scholarly journals Identification and functional analysis of bacteria in sclerotia of Cordyceps militaris

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12511
Author(s):  
Li Luo ◽  
Jiaxi Zhou ◽  
Zhongshun Xu ◽  
Jingqiang Guan ◽  
Yingming Gao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Extracellular Polysaccharide ◽  
Cordyceps Militaris ◽  
Liaoning Province ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Sequencing Technology ◽  
Ecological Functions ◽  
Three Samples ◽  
And Function

Background Cordyceps militaris is a fungus that parasitizes insects. Compounds from C. militaris are valuable in medicine and functional food. There are many kinds of bacteria in the natural sclerotia of C. militaris. However, the community structure of microorganisms in samples from different places may be different, and their corresponding ecological functions require experimental verification. Methods We used high-throughput sequencing technology to analyze bacterial 16S rRNA gene sequences in sclerotia of three samples of C. militaris from Liaoning Province, China. We isolated, identified and verified the function of culturable bacterial strains from the sclerotia. Results Pseudomonas, Pedobacter, Sphingobacterium, and Serratia were the dominant bacterial genera in the sclerotia. And function prediction showed that Pseudomonas and Pedobacter could be heterotrophic, Sphingobacterium could decompose urea, and Serratia could reduce nitrate. Two strains of bacteria isolated from the sclerotia of C. militaris, N-2 and N-26, were identified as Stenotrophomonas maltophilia and Pseudomonas baetica, respectively, based on culture and biochemical characteristics. When these isolated strains were co-cultured with C. militaris, the mycelium biomass and mycelium pellet diameter decreased, and the content of extracellular polysaccharide increased. Strain N-26 decreased the cordycepin content in C. militaris. Conclusions Bacteria in sclerotia have an important effect on the growth of C. militaris and the production of its metabolites.

scholarly journals Identification and functional analysis of bacteria in sclerotia of Cordyceps militaris

2021 ◽  
Author(s):  
Li Luo ◽  
Jia-Xi Zhou ◽  
Zhong-Shun Xu ◽  
Ying-Ming Gao ◽  
Xiao Zou
Keyword(s):  
Functional Food ◽  
High Throughput Sequencing ◽  
Cordyceps Militaris ◽  
Liaoning Province ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Sequencing Technology ◽  
Ecological Functions ◽  
Three Samples ◽  
Mycelium Biomass

Abstract Background Cordyceps militaris is a fungus that parasitizes insects. Compounds from C. militaris are valuable in medicine and functional food. There are many kinds of bacteria in the natural sclerotia of C. militaris. However, the community structure of microorganisms in samples from different places may be different, and the corresponding ecological functions require experimental verification. Results We used high-throughput sequencing technology to analyze bacterial 16S rRNA gene sequences in sclerotia of three samples of C. militaris from Liaoning Province, China. Pseudomonas, Pedobacter, Sphingobacterium, and Serratia were the dominant bacterial genera in the sclerotia. Pseudomonas and Pedobacter are heterotrophic, Sphingobacterium decomposes urea, and Serratia reduce nitrate. Two strains of bacteria, N-2 and N-26, were isolated from the sclerotia of the C. militaris, cultured, biochemically characterized, and identified as Stenotrophomonas maltophilia and Pseudomonas baetica, respectively. When these isolated strains were respectively cocultured with C. militaris, the mycelium biomass, mycelium pellet diameter, and cordycepin content decreased. Conclusions Bacteria in sclerotia have an important effect on the growth of C. militaris and the production of its metabolites.

scholarly journals Characterization of the salivary microbiome in people with obesity

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4458 ◽  
Author(s):  
Yujia Wu ◽  
Xiaopei Chi ◽  
Qian Zhang ◽  
Feng Chen ◽  
Xuliang Deng
Keyword(s):  
High Throughput Sequencing ◽  
Periodontal Diseases ◽  
Illumina Miseq ◽  
Normal Weight ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Diseases ◽  
And Function ◽  
Healthy Participants

Background The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs. Methods We characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases. Results The salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus Prevotella, Granulicatella, Peptostreptococcus, Solobacterium, Catonella, and Mogibacterium were significantly more abundant in the obesity group; meanwhile the genus Haemophilus, Corynebacterium, Capnocytophaga, and Staphylococcus were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls. Discussion Our study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral diseases.

scholarly journals Bacterial Diversity and Community in Regional Water Microbiota between Different Towns in World’s Longevity Township Jiaoling, China

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 361
Author(s):  
Lei Wu ◽  
Xinqiang Xie ◽  
Jumei Zhang ◽  
Yu Ding ◽  
Qingping Wu
Keyword(s):  
16S Rrna ◽  
High Throughput Sequencing ◽  
The Other ◽  
Rrna Gene ◽  
Metabolic Characteristics ◽  
Kegg Pathways ◽  
Healthy Longevity ◽  
And Function ◽  
Regional Water

Healthy longevity is associated with many factors, however, the potential correlation between longevity and microbiota remains elusive. To address this, we explored environmental microbiota from one of the world’s longevity townships in China. We used 16S rRNA gene high-throughput sequencing to analyze the composition and function of water microbiota. The composition and diversity of water microbiota significantly differed between the towns. Lactobacillus, Streptococcus, Bacteroides, Faecalibacterium, and Stenotrophomonas were only dominant in Xinpu, a town with an exceptionally high centenarian population. Several biomarkers were identified, including Flavobacterium, Acinetobacter, Paracoccus, Lactobacillales, Psychrobacter, Bacteroides, Ruminococcaceae, and Faecalibacterium, and these shown to be responsible for the significant differences between towns. The main species contributing to the differences between towns were Cyanobacteria, Cupriavidus and Ralstonia. Based on KEGG pathways showed that the predicted metabolic characteristics of the water microbiota in Xinpu towns were significantly different to those of the other towns. The results revealed significant differences in the composition and diversity of water microbiota in the longevity township. These findings provide a foundation for further research on the role of water microbiota in healthy longevity.

scholarly journals Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Jessica Chopyk ◽  
Daniel J. Nasko ◽  
Sarah Allard ◽  
Anthony Bui ◽  
Mihai Pop ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Antibiotic Resistance Genes ◽  
Pond Water ◽  
Taxonomic Composition ◽  
Storm Event ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Culture Independent ◽  
Freshwater Habitats ◽  
And Function

Abstract Background Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. Results Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. Conclusions Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

scholarly journals Culture-independent analysis of the bacterial communities in Chinese fermented vegetables and genomic analysis of lactic acid bacteria

2021 ◽  
Author(s):  
Jianming Zhang ◽  
Hye Seon Song ◽  
Chengcheng Zhang ◽  
Yeon Bee Kim ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Whole Genome Analysis ◽  
Sequencing Platform ◽  
Tuber Mustard ◽  
Fermented Vegetables

Abstract Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial communities using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from six samples. Firmicutes and Proteobacteria were the main phyla in all of samples. Meanwhile, Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated there were clear differences between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole genome analysis of Lactobacillus suantsaii, Lactobacillus sakei subsp. sakei, and Weissella cibaria showed they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.

scholarly journals Screening and Characterization of Two Extracellular Polysaccharide-Producing Bacteria from the Biocrust of the Mu Us Desert

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5521
Author(s):  
Zhanfang Xue ◽  
Shuting Zhao ◽  
Nomin Bold ◽  
Jianguo Zhang ◽  
Zhimin Hu ◽  
...  
Keyword(s):  
Sinorhizobium Meliloti ◽  
Lipid Analysis ◽  
16S Rrna Gene Sequencing ◽  
Extracellular Polysaccharide ◽  
Preliminary Evidence ◽  
Shaanxi Province ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Mu Us Desert ◽  
Rrna Gene Sequencing

The extracellular polysaccharide (EPS) matrix embedding microbial cells and soil particles plays an important role in the development of biological soil crusts (BSCs), which is widely recognized as beneficial to soil fertility in dryland worldwide. This study examined the EPS-producing bacterial strains YL24-1 and YL24-3 isolated from sandy soil in the Mu Us Desert in Yulin, Shaanxi province, China. The strains YL24-1 and YL24-3 were able to efficiently produce EPS; the levels of EPS were determined to be 257.22 μg/mL and 83.41 μg/mL in cultures grown for 72 h and were identified as Sinorhizobium meliloti and Pedobacter sp., respectively. When the strain YL24-3 was compared to Pedobacter yulinensis YL28-9T using 16S rRNA gene sequencing, the resemblance was 98.6% and the strain was classified as Pedobacter sp. using physiological and biochemical analysis. Furthermore, strain YL24-3 was also identified as a subspecies of Pedobacter yulinensis YL28-9T on the basis of DNA–DNA hybridization and polar lipid analysis compared with YL28-9T. On the basis of the EPS-related genes of relevant strains in the GenBank, several EPS-related genes were cloned and sequenced in the strain YL24-1, including those potentially involved in EPS synthesis, assembly, transport, and secretion. Given the differences of the strains in EPS production, it is possible that the differences in gene sequences result in variations in the enzyme/protein activities for EPS biosynthesis, assembly, transport, and secretion. The results provide preliminary evidence of various contributions of bacterial strains to the formation of EPS matrix in the Mu Us Desert.

scholarly journals Relationship between the True Digestibility of Dietary Calcium and Gastrointestinal Microorganisms in Goats

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 875
Author(s):  
Yuehui Liu ◽  
Ali Mujtaba Shah ◽  
Lizhi Wang ◽  
Lei Jin ◽  
Zhisheng Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Sequencing Technology ◽  
Experimental Animals ◽  
Healthy Female ◽  
True Digestibility ◽  
The Relationship ◽  
Bacterial 16S Rrna Gene

The current study was performed to examine the relationship between the true digestibility of calcium (TDC) in the diet and bacterial community structure in the gastrointestinal tract (GIT) of goats. Twenty-six Nubian healthy female goats were selected as experimental animals, and their TDC was determined using metabolic experiments. Eight goats were grouped into the high digestibility of Calcium (HC) phenotype, and another eight were grouped into the low digestibility of Calcium (LC) phenotype. Their bacterial 16S rRNA gene amplicons from the rumen, abomasum, jejunum, cecum, and colon contents were sequenced using next-generation high-throughput sequencing technology. In the rumen, 239 genera belonging to 23 phyla, 319 genera belonging to 30 phyla in the abomasum, 248 genera belonging to 36 phyla in the jejunum, 248 genera belonging to 25 phyla in the colon and 246 genera belonging to 23 phyla in the cecum were detected. In addition, there was a significant correlation between the TDC and the relative abundance of Candidatus_Saccharimonas, Christensenellaceae_R-7_group, Mogibacterium, Prevotella_1, Prevotella_UCG_004, Ruminococcus_2, Saccharibacteria in the rumen, Eubacterium_coprostanoligens_group, Lachnospiraceae_ND3007_group, Lachnospiraceae_NK3A20_group, p-1088-a5_gut_group, and Planctomycetes in the abomasum, Butyrivibrio in the cecum, and Fibrobacter in the cecum were observed. This study suggests an association of GIT microbial communities as a factor influencing TDC in goats.

scholarly journals Bacterial community and composition of soil in world’s longevity township Jiaoling, China by 16S rRNA high-throughput sequencing

2021 ◽  
Author(s):  
Lei Wu ◽  
Xinqiang Xie ◽  
Jun Ma ◽  
Jumei Zhang ◽  
Yu Ding ◽  
...  
Keyword(s):  
16S Rrna ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Soil Microbiota ◽  
Healthy Longevity ◽  
Underlying Mechanisms ◽  
And Function ◽  
Dominant Bacteria

Abstract Healthy longevity is a complicated process, however, the underlying mechanisms between longevity and microbiota warrant investigation. To address this, we characterized a longevity trajectory of environmental microbiota in a longevity township. We used high-throughput sequencing of the 16S rRNA gene to analyse the composition and function of soil microbiota. The composition and diversity of soil microbiota significantly differed between towns. The dominant bacteria at the phylum level included Proteobacteria, Firmicutes, and Acidobacteria. At the genus level, Chujaibacter, Acidipila, and Lactobacillus were dominant. However, Steroidobacter, Comamonas, and Pseudoxanthomonas were only dominant in Xinpu with high centenarian population. Twelve biomarkers were responsible for significant differences between towns, including Lactobacillus, Muribaculaceae, Ruminococcaceae, Lachnospiraceae, and Chitinophagales, etc. The main species contributing to the differences of towns were Chujaibacter, Acidipila, Lactobacillus, Rhodanobacter, Lysobacter, Bryobacter, Granulicella, Flavobacterium, and Mizugakiibacter. The function of exosome, cysteine and methionine metabolism, amino acid-related enzymes, peptidases, starch and sucrose metabolism, etc., were predicted. Thus, we have revealed significant differences in the composition and diversity of soil microbiota in the world’s longevity township, the relationship between soil microbiota and long-lived people. These findings provide a research foundation for the role of soil microbiota in healthy longevity.

scholarly journals Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3277 ◽  
Author(s):  
Tasha M. Santiago-Rodriguez ◽  
Yvonne Narganes-Storde ◽  
Luis Chanlatte-Baik ◽  
Gary A. Toranzos ◽  
Raul J. Cano
Keyword(s):  
Puerto Rico ◽  
Dental Plaque ◽  
High Throughput Sequencing ◽  
Dietary Habits ◽  
Microbial Evolution ◽  
Structure And Function ◽  
Oral Disease ◽  
Rrna Gene ◽  
Disease States ◽  
And Function

Background The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet. Methods Dental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project. Results Actinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including Streptococcus sp., Veillonella dispar and Rothia mucilaginosa. Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome. Discussion Results suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles.

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