Bacterial 16S rDNA Sequences Research Articles

Microbial communities in rural and urban homes and their relationship to surrounding land use, household characteristics, and asthma status

The relationships between the microbial communities that develop within homes and local outdoor features, household conditions and respiratory health outcomes are not well understood. In this study, high-throughput bacterial 16S and fungal ITS rDNA sequencing were coupled with a quantitative, GIS-based land use approach in a sample of 95 homes in adjacent urban and rural areas to investigate how local land use features surrounding homes relate to the home microbiome. Bacterial richness was higher in homes surrounded by less development while fungal richness was higher in homes surrounded by more development. Home mycobiomes in less developed areas were enriched with crop-associated taxa whereas in more developed areas human-associated bacterial taxa and wood decaying fungal taxa predominated. Not all vegetation had the same effect on the home microbiome and distinct differences were observed between bacterial and fungal communities, and the distance between home and vegetation. Crops and tree coverage were strongly related to indoor mycobiomes due to the abundance of crop-related taxa and wood decaying taxa, respectively. Regarding asthma, the microbiomes in homes with asthmatic children had greater bacterial diversity and lower fungal diversity compared to homes without asthmatic children. In addition, ‘protective’ taxa were enriched in non-asthmatic homes. The buffer-based approach used for quantitatively categorizing land use and development levels around homes identified specific outdoor environmental factors that affect the indoor microbiomes in urban and rural homes. The study also supports the growing body of scientific evidence that the indoor microbiome can affect health outcomes such as childhood asthma.

Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome?

Soil microbiota underpin ecosystem functionality yet are rarely targeted during ecosystem restoration. Soil microbiota recovery following native plant revegetation can take years to decades, while the effectiveness of soil inoculation treatments on microbiomes remains poorly explored. Therefore, innovative restoration treatments that target soil microbiota represent an opportunity to accelerate restoration outcomes. Here, we introduce the concept of ecological phage therapy-the application of phage for the targeted reduction of the most abundant and dominant bacterial taxa present in degraded ecosystems. We propose that naturally occurring bacteriophages-viruses that infect bacteria-could help rapidly shift soil microbiota towards target communities. Bacteriophages sculpt the microbiome by lysis of specific bacteria, and if followed by the addition of reference soil microbiota, such treatments could facilitate rapid reshaping of soil microbiota. Here, we experimentally tested this concept in a pilot study. We collected five replicate pre-treatment degraded soil samples, then three replicate soil samples 48 hours after phage, bacteria, and control treatments. Bacterial 16S rDNA sequencing showed that phage-treated soils had reduced bacterial diversity; however, when we combined ecological phage therapy with reference soil inoculation, we did not see a shift in soil bacterial community composition from degraded soil towards a reference-like community. Our pilot study provides early evidence that ecological phage therapy could help accelerate the reshaping of soil microbiota with the ultimate aim of reducing timeframes for ecosystem recovery. We recommend the next steps for ecological phage therapy be (a) developing appropriate risk assessment and management frameworks, and (b) focussing research effort on its practical application to maximise its accessibility to restoration practitioners.

Microalgae-bacteria consortia for the treatment of raw dairy manure wastewater using a novel two-stage process: Process optimization and bacterial community analysis

The major objective of this study was to develop a functional microalgae-bacteria consortium for the treatment of dairy manure wastewater (DMW). Chlorella sorokiniana AK-1 was selected as the proficient microalgal strain for treating unsterilized DMW. AK-1 was directly grown in 50% raw DMW, and the addition of an acclimated mixed bacterial culture enriched from dairy manure improved treatment efficiency. Culture conditions for DMW treatment using the AK-1 mixed bacterial consortium were optimized as follows: 50% raw DMW, 0.4 g/L mixed bacterial inoculum on day 1, followed by 0.1 g/L AK-1 inoculum on day 3, and further incubation for 3 days. The achieved removal efficiencies for COD, BOD, TN, NH3-N, and TP were 84.3%, 97.8%, 90.2%, 99.1%, and 100%, respectively. Bacterial 16S rDNA sequencing was conducted to analyze the shift in the bacterial community during wastewater treatment. In DMW, Firmicutes emerged as the dominant phylum, whereas Proteobacteria took over after microalgal inoculation. Additionally, Actinobacteria and Bacteroidetes were consistently present in all samples. Interestingly, Patescibacteria and Planctomycetes were found in varying proportions. At the species level, the predominant bacteria identified during the treatment process were Rhizobiaceae, Sericytochromatia_unclassified, Pirellula_sp, Owenweeksia, Devosia_unclassified, Acinetobacter_towneri, and Acinetobacter_unclassified. Despite the significant diversity of the microbial community among the different processes, optimal microalgal biomass production and maximum nutrient removal efficiencies were achieved using this designer microalgae-bacteria consortium.

Endophytic bacteria improve jute growth through induction of phytohormones-related gene expression

Plants coexist with complex populations of microorganisms, including Plant Growth-Promoting Rhizobacteria (PGPR). PGPR bacteria help in plant development by secreting numerous plan growth-promoting compounds like IAA, gibberellin, siderophore, and cytokinin. They also provide resistance to plants against different pathogens. Jute fibre is the second most important fibre next to cotton, obtained from the bark of plant through microbial retting process. Hence, increased plant growth means increased bark i.e., increased fibre. This study aims to identify the molecular, physiological and growth promotion characteristics of non-rhizobial bacterial specie from the surface-sterilized root of healthy and biotic stressed (nematode-infested) jute (Corchorus capsularis; Corchorus olitorius and an advanced variety of C. olitorius, Robi-1). We have identified 62 culturable bacterial isolates from healthy and nematode-infected jute plant using bacterial 16S rDNA sequencing. All the isolates were distributed to Bacillus, Staphylococcus and Ensifer genera, respectively. B. cereus, S. hominis and a consortium increased the growth phenotype (Root length, shoot length, germination rate, root and shoot biomass) of C. capsularis (CVL-1), C. olitorius (O-9897), and an advanced variety of C. olitorius (Robi-1), respectively. Increased expression (qRT-PCR analysis) of growth hormones GA-20 and GA-03 oxidase corroborates plant growth induction by increased production of the growth hormone gibberellin. Taken together, our results suggest that plant-growth promotion by endophytic bacteria may involve the increased expression of growth hormone gibberellin and nutrient uptake. B. cereus and S. hominis having plant growth-promoting traits could be useful in sustainable agriculture practice.

Measurement of lactate in pleural fluid rapidly identify infection and guide therapy

Background Measurements of pleural fluid biomarkers for rapid identification of complicated parapneumonic effusion (CPPE) are crucial for optimal management. Previous studies for biomarker evaluation were however based on pleura culture, not modern DNA technique. Lactate has not been thoroughly studied earlier as a potential biomarker in this regard. Objectives To evaluate whether the routine biomarkers pH, glucose, lactate dehydrogenase (LDH) measured in pleural fluid in a microbiological well characterised cohort could differentiate simple parapneumonic effusion (SPPE) from CPPE and if pleural fluid lactate could be of additional use in this discrimination. Methods Pleural fluid prospectively collected from adult patients (n = 112) with PPE admitted to the Departments of Infectious Diseases (DIDs) at four Stockholm County hospitals were characterised microbiologically with bacterial culture and 16S rDNA sequencing, and biochemically with pH, glucose, LDH and lactate. Results Forty and seventy two patients were categorised as SPPE/CPPE. The median values between SPPE/CPPE differed significantly for all biomarkers with varying overlap. Receiver operating characteristics (ROC) curves showed the area under the curve (AUC) for pH 0.905 (CI 0.847–0.963), glucose 0.861 (CI 0.79–0.932), LDH 0.917 (CI 0.860–0.974) and lactate 0.927 (CI 0.877–0.977), corresponding to best cut-off levels and sensitivity/specificity for pH of 7.255, 0.819/0.9, glucose 5.35 mmol/L, 0.847/0.775, LDH 9.8 µcat/L, 0.905/0.825 and lactate 4.9 mmol/L, 0.875/0.85. Conclusions To distinguish between SPPE/CPPE, pH and LDH performed well, but optimal cut-off values differed from earlier established recommendations. Pleura lactate had the largest AUC of the investigated biomarkers and may be used in the analyses of PPE-staging.

1725P Metastasis-resident bacteria in advanced hormone receptor-positive breast cancer are related to primary tumor microbiota and show distinct composition

Tumor-resident bacteria are an emerging component of the tumor microenvironment. Recent studies have shown their presence over multiple cancer types. Lately, mechanistic evidence in a murine breast cancer model indicates that these bacteria promote the metastatic process. However, the presence and conformation of the microbiome of human metastatic tumors have not been determined. Here, we characterized tumor-resident bacteria in a cohort of metastatic hormone receptor-positive breast cancer (MHRBC) patients with matched primary tumors. We performed bacterial 16S rDNA sequencing targeting hypervariable regions V2-4 and V6-9 on FFPE tissues from 40 patients with MHRBC and their matched primary tumors. Sequence data were processed using high resolution sample inference with DADA2. Controls included normal breast tissue, paraffin from all blocks and a simulated bacterial community, comprising known intra and extracellular bacteria. Taxonomy was assigned using the SILVA database v138. Feature selection was used to determine amplicon sequences in primary tumors related to their metastasis. A machine learning classifier was generated to predict the metastatic site from selected amplicons. α-diversity was similar among sample types, while β-diversity showed segregation between metastatic and primary tumors. Alphaproteobacteria, Gammaproteobacteria and Bacilli had increased relative abundance across metastatic and primary tumors. Differential abundance of Proteobacteria and Firmicutes species was identified in metastatic tumors. A machine learning classifier using the 5 top ranked amplicons in primary tumors was capable of 100% precision and high recall for prediction of bone and liver metastatic site, but not lung metastases. We identified and categorized the tumor-resident bacteria of MHRBC. To our knowledge, this is the first study looking at the composition of metastatic breast cancer microbiome. While insights have been gained on primary tumor microbiota, the role of metastasis-resident bacteria including local immunity and treatment resistance warrants further study.

Metabarcoding of organic tea (Camellia sinensis L.) chronosequence plots elucidates soil acidification-induced shifts in microbial community structure and putative function

Tea (Camellia sinensis L.) agroecosystem soil acidification (TASA) is occurring at epidemic rates relative to other crops, however TASA remains poorly defined in its pathogenesis and effects on soil microbiota. The present study examined bulk soil physicochemical and bacterial 16S rDNA sequence data to elucidate TASA-associated changes through 10 tea agroecosystem sites, including an organic-certified tea field chronosequence of 3-year- (Young), 8-year- (Middle), and 13-year-old (Old) plots. Soil pH declined linearly with age through chronosequence plots. Hierarchical clustering based on community β-diversity revealed a tipping point in community composition as soil acidified below pH 4.5, which had occurred between Middle and Old plots. Tipping point-associated changes in predicted community functionality included a precipitous decline in nitrogenase-encoding communities and concurrent proliferations of Al-detoxifiers, anti-oxidative specialists, and pathogen virulence factor-encoding communities. PERMANOVA modeling revealed that Streptomyces was the genus with population abundance corresponding most significantly with whole microbiome composition at both OTU- (r2 = 0.460, p < 0.001) and genus-levels (r2 = 0.512, p < 0.001), despite ranking 74th in total abundance among 186 core genera, providing computationally-modeled evidence of a keystone role of Streptomyces under tea agroecosystem conditions. Correlations of soil pH with Rhizobiales (r = 0.713, p < 0.001), Acidibacter (r = −0.717, p < 0.001), and predicted β-glucosidase-encoding communities (r = −0.622, p < 0.001) across all samples indicated potential utility as community-level TASA biomarkers. Moreover, two phylogenetically diverse OTU co-abundance modules also corresponded (p < 0.01) with soil pH across all samples, suggesting that TASA-induced shifts were interfaced by networks of diverse and interactive taxa, or keystone guilds. Presently, organic management per se was unable to retain soil pH within the optimal range for tea plant cultivation (pH 4.5–5.5), therefore additional considerations not currently encompassed by organic management guidelines, such as lower tea planting density, may be necessary to avoid the detrimental effects of soil acidification described above. Moreover, future studies may seek to further elucidate the keystone functions of Streptomyces spp. under tea agroecosystem conditions.

Comparison of ready-to-eat "organic" antimicrobials, sodium bisulfate, and sodium lactate, on Listeria monocytogenes and the indigenous microbiome of organic uncured beef frankfurters stored under refrigeration for three weeks.

Listeria monocytogenes has been implicated in several ready-to-eat (RTE) foodborne outbreaks, due in part to its ability to survive under refrigerated conditions. Thus, the objective of this study was to evaluate the effects of sodium bisulfate (SBS), sodium lactate (SL), and their combination as short-duration antimicrobial dips (10-s) on L. monocytogenes and the microbiome of inoculated organic frankfurters (8 Log10 CFU/g). Frankfurters were treated with tap water (TW), SBS0.39%, SBS0.78%, SL0.78%, SL1.56%, SBS+SL0.39%, SBS+SL0.78%. In addition, frankfurters were treated with frankfurter solution water (HDW)+SBS0.78%, HDW+SL1.56%, and HDW+SBS+SL0.78%. After treatment, frankfurters were vacuum packaged and stored at 4°C. Bacterial enumeration and 16S rDNA sequencing occurred on d 0, 7, 14, 21. Counts were Log10 transformed and calculated as growth potential from d 0 to d 7, 14, and 21. Data were analyzed in R using mixed-effects model and One-Way ANOVA (by day) with differences separated using Tukey’s HSD at P ≤ 0.05. The 16S rDNA was sequenced on an Illumina MiSeq and analyzed in Qiime2-2018.8 with significance at P ≤ 0.05 and Q ≤ 0.05 for main and pairwise effects. An interaction of treatment and time was observed among the microbiological plate data with all experimental treatments reducing the growth potential of Listeria across time (P < 0.0001). Efficacy of treatments was inconsistent across time; however, on d 21, SBS0.39% treated franks had the lowest growth potential compared to the control. Among diversity metrics, time had no effect on the microbiota (P > 0.05), but treatment did (P < 0.05). Thus, the treatments potentially promoted a stable microbiota across time. Using ANCOM, Listeria was the only significantly different taxa at the genus level (P < 0.05, W = 52). Therefore, the results suggest incorporating SBS over SL as an alternative antimicrobial for the control of L. monocytogenes in organic frankfurters without negatively impacting the microbiota. However, further research using multiple L. monocytogenes strains will need to be utilized in order to determine the scope of SBS use in the production of RTE meat.

Hyaluronic Acid-Melatonin Nanoparticles Improve the Dysregulated Intestinal Barrier, Microbiome and Immune Response in Mice with Dextran Sodium Sulfate-Induced Colitis.

Although the cause of inflammatory bowel disease (IBD) is unclear, current studies have found that the main factors involved in its pathogenesis include imbalance of mucosal immune response, intestinal dysbiosis, and destruction of the intestinal barrier. We synthesized an amphiphilic conjugate of hyaluronic acid (HA) and melatonin (MT), which have established immunomodulatory and antioxidant properties, by stimulating their nano-aggregation. Inducing colitis by dextran sodium sulfate (DSS), HA-MT accumulated in the inflamed colon epithelium of colitis mice, and markedly improved the colitis symptoms, repaired the damaged intestinal barrier and inhibited colon inflammation. In addition, through bacterial 16S rDNA sequencing, it was found that HA-MT can restore the ratio of Firmicutes/Bacteroidetes by increasing the overall microbial richness and diversity, and alleviate the intestinal dysbiosis of mice with colitis. In the analysis of the intestinal flora at the species level, the abundance of Lactobacillus increased in colitis mice treated with HA-MT while that of Bacteroides, Blautia and Streptococcus decreased in the colitis mice treated with HA-MT. Our findings suggest that the HA-MT system is a promising prebiotic, which can relieve the symptoms of IBD by regulating the intestinal microflora and restoring intestinal homeostasis, inhibiting inflammation.

Cadmium exposure modulates the gut-liver axis in an Alzheimer\u2019s disease mouse model

The human Apolipoprotein E4 (ApoE4) variant is the strongest known genetic risk factor for Alzheimer’s disease (AD). Cadmium (Cd) has been shown to impair learning and memory at a greater extent in humanized ApoE4 knock-in (ApoE4-KI) mice as compared to ApoE3 (common allele)-KI mice. Here, we determined how cadmium interacts with ApoE4 gene variants to modify the gut-liver axis. Large intestinal content bacterial 16S rDNA sequencing, serum lipid metabolomics, and hepatic transcriptomics were analyzed in ApoE3- and ApoE4-KI mice orally exposed to vehicle, a low dose, or a high dose of Cd in drinking water. ApoE4-KI males had the most prominent changes in their gut microbiota, as well as a predicted down-regulation of many essential microbial pathways involved in nutrient and energy homeostasis. In the host liver, cadmium-exposed ApoE4-KI males had the most differentially regulated pathways; specifically, there was enrichment in several pathways involved in platelet activation and drug metabolism. In conclusion, Cd exposure profoundly modified the gut-liver axis in the most susceptible mouse strain to neurological damage namely the ApoE4-KI males, evidenced by an increase in microbial AD biomarkers, reduction in energy supply-related pathways in gut and blood, and an increase in hepatic pathways involved in inflammation and xenobiotic biotransformation.

Microbial Response to Fungal Infection in a Fungus-Growing Termite, Odontotermes formosanus (Shiraki).

The crosstalk between gut microbiota and host immunity has emerged as one of the research foci of microbiome studies in recent years. The purpose of this study was to determine how gut microbes respond to fungal infection in termites, given their reliance on gut symbionts for food intake as well as maintaining host health. Here, we used Metarhizium robertsii, an entomopathogenic fungus, to infect Odontotermes formosanus, a fungus-growing termite in the family Termitidae, and documented changes in host gut microbiota via a combination of bacterial 16S rDNA sequencing, metagenomic shotgun sequencing, and transmission electron microscopy. Our analyses found that when challenged with Metarhizium, the termite gut showed reduced microbial diversity within the first 12 h of fungal infection and then recovered and even surpassed pre-infection flora levels. These combined results shed light on the role of gut flora in maintaining homeostasis and immune homeostasis in the host, and the impact of gut flora dysbiosis on host susceptibility to infection.

Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava (Manihot esculenta Crantz) Genotypes.

Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.

Dihydromyricetin improves DSS-induced colitis in mice via modulation of fecal-bacteria-related bile acid metabolism

Recent studies show that the nutraceutical supplement dihydromyricetin (DHM) can alleviate IBD in murine models by downregulating the inflammatory pathways. However, the molecular mechanistic link between the therapeutic efficiency of DHM, gut microbiota, and the metabolism of microbial BAs remains elusive. In this study, we explored the improvement of DHM on the dysregulated gut microbiota of mice with dextran sulfate sodium (DSS)-induced colitis. We found that DHM could markedly improve colitis symptoms, gut barrier disruption, and colonic inflammation in DSS-treated mice. In addition, bacterial 16S rDNA sequencing assay demonstrated that DHM could alleviate gut dysbiosis in mice with colitis. Furthermore, antibiotic-mediated depletion of the gut microflora and fecal microbiome transplantation (FMT) demonstrated that the therapeutic efficiency of DHM was closely associated with gut microbiota. BA-targeted metabolomics analysis revealed that DHM restored the metabolism of microbial BAs in the gastrointestinal tract during the development of colitis. DHM significantly enriched the proportion of the beneficial Lactobacillus and Akkermansia genera, which were correlated with increased gastrointestinal levels of unconjugated BAs involving chenodeoxycholic acid and lithocholic acid, enabling the BAs to activate specific receptors, such as FXR and TGR5, and maintaining intestinal integrity. Taken together, DHM could alleviate DSS-induced colitis in mice by restoring the dysregulated gut microbiota and BA metabolism, leading to improvements in intestinal barrier function and colonic inflammation. Increased microbiota-BAs-FXR/TGR5 signaling may be the potential targets of DHM in colitis. Therefore, our findings provide novel insights into the development of novel DHM-derived drugs for the management of IBD.

Evidence for Differentiation of Colon Tissue Microbiota in Patients with and without Postoperative Hirschsprung's Associated Enterocolitis: A Pilot Study.

PurposeTo investigate the differences in the colon microbiota composition of Hirschsprung's disease (HSCR) patients with and without a history of postoperative Hirschsprung's associated enterocolitis (HAEC).MethodsColon tissue microbiota was characterized by bacterial deoxyribonucleic acid (DNA) extraction and 16S rDNA sequencing for taxonomic classification and comparison.ResultsThe sequence diversity richness within samples was significantly higher in samples from patients with a history of postoperative HAEC. We observed an increased relative abundance of the phyla Bacteroidetes, Firmicutes and Cyanobacteria in HAEC patients and Fusobacteria, Actinobacteria and Proteobacteria in HSCR patients and, an increased relative abundance of the genera Dolosigranulum, Roseouria and Streptococcus in HAEC patients and Propionibacterium and Delftia in HSCR patients.ConclusionOur findings provide evidence that the colon tissue microbiota composition is different in HSCR patients with and without postoperative HAEC.

Investigation of microbial composition and functional characterization of Zangqu using high throughput sequencing

Zangqu is a saccharifying starter used in the production of highland barley wine, which is a traditional Chinese liquor. The objective of this study was to explore microbial composition and function of Zangqu. 16 Zangqu samples were collected from seven different locations in Tibet were analyzed microbial communities using high throughput sequencing technology. The sequenceing analysis revealed 1 340 734 fungal Internal Transcribed Spacer (ITS) reads and 737 185 high quality bacterial 16S rDNA sequences, which were used for taxonomic classification. A total of four fungal and six bacterial phyla were predominantly present in Zangqu samples. Saccharomycopsis, Rhizopus, and Aspergillus were the most abundantly present fungal genera, and Lactobacillus and Leuconostoc were the most abundantly present bacterial genera. The saccharifying ability and protease activity are widely used to evaluate the quality of Zangqu. 57 strains were isolated from all samples using traditional culture medium screening method, as well as molecular biological analysis. Rhizopus oryzaeM12 had the highest saccharifying ability, which was 1382 ± 77.38 mg/g min.Bacillus amyloliquefaciensQ4 had the highest protease activity, which was 1035.56 ± 40.09 μg/g min. We hope that our research analysis can provide statistical support for establishing microbial database and for screening of functional microorganisms.

The Diversity and Geographic Distribution of Cultivable Bacillus-Like Bacteria Across Black Soils of Northeast China.

Bacillus-like species are gram-positive bacteria that are ubiquitous in soils. Many of Bacillus-like bacteria are demonstrated as beneficial microbes widely used in industry and agriculture. However, the knowledge related to their diversity and distribution patterns in soils is still rudimentary. In this study, we developed a combined research method of using culture-dependent and high-throughput sequencing to investigate the composition and diversity of cultivable Bacillus-like bacterial communities across 26 soil samples obtained from the black soil zone in northeast China. Nearly all bacterial 16S rDNA sequences were classified into the order Bacillales. Fifteen genera were detected, with Bacillus, Paenibacillus, and Brevibacillus being the three most abundant genera. Although more than 2,000 OTUs were obtained across all samples, 33 OTUs were confirmed as the abundant species with a relative abundance over 5% in at least one sample. Pairwise analysis showed that the diversity of Bacillus-like bacterial communities were significantly and positively correlated with soil total carbon contents and soil sampling latitudes, which suggests that a latitudinal gradient diversity of Bacillus-like bacterial communities exists in the black soil zone. The principal coordinates analysis revealed that the Bacillus-like bacterial communities were remarkably affected by soil sampling latitudes and soil total carbon content. In general, this study demonstrated that a distinct biogeographic distribution pattern of cultivable Bacillus-like bacterial communities existed in the black soil zone, which emphasizes that the strategy of local isolation and application of beneficial Bacillus-like strains is rather important in black soil agriculture development.

Characterization of Bacterial Community Associated with Four Organs of the Yesso Scallop (Patinopecten yessoensis) by High-Throughput Sequencing

We used Illumina high-throughput sequencing of PCR-amplified V3-V4 16S rRNA gene regions to characterize bacterial communities associated with the adductor muscles, gills, gonads and intestines of the Yesso scallop (Patinopecten yessoensis) from waters around Zhangzidao, Dalian, China. Overall, 421,276 optimized reads were classified as 25 described bacterial phyla and 308 genera. Firmicutes, Proteobacteria, Tenericutes, Bacteroidetes, Chlamydiae and Spirochaetae accounted for > 97% of the total reads in the four organs. The bacterial 16S rDNA sequences assigned to Firmicutes and Proteobacteria were abundant in the adductor muscles, gills and gonads; while reads from Tenericutes were dominant in the intestines, followed by those from Firmicutes, Chlamydiae, Proteobacteria and Bacteroidetes. At the genus level, the dominant genera in the adductor muscles, gills and gonads appeared to be Bacillus, Enterococcus and Lactococcus, whereas Mycoplasma was dominant in the intestines. The relative abundances of Bacillus, Enterococcus, Lactococcus, Alkaliphilus, Raoultella, Paenibacillus and Oceanobacillus were significantly lower in the intestine than in the other three organs. Cluster analysis and principal coordinates analysis of the operational taxonomy units profile revealed significant differences in the bacterial community structure between the intestine and the other three organs. Taken together, these results suggest that scallops have intestine-specific bacterial communities and the adductor muscles, gills and gonads harbor similar communities. The difference in the bacterial community between organs may relate to unique habitats, surroundings, diet and their respective physiological functions.

Screening of Rice Endophytic Biofertilizers with Fungicide Tolerance and Plant Growth-Promoting Characteristics

The application of pesticides is unavoidable in conventional agricultural practice. To develop effective biofertilizers, bacterial strains with both pesticide tolerance and plant growth-promoting (PGP) traits were isolated for further testing. Seedlings of rice (Oryza sativa) were planted in soil with 1, 5, or 10 times the recommended rates of the fungicides etridiazole, metalaxyl, and tricyclazole. Endophytic bacteria were isolated from roots of rice seedlings. The bacterial 16S rDNA sequences and related PGP characteristics including potential nitrogen fixation, phosphorus-solubilizing and indole acetic acid (IAA) production ability were further examined. In all, 17 different strains were obtained from rice seedling roots; five strains with both nitrogen fixation potential and IAA production ability included Rhizobium larrymoorei E2, Bacillus aryabhattai E7, Bacillus aryabhattai MN1, Pseudomonas granadensis T6, and Bacillus fortis T9. Except for T9, all strains could tolerate two or more fungicides. We inoculated rice roots with the endophytic bacteria and all conferred rice growth-promoting ability. Bacillus aryabhattai MN1 was further tested and showed high tryptophan dose-dependent IAA production ability, tolerance towards etridiazole and metalaxyl application and should be considered a potential bacterial biofertilizer.

Conjunctival microbiome changes associated with fungal keratitis: metagenomic analysis.

To investigate the ocular surface microbiome profile of patients with fungal keratitis (FK) through bacterial 16S rDNA sequencing. The swab samples were collected from 8 patients with FK (Group 1 from the corneal ulcer, Group 2 from the conjunctival sac of the infected eyes, and Group 3 from the conjunctival sac of the fellow eyes) and 10 healthy eyes (Group 4 from the conjunctival sac). Bacterial 16S rDNA V4-V5 region sequencing was performed to characterize the bacterial communities on the ocular surfaces of the patients with FK. Our metagenomic data showed that 97% of the sequence reads were categorized into 245 distinct bacterial genera, with 67.75±7.79 genera detected in Group 1, 73.80±13.44 in Group 2, 74.57±14.14 in Group 3, and 89.60±27.49 in Group 4. Compared with the healthy eyes (Group 4), both infected (Groups 1 and 2) and fellow eyes (Group 3) of the patients with FK showed reduced bacterial diversity and altered ocular surface microbiota compositions, with lower abundance of Corynebacterium and Staphylococcus and higher abundances of Pseudomonas, Achromobacter, Caulobacter and Psychrobacter. Our report depicts the altered ocular surface bacterial community structures both in the affected and fellow eyes of patients with FK. These changes may contribute to the pathogenesis of FK or the increased risk for FK.

Fecal Bacterial Communities in Insectivorous Bats from the Netherlands and Their Role as a Possible Vector for Foodborne Diseases

Bats are commonly regarded as vectors for viruses, but little is known about bacterial communities in bats and the possible role of bats in the transmission cycle of foodborne diseases. To gain more insight, microbial communities in fecal samples from 37 insectivorous bats of different species from the Netherlands were investigated by polymerase chain reaction and denaturant gradient gel electrophoresis (PCR-DGGE). Subsequently, 10 samples from the following bat species: common pipistrelle (Pipistrellus pipistrellus; n = 3), Daubenton's bat (Myotis daubentonii; n = 3), serotine bat (Eptesicus serotinus; n = 1), whiskered bat (Myotis mystacinus; n = 1), Geoffroy's bat (Myotis emarginatus; n = 1) and Natterer's bat (Myotis nattereri; n = 1) were selected and used in bacterial 16S rDNA cloning and sequencing. The fecal microbiota in bats was found to be diverse with predominant bacterial genera Carnobacterium, Serratia, Pseudomonas, Enterococcus and Yersinia. The presence of opportunistic pathogens Citrobacter freundii, Escherichia coli, Enterococcus faecalis, Serratia fonticola and Rahnella aquatilis was also recorded. Based on cloning results, we found no proof that bats in the Netherlands are a major vector for the transmission of bacterial zoonotic diseases, although previous findings in literature reported isolation of foodborne pathogens from bats.