Core Operational Taxonomic Units Research Articles

Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks.

Twelve mature (aged 5–16 years) horses and ponies of mixed breed and type were fed restricted (1.25% BM Dry matter) quantities of one of two fiber based diets formulated to be iso-caloric. Diet 1 comprised of 0.8% body mass (BM) of chaff based complete feed plus 0.45% BM low energy grass hay (the same hay used for both diets). Diet 2 comprised 0.1% BM of a nutrient balancer plus 1.15% BM grass hay. Fecal samples were collected at week 10 and week 16. DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the bacterial microbiome of the horse. The two most abundant phyla found in both diets and sampling periods were the Firmicutes and Bacteroidetes. There was a clear reduction in Bacteroidetes with a concordant increase in Firmicutes over time. There was a limited degree of stability within the bacterial community of the hindgut of horses, with 65% of bacteria retained, over a 6 week period whilst on a uniform diet. The presence of a core community defined by being present in all samples (each animal/diet combination) included in the study and being present at 0.1% relative abundance (or greater) was identified. In total 65 operational taxonomic units (OTUs) were identified that fit the definition of core making up 21–28% of the total sequences recovered. As with total population the most abundant phyla were the Bacteroidetes followed by the Firmicutes, however there was no obvious shift in phyla due to period. Indeed, when the relative abundance of OTUs was examined across diets and periods there was no significant effect of diet or period alone or in combination on the relative abundance of the core OTUs.

Composition and abundance of microbiota in the pharynx in patients with laryngeal carcinoma and vocal cord polyps.

The pharynx is an important site of microbiota colonization, but the bacterial populations at this site have been relatively unexplored by culture-independent approaches. The aim of this study was to characterize the microbiota structure of the pharynx. Pyrosequencing of 16S rRNA gene libraries was used to characterize the pharyngeal microbiota using swab samples from 68 subjects with laryngeal cancer and 28 subjects with vocal cord polyps. Overall, the major phylum was Firmicutes, with Streptococcus as the predominant genus in the pharyngeal communities. Nine core operational taxonomic units detected from Streptococcus, Fusobacterium, Prevotella, Granulicatella, and Veillonella accounted for 21.3% of the total sequences detected. However, there was no difference in bacterial communities in the pharynx from patients with laryngeal cancer and vocal cord polyps. The relative abundance of Firmicutes was inversely correlated with Fusobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. The correlation was evident at the genus level, and the relative abundance of Streptococcus was inversely associated with Fusobacterium, Leptotrichia, Neisseria, Actinomyces, and Prevotella. This study presented a profile for the overall structure of the microbiota in pharyngeal swab samples. Inverse correlations were found between Streptococcus and other bacterial communities, suggesting that potential antagonism may exist among pharyngeal microbiota.

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time.

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs’ microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealed Propionibacterium acnes and Haemophilus sp. as key members of the dog skin bacterial community, along with Corynebacterium sp. and Staphylococcus epidermidis. This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease.

BackgroundThe preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <32 weeks gestation, we selected 7 infants who developed NEC (defined rigorously) and 28 matched controls. We performed detailed temporal bacterial (n = 641) and metabolomic (n = 75) profiling of the gut microbiome throughout the disease.ResultsA core community of Klebsiella, Escherichia, Staphyloccocus, and Enterococcus was present in all samples. Gut microbiota profiles grouped into six distinct clusters, termed preterm gut community types (PGCTs). Each PGCT reflected dominance by the core operational taxonomic units (OTUs), except of PGCT 6, which had high diversity and was dominant in bifidobacteria. While PGCTs 1–5 were present in infants prior to NEC diagnosis, PGCT 6 was comprised exclusively of healthy samples. NEC infants had significantly more PGCT transitions prior to diagnosis. Metabolomic profiling identified significant pathways associated with NEC onset, with metabolites involved in linoleate metabolism significantly associated with NEC diagnosis. Notably, metabolites associated with NEC were the lowest in PGCT 6.ConclusionsThis is the first study to integrate sequence and metabolomic stool analysis in preterm neonates, demonstrating that NEC does not have a uniform microbial signature. However, a diverse gut microbiome with a high abundance of bifidobacteria may protect preterm infants from disease. These results may inform biomarker development and improve understanding of gut-mediated mechanisms of NEC.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0216-8) contains supplementary material, which is available to authorized users.

Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation.

BackgroundAnnual hibernation is an adaptation that helps many animals conserve energy during food shortage in winter. This natural cycle is also accompanied by a remodeling of the intestinal immune system, which is an aspect of host biology that is both influenced by, and can itself influence, the microbiota. In amphibians, the bacteria in the intestinal tract show a drop in bacterial counts. The proportion of pathogenic bacteria is greater in hibernating frogs than that found in nonhibernating frogs. This suggests that some intestinal gut microbes in amphibians can be maintained and may contribute to the functions in this closed ecosystem during hibernation. However, these results were derived from culture-based approaches that only covered a small portion of bacteria in the intestinal tract.MethodsIn this study, we use a more comprehensive analysis, including bacterial appearance and functional prediction, to reveal the global changes in gut microbiota during artificial hibernation via high-throughput sequencing technology.ResultsOur results suggest that artificial hibernation in the brown tree frog (Polypedates megacephalus) could reduce microbial diversity, and artificially hibernating frogs tend to harbor core operational taxonomic units that are rarely distributed among nonhibernating frogs. In addition, artificial hibernation increased significantly the relative abundance of the red-leg syndrome-related pathogenic genus Citrobacter. Furthermore, functional predictions via PICRUSt and Tax4Fun suggested that artificial hibernation has effects on metabolism, disease, signal transduction, bacterial infection, and primary immunodeficiency.ConclusionsWe infer that artificial hibernation may impose potential effects on primary immunodeficiency and increase the risk of bacterial infections in the brown tree frog.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3318-6) contains supplementary material, which is available to authorized users.

Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling.

Pepper pericarp microbiota plays an important role in the pepper peeling process for the production of white pepper. We collected pepper samples at different peeling time points from Hainan Province, China, and used a metagenomic approach to identify changes in the pericarp microbiota based on functional gene analysis. UniFrac distance-based principal coordinates analysis revealed significant changes in the pericarp microbiota structure during peeling, which were attributed to increases in bacteria from the genera Selenomonas and Prevotella. We identified 28 core operational taxonomic units at each time point, mainly belonging to Selenomonas, Prevotella, Megasphaera, Anaerovibrio, and Clostridium genera. The results were confirmed by quantitative polymerase chain reaction. At the functional level, we observed significant increases in microbial features related to acetyl xylan esterase and pectinesterase for pericarp degradation during peeling. These findings offer a new insight into biodegradation for pepper peeling and will promote the development of the white pepper industry.

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats.

Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Microbial composition in different gut locations of weaning piglets receiving antibiotics.

ObjectiveThe aim of this study was to examine shifts in the composition of the bacterial population in the intestinal tracts (ITs) of weaning piglets by antibiotic treatment using high-throughput sequencing.MethodsSixty 28-d-old weaning piglets were randomly divided into two treatment groups. The Control group was treated with a basal diet without antibiotics. The Antibiotic group’s basal diet contained colistin sulfate at a concentration of 20 g per ton and bacitracin zinc at a concentration of 40 g per ton. All of the pigs were fed for 28 days. Then, three pigs were killed, and the luminal contents of the jejunum, ileum, cecum, and colon were collected for DNA extraction and high-throughput sequencing.ResultsThe results showed that the average daily weight gain of the antibiotic group was significantly greater (p<0.05), and the incidence of diarrhea lower (p>0.05), than the control group. A total of 812,607 valid reads were generated. Thirty-eight operational taxonomic units (OTUs) that were found in all of the samples were defined as core OTUs. Twenty-one phyla were identified, and approximately 90% of the classifiable sequences belonged to the phylum Firmicutes. Forty-two classes were identified. Of the 232 genera identified, nine genera were identified as the core gut microbiome because they existed in all of the tracts. The proportion of the nine core bacteria varied at the different tract sites. A heat map was used to understand how the numbers of the abundant genera shifted between the two treatment groups.ConclusionAt different tract sites the relative abundance of gut microbiota was different. Antibiotics could cause shifts in the microorganism composition and affect the composition of gut microbiota in the different tracts of weaning piglets.

Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study.

This population-based study determined the salivary microbiota composition of 2,343 adult residents of Hisayama town, Japan, using 16S rRNA gene next-generation high-throughput sequencing. Of 550 identified species-level operational taxonomic units (OTUs), 72 were common, in ≥75% of all individuals, as well as in ≥75% of the individuals in the lowest quintile of phylogenetic diversity (PD). These “core” OTUs constituted 90.9 ± 6.1% of each microbiome. The relative abundance profiles of 22 of the core OTUs with mean relative abundances ≥1% were stratified into community type I and community type II by partitioning around medoids clustering. Multiple regression analysis revealed that a lower PD was associated with better conditions for oral health, including a lower plaque index, absence of decayed teeth, less gingival bleeding, shallower periodontal pockets and not smoking, and was also associated with tooth loss. By contrast, multiple Poisson regression analysis demonstrated that community type II, as characterized by a higher ratio of the nine dominant core OTUs, including Neisseria flavescens, was implicated in younger age, lower body mass index, fewer teeth with caries experience, and not smoking. Our large-scale data analyses reveal variation in the salivary microbiome among Japanese adults and oral health-related conditions associated with the salivary microbiome.

Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments.

Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultivation was implemented to selectively enrich and isolate crystalline iron(III) oxide reducing microorganisms in soils and sediments. Firstly, iron reducers were enriched and other untargeted eutrophs were depleted by 2-years successive culture on a crystalline ferric iron oxide (i.e., goethite, lepidocrocite, hematite, or magnetite) as electron acceptor. Fifty-eight out of 136 incubation conditions allowed the continued existence of microorganisms as confirmed by PCR amplification. High-throughput Illumina sequencing and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures on each of the ferric iron oxides contained bacteria belonging to the Deltaproteobacteria (mainly Geobacteraceae), followed by Firmicutes and Chloroflexi, which also comprised most of the operational taxonomic units (OTUs) identified. Venn diagrams indicated that the core OTUs enriched with all of the iron oxides were dominant in the Geobacteraceae while each type of iron oxides supplemented selectively enriched specific OTUs in the other phylogenetic groups. Secondly, 38 enrichment cultures including novel microorganisms were transferred to soluble-iron(III) containing media in order to stimulate the proliferation of the enriched iron reducers. Through extinction dilution-culture and single colony isolation, six strains within the Deltaproteobacteria were finally obtained; five strains belonged to the genus Geobacter and one strain to Pelobacter. The 16S rRNA genes of these isolates were 94.8–98.1% identical in sequence to cultured relatives. All the isolates were able to grow on acetate and ferric iron but their physiological characteristics differed considerably in terms of growth rate. Thus, the novel strategy allowed to enrich and isolate novel iron(III) reducers that were able to thrive by reducing crystalline ferric iron oxides.

Fungal communities in wheat grain show significant co-existence patterns among species

The wheat grain mycobiome is only scarcely investigated and focus has been on seed-transmitted wheat pathogens of agricultural importance. In this study, we used next generation sequencing to study the mycobiome of Danish wheat grain samples at harvest. In total 228,421 sequences were obtained from 90 samples that were taken from locations across Denmark during three years. These sequences could be grouped into 173 non-singleton operational taxonomic units (OTUs) of which 21 OTUs, identified as belonging to genera such as Fusarium, Alternaria, Cladosporium. Phaeosphaeria and Microdochium, were identified as ‘core’ OTUs as they were found in all or almost all samples and accounted for almost 99 % of all sequences. The remaining OTUs were only sporadically found and only in small amounts. Cluster and factor analyses showed patterns of co-existence among the core species. Cluster analysis grouped the 21 core OTUs into three clusters: cluster 1 consisting of saprotrophs, cluster 2 consisting mainly of yeasts and saprotrophs and cluster 3 consisting of wheat pathogens. Principal component extraction showed that the Fusarium graminearum group was inversely related to OTUs of clusters 1 and 2.

Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients

In this study, 454 pyrosequencing of the 16S rRNA gene was used to investigate sediment bacterial community response to contaminant disturbance across six estuaries with differing levels of 'modification'. We observed a significant influence of metal and polycyclic aromatic hydrocarbon contaminants in shaping bacterial community composition, structure and diversity, with metals being the more influential contaminant. An abundant and pervasive 'core' set of bacteria found in every sample were largely responsible for mediating community response to contamination. These 13 core operational taxonomic units were mostly comprised of Gamma-, Delta-, Alphaproteobacteria and Acidobacteria. Sediment silt and metals together explained the most variation in bacterial community composition (19.7%). Following this strong contaminant signature, salinity and temperature represented important environmental variables predicting 10.9% of community variation. While overall network connectivity measures supported the idea of an inherently diverse soil microbiome with some degree of functional redundancy, lower values observed in contaminated sediments indicate potential structural perturbations in the community from fracturing or loss of bacterial associations. The large number of unclassified sequences obtained in this study contribute to improving our understanding of environmentally relevant strains in relation to anthropogenic contamination, which have been overlooked in laboratory studies.

Distribution and abundance of Spirochaetes in full-scale anaerobic digesters

To investigate the distribution and abundance of spirochaetal communities within anaerobic digesters, pyrosequencing of the 16S rRNA gene was conducted. Phylogenetic analysis identified a cluster which included the majority of core spirochaetal operational taxonomic units (OTUs) and environmental clones but no pure-culture strains. Distribution of the core OTUs demonstrated an importance of local factors in shaping the structure of Spirochaetes. Spirochaetal to bacterial 16S rRNA gene copy numbers varied from 1.3% to 30.0% depending on digester samples. Environmental variables were found to influence the relative abundance of Spirochaetes. In a batch anaerobic digestion experiment testing the response to different substrates, acetate most stimulated the activity of Spirochaetes, suggesting possible acetate oxidation by syntrophic acetate oxidation process. Taken together, the results obtained in this study provides an insight into the ecology of Spirochaetes in anaerobic digesters and a basis for future studies examining ecological function of these bacteria.

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data

Local similarity analysis of biological time series data helps elucidate the varying dynamics of biological systems. However, its applications to large scale high-throughput data are limited by slow permutation procedures for statistical significance evaluation. We developed a theoretical approach to approximate the statistical significance of local similarity analysis based on the approximate tail distribution of the maximum partial sum of independent identically distributed (i.i.d.) random variables. Simulations show that the derived formula approximates the tail distribution reasonably well (starting at time points > 10 with no delay and > 20 with delay) and provides P-values comparable with those from permutations. The new approach enables efficient calculation of statistical significance for pairwise local similarity analysis, making possible all-to-all local association studies otherwise prohibitive. As a demonstration, local similarity analysis of human microbiome time series shows that core operational taxonomic units (OTUs) are highly synergetic and some of the associations are body-site specific across samples. The new approach is implemented in our eLSA package, which now provides pipelines for faster local similarity analysis of time series data. The tool is freely available from eLSA's website: http://meta.usc.edu/softs/lsa. Supplementary data are available at Bioinformatics online. fsun@usc.edu.

Comparative analysis of yellow microbial communities growing on the walls of geographically distinct caves indicates a common core of microorganisms involved in their formation

Morphologically similar microbial communities that often form on the walls of geographically distinct limestone caves have not yet been comparatively studied. Here, we analysed phylotype distribution in yellow microbial community samples obtained from the walls of distinct caves located in Spain, Czech Republic and Slovenia. To infer the level of similarity in microbial community membership, we analysed inserts of 474 16S rRNA gene clones and compared those using statistical tools. The results show that the microbial communities under investigation are composed solely of Bacteria. The obtained phylotypes formed three distinct groups of operational taxonomic units (OTUs). About 60% of obtained sequences formed three core OTUs common to all three sampling sites. These were affiliated with actinobacterial Pseudonocardinae (30-50% of sequences in individual sampling site libraries), but also with gammaproteobacterial Chromatiales (6-25%) and Xanthomonadales (0.5-2.0%). Another 7% of sequences were common to two sampling sites and formed eight OTUs, while the remaining 35% were site specific and corresponded mostly to OTUs containing single sequences. The same pattern was observed when these data were compared with sequence data available from similar studies. This comparison showed that distinct limestone caves support microbial communities composed mostly of phylotypes common to all sampling sites.

Monitoring bacterial community structure and variability in time scale in full-scale anaerobic digesters

Using a high-throughput pyrosequencing technology, this study assessed bacterial community structure and time-scale variability in great detail in seven full-scale anaerobic digesters operated variously in terms of influent substrate, digestion temperature, and reactor configuration. Pyrosequencing generated a total of 83,774 sequence reads from 40 digester sludge samples collected monthly for six months. The highest number of sequence reads were detected within Proteobacteria (20.5%), followed by those within Bacteroidetes (19.7%), Firmicutes (17.8%), and Chloroflexi (4.8%). The relative composition of bacterial populations was varied within the digesters as well as between the digesters, and the bacterial community structures were mainly influenced by digestion temperature. Detailed bacterial community structures were assessed by analyzing the operational taxonomic units (OTUs) based on 97% sequence similarity, which resulted in a total of 9051 OTUs. Among these, a total of 31 core OTUs were analyzed and inferred phylogenetically, which enabled us to classify the sequences within an unclassified phylum. Unclassified sequences were mostly affiliated with the sequences within Spirochaetes and Firmicutes. Interestingly, numerically dominant novel phylotypes (18% of the total sequence reads) presumably involved in anaerobic digestion within Spirochaetes were identified. Temporal variability was further explored using a non-metric multidimensional scaling ordination which demonstrated that the variability of the bacterial community within the digesters was smaller than between digesters. Correlation analysis demonstrated that digester performance and operational conditions affected the pattern of bacterial community in the ordination. Additionally, a multi-response permutation procedure revealed that the bacterial communities within the digesters were more similar than those belonging to other digesters statistically, demonstrating a patchiness of the digesters in the distribution of bacterial populations. Overall, this study revealed the correlation of bacterial community structure and time-scale variability with digester performance and operating conditions.

Comparison of the structure and composition of bacterial communities from temperate and tropical freshwater ecosystems

We used a partial 16S rRNA sequencing approach to compare the structure and composition of the bacterial communities in three large, deep subalpine lakes in France with those of communities in six shallow tropical reservoirs in Burkina Faso. Despite the very different characteristics of these ecosystems, we found that their bacterial communities share the same composition in regard to the relative proportions of the different phyla, suggesting that freshwater environmental conditions lead to convergence in this composition. In the same way, we found no significant difference in the richness and diversity of the bacterial communities in France and Burkina Faso. We defined core and satellite operational taxonomic units (OTUs) (sequences sharing at least 98% identity) on the basis of their abundance and their geographical distribution. The core OTUs were found either ubiquitously or only in temperate or tropical and subtropical areas, and they contained more than 70% of all the sequences retrieved in this study. In contrast, satellite OTUs were characterized by having a more restricted geographical distribution and by lower abundance. Finally, the bacterial community composition of these freshwater ecosystems in France and Burkina Faso was markedly different, showing that the history of these ecosystems and regional environmental parameters have a greater impact on the relative abundances of the different OTUs in each bacterial community than the local environmental conditions.