Abundance-based Coverage Estimator Research Articles

Alternation of Gut Microbiota in Patients with Pulmonary Tuberculosis.

One-third of the world's population has been infected with Mycobacterium tuberculosis (M. tuberculosis), a primary pathogen of the mammalian respiratory system, while about 10% of latent infections progress to active tuberculosis (TB), indicating that host and environmental factors may determine the outcomes such as infection clearance/persistence and treatment prognosis. The gut microbiota is essential for development of host immunity, defense, nutrition and metabolic homeostasis. Thus, the pattern of gut microbiota may contribute to M. tuberculosis infection and prognosis. In current study we characterized the differences in gut bacterial communities in new tuberculosis patients (NTB), recurrent tuberculosis patients (RTB), and healthy control. The abundance-based coverage estimator (ACE) showed the diversity index of the gut microbiota in the patients with recurrent tuberculosis was increased significantly compared with healthy controls (p < 0.05). At the phyla level, Actinobacteria and Proteobacteria, which contain many pathogenic species, were significantly enriched in the feces RTB patients. Conversely, phylum Bacteroidetes, containing a variety of beneficial commensal organisms, was reduced in the patients with the recurrent tuberculosis compared to healthy controls. The Gram-negative genus Prevotella of oral origin from phylum of Bacteroidetes and genus Lachnospira from phylum of Firmicutes were significantly decreased in both the new and recurrent TB patient groups, compared with the healthy control group (p < 0.05). We also found that there was a positive correlation between the gut microbiota and peripheral CD4+ T cell counts in the patients. This study, for the first time, showed associations between gut microbiota with tuberculosis and its clinical outcomes. Maintaining eubiosis, namely homeostasis of gut microbiota, may be beneficial for host recovery and prevention of recurrence of M. tuberculosis infection.

Combination of amplified rDNA restriction analysis and high-throughput sequencing revealed the negative effect of colistin sulfate on the diversity of soil microorganisms

Colistin sulfate is widely used in both human and veterinary medicine. However, its effect on the microbial ecologyis unknown. In this study, we determined the effect of colistin sulfate on the diversity of soil microorganisms by amplified rDNA restriction analysis (ARDRA) and high-throughput sequencing.ARDRAshowed that the diversity of DNA from soil microorganisms was reduced after soil was treated with colistin sulfate, with the most dramatic reductionobserved after 35days of treatment. High-throughput sequencing showed that the Chao1 and abundance-based coverage estimators (ACE) were reduced in the soils treated with colistin sulfate for 35 dayscompared to those treated with colistin sulfate for 7days. Furthermore, Chao1 and ACE tended to be lower when higher concentration of colistin sulfate was used, suggesting that the microbial abundance is reduced by colistin sulfate in a dose-dependent manner. Shannon index showed that the diversity of soil microorganism was reduced upon treatment with colistin sulfate compared to the untreated control group. Following 7days of treatment, Bacillus, Clostridiumand Sphingomonas were sensitive to all the concentration of colistin sulfate used in this study. Following 35days of treatment, the abundance of Choroplast, Haliangium, Pseudomonas, Lactococcus, and Clostridium was significantly decreased. Our results demonstrated that colistin sulfate especially at high concentration (≥5mg/kg) could alter the population structure of microorganisms and consequently the microbial community function in soil.

Bacterial diversity in goat milk from the Guanzhong area of China

In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator. Functional genes and their likely metabolic pathways were predicted, which demonstrated that the functional genes present in the bacteria in goat milk were enriched in pathways for amino acid metabolism and carbohydrate metabolism, which represented 11.93 and 11.23% of functional genes, respectively. Physicochemical properties such as pH, protein, fat, and AA levels were also determined and correlations made with microbial diversity. We detected a significant difference in the content of lactose and 6 AA, which were higher in Saanen milk than in Guanzhong milk, and positively correlated with microbial carbohydrate metabolism and AA metabolism. Lactococcus, Lactobacillus, Bifidobacterium, Enterococcus, and Streptococcus, which are lactose-utilizing genera, were more abundant in Saanen milk than in Guanzhong milk. Higher levels of lactose in Saanen goat milk may explain its greater microbial diversity. We also demonstrated that most of the AA metabolism-related bacterial genera (e.g., Massilia, Bacteroides, Lysobacter) were enriched in Saanen goat milk. In this research, both probiotic and pathogenic bacteria were identified in goat milk, which provided the microbial information necessary to direct the utilization of beneficial microbial resources and prevent the development of harmful organisms in goat milk.

GUT MICROBIOME ALTERATIONS IN ALZHEIMER'S DISEASE AND THE RELATIONSHIP WITH CSF BIOMARKERS

The etiology of dementia due to Alzheimer's disease (AD) is not completely understood. Recent studies suggest that alterations in human gut microbiota contribute to neurological conditions including multiple sclerosis and Parkinson's disease, yet the contribution of the gut microbiota to the development of AD neuropathology and dementia is unknown. We investigated this by examining gut microbiota among participants in the Wisconsin Registry for Alzheimer's Prevention and Wisconsin ADRC, with and without a clinical diagnosis of mild cognitive impairment (MCI) or AD. Secondary analysis examined the extent to which cerebrospinal fluid (CSF) biomarkers of AD were associated with the composition of the gut microbiome. Bacterial 16S rRNA gene sequencing was performed on DNA extracted from fecal samples collected from AD/MCI patients (n=16), age- and sex-matched control participants (n=18), and asymptomatic middle-aged participants (n=52). Sequence processing was performed in mothur, and richness, alpha, and beta diversity metrics were calculated using normalized OTU-level data. Metastats was used to detect differential abundance between AD/MCI and controls at the family taxonomic level. Among participants who had previously undergone lumbar puncture (n=31), we tested the relationship between microbiome phylogenetic diversity and CSF levels of Aβ42 and phosphorylated tau. The microbiome of AD/MCI participants showed significantly less richness and alpha diversity (Figure 1), and a significant difference in beta diversity compared to control participants. AD/MCI participants showed elevated abundance of Lachnospiraceae, Bacteroidaceae, and Streptococcaceae, with decreased levels of Ruminococcaceae (Figure 2). Among participants with CSF data, an interaction between diagnosis and phylogenetic diversity was observed for CSF phosphorylated tau and the ratio of ptau/Aβ42 (Figure 3). Decreased richness and alpha diversity in the microbiome of AD/MCI participants parallels results observed in other conditions associated with gut dysbiosis including diabetes and obesity. Moreover, we observed that decreased microbial diversity was associated with greater AD pathology in CSF. Additional work, including animal studies and longitudinal human studies, are needed to determine the potential contribution of gut microbiota to the development of AD. Gut microbiome in AD/MCI displays decreased richness (Abundance-based coverage estimator (ACE), Chaol) and alpha diversity (Shannon Index, Faith's Phylogenetic Diversity) metrics. *p<0.05. Relative abundance differences at family taxonomic level between AD/MCI and age- and sex-matched control participants as identified by Metastats. *p<0.05 (FDR). Relationship between gut microbiome phylogenetic diversity and CSF phosphorylated tau and the ratio of tau/Aβ42.

Rumen microbial and fermentation characteristics are affected differently by acarbose addition during two nutritional types of simulated severe subacute ruminal acidosis in vitro

Little information is available on whether or not the effect of an alpha-glucosidase inhibitor on the prevention of ruminal acidosis is influenced by the type of diet during ruminant feeding. This study was conducted to explore the effect of acarbose addition on the prevention of severe subacute ruminal acidosis induced by either cracked wheat or beet pulp in vitro. Cracked wheat and beet pulp were fermented in vitro by rumen microorganisms obtained from three dairy cows. When cracked wheat was used as the substrate and fermented for 24 h, compared with the control, acarbose addition decreased the concentrations of acetate, propionate, butyrate, total volatile fatty acids, and lactate (P < 0.05), while linearly increased the ratio of acetate to propionate, pH value, and the ammonia-nitrogen level (P < 0.05). Applying Illumina MiSeq sequencing of a fragment of the 16S rRNA gene revealed that the relative abundance of Firmicutes and Bacteroidetes as well as the ACE (abundance-based coverage estimator) value, Chao 1 value, and Shannon index increased significantly (P < 0.05), while there was a significant reduction (P < 0.05) in the relative abundance of Tenericutes as well as Proteobacteria after adding acarbose compared to the control. On the other hand, when beet pulp was used as the substrate, acarbose addition had no significant effects (P > 0.05) on the fermentation parameters and the Chao 1 value, the Shannon index, and the proportion of Firmicutes and Bacteroidetes. In general, these findings indicate that acarbose had more effects on ruminal fermentation when wheat was used as the substrate, whereas it exhibited little effect on ruminal fermentation when beet pulp was used as the substrate.

The normal vaginal and uterine bacterial microbiome in giant pandas (Ailuropoda melanoleuca)

While the health effects of the colonization of the reproductive tracts of mammals by bacterial communities are widely known, there is a dearth of knowledge specifically in relation to giant panda microbiomes. In order to investigate the vaginal and uterine bacterial diversity of healthy giant pandas, we used high-throughput sequence analysis of portions of the 16S rRNA gene, based on samples taken from the vaginas (GPV group) and uteri (GPU group) of these animals. Results showed that the four most abundant phyla, which contained in excess of 98% of the total sequences, were Proteobacteria (59.2% for GPV and 51.4% for GPU), Firmicutes (34.4% for GPV and 23.3% for GPU), Actinobacteria (5.2% for GPV and 14.0% for GPU) and Bacteroidetes (0.3% for GPV and 10.3% for GPU). At the genus level, Escherichia was most abundant (11.0%) in the GPV, followed by Leuconostoc (8.7%), Pseudomonas (8.0%), Acinetobacter (7.3%), Streptococcus (6.3%) and Lactococcus (6.0%). In relation to the uterine samples, Janthinobacterium had the highest prevalence rate (20.2%), followed by Corynebacterium (13.2%), Streptococcus (19.6%), Psychrobacter (9.3%), Escherichia (7.5%) and Bacteroides (6.2%). Moreover, both Chao1 and abundance-based coverage estimator (ACE) species richness indices, which were operating at the same sequencing depth for each sample, demonstrated that GPV had more species richness than GPU, while Simpson and Shannon indices of diversity indicated that GPV had the higher bacterial diversity. These findings contribute to our understanding of the potential influence abnormal reproductive tract microbial communities have on negative pregnancy outcomes in giant pandas.

沙埋对干旱沙区真藓结皮层细菌群落结构和多样性的影响

PDF HTML阅读 XML下载 导出引用 引用提醒 沙埋对干旱沙区真藓结皮层细菌群落结构和多样性的影响 DOI: 10.5846/stxb201601010002 作者: 作者单位: 中国科学院寒区旱区环境与工程研究所,中国科学院寒区旱区环境与工程研究所,中国科学院寒区旱区环境与工程研究所 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（41371099，41301080，41530746）；中国科学院"西部之光"人才培养引进计划 Impact of sand burial on bacterial community structure and diversity within biocrusts dominated by Bryum argenteum Author: Affiliation: Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences,Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences,Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:作为干旱沙区常见干扰之一的沙埋显著影响着生物结皮的结构和功能，但其内在的生物学机理还不清楚。利用高通量测序技术，通过对0（对照）、0.5（浅层）、2和10 mm（深层）沙埋处理后的腾格里沙漠东南缘沙坡头地区真藓（Bryum argenteum）结皮层细菌群落物种组成与丰度的测定，研究了沙埋对真藓结皮层细菌群落结构和多样性的影响。结果表明：（1）共检测到沙坡头地区真藓结皮层细菌38门106纲181属，以放线菌、变形菌、蓝藻、浮霉菌、拟杆菌和酸杆菌等为主（占细菌群落的78.4%-83.0%）；（2）PCA分析表明沙埋导致该地区真藓结皮层细菌群落结构组成发生明显改变。无沙埋时，真藓结皮层细菌群落中相对丰度最高的是蓝藻（18.6%），随着沙埋厚度的增加，依次变为变形菌（21.5%，沙埋厚度0.5 mm）、浮霉菌（21.5%，沙埋厚度2 mm）和放线菌（23.3%，沙埋厚度10 mm）；浅层沙埋显著增加了真藓结皮层细菌群落中光合菌、固氮菌和产菌丝体细菌等关键功能菌的丰度，但深层沙埋降低了它们的丰度；（3）沙埋显著增加了真藓结皮层细菌群落多样性（P<0.05）和物种丰富度（P<0.05），0.5 mm沙埋后的细菌群落丰富度指数最高，2 mm沙埋后的结皮层细菌群落多样性指数最高。揭示了沙埋对干旱沙区真藓结皮层细菌群落结构与多样性的影响，为深入理解沙埋对沙区生物结皮结构和生态功能影响的生物学机制提供了一定的理论依据。 Abstract:Bacteria, as a key component of biocrusts, which constitute up to or more than 70% of the living cover in arid and semiarid lands worldwide, play the primary role in carbon and nitrogen inputs in deserts. Thus, changes in bacterial community structure and diversity can significantly alter their ecological processes and the functions of biocrusts. Sand burial is a common environmental stress of the biocrusts in arid and semiarid areas, yet little information is available regarding the effects of sand burial on bacterial community structure and diversity within biocrusts. Therefore, we adopted the high-throughput sequencing techniques to investigate the effects of sand burial on bacterial community structure and diversity of biocrusts dominated by Bryum argenteum following sand burial of 0 (control), 0.5, 2 and 10 mm in Shapotou, southeastern edge of the Tengger Desert. Bacterial community species composition, abundance variation, and diversity indices including the Shannon-Wiener diversity and the richness indices Chao and abundance-based coverage estimator were compared among biocrusts that suffered sand burial at various depths. The results showed the following:(1) In total, 38 phyla, 106 classes, and 181 genera were identified within biocrusts dominated by B. argenteum, of which the dominant bacterial phyla included Actinobacteria, Proteobacteria, Cyanobacteria, Planctomycetes, Bacteroidetes, and Acidobacteria, which comprised 78.4%-83.0% of the whole community. (2) Principal component analysis showed that, compared to the control, the bacterial community structure was the most variable in soils at 2 and 10 mm depths. Sand burial induced significant changes in bacterial community composition; with the highest abundance were Cyanobacteria, Proteobacteria, Planctomycetes and Actinobacteria following 0, 0.5, 2 and 10 mm burial depths, respectively. With the increase in burial depth, the relative abundance of Actinobacteria, Proteobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gemmatimonadetes, and FBP increased, while that of the phyla Cyanobacteria, Acidobacteria, and Chloroflexi decreased. In addition, the abundance of photosynthetic bacteria, nitrogen fixing bacteria, and mycelial genera of Actinobacteria all increased largely at 0.5 mm burial depth and decreased sharply at 2 and 10 mm burial depths. (3) The total count of bacteria, species richness, and microbial diversity of biocrusts dominated by B. argenteum increased following sand burial, among which the biocrusts subjected to 0.5 mm burial depth had the highest richness indices and biocrusts subjected to 2 mm burial depth had the highest diversity indices. The study demonstrated that various depths of sand burial had significant effects on bacterial community and diverse features within biocrusts dominated by B. argenteum in Shapotou and thus offered the theoretical foundation for further understanding of the influence mechanism of sand burial on the structure and ecological functions of biocrusts in arid desert areas. 参考文献 相似文献 引证文献

Shifts in soil bacterial communities induced by the controlled-release fertilizer coatings

Coated controlled-release fertilizers (CRFs) have been widely applied in agriculture due to their increased efficiency. However, the widespread and a lot of coated CRFs application may leave undesired coating residues in the soil due to their slow degradation. Limited information is available on the effects of substantial residual coatings on the soil bacterial community. By adding 0, 5, 10, 20, and 50 times quantities of residual coating from conventional application amount of resin and water-soluble coated CRFs, we studied the responses of soil properties and bacterial community composition to these two residual coatings in black soil. The results showed that the resin and water-soluble coatings did not essentially alter the properties of black soil or cause dramatic changes to bacterial diversity within the test concentration range. The residual resin and water-soluble coatings also did not distinctly alter the relative abundance of the top ten bacteria at phylum level. Heatmap results suggested that the treatments were basically clustered into two groups by concentration rather than types of coating material. Pearson correlation analysis showed that the Simpson's diversity index of the bacterial community was significantly correlated with microbial biomass carbon (MBC, r=0.394, P<0.05), and the richness index abundance-based coverage estimator (ACE) of the bacterial community was significantly correlated with microbial biomass nitrogen (MBN, r=0.407, P<0.05). Overall, results of this study suggested that substantial residual resin and water-soluble coatings with 0–50 times quantities of residual coating from conventional application amount of coated CRFs did not generate obviously negative impacts on the bacterial community in black soil.

Novel application of species richness estimators to predict the host range of parasites

Host range is a critical life history trait of parasites, influencing prevalence, virulence and ultimately determining their distributional extent. Current approaches to measure host range are sensitive to sampling effort, the number of known hosts increasing with more records. Here, we develop a novel application of results-based stopping rules to determine how many hosts should be sampled to yield stable estimates of the number of primary hosts within regions, then use species richness estimation to predict host ranges of parasites across their distributional ranges. We selected three mistletoe species (hemiparasitic plants in the Loranthaceae) to evaluate our approach: a strict host specialist (Amyema lucasii, dependent on a single host species), an intermediate species (Amyema quandang, dependent on hosts in one genus) and a generalist (Lysiana exocarpi, dependent on many genera across multiple families), comparing results from geographically-stratified surveys against known host lists derived from herbarium specimens. The results-based stopping rule (stop sampling bioregion once observed host richness exceeds 80% of the host richness predicted using the Abundance-based Coverage Estimator) worked well for most bioregions studied, being satisfied after three to six sampling plots (each representing 25 host trees) but was unreliable in those bioregions with high host richness or high proportions of rare hosts. Although generating stable predictions of host range with minimal variation among six estimators trialled, distribution-wide estimates fell well short of the number of hosts known from herbarium records. This mismatch, coupled with the discovery of nine previously unrecorded mistletoe-host combinations, further demonstrates the limited ecological relevance of simple host-parasite lists. By collecting estimates of host range of constrained completeness, our approach maximises sampling efficiency while generating comparable estimates of the number of primary hosts, with broad applicability to many host-parasite systems.

Bacterial composition, abundance and diversity in fish polyculture and mussel-fish integrated cultured ponds in China

Bacterial community and abiotic environmental parameters in twelve freshwater aquaculture ponds were analysed. According to the major component of stocked animals, the ponds were grouped into four types: black carp Mylopharyngodon piceus, largemouth bass Micropterus salmoides, yellow catfish Pelteobagrus fulvidraco and pearl mussel Hyriopsis cumingii ponds. Each type of pond was stocked with three species of Chinese carps (silver carp, bighead carp and gibel carp) to form a unique mode of fish polyculture or mussel–fish integrated culture. The bacterial composition was identified using 16S rDNA sequencing. Totally, 3701 and 11 150 operational taxonomic units (OTUs) were identified from the water and sediment samples respectively. The number of OTUs, abundance-based coverage estimator, Chao1 index and Shannon diversity index were lower in the water column than in the sediment, suggesting that diversity and stability of bacterial community were higher in the sediment. In the water column, Proteobacteria, Actinobacteria and Bacteroidetes dominated at the phylum level, and 26 dominant genera were identified. In the sediment, Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria and Nitrospirae dominated at the phylum level, and 25 dominant genera were identified. Bacterial compositions between the ponds with different aquaculture modes were similar at the phylum levels, but varied at the genus levels. The bacterial composition in the ponds was correlated with hardness, ammonia and total nitrogen in the water column. This study indicates that the type of aquaculture mode is a factor regulating the microbial community, which provides an insight towards microbial management through probiotic manipulation in pond culture.

Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants.

Few studies have systematically assessed the influence of gut microbiota on cardiovascular disease (CVD) risk. To examine the association between gut microbiota and lifetime CVD risk profile among 55 Bogalusa Heart Study participants with the highest and 57 with the lowest lifetime burdens of CVD risk factors. 16S ribosomal RNA sequencing was conducted on microbial DNA extracted from stool samples of the Bogalusa Heart Study participants. α Diversity, including measures of richness and evenness, and individual genera were tested for associations with lifetime CVD risk profile. Multivariable regression techniques were used to adjust for age, sex, and race (model 1), along with body mass index (model 2) and both body mass index and diet (model 3). In model 1, odds ratios (95% confidence intervals) for each SD increase in richness, measured by the number of observed operational taxonomic units, Chao 1 index, and abundance-based coverage estimator, were 0.62 (0.39-0.99), 0.61 (0.38-0.98), and 0.63 (0.39-0.99), respectively. Associations were consistent in models 2 and 3. Four genera were enriched among those with high versus low CVD risk profile in all models. Model 1 P values were 2.12×10(-3), 7.95×10(-5), 4.39×10(-4), and 1.51×10(-4) for Prevotella 2, Prevotella 7, Tyzzerella, and Tyzzerella 4, respectively. Two genera were depleted among those with high versus low CVD risk profile in all models. Model 1 P values were 2.96×10(-6) and 1.82×10(-4) for Alloprevotella and Catenibacterium, respectively. The current study identified associations of overall microbial richness and 6 microbial genera with lifetime CVD risk.

Microbial communities of an arable soil treated for 8 years with organic and inorganic fertilizers

The use of organic compost combined with inorganic fertilizer can enable balanced fertilization under intensive farming conditions, but little is known about how these fertilization practices affect the composition of microbial in arable soils. In this study, a field trial of a rice–wheat cropping system was established to examine the effects of 8 years of fertilization with inorganic fertilizers (IFs) and the organic manure–inorganic fertilizers (OMIFs) on composition of microbial communities. The fungal 18S and bacterial 16S rRNA gene fragments were amplified from each soil sample and sequenced. Significantly lower fungal richness and higher bacterial richness were observed for the OMIF treatment compared to the other treatments. No obvious changes in fungal diversity were observed among the treatments, with a decrease bacterial diversity detected in the IF treatment. Variations in relative abundance were observed in the fungal phyla Glomeromycota, Blastocladiomycota, and Schizoplasmodiida and in the bacterial phyla Acidobacteria, Gemmatimonadetes, and Cyanobacteria, most of which were significantly correlated with soil organic matter (OM) and/or nitrate N (NO3 −-N) contents. Additionally, the fungal abundance-based coverage estimator (ACE) showed a significant negative correlation with the soil NO3 −-N/OM content, while the correlation was positive for the bacterial ACE estimate. This study suggests that the fungal and bacterial communities respond differently to the long-term organic-inorganic fertilization, which may result from different effects of NO3 −-N/OM content of soil on the composition of fungal and bacterial communities.

Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population

BackgroundReports on the composition of oral bacteriome in Arabs are lacking. In addition, the majority of previous studies on other ethnic groups have been limited by low-resolution taxonomic assignment of next-generation sequencing reads. Furthermore, there has been a conflict about the existence of a ‘core’ bacteriome.ObjectiveThe objective of this study was to characterize the healthy core oral bacteriome in a young Arab population at the species level.MethodsOral rinse DNA samples obtained from 12 stringently selected healthy young subjects of Arab origin were pyrosequenced (454's FLX chemistry) for the bacterial 16S V1–V3 hypervariable region at an average depth of 11,500 reads. High-quality, non-chimeric reads ≥380 bp were classified to the species level using the recently described, prioritized, multistage assignment algorithm. A core bacteriome was defined as taxa present in at least 11 samples. The Chao2, abundance-based coverage estimator (ACE), and Shannon indices were computed to assess species richness and diversity.ResultsOverall, 557 species-level taxa (211±42 per subject) were identified, representing 122 genera and 13 phyla. The core bacteriome comprised 55 species-level taxa belonging to 30 genera and 7 phyla, namely Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Fusobacteria, Saccharibacteria, and SR1. The core species constituted between 67 and 87% of the individual bacteriomes. However, the abundances differed by up to three orders of magnitude among the study subjects. On average, Streptococcus mitis, Rothia mucilaginosa, Haemophilus parainfluenzae, Neisseria flavescence/subflava group, Prevotella melaninogenica, and Veillonella parvula group were the most abundant. Streptococcus sp. C300, a taxon never reported in the oral cavity, was identified as a core species. Species richness was estimated at 586 (Chao2) and 614 (ACE) species, whereas diversity (Shannon index) averaged at 3.99.ConclusionsA species-level core oral bacteriome representing the majority of reads was identified, which can serve as a reference for comparison with oral bacteriomes of other populations as well as those associated with disease.

Vertical stratification of beetles in tropical rainforests as sampled by light traps in North Queensland, Australia

How arthropods are distributed within the vertical structure of tropical rainforests is of considerable interest to ecologists. Here, we examine how light trapped beetles are distributed in tropical rainforest in North Queensland, Australia. In January and July 2012, traps were suspended 0 m, 10 m, 20 m and 30 m above the ground in five locations with no more than one trap at any single location on any night. Maximum canopy height at the sites was 35 m. A total of 7299 individuals of 492 morphospecies and 66 families were collected. The species abundance-based coverage estimator predicted a total species richness of 765. Sample completeness decreases with increasing height from the ground suggesting higher strata were less well sampled. Distance-based redundancy analysis showed species richness was significantly different between 30 m and all other levels but not between other paired strata. In contrast, both species composition and family composition were significantly distinct for all strata pairs except 10 m with 20 m, and 20 m with 30 m, suggesting that the most distinct strata were 0 m and 30 m. The first two axes of ordination and hierarchical clustering accounted for 46.5% and 17.4% of species composition variation corresponding with season and stratum, respectively. Family level analyses gave similar results to those at the species level. We found stratification of different feeding guilds with herbivores comprising a larger percentage of species in higher strata, whereas saprophages were restricted to the lower strata, reflecting the availability of key resources for these guilds. Fewer species or families were found to be indicators of strata, as measured using IndVal, than for Malaise and flight interception traps (FIT). Dytiscidae and Hydraenidae were abundant but had not been collected using Malaise and FIT. Which species or families are indicators of strata depends on sampling method suggesting multiple sampling methods should be used to establish indicators.

Comparison of bacterial communities in soil between nematode-infected and nematode-uninfected Pinus massoniana pinewood forest

Few studies have investigated the soil properties and bacterial communities in Bursaphelenchus xylophilus-infected Pinus massoniana (Chinese red pine) forests. Herein, soil samples were collected from B. xylophilus-uninfected (control) and B. xylophilus-infected Chinese red pine forests in Small Huangshan, Anhui Province, China to investigate the effects of B. xylophilus on soil bacterial composition and diversity by 16S rRNA clone library analysis. The results showed that pH, microbial biomass-associated carbon and nitrogen were lower in the infected soils relative to the control soils while other properties were elevated. In addition, the soil bacterial community abundance followed the order of Acidobacteria>Proteobacteria>Bacteroidetes>Verrucomicrobia>Cyanobacteria/Chloroplast. Shannon–Wiener index, Jaccard index, Shannon evenness, abundance-based coverage estimator (ACE) and species richness estimator (SChao1) decreased below the control levels. B. xylophilus infection led to a reduction in soil bacterial diversity, and Proteobacteria>Acidobacteria>Planctomycetes>Firmicutes in the control soils. Therefore, we suggest that pinewood infections by B. xylophilus can alter the physicochemical properties of forest soils and thus cause changes in the composition and diversity of resident bacterial communities.

Community assembly during recovery of tropical lowland rain forest from abandoned shift-ing cultivation lands on Hainan Island, China

Aims A major challenge in studies of tropical forest successional dynamics is to reveal the relative importance of deterministic versus stochastic processes affecting species composition, spatial distributions and their rates of change. Here, we tested succession trajectory of tropical secondary forests follow equilibrium or non-equilibrium dynamics by evaluating community reassembly for tropical lowland rainforest recovery on the abandoned shifting cultivation lands on Hainan Island of south China. Methods We explored species composition and dominance of different size classes (seedlings, saplings and adult trees) of communities along a chronosequence of secondary forest plots ranging from 15 to 60 years since abandonment after shifting cultivation. We included two old-growth forest plots for comparison. Important findings Both species diversity for the three size classes and the species similarity index among size classes in old-growth forests were significantly higher than in secondary forests. However, the proportion of dominant species in old-growth community was lower than that of secondary forests. Species similarity between secondary forests and old-growth forests increased with forest recovery, supporting the view of equilibrium succession dynamics. In each recovery stage, the number of individuals, species richness and abundance-based coverage estimator of seedlings were lower than those of both saplings and adult trees. Moreover, the species composition of seedlings in secondary forests differed significantly from that of both saplings and adult trees, suggesting that seedling recruitment might be an unpredictable process. Our results highlighted that the community assembly processes during secondary forest recovery are driven simultaneously by stochastic and deterministic processes.

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland

Subglacial lakes beneath the Vatnajökull ice cap in Iceland host endemic communities of microorganisms adapted to cold, dark and nutrient-poor waters, but the mechanisms by which these microbes disseminate under the ice and colonize these lakes are unknown. We present new data on this subglacial microbiome generated from samples of two subglacial lakes, a subglacial flood and a lake that was formerly subglacial but now partly exposed to the atmosphere. These data include parallel 16S rRNA gene amplicon libraries constructed using novel primers that span the v3-v5 and v4-v6 hypervariable regions. Archaea were not detected in either subglacial lake, and the communities are dominated by only five bacterial taxa. Our paired libraries are highly concordant for the most abundant taxa, but estimates of diversity (abundance-based coverage estimator) in the v4-v6 libraries are 3-8 times higher than in corresponding v3-v5 libraries. The dominant taxa are closely related to cultivated anaerobes and microaerobes, and may occupy unique metabolic niches in a chemoautolithotrophic ecosystem. The populations of the major taxa in the subglacial lakes are indistinguishable (>99% sequence identity), despite separation by 6 km and an ice divide; one taxon is ubiquitous in our Vatnajökull samples. We propose that the glacial bed is connected through an aquifer in the underlying permeable basalt, and these subglacial lakes are colonized from a deeper, subterranean microbiome.

Estimating the Number of One-step Beneficial Mutations

Mutations that confer a selective advantage to an organism are the raw material upon which natural selection acts. The number of such mutations that are available is a central quantity of interest for understanding the tempo and trajectory of adaptive evolution. While this quantity is typically unknown, it can be estimated with varying levels of accuracy based on data obtained experimentally. We propose a method for estimating the number of beneficial mutations that accounts for the evolutionary forces that generate the data. Our model-based parametric approach is compared to an adjusted nonparametric abundance-based coverage estimator. We show that, in general, our estimator performs better. When the number of mutations is small, however, the performances of the two estimators are similar.

Microbial Diversity of an Anoxic Zone of a Hydroelectric Power Station Reservoir in Brazilian Amazonia

Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40m) and sediment (60m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.

Microbial diversity in saliva of oral squamous cell carcinoma

In the oral cavity, chronic inflammation has been observed at various stages of oral squamous cell carcinomas (OSCC). Such inflammation could result from persistent mucosal or epithelial cell colonization by microorganisms. There is increasing evidence of the involvement of oral bacteria in inflammation, warranting further studies on the association of bacteria with the progression of OSCC. The objective of this study was to evaluate the diversity and relative abundance of bacteria in the saliva of subjects with OSCC. Using 454 parallel DNA sequencing, ∼58,000 PCR amplicons that span the V4-V5 hypervariable region of rRNAs from five subjects were sequenced. Members of eight phyla (divisions) of bacteria were detected. The majority of classified sequences belonged to the phyla Firmicutes (45%) and Bacteroidetes (25%). Further, 52 different genera containing approximately 860 (16.51%) known species were identified and 1077 (67%) sequences belonging to various uncultured bacteria or unclassified groups. The species diversity estimates obtained with abundance-based coverage estimators and Chao1 were greater than published analyses of other microbial profiles from the oral cavity. Fifteen unique phylotypes were present in all three OSCC subjects.