, Clostridium and Oscillibacter, as the core gut microbial genera, all had high abundance in BG and WG group. Only the Bacteroides and Bacteroidaceae 5-7N15 were the different genera between the BG and WG group, of which Bacteroides overlapped with the core genera and enriched in the WG group. Besides, PICRUSt analysis showed that there was a high abundance in the secondary metabolic pathways including membrane transport, replication and repair, carbohydrate metabolism and amino acid metabolism. We found the intestinal microbial species of black goats and white goats were very similar for living in the identical growing environment and feeding conditions, but there was still a slight difference in the content. On the one hand, it was proved that the small effect of genotype and the great effect of diet affected the intestinal microbiota together. On the other hand, it was also proved that these different traits of first filial generation (F1) hybrids may not related to gut microbiota and only because of different genotype. Moreover, characterization of the gut microbiota in BG and WG will be useful in goats gut microbiota research. , et al. (2020) The distal intestinal microbiome of hybrids of Hainan black goats and Saanen goats. PLoS ONE 15(1): e0228496. https://

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Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food

Cited by 75 publications

References 33 publications

Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut (Arachis hypogaea L.) Cultivars

Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut (Arachis hypogaea L.) Cultivars

Bacterial diversity in goat milk from the Guanzhong area of China

The distal intestinal microbiome of hybrids of Hainan black goats and Saanen goats

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