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Background Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions. The aim of this study was to investigate the bacterial communities profiles in the Moroccan phosphate mine using 16S metagenomics sequencing. Taxonomic resolution of six hypervariable regions of the 16S rRNA was assessed in the collected samples and mock standard community. The bacterial functions enriched in the samples were also predicted to assess the contribution of the proposed low cost approach in the description of bacterial diversity and functionality in soil and plant. Methods The Ion 16S™ metagenomics kit was used to compare the discriminatory potential of the six targeted hypervariable regions of the 16S rRNA gene in the description of the bacterial communities. Alpha and beta diversity analysis were also performed accordingly in the studied samples. The later were collected from the bulk phosphate mine and the soils attached to roots of three different wild plants, that natively grow in this environment. Samples from the rhizosphere of wheat plants in cropping system were also studied. Actinobacteria related sequences were compared between the samples to investigate their possible origin between the bulk mine and the wild plants rhizosphere. The prediction of 82 bacterial functions related to nitrogen and phosphate metabolism along with stress was performed using Tax4fun bioinformatics tool. Results The rhizosphere of the three wild plants in the Moroccan phosphate mine is characterized by interesting bacterial diversity including Proteobacteria (62,24%, 71,15% and 65,61%), Actinobacteria (22,53%, 15,24%, 22,30%), Bacteroidetes (7,57% ; 4,23% ; 7,63%), and Firmicutes (5,82%; 1,17% ; 2,83%). Broad taxonomic diversity of minor phyla was also found in the native plants samples and included Acidobacteria, Armatimonadetes, Chloroflexi, Cyanobacteria, Gemmatimonadetes and Verrucomicrobia. The bulk phosphate mine samples were dominated by Actinobacteria with average relative abundance of 97,73% and Proteobacteria was Less abundant phylum in these samples. V3, V4 and V67 regions performed better in the taxonomic resolution at different levels e.g., phylum, family and genus. However, V8 and V9 regions gave the lesser taxonomic resolution and V9 region identified only Proteobacteria phylum in the mock standard sample. Alpha and beta diversity analysis indicated low abundance of observed OTUs and diversity in the bulk samples compared with the rhizosphere samples of the native plants in the phosphate mine. Moreover, significant (p = 0,021) differences in bacterial diversity were observed among at least three kind of samples : The bulk phosphate mine, the rhizosphere of the native wild plants of the phosphate mine and the rhizosphere of the wheat crop. The results indicated that both plant genotype and mainly soil conditions may be involved in the shaping of bacterial diversity. Such indication was also confirmed by the prediction of functional profiles that showed enrichment of many functions related to biological nitrogen fixation in the rhizosphere of native plants and the stress related functions in the bulk phosphate mine in comparison with the wheat rhizosphere samples Conclusion The proposed amplicon sequencing approach combined to bioinformatic prediction of bacterial functions could be considered as low-cost method to study the bacterial communities in soils and plants. The application of such approach to samples from the phosphate mines and wild plants revealed the need to consider at least V3, V4 and V6-7 hypervariable regions of the 16S rRNA gene in the taxonomic resolution of bacterial diversity in soil samples. This approach revealed also interesting bacterial diversity governed by the plant genotypes and the local conditions with interesting predicted functionalities involved in plant growth and development and stress tolerance in extreme environments. Further studies could target some interesting identified phyla and predicted bacterial functionalities, such studies could also deeply investigate the origin of the bacterial diversity in these native plants to develop new generation of bacterial inoculants for sustainable agriculture.

Bovine mastitis is the persistent, inflammatory reaction of the udder due to physical trauma or microorganism infection. The milk from healthy and mastitis cows presents an ecosystem of microbial communities, which can influence the mechanisms and pathophysiology of mastitis. Hence, there is a possible shift in microbiome composition in healthy, subclinical and clinical mastitis. This study reported the composition of microbiota in the udder of Jersey Friesian cows in one of the local farms located in Pahang, Malaysia. From the 16s amplicon sequencing analysis, the core microbiota was dominated by phyla of Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota. Most of the predominant genera from healthy groups were mainly Ralstonia, Staphylococcus, Corynebacterium, Turicibacter, Acinetobacter, Escherichia, Aerococcus, and Streptococcus. Furthermore, the majority of subclinical mastitis milk was populated by genera of Ralstonia, Escherichia, Aerococcus, and Corynebacterium, whereas, Streptococcus, Ralstonia and Escherichia were predominant in clinical mastitis samples. The alpha and beta diversity analysis indicated that microbiota from healthy and subclinical were more diverse compared to clinical mastitis microbiota. Therefore, predominant genera from clinical mastitis samples might be the potential of causative mastitis pathogens in the respective farm. The use of culture-independent analysis presented here revealed a wide bacterial diversity and variation between different clinical statuses.

Background: Microbes are an important part of the vineyard ecosystem, which significantly influence the growth and development of grapevines. High-throughput microbiome sequencing can fully identify the microbial communities so as to help to guide viticulture and disease control. Previously, we identified a bud mutant variety, named ‘Fengzao’, from ‘Kyoho’ grapes. With both ‘Fengzao’ and ‘Kyoho’, we conducted high-throughput microbiome sequencing and investigated their microbial communities in different tissues. Methods: Samples of fruit, stem and leaf were separately collected from ‘Fengzao’ and ‘Kyoho’. After microbiome sequencing, analysis of OTU (Operational Taxonomic Unit) and taxonomy were conducted. The species diversity among different samples were analyzed by performing alpha and beta diversity analysis. Results: A total of 34 OTUs were identified from the different tissues of ‘Fengzao’ and ‘Kyoho’. There were obvious differences in the microbial communities between ‘Fengzao’ and ‘Kyoho’. The fruit and the stem are the tissues with relatively higher abundance of microbes, while the leaves contained less microbes. The fruit and stem of ‘Kyoho’ and the stem of ‘Fengzao’ had relatively higher species diversity based on the alpha diversity analysis. Proteobacteria, Enterobacteriaceae and Rhodobacteraceae had significantly high abundance in ‘Fengzao’. Firmicutes and Pseudomonas were highly abundant in the stems of ‘Kyoho’, and family of Spirochaetaceae, Anaplasmataceae, Chlorobiaceae, and Sphingomonadaceae, and genera of Spirochaeta, Sphingomonas, Chlorobaculum and Wolbachia were abundant in the fruits of ‘Kyoho’. Conclusion: The fruit and the stem (but not leaf) of grapevines are important hosts for microbes, and there are significant differences in microbial compositions between ‘Fengzao’ and ‘Kyoho’. These identified microbes will be significant resources for the future researches on the quality regulation and disease control of grapevines.

IntroductionCommensal microbiota dysbiosis is associated with the development of lung cancer. The current studies about composition of respiratory microbiota in lung cancer patients yielded inconsistent results. This study aimed to examine the association between airway microbiota and lung cancer clinicopathological characteristics.MethodsSurgically removed lesion tissues from 75 non-small cell lung cancer patients and 7 patients with benign pulmonary diseases were analyzed by 16S rRNA sequencing. Taxonomy, relative abundance, and diversity of respiratory microbiota were compared among lung cancer of different pathology and TNM stages. The effects of antibiotic and cigarette exposure on respiratory microbiota in lung cancer patients were also evaluated.ResultsBacterial relative abundance and alpha- and beta-diversity analysis of lung microbiota showed significant differences among lung cancer of different pathology and benign pulmonary diseases. At the genus level, the abundance differences of 13 taxa between lung squamous cell carcinoma and lung adenocarcinoma, 63 taxa between lung squamous cell carcinoma and benign pulmonary diseases, and 4 taxa between lung adenocarcinoma and benign pulmonary diseases reached statistical significance. In contrast, diversity differences were not as significant across lung cancer of different stages. No significant differences were observed in tissue taxonomic abundances and diversity at all taxonomic levels between lung cancer patients with and without antibiotic exposure 3 months prior to surgery. For lung adenocarcinoma, respiratory bacterial abundance and diversity at all taxonomic levels did not show significant differences between smokers and non-smokers.ConclusionsOur results confirm significantly differential respiratory microbiome taxa, abundance, and diversity in lung cancer of different pathology and some stages. Short-term antibiotic application might play a minor role in molding airway microbiota in lung cancer patients. Composition and diversity of respiratory microbiota in lung adenocarcinoma are not affected by cigarette exposure.

Agri-environment schemes (AES) are expected to counteract the negative impacts of intensive agriculture on biodiversity. These schemes were specifically designed to target farmland biodiversity and included, for instance, ecological focus areas (EFAs). In Switzerland, in order to qualify for direct payments, farmers must manage 7% or more of their land as biodiversity promotion areas (BPAs). BPAs encompass extensively managed and low intensity hay meadows, fallows (wildflower strips), traditional orchards with high-stem trees and hedgerows. Evaluation of AES delivery for biodiversity is of crucial importance but must be performed across several years and considering the various components of species diversity to avoid incomplete or wrong conclusions. From a complex study design comprising 478 fields in three regions and sampling over 7 years with four sampling times, spider assemblages of BPA habitats were compared to corresponding conventionally managed fields. A battery of investigations was performed including alpha- and beta-diversity analysis, multivariate dispersion, indicator species and species specificity to understand what BPAs deliver for spiders in the habitat scale and farming landscape. Results showed that alpha-diversity (average number of species) was usually higher in BPA habitats than in conventionally managed fields but the species composition (beta-diversity) had more power to perceive AES impact. Furthermore, the various environmental conditions of BPAs in the farming landscape led to highly diverse spider assemblages (multivariate dispersion) emphasizing that not only the agricultural management plays a role in determining species diversity but the environmental heterogeneity. Indicator (and rare) species were mostly found in woody BPAs (hedges and high-stem tree orchards) revealing the high importance of these BPA habitats for spider conservation. At regional scale, BPA hedges contributed most to the regional diversity of spiders in grassland and mixed regions while BPA meadows and wildflower strip BPAs were first delivering in the region of arable crops. Recommendations highlight the role of the woody habitats and of the environmental heterogeneity in the farming landscape as well as of regional planning to make AES effective.

Vaginal and cervical canal bacteria are associated with women’s health and pregnancy outcomes. Here, we compared their composition and characteristics in 37 reproductive-aged Chinese women including 24 pregnant women with cervical incompetence (vaginal and cervical canal bacteria formed Groups A and B, respectively) and 13 healthy pregnant women (vaginal and cervical canal bacteria formed Groups C and D, respectively) using high-throughput sequencing of the V4 region of 16S rRNA gene. The results of alpha and beta diversity analysis, respectively, indicated no statistical differences between Groups A and B (p = 0.32, 0.06), nor Groups B and D (p = 0.69, 0.74); however, differences were found between Groups C and D (p = 0.02, 0.01) and between Groups A and C (p = 0.04, 0.02). PLS-DA analysis showed that the individuals from each group were irregularly distributed according to their clade. Lactobacillus, Bifidobacterium and Ureaplasma were the dominant genera in all groups. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSts) analysis identified 31 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs associated with the bacterial communities from the four groups, including membrane transport, folding, sorting and degradation, xenobiotics biodegradation and metabolism, and nucleotide metabolism. We further determined relationships between pregnancy outcomes (Apgar scores) and certain bacterial species. A significant positive correlation was found between Apgar scores and Actinomyces neuii and Anoxybacillus flavithermus in the vagina and cervical canal of pregnant women with cervical incompetence while Bacteroides plebeius, Bifidobacterium pseudopodium and Staphylococcus petrasii in the cervical canal displayed negative correlations with Apgar scores. Moreover, Clostridium fimetarium, Methanobacterium congolense, Pseudomonas chlororaphis, and Psychrobacter nivimaris in the vagina were negatively correlated with Apgar scores. These bacteria may serve as potential biomarkers, however, additional research is warranted to verify their role in clinical outcomes.

To analyze the gut microbiota of patients with rheumatoid arthritis (RA) according to disease activity.An observational cross-sectional study of 110 patients with RA and 110 age- and sex-matched controls was performed. Patients were classified according to the disease activity (DAS28 ≥3.2 or DAS28 3.2). Clinical and epidemiological variables were included. The gut microbiota was analyzed using 16S rRNA sequencing and bioinformatics analysis based on QIIME and PICRUSt. A multivariate analysis was performed to identify factors associated with inflammatory activity.The mean DAS28 indicated remission/low inflammatory activity in 71 patients (64.5 %) and moderate/high activity in 39 (35.5 %) during follow-up. Alpha and beta diversity analysis revealed differences in gut microbiota between the 3 study groups. In the moderate/high activity RA, we observed a significant change in the abundance of genera compared with the other groups. The abundance of Collinsella and Bifidobacterium was increased in RA patients compared with controls. The metabolic profile of gut microbiota was characterized by differences in pathways related to Biosynthesis, Generation of Precursor Metabolites/Energy, and Degradation/Utilization/Assimilation between the 3 groups. The factors associated with cumulative inflammatory activity in RA were age (OR [95 % CI], 1.065 [1.002-1.131]), obesity (OR [95% CI], 3.829 [1.064-8.785]), HAQ score (OR [95% CI], 2.729 [1.240-5.009]), and expansion of the genus Collinsella (OR [95% CI], 3.000 [1.754-9.940]).The composition of gut microbiota differed between patients with RA and moderate/high activity, patients with remission/low activity, and controls. The genus Collinsella, age, obesity, and physical function were associated with cumulative inflammatory burden in RA.

Shugan Jieyu Capsule (SG) has been widely used in China to treat mild to moderate depression. Hypericum perforatum L. (St John’s Wort, SJW) is the main ingredient of SG and has been used as herbal medicine to treat depression in western countries. However, it is known that SJW has low bioavailability and does not easily get through the blood-brain barrier. Therefore, how SG plays an antidepressant effect in the central nervous system (CNS) remains an urgent problem to be solved. Mounting research has described the relationship between antidepressants and intestinal microbiota to illuminate antidepressive mechanisms in the CNS. We aimed to investigate the effects of therapy with SG on the function of gut microbiota and intestinal microbiota in rats with chronic unpredictable mild stress (CUMS)-induced depression. The psychophysiological state and the hypothalamic-pituitary-adrenal axis function of rats are evaluated through behavioral experiments, corticosterone levels, serotonin levels, and adrenal index measurements. 16S rDNA amplicon sequencing is used to test the changes in gut microbiota and make functional predictions of genes. With treatment of SG, the depression-like behaviors of CUMS-induced rats were reversed; the corticosterone levels and the adrenal index decreased significantly; the level of serotonin increased significantly; and the alpha and beta diversity analysis of microbiota showed an increase in the richness and uniformity of the flora were increased. SG regulated the relative abundance of Actinobacteria, Erysipelotrichaceae, Bifidobacteriaceae, Atopobiaceae, Dubosiella, and Bifidobacterium; Linear discriminant analysis effect size analysis demonstrated that Lactobacillaceae (family level), Lactobacillus (genus level), Lactobacillales (order level), Bacilli (class level), and Lactobacillus-reuteri (species level) were biomarkers in the SG group samples, and also likely to modulate metabolic pathways, such as those involved in carbohydrate metabolism, amino acid metabolism, and signal transduction. These data clearly illustrated the effect of SG on gut microbiome, thus laying the foundation for uncovering more insights on the therapeutic function of the traditional Chinese antidepressants. The potential of SG on mechanisms of antidepression to alter gut microbiota and intestinal microbiome function exposed to CUMS can be explored.

Additional file 2. Fig. S1 Alpha and beta diversity analysis of intestinal microbiota among the naïve, sham and TCI groups. Fig. S2 Confirmation of microbiota dysregulation induced by TCI. Fig. S3 KEGG analysis to show the associated pathways in the environmental information processing, human diseases and organismal systems categories based on 16S rRNA sequencing data. KEGG Kyoto Encyclopedia of Genes and Genomes. Fig. S4 Oral gavage of Asn or IPA extends the survival time of TCI rats. Fig. S5 Administration of Asn plus IPA mitigates intestinal microbiota dysbiosis induced by TCI. Fig. S6 Asn and IPA supplementation ameliorates intestinal hyperpermeability and intestinal microbiota dysbiosis induced by TCI through Akt activation in intestinal epithelium. Fig. S7 Oral administration of Asn prolongs survival time and promotes intestinal recovery through activating PI3K/Akt pathway in intestinal epithelium. Fig. S8 Asn administration mitigates intestinal microbiota dysbiosis through phosphorylating PI3K in intestinal epithelium. Fig. S9 Oral administration of IPA prolongs survival time and restores intestinal functions through activating PDK1/Akt pathway in intestinal epithelium. Fig. S10 IPA administration mitigates intestinal microbiota dysbiosis through phosphorylating PDK1 in intestinal epithelium.

A lichen is a composite organism formed of algae or cyanobacteria that live in a mutually advantageous symbiotic relationship with the filaments (hyphae) of fungus. Three lichen samples were obtained from diverse sites at a terrestrial habitat located in Coimbatore and coastal habitats located in Kanyakumari and Nagapattinam districts of Tamil Nadu. Amplification and sequencing of 16S rRNA V3-V4 regions were used for metagenomic study. Aside from the Next-Generation Sequencing data (NGS), distinct types of lichen microbiome profiles were clearly revealed. The bacterial diversity in the lichen genera of Roccella montagnei growing in coastal and terrestrial environments was further investigated using common and unique operational taxonomic units (OTUs) and the QIIME pipeline (1.9.1). Using similarity clustering, the heat map analysis depicts the abundance information of chosen OTUs as well as the similarity and difference between OTUs and lichen samples. Using multiple methods, the alpha and beta diversity analysis revealed that there were differences in all of the samples. However, UPGMA tree inference of comparable bacterial community in coastal habitat lichen samples compared to terrestrial habitat validates their evolutionary lineage. As a result, the bacterial population associated with corticolous lichen is dependent on geographic locations, growth substrate, and climatic circumstances of similar lichen genera produced in different habitats and tree substrates.

A lichen is a composite organism formed of algae or cyanobacteria that live in a mutually advantageous symbiotic relationship with the filaments (hyphae) of fungus. Three lichen samples were obtained from diverse sites at Kuppanasamy temple, Pollachi, a terrestrial habitat located in Coimbatore, Nithiravilai, Nagercoil, and Ramarpatham, Vedaranyam, both coastal habitats located in Kanyakumari and Nagapattinam districts of Tamil Nadu, for this study. Amplification and sequencing of 16S rRNA V3 - V4 regions were used for metagenomic study. Aside from the NGS data, distinct types of lichen microbiome profiles were clearly shown. The bacterial diversity in the lichen genera of Roccella montagnei growing in coastal and terrestrial environments was further investigated using common and unique operational taxonomic units (OTUs) and the QIIME pipeline (1.9.1). By using similarity clustering, the heat map analysis depicts the abundance information of chosen OTUs as well as the similarity and difference between OTUs and lichen samples. Using multiple methods, the Alpha and Beta diversity analysis revealed that there were differences in all of the samples. However, UPGMA tree inference of comparable bacterial community in coastal habitat lichen samples compared to terrestrial habitat validates their evolutionary lineage. As a result, the bacterial population associated with corticolous lichen is dependent on geographic locations, growth substrate, and climatic circumstances of similar lichen genera produced in different habitats and tree substrates.

Rice is a major food crop cultivated around the globe. Specially scented rice varieties are of commercial importance but they are low-yielding. The rhizospheric microflora plays a significant role in improving yield and aroma. However, the core microbiome of the scented rice rhizosphere is comparatively less explored. Here, we analyzed the core microbiome associated with the rhizosphere of the scented (Ambemohar-157 and Dehradun basmati) in comparison with non-scented rice (Kolam and Arize 6444 Gold) cultivated at two different geoclimatic zones of India (Maharashtra and Uttarakhand) using the metagenomics approach. The alpha and beta diversity analysis showed that the microbial communities associated with scented and non-scented varieties significantly changes with respect to richness, diversity, and evenness. The taxonomic profiling revealed the variation in composition, diversity, and abundance of the microbiome in terms of phyla and genera associated with scented rice varieties over non-scented. The cluster analysis distinguishes the microbial communities based on their geographical positions. The core microbiome analysis revealed that scented rice rhizosphere shelters distinct and unique microbiota. 28.6 % of genera were exclusively present only in the scented rice rhizosphere. The putative functional gene annotation revealed the high abundance of genes related to the biosynthesis of 2-acetyl-1-pyrroline (2AP) precursors in scented rice. The precursor feeding analysis revealed proline as a preferred substrate by 2AP synthesizing bacteria. The 2AP precursor proline and proline metabolism genes showed a positive correlation. The scented rice-specific rhizobacteria pointed out in this study can be used as bio-inoculants for enhancing aroma, yield, and sustainable rice cultivation.

In the first few weeks of a calf's life, the early colonization of microbes throughout the gastrointestinal tract (GIT) is critical in its digestive system and immunity development. Analyses of data generated from next-generation sequencing platforms have revolutionized the understanding of host-associated microbial communities; these analyses can be done through a variety of bioinformatics pipelines. This study aimed to describe the diversity and evolution of gastrointestinal tract microbial communities in the first days of life of calves; for which we used the USEARCH and KRAKEN2 algorithms, in terms of alpha and beta diversity analysis in the rumen and jejunum contents of calves from 0, 7, 28, 42 days-born in the Mexican Tropic and its changes. The two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes. The present study revealed the changes occurring in the rumen and jejunum ecosystem in the first week of life, reflected by a decline in the phylum Proteobacteria and an increase in phylum Bacteroidetes in rumen and Firmicutes in the jejunum. We observed an increase in the similarity in the phylum taxa with age, suggesting a homogeneous and specific mature community, compared with the primary community.

Oysters are one of the main aquatic products sold in coastal areas worldwide and are popular among consumers because of their delicious taste and nutritional value. However, the microorganisms present in oysters may pose health risks to consumers. In this study, the microbial communities of Pacific oysters (Crassostrea gigas) collected from aquatic product markets in three cities (Guangzhou, Zhuhai, and Jiangmen) of Guangdong Province, China, where raw oysters are popular, were investigated. The plate counts of viable bacteria in oysters collected in the three cities were all approximately 2 log colony-forming units/g. High-throughput sequencing analysis of the V3–V4 region of the 16Sribosomal DNA gene showed a high level of microbial diversity in oysters, as evidenced by both alpha and beta diversity analysis. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla of the microorganisms present in these samples. A variety of pathogenic bacteria, including the fatal foodborne pathogen Vibrio vulnificus, were found, and Vibrio was the dominant genus. Additionally, the relationship between other microbial species and pathogenic microorganisms may be mostly symbiotic in oysters. These data provide insights into the microbial communities of retail oysters in the Guangdong region and indicate a considerable risk related to the consumption of raw oysters.

IntroductionMicrobial structure is closely associated with the initiation and development of various diseases. However, the roles of urine flora in prostate diseases, including prostate cancer (PCa) and benign prostatic hyperplasia (BPH), are still unclear.Material and methodsIn this study, clinical samples were collected from PCa (n = 21) and BPH (n = 19) patients and healthy people (n = 12). The analysis of urine flora DNA sequencing and hematological testing results between groups was performed using bioinformatic methods, including alpha and beta diversity analysis, and functional PICRUSt analysis.ResultsThe results showed that the microbial structure in PCa and BPH differed from the healthy control. Abundance of Escherichia coli was higher in PCa and BPH patients, while probiotics, such as Lactobacillus helveticus and Lactobacillus iners, were lower. Moreover, beta diversity in the PCa group was significantly different from the control group, while alpha diversity was not. Spearman analysis showed that Escherichia coli was negatively correlated with Lactobacillus helveticus and Lactobacillus iners. Functional analysis showed that microbial imbalance was associated with energy metabolism in PCa, and with cell motility, energy metabolism, and intracellular trafficking, secretion, and vesicular transport in BPH. Moreover, microbial imbalance was associated with nervous disorders and infectious diseases in PCa, and with metabolic system, infectious diseases, and signal transduction in BPH.ConclusionsTaken together, microbial imbalance may be associated with PCa and BPH. The increase of Escherichia coli was accompanied by the decrease of probiotics, such as Lactobacillus helveticus and Lactobacillus iners. These may be biomarkers for risk prediction and early treatment for prostate disease.

Oysters are one of the main aquatic products sold in coastal areas worldwide and are popular among consumers because of their delicious taste and nutritional value. However, the microorganisms present in oysters may pose health risks to consumers. In this study, the microbial communities of Pacific oysters (Crassostrea gigas) collected from aquatic product markets in three cities (Guangzhou, Zhuhai, and Jiangmen) of Guangdong Province, China, where raw oysters are popular, were investigated. The plate counts of viable bacteria in oysters collected in the three cities were all approximately 2 log colony-forming units/g. High-throughput sequencing analysis of the V3–V4 region of the 16Sribosomal DNA gene showed a high level of microbial diversity in oysters, as evidenced by both alpha and beta diversity analysis. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla of the microorganisms present in these samples. A variety of pathogenic bacteria, including the fatal foodborne pathogen Vibrio vulnificus, were found, and Vibrio was the dominant genus. Additionally, the relationship between other microbial species and pathogenic microorganisms may be mostly symbiotic in oysters. These data provide insights into the microbial communities of retail oysters in the Guangdong region and indicate a considerable risk related to the consumption of raw oysters.

Theaflavins (TFs) are the main bioactive component in black tea. At present, little effort has been done to evaluate the influence of TFs when included in the toothpaste on the diversity of oral microbiota. In this study, eighty samples collected from the saliva and supragingival plaque of 20 healthy adults using toothpaste with the absence or presence of TFs for a period of 4 weeks were used for the oral microbiome analysis by 16S rRNA gene sequencing. Alpha and beta diversity analysis showed that tooth brushing using the toothpaste with TFs significantly increased the microbial abundance in the saliva samples, and altered the oral microbiota obtained from the saliva and supragingival plaque. The linear discriminant analysis revealed that the use of toothpaste with TFs significantly reduced the abundance of oral pathogens (e.g., Prevotella, Selenomonas, and Atopobium) while increased the abundance of oral-health associated bacteria (e.g., Streptococcus and Rothia). In addition, using toothpaste with TFs reduced the functional pathways abundance relevance to the extracellular polymeric substance (EPS) synthesis while enriched the functions in transporters, ABC transporters, two-component system, and amino acid metabolism. Collectively, our results provide evidence for the application of toothpaste containing TFs as a promising oral care product. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02699-7.

Background: It has not been fully elucidated whether the change of the uterus flora is correlated to impaired fecundity. This case-control study aimed to analyze the differences in uterus microbial flora between women with post-cesarean section (CS) scar diverticulum (PCSD) (CS group) and women after vaginal delivery (control group), exploring the correlation between differentially expressed microbial flora and inflammation.Methods: Infertile women who underwent hysteroscopy were enrolled in this case-control study. The swab samples were classified into four subgroups: CS cervix group, CS endometrium group, control cervix group, and control endometrium group. The total DNA obtained from 16 women (a total of 31 samples, the cervix or endometrium) was extracted for 16S recombinant DNA (rDNA) analysis. The Luminex platform was used to detect the abundance of 34 kinds of local inflammatory cytokines in 32 endometrium samples, and the correlation between microbial flora and inflammatory cytokines was analyzed.Results: The alpha and beta diversity analysis indicated that the microbial diversity was higher in the CS group compared to the control group, especially in endometrium tissues. The heatmaps revealed that the microbial flora structure differs at each level of the phylum-class-order-family-genus among the groups. The analysis of four of the most prominently changed microbial flora revealed that Lactobacillus in the cervix was significantly higher in the control group when compared with the cesarean section group (P < 0.05). Furthermore, Proteobacteria and Neisseriaceae had a higher abundance in the CS groups, especially in the cervical tissue (P < 0.05), while Staphylococcaceae increased only in the CS endometrium tissue (P < 0.05). Next, these women were re-divided into the high- and low-Staphylococcaceae, and the abundance of 34 kinds of local inflammation cytokines was compared between groups. It was found that there was a positive correlation between Staphylococcaceae and IL-2, and a negative correlation between Staphylococcaceae and IL-8 (P < 0.05).Conclusion: The present results suggest that the disrupted uterus microbiota composition in women with CS may be closely associated with local inflammation. The interplay between the microbiota and the immune system may be linked to clinical disorders. The potential mechanisms require further exploration.

Chronic atrophic gastritis (CAG) is well-known related with multiple pathogenic factors and normally therapies comprised by western or Chinese medicines. The present study was designed to identify the bacterial community characterized by 16S rRNA amplicon sequencing and determine the modulate affection of bacterial composition response western and Chinese medicine Qinghuayin (QHY) as well as antibiotic on model rats. The result shown the overall structure alteration of bacterial appeared under medicine intervened, antibiotic caused a marked depletion in bacterial diversity and richness. The enrichments of Firmicutes (85.1-90.7%) in antibiotic-free converts into Bacteroidetes (30.7-34.6%) in antibiotic-added model rat were demonstrated. Firmicutes as the most dominant phylum in antibiotic-free treatments and significantly decreased till 21.9%-68.5% in antibiotic-added treatments. Especially QHY-treated rats showed highest RA of Firmicutes (90.7%) and the amelioration of CAG using QHY attributed by beneficial bacterial enrichment, especially Ruminococcus, Lactobacillus and Bifidobacterium. In addition, alpha and beta diversity analysis also demonstrated the clear dispersion and aggregation that revealed the alteration and steady of bacterial community structures. In summary, QHY has potential application value in the treatment of CAG, which attributed to close relation with the modulatory of internal bacterial communities.

Additional file 1: Figure S1. MiniBioReactor Array (MBRA) system and experiment outline. A: Overview of the MBRA system installed within an anaerobic chamber. B: MBRA system after inoculation and stabilization with human microbiota. C: Experimental plan used and schedule of samples collection. D: Microbiota stability after MBRA inoculation with human feces. At each time points, the number of unique OTU per 15,000 sequences is represented. Values are mean +/- S.E.M., N = 3. Figure S2. Example of the data presentation used in this study. In order to account for the high number of time points analyzed (17) during the three phases of the MBRA experiments (pre-treatment, treatment and post-treatment), data of bacterial density, alpha and beta diversity analysis of microbiota composition and pro-inflammatory potential were processed and presented as exemplified here for the Jaccard measurement of beta diversity of microbiota composition. A. Principal coordinate analysis at each individual time points. B. Histograms of Jaccard distance separating control samples from every other condition – including control themselves. C-D. These various time points were subsequently combined in a XY representation with two normalizations steps : the distance separating control samples from themselves were normalized as 1 (C) in order to account for inter-chambers and day-to-day variations, and the distance observed at the 24 h time point were normalize as 1 (D) in order to account for pre-treatment inter-chambers variations. E. Finally, area under the curve was determined for the treatment phase (72 h > 216 h) and the post-treatment phase (216 h > 274 h) in order to present, for both phases, the global impact of emulsifier exposure on microbiota composition and function. Data are the means +/- S.E.M (N = 3). *P

Gut microbes play critical roles in host nutrition, physiology, and behavior. Periplaneta americana is a famous urban pest which is widely distributed in the tropics and subtropics, but very few information is available on the gut microbiome of Periplaneta americana, particularly in its different life stages. Here, we characterized the diversity and structure of gut microbiome in eggs, nymph and adult life stages of Periplaneta americana using high-throughput 16S rRNA genes sequencing. Both the results of Alpha- and Beta-diversity analysis showed the diversity and structure of gut microbiome were significant different among the eggs, nymph and adult stages. The result of species distribution showed the predominant phyla in three life stages were Bacteroidetes , Firmicutes and Proteobacteria , but the relative abundances of these bacteria were significant different among each life stage. 1,169 operational taxonomic units were shared by three stages, which indicating the gut microbiome may be inherited to offspring from parents of Periplaneta americana. According to the prediction of functional genes in metabolic pathways, most of them were distributed in the metabolic pathways of basic physiology such as nutrition, growth, development and immunity, etc. The relative abundances of functional genes in metabolic pathways were significant different among life stages of Periplaneta americana, indicating the gut microbiome might play an important role in the physiology across its different life stages. This study revealed the diversity and structure of gut microbiome in different life stages of Periplaneta americana, which may contribute to us to understand it’s physiology and behaviors.

16S rRNA gene sequencing is a cost-effective method for profiling the bacterial component of a microbiome. Nevertheless, processing and analysis of the resulting sequencing data is often constrained by the availability of dedicated bioinformaticians - creating a bottleneck for biological interpretation. Multiple visualisation and analysis tools now exist for downstream analysis of 16S rRNA data. These tools are designed with biological scientists in mind and therefore consist of a graphical user interface that interacts with taxonomic counts tables to perform tasks such as alpha- and beta-diversity analysis and differential abundance. However, generating the input to these applications still relies on bioinformatics experience, creating a disconnect between data processing and data analysis. We aimed to bridge the gap between data processing and data analysis. To do this we have created two tools - OCMS_16S and OCMSlooksy - that perform data processing and data visualisation/analysis, respectively. OCMS_16S is a cgat-core based pipeline that wraps DADA2 functionality in order to facilitate processing of raw sequence reads into tables of amplicon sequence variant (ASV) counts using a simple command line interface. OCMSlooksy is an RShiny application that takes an OCMS_16S-generated SQLite database as input to facilitate data exploration and analysis. Combining these tools provides a simple, user-friendly workflow to facilitate 16S rRNA gene amplicon sequencing data analysis from raw reads to results.

Organic farming can increase the diversity of soil bacterial. This research aimed to compare the profile of microbial community of organic and conventional rice fields in early (0 Day After Planting/DAP), mid (15 DAP), and late (45 DAP) fertilizer application period. The total DNA genome from the soil sample was extracted then analyzed metagenomically using Next Generation Sequencing (NGS). There was nine genus of bacteria found in high relative abundance, 95.28%, while 4.72% included in Domain of Archaea (genus Methanosaeta). Phylum of Firmicutes (genus Clostridium has 24.50% relative abundance, Bacillus 11.90%, Lactobacillus 9.69%); Proteobacteria (genus Defluviicoccus 12.10%, Buchnera 18.46%, Rosenbergiella 2.46%); and Actinobacteria (genus Nocardioides 12.21%, and Streptomyces 3.96%). Meanwhile, the average plant height of organic rice fields was shorter than conventional rice fields got directly measured coincided with soil sampled. Based on alpha and beta diversity analysis, the highest community diversity and abundance were found in organic rice field soil samples taken at 45 DAP, i.e., at the end of the fertilizer application period. However, in both organic and conventional rice field soils, there was almost no significant difference in the bacterial community, so it impacts that organic and conventional systems do not make a real difference in the total N, P available, CEC, and pH values. It makes a significant difference in organic C and organic matters.

Projected population growth and climate change will make it inevitable to convert neglected and marginal land into productive arable land. We investigate the influence of agricultural management practices on nutrient stocks and soil functions during the conversion of former extensively used grassland to arable land. Effects of grassland removal, tillage, intercropping with faba bean (Vicia faba) and its later incorporation were studied with respect to soil properties and bacterial community structure. Therefore, composite samples were collected with a core sampler from the topsoil (0–20 cm) in (a) the initial grassland, (b) the transitional phase during the vegetation period of V. faba, (c) after ploughing the legume in, and (d) untreated controls. In all samples, nitrate-N, ammonium-N, dissolved organic carbon (DOC) and total nitrogen bound (TNb) were analyzed and comparisons of the bacterial community structure after 16S-amplicon sequencing were performed to assess soil functions. Mineralization after grassland conversion followed by the biological nitrogen fixation of broad beans enhanced the nitrate-N content in bulk soil from 4 to almost 50 μg N g−1 dw. Bacterial community structure on phylum level in bulk soil was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes and remained almost stable. However, alpha and beta-diversity analysis revealed a change of the bacterial composition at the final state of the conversion. This change was primarily driven by increasing abundances of the genera Massilia and Lysobacter, both members of the Proteobacteria, after the decay of the leguminous plant residues. Furthermore, increasing abundances of the family Gaiellaceae and its genus Gaiella fostered this change and were related to the decreasing carbon to nitrogen ratio. In short, gentle management strategies could replace the input of mineral fertilizer with the aim to contribute to future sustainable and intensified production even on converted grassland.

The purpose of this study is to compare the microbiological results of debridement bone samples with those of corresponding results of operation bone samples for patients with diabetic foot osteomyelitis, using 16s rRNA high-throughput sequencing approach. We prospectively recruited 24 diabetic foot patients with osteomyelitis, and obtained 9 bone samples during surgery(Ds-Group) and 16 bone samples from debridement(Dd-Group). We compared the differences between debridement and operation procedures based on microbiological study of bone samples via 16s rRNA sequencing, using Ion PGM™ System Sequencer. It was obvious that microbes in Ds-Group, with narrower distribution, were more stable in alpha and beta diversity analysis. As for genera, totally 14 dominant genera were separated, and the average of Ds-Group and Dd-Group were respectively 10.44 and 9.44, with no statistically significant difference(P>0.05). Halomonas spp. and Prevotella spp. were the predominant genera of Ds-Group and Dd-Group respectively. Ds-Group had significant more Anaerococcus spp., Dialister spp. and Pseudomonas spp. than Dd-Group(P0.05). We might draw a conclusion that though surgical operation was a little bit more accurate than debridement, microbiological study of bone samples from debridement could be capable enough for the diagnosis and treatment guidance of diabetic foot osteomyelitis. Disclosure M. Zou: None. P. Hu: None. Y. Pan: None. X. Luo: None. Y. Jiang: None. Y. Xue: None. Y. Cao: None. F. Gao: None.

Purpose: Fluoroquinolone-resistant (FQR) Escherichia coli causes transrectal prostate biopsy infections. In order to reduce colonization of these bacteria in carriers, we would like to understand the surrounding microbiome to determine targets for decolonization. Materials and Methods: We perform an observational study to investigate the microbiome differences in men with and without FQR organisms found on rectal culture. A rectal swab with two culturettes was performed on men before an upcoming prostate biopsy procedure as standard of care to perform “targeted prophylaxis.” Detection of FQR was performed by the standard microbiology lab inoculates the swab onto MacConkey agar containing ciprofloxacin. The extra swab was sent for 16S rRNA amplicon sequencing (MiSeq paired-end) using the V1V2 primer. Alpha and beta-diversity analysis were performed using QIIME. We used PERMANOVA to evaluate the statistical significance of beta-diversity distances within and between groups of interest. Results: We collected 116 rectal swab samples before biopsy for 16S rRNA amplicon sequencing. We identified 18 isolates (15.5%, 18/116) that were positive and had relative reduced diversity profiles (p