Relative Abundance Of Specific Taxa Research Articles

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication.

BackgroundPremastication, the transfer of pre-chewed food, is a common infant and young child feeding practice among the Tsimane, forager-horticulturalists living in the Bolivian Amazon. Research conducted primarily with Western populations has shown that infants harbor distinct oral microbiota from their mothers. Premastication, which is less common in these populations, may influence the colonization and maturation of infant oral microbiota, including via transmission of oral pathogens. We collected premasticated food and saliva samples from Tsimane mothers and infants (9–24 months of age) to test for evidence of bacterial transmission in premasticated foods and overlap in maternal and infant salivary microbiota. We extracted bacterial DNA from two premasticated food samples and 12 matched salivary samples from maternal-infant pairs. DNA sequencing was performed with MiSeq (Illumina). We evaluated maternal and infant microbial composition in terms of relative abundance of specific taxa, alpha and beta diversity, and dissimilarity distances.ResultsThe bacteria in saliva and premasticated food were mapped to 19 phyla and 400 genera and were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The oral microbial communities of Tsimane mothers and infants who frequently share premasticated food were well-separated in a non-metric multi-dimensional scaling ordination (NMDS) plot. Infant microbiotas clustered together, with weighted Unifrac distances significantly differing between mothers and infants. Infant saliva contained more Firmicutes (p < 0.01) and fewer Proteobacteria (p < 0.05) than did maternal saliva. Many genera previously associated with dental and periodontal infections, e.g. Neisseria, Gemella, Rothia, Actinomyces, Fusobacterium, and Leptotrichia, were more abundant in mothers than in infants.ConclusionsSalivary microbiota of Tsimane infants and young children up to two years of age do not appear closely related to those of their mothers, despite frequent premastication and preliminary evidence that maternal bacteria is transmitted to premasticated foods. Infant physiology and diet may constrain colonization by maternal bacteria, including several oral pathogens.

Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers

Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv. ‘BHN602’ grown in soils amended with fresh poultry litter, commercially available sterilized poultry litter pellets, vermicompost or synthetic fertilizer was described. Culture independent DNA was extracted from bulk and rhizosphere soils, and washes of tomato blossoms and ripe fruit. PCR amplicons of hypervariable regions of the 16S rRNA gene were sequenced and profiled using the QIIME pipeline. Bulk and rhizosphere soil, and blossom and fruit surfaces all supported distinct bacterial communities according to principal coordinate analysis and ANOSIM (R=0.87, p=0.001 in year 1; R=0.93, p=0.001 in year 2). Use of microbiologically diverse organic fertilizers generally did not influence bacterial diversity, community structure or relative abundance of specific taxa on any plant organ surface. However, statistically significant differences in sand and silt contents of soil (p<0.05) across the field and corresponding shifts in water activity were positively (R2=0.52, p=0.005) and negatively (R2=0.48, p=0.009) correlated with changes in bacterial community structure in the rhizosphere, respectively. Over two harvest seasons, this study demonstrated that the application of raw poultry manure, poultry litter pellets and vermicompost had little effect on the tomato microbiome in the rhizosphere and phyllosphere, when compared to synthetically fertilized plants. Plant anatomy, and other factors related to field location, possibly associated with edaphic and air characteristics, were more influential drivers of different tomato organ microbiomes than were diverse soil amendment applications.

Temporal Stability in Chronic Wound Microbiota Is Associated With Poor Healing

Microbial burden of chronic wounds is believed to play an important role in impaired healing and the development of infection-related complications. However, clinical cultures have little predictive value of wound outcomes, and culture-independent studies have been limited by cross-sectional design and small cohort size. We systematically evaluated the temporal dynamics of the microbiota colonizing diabetic foot ulcers, a common and costly complication of diabetes, and its association with healing and clinical complications. Dirichlet multinomial mixture modeling, Markov chain analysis, and mixed-effect models were used to investigate shifts in the microbiota over time and their associations with healing. Here we show, to our knowledge, previously unreported temporal dynamics of the chronic wound microbiome. Microbiota community instability was associated with faster healing and improved outcomes. Diabetic foot ulcer microbiota were found to exist in one of four community types that experienced frequent and nonrandom transitions. Transition patterns and frequencies were associated with healing time. Exposure to systemic antibiotics destabilized the wound microbiota, rather than altering overall diversity or relative abundance of specific taxa. This study provides evidence that the dynamic wound microbiome is indicative of clinical outcomes and may be a valuable guide for personalized management and treatment of chronic wounds.

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis.

BackgroundUpper respiratory infections (URI) and their complications are a major healthcare burden for pediatric populations. Although the microbiology of the nasopharynx is an important determinant of the complications of URI, little is known of the nasopharyngeal (NP) microbiota of children, the factors that affect its composition, and its precise relationship with URI.ResultsHealthy children (n = 47) aged 49–84 months from a prospective cohort study based in Wisconsin, USA, were examined. Demographic and clinical data and NP swab samples were obtained from participants upon entry to the study. All NP samples were profiled for bacterial microbiota using a phylogenetic microarray, and these data were related to demographic characteristics and upper respiratory health outcomes. The composition of the NP bacterial community of children was significantly related prior to the history of acute sinusitis (R2 = 0.070, P < 0.009). History of acute sinusitis was associated with significant depletion in relative abundance of taxa including Faecalibacterium prausnitzii and Akkermansia spp. and enrichment of Moraxella nonliquefaciens. Enrichment of M. nonliquefaciens was also a characteristic of baseline NP samples of children who subsequently developed acute sinusitis over the 1-year study period. Time to develop URI was significantly positively correlated with NP diversity, and children who experienced more frequent URIs exhibited significantly diminished NP microbiota diversity (P ≤ 0.05).ConclusionsThese preliminary data suggest that previous history of acute sinusitis influences the composition of the NP microbiota, characterized by a depletion in relative abundance of specific taxa. Diminished diversity was associated with more frequent URIs.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0179-9) contains supplementary material, which is available to authorized users.

Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR.

Changes in the composition of microbial communities are often examined using high-throughput sequencing (HTS). Here we analyzed bar-coded Illumina sequencing data from a previous work describing the microbial community found in the sputum of a cystic fibrosis patient by itself or in combination with qPCR to measure the absolute abundance of Pseudomonas aeruginosa and Burkholderia multivorans. Through this comparison we were able to determine the computational analysis accuracy of sequencing data to measure the relative abundance of specific taxa. While no correlation was found between relative abundance and absolute abundance of P. aeruginosa or B. multivorans, we did find conclusions derived from HTS data alone differed from those derived from a combination of HTS and qPCR. Our results highlight the importance of using qPCR with HTS when characterizing organisms in microbial communities having a dominant taxon.

Different genotypes of Silene vulgaris (Moench) Garcke grown on chromium-contaminated soils influence root organic acid composition and rhizosphere bacterial communities.

Plant-microbe interactions are considered to be important processes determining the efficiency of phytoremediation of heavy metal-contaminated soils. However, relatively little is known about how these interactions are influenced by chromium (Cr) contamination. The effect of Cr stress on metal uptake, root organic acid composition, and rhizosphere bacterial communities was studied using two genotypes of the metallophyte Silene vulgaris, which have shown different tolerance to Cr(VI). The results indicated that root biomass and shoot biomass were not significantly influenced by Cr treatment, but metal uptake in shoots and roots was significantly impacted by the genotype. Principal component analyses (PCA) showed that variation in organic acids oxalic, citric, malic, formic, lactic, acetic, and succinic differed between genotypes. Changes in root organic acid contents in response to Cr revealed a significant increase of oxalic acid in genotype SV-21. The denaturing gradient gel electrophoresis (DGGE) cluster analysis showed that the community structure (determined by PCR-DGGE) was affected by plant genotype and, to a lesser extent, by Cr contamination, the first being the most influential factor shaping the rhizosphere microbiome. Under Cr pollution, a shift in the relative abundance of specific taxa was found and dominant phylotypes were identified as Variovorax in SV-21 and Chitinophaga niastensis, Pontibacter sp., and Ramlibacter sp. in SV-38. These results provided the basis for further studies aimed at the combined use of plants and soil microorganisms in the remediation of Cr-polluted soils.

Aging and serum MCP-1 are associated with gut microbiome composition in a murine model.

Introduction. Age is the primary risk factor for major human chronic diseases, including cardiovascular disorders, cancer, type 2 diabetes, and neurodegenerative diseases. Chronic, low-grade, systemic inflammation is associated with aging and the progression of immunosenescence. Immunosenescence may play an important role in the development of age-related chronic disease and the widely observed phenomenon of increased production of inflammatory mediators that accompany this process, referred to as “inflammaging.” While it has been demonstrated that the gut microbiome and immune system interact, the relationship between the gut microbiome and age remains to be clearly defined, particularly in the context of inflammation. The aim of our study was to clarify the associations between age, the gut microbiome, and pro-inflammatory marker serum MCP-1 in a C57BL/6 murine model.Results. We used 16S rRNA gene sequencing to profile the composition of fecal microbiota associated with young and aged mice. Our analysis identified an association between microbiome structure and mouse age and revealed specific groups of taxa whose abundances stratify young and aged mice. This includes the Ruminococcaceae, Clostridiaceae, and Enterobacteriaceae. We also profiled pro-inflammatory serum MCP-1 levels of each mouse and found that aged mice exhibited elevated serum MCP-1, a phenotype consistent with inflammaging. Robust correlation tests identified several taxa whose abundance in the microbiome associates with serum MCP-1 status, indicating that they may interact with the mouse immune system. We find that taxonomically similar organisms can exhibit differing, even opposite, patterns of association with the host immune system. We also find that many of the OTUs that associate with serum MCP-1 stratify individuals by age.Discussion. Our results demonstrate that gut microbiome composition is associated with age and the pro-inflammatory marker, serum MCP-1. The correlation between age, relative abundance of specific taxa in the gut microbiome, and serum MCP-1 status in mice indicates that the gut microbiome may play a modulating role in age-related inflammatory processes. These findings warrant further investigation of taxa associated with the inflammaging phenotype and the role of gut microbiome in the health status and immune function of aged individuals.

Differential susceptibility to colorectal cancer due to naturally occurring gut microbiota.

Recent studies investigating the human microbiome have identified particular bacterial species that correlate with the presence of colorectal cancer. To evaluate the role of qualitatively different but naturally occurring gut microbiota and the relationship with colorectal cancer development, genetically identical embryos from the Polyposis in Rat Colon (Pirc) rat model of colorectal cancer were transferred into recipients of three different genetic backgrounds (F344/NHsd, LEW/SsNHsd, and Crl:SD). Tumor development in the pups was tracked longitudinally via colonoscopy, and end-stage tumor burden was determined. To confirm vertical transmission and identify associations between the gut microbiota and disease phenotype, the fecal microbiota was characterized in recipient dams 24 hours pre-partum, and in Pirc rat offspring prior to and during disease progression. Our data show that the gut microbiota varies between rat strains, with LEW/SsNHsd having a greater relative abundance of the bacteria Prevotella copri. The mature gut microbiota of pups resembled the profile of their dams, indicating that the dam is the primary determinant of the developing microbiota. Both male and female F344-Pirc rats harboring the Lewis microbiota had decreased tumor burden relative to genetically identical rats harboring F344 or SD microbiota. Significant negative correlations were detected between tumor burden and the relative abundance of specific taxa from samples taken at weaning and shortly thereafter, prior to observable adenoma development. Notably, this naturally occurring variation in the gut microbiota is associated with a significant difference in severity of colorectal cancer, and the abundance of certain taxa is associated with decreased tumor burden.

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils.

This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes, dominated by fermenters (Bacteroidetes and Firmicutes).

Microbiome/Metabolic Syndrome/Diabetes and CVD

We have carried out taxonomic profiling of gut microbiota in a population of about 100 commercially available inbred strains of mice termed the Hybrid Mouse Diversity Panel (HMDP). This panel has been developed as a systems genetics resource and can be used for high resolution association mapping of complex traits. When maintained under controlled environmental conditions, the gut microbiota composition exhibits high heritability in the HMDP as calculated using a linear mixed model assuming additive genetic effects. Genome‐wide association analysis with informative SNPs identified significant loci in the mouse genome associated with relative abundances of specific taxa. The HMDP mice have been typed for a number of cardiovascular, metabolic, and other clinical traits, allowing correlation analysis of gut microbiota composition with clinical traits. Some of these associations, such as the association between Akkermansia muciniphila levels and high fat diet response, have subsequently been confirmed in published experimental studies. A number of novel associations are presently being tested using co‐fostering of different inbred strains or experimental introduction of cultured bacterial species. A variety of diets have been studied across the HMDP. In conclusion, studies of natural variations in gut microbiota composition in mice may help identify regulatory host factors as well as providing a global view of the relationships between microbiota and clinically relevant traits.

Abstract 4143: Oral microbiome and risk of head and neck cancer, a nested case-control study

Abstract Introduction: The oral microbiome is intimately involved in inflammatory processes in the oral cavity and may be involved in metabolism of carcinogens in tobacco smoke. Our hypothesis is that oral microbiota may promote head and neck carcinogenesis, possibly related to smoking. To test this hypothesis, we conducted a nested case-control study to prospectively examine the role of the oral microbiome in head and neck cancer, in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial cohort. Methods: Subjects in the PLCO Trial completed risk factor questionnaires and provided oral wash samples. Trial participants were followed for cancer incidence by annual follow-up, medical chart review and search of mortality databases. During follow-up, 87 histologically confirmed head and neck cancer cases occurred subsequent to oral wash sample collection. We matched these cases to 174 cohort-nested controls (matched by age, gender, and race). DNA was extracted from oral wash samples, 16S rRNA genes were amplified by universal primers, and product was bar-coded and sequenced by 454 FLX technology. 16S rRNA bacterial gene sequences were binned into operational taxonomic units (based on 97% identity) and further assigned to taxonomy in the QIIME pipeline. We performed nonparametric Wilcoxon signed-rank tests and conditional logistic regression to compare differences between head and neck cancer cases and controls, with respect to overall bacterial community structure and relative abundance of specific taxa. Results: From 261 oral samples, we obtained 2,548,067 high quality 16S rRNA gene sequence reads. Overall community structure, based on a weighted UniFrac phylogenetic distance index, did not differ significantly between cases and controls (p&amp;gt;0.05). The major phyla in controls were Firmicutes (59.5%), Actinobacteria (15.5%), Bacteroidetes (11.3%), Proteobacteria (10.3%), and Fusobacteria (2.8%). Decreased abundance of Proteobacteria was observed in cases (7.8%) compared to controls (Wilcoxon test, p = 0.008, FDR controlled p=0.041). After consideration of age, race and sex in conditional logistic regression analysis, an inverse association of Proteobacteria with head and neck cancer risk was observed in smokers (OR comparing extreme tertiles =0.34, 95% CI 0.15-0.79; ptrend = 0.009 [FDR controlled p=0.065]), but not in non-smokers (ptrend=0.62). We also noted a relative increase in abundance of Bifidobacteriales order (multivariate p=0.002, FDR controlled p=0.045) and Lactobacillaceae family (multivariate p=0.005, FDR controlled p&amp;gt;0.05) in cases compared with controls. Conclusion: This first prospective study of the oral microbiome and head and neck cancer suggests that Proteobacteria and Bifidobacteriales are related to risk of head and neck cancer. Replication of these first observations is needed. Citation Format: Jiyoung Ahn, Yingfei Ma, Mark P. Purdue, Neal D. Freedman, Susan M. Gapstur, Liying Yang, Richard B. Hayes, Zhiheng Pei. Oral microbiome and risk of head and neck cancer, a nested case-control study. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4143. doi:10.1158/1538-7445.AM2014-4143

Abstract 2290: Human gut microbiome and risk of colorectal cancer, a case-control study.

Abstract Introduction: Inflammatory responses play a decisive role in colorectal cancer etiology, yet specific causes remain unclear. Our hypothesis is that gut microbial alterations promote colorectal carcinogenesis, possibly through inflammation. To test this hypothesis, we conducted a case-control study of the gut microbiome in 47 histologically confirmed colorectal cancer cases and 94 non-cancer controls (matched by gender and body mass index) who were previously recruited (Schiffman et al, 1989). Demographic and clinical information was assessed by questionnaire and medical chart review, and lyophilized fecal biospecimens for gut microbiome analysis were obtained before initiation of any treatment. Methods: Ribosomal 16S rRNA genes in fecal DNA were amplified by universal primers, bar coded and sequenced by 454 FLX technology. 16S rRNA bacterial gene sequences were binned into operational taxonomic units (OTUs) with 97% identity and aligned to fully sequenced microbial genomes (IMG/GG GreenGenes) in the QIIME pipeline. We performed t-tests and nonparametric Wilcoxon signed-rank tests to compare differences between colorectal cancer cases than controls on alpha diversity (Shannon's diversity index) and relative abundance of specific taxa, respectively, unadjusted for multiple comparisons. Results: From 141 fecal samples, we have obtained 794,217 16S rRNA gene sequence reads. Shannon's diversity index was significantly lower in cases (p=0.02; 7.86 for cases; 8.33 for controls). In taxonomy-based analyses, Fusobacterium genus was significantly enriched in the colorectal cancer cases compared with control group (p=0.003). Relative abundance of Fusobacterium sequences ranged from 0-28.9% in cases (median 0.072%) compared to 0-1.3% in controls (median 0.027%). We also noted a relative decrease in abundance of Clostridia (p=0.01, class) and Actinobacteria (p=0.03, phylum) in the colorectal cancer group compared with controls. Conclusion: This first study of the gut microbiome in colorectal cancer patients compared with non-cancer controls suggests that the differential abundances in stool of Fusobacteria, and possibly Clostridia and Actinobacteria, are associated with risk of colorectal cancer. Consistent with our results, two recent studies reported that Fusobacterium sequences were enriched in human colorectal tumor tissue compared to adjacent normal tissue (Kostic et al, 2012 and Castellarin et al, 2012). Fusobacterium is an anaerobic, Gram-negative bacteria, with invasive and proinflammatory characteristics through lipopolysaccharides. Further study is needed to define its role in colorectal carcinogenesis. Citation Format: Jiyoung Ahn, Rashmi Sinha, Zhiheng Pei, Christine Dominianni, James J. Goedert, Richard B. Hayes, Liying Yang. Human gut microbiome and risk of colorectal cancer, a case-control study. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2290. doi:10.1158/1538-7445.AM2013-2290

Soil bacterial community structure in five tropical forests in Malaysia and one temperate forest in Japan revealed by pyrosequencing analyses of 16S rRNA gene sequence variation

Bacterial community structure was investigated in five tropical rainforests in Sarawak, Malaysia and one temperate forest in Kyoto, Japan. A hierarchical sampling approach was employed, in which soil samples were collected from five sampling-sites within each forest. Pyrosequencing was performed to analyze a total of 493,790 16S rRNA amplicons. Despite differences in aboveground conditions, the composition of bacterial groups was similar across all sampling-sites and forests, with Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes accounting for 90% of all Phyla detected. At higher taxonomic levels, the same taxa were predominant, although there was significant heterogeneity in relative abundance of specific taxa across sampling-sites within one forest or across different forests. In all forests, the level of bacterial diversity, estimated using the Chao1 index, was on the order of 1,000, suggesting that tropical rainforests did not necessarily have a large soil bacterial diversity. The average number of reads per species (OTUs) per sampling-site was 8.0, and more than 40-50% of species were singletons, indicating that most bacterial species occurred infrequently and that few bacterial species achieved high predominance. Approximately 30% of species were specific to one sampling-site within a forest, and 40-60% of species were uniquely detected in one of the six forests studied here. Only 0.2% of species were detected in all forests, while on average 32.1% of species were detected in all sampling-sites within a forest. The results suggested that bacterial communities adapted to specific micro- and macro-environments, but macro-environmental diversity made a larger contribution to total bacterial diversity in forest soil.