Distribution Of Operational Taxonomic Units Research Articles

Microbiome Analysis of the Bamboo Aphid Melanaphis bambusae Infected with the Aphid Obligate Pathogen Conidiobolus obscurus (Entomophthoromycotina).

Insect-associated microbes exert diverse effects on host fitness. This study provides insights into the microbiota of the bamboo aphid, Melanaphis bambusae, and their response to Conidiobolus obscurus infection. 16S rRNA and ITS sequencing data were used to analyze the bacterial and fungal samples associated with healthy, infected, and starved aphids. At ≥97% nucleotide similarity, the total reads were clustered into 79 bacteria and 97 fungi operational Taxonomic Units (OTUs). The phyla Proteobacteria and Ascomycota dominated the bacterial and fungal communities, respectively. The significant divergence in OTU distribution presented differential profiles of the microbiota in response to host conditions. Lower α-diversity indices were found in bacterial and fungal diversity when the aphids were experiencing fungal infection and starvation stresses, respectively. The β-diversity analyses of the communities showed significant differences among the three host conditions, demonstrating that aphid-associated microbiota could significantly shift in response to varying host conditions. Moreover, some OTUs increased under fungal infection, which potentially increased aphid susceptibility. Presumably, C. obscurus infection contributed to this increase by causing the disintegration of host tissues other than host starvation. In conclusion, understanding the differentiation of aphid microbiota caused by fungal entomopathogens helped facilitate the development of novel pest management strategies.

The diversity and composition of the human gut lactic acid bacteria and bifidobacterial microbiota vary depending on age.

Aging is associated with gut microbiota alterations, characterized by changes in intestinal microbial diversity and composition. However, no study has yet focused on investigating age-related changes in the low-abundant but potentially beneficial subpopulations of gut lactic acid bacteria (LAB) and Bifidobacterium. Our study found that the subjects' age correlated negatively with the alpha diversity of the gut bifidobacterial microbiota, and such correlation was not observed in the gut LAB subpopulation. Principal coordinate analysis (PCoA) and analysis of distribution of operational taxonomic units (OTUs) revealed that the structure and composition of the gut bifidobacterial subpopulation of the longevous elderly group were rather different from that of the other three age groups. The same analyses were applied to identify age-dependent characteristics of the gut LAB subpopulation, and the results revealed that the gut LAB subpopulation of young adults was significantly different from that of all three elderly groups. Our study identified several potentially beneficial bacteria (e.g., Bifidobacterium breve and Bifidobacterium longum) that were enriched in the longevous elderly group (P < 0.05), and the relative abundance of Bifidobacterium adolescentis decreased significantly with the increase in age (P < 0.05). Although both bifidobacteria and LAB are generally considered as health-promoting taxa, their age-dependent distribution varied from each other, suggesting their different life stage changes and potentially different functional roles. This study provided novel species-level gut bifidobacterial and LAB microbiota profiles of a large cohort of subjects and identified several age-or longevity-associated features and biomarkers. KEY POINTS: • The alpha diversity of the gut bifidobacterial microbiota decreased with age, while LAB did not change. • The structure and composition of the gut bifidobacterial subpopulation of the longevous elderly group were rather different from that of the other three age groups. • Several potentially beneficial bacteria (e.g., Bifidobacterium breve and Bifidobacterium longum) that were enriched in the longevous elderly group.

Impacts of mountain forest dieback on aquatic insect communities: A DNA metabarcoding analysis of samples from the Bavarian Forest

Mountain forests are increasingly affected by changes in rainfall and pest outbreaks, and the way forests are managed can have direct consequences for the streams flowing through forests. Aquatic macroinvertebrate communities are great bioindicators and changes to their ecosystem likely translates to changes in their overall composition and abundance. The Bavarian Forest National Park (SE Germany) is dominated by the Norway spruce (Picea abies) which, weakened by storms and other stressors, is susceptible to infestation by the European spruce bark beetle (Ips typographus). The result is large scale forest dieback in some areas, and forest management practices that lead to a predominance of three different forest types (hereafter habitats): Intact forest that is healthy and not impacted by Ips typographus; Disturbed forest that was impacted by Ips typographus, left to regenerate naturally, and from which deadwood was not removed; and Salvaged forest that was heavily impacted by Ips typographus with the same consequences, but from which deadwood was removed, creating a treeless forest meadow. Intact forest that is healthy and not impacted by Ips typographus; Disturbed forest that was impacted by Ips typographus, left to regenerate naturally, and from which deadwood was not removed; and Salvaged forest that was heavily impacted by Ips typographus with the same consequences, but from which deadwood was removed, creating a treeless forest meadow. To analyze the impacts these different forest management strategies have on the aquatic insect communities, 30 samples from 11 different streams were taken using kick-sampling. Operational taxonomic units (OTUs) were identified by bulk metabarcoding of dried, ground samples. A mock community was used to verify the setup and a DNA spike-in with three foreign OTUs was added to each sample to measure the biases introduced by PCR amplification and sequencing. Biases varied across samples, but spike-in OTUs produced a pattern indicating predictable biases which could lead to quantifiable metabarcoding results in the future. In total, 260 macroinvertebrate OTUs were identified. In comparison, a morphological study by Bojková et al. (2018) in the same region with twice the number of sampling sites collected 194 taxa in the same month as our samples. This underlines the potential for metabarcoding in evaluating species richness. Species richness was high across all habitats. A significant difference between the forest conditions was detected: The number of detected Diptera OTUs was lowest in disturbed habitats (55) and highest in salvaged areas (73). A permutational multivariate analysis of variance (PERMANOVA) indicated that habitat (i.e., intact, disturbed, salvaged) had an effect on the observed OTU distribution (9.2%), but that the stream catchment had a much larger effect (39.3%) regardless of the habitat. Our findings indicate that forest management can affect stream macroinvertebrate communities, and that this was most pronounced for the Diptera, a group for which DNA metabarcoding is particularly well suited because of their small size and high diversity.

Cosmopolitan Distribution of Endozoicomonas-Like Organisms and Other Intracellular Microcolonies of Bacteria Causing Infection in Marine Mollusks.

Intracellular microcolonies of bacteria (IMC), in some cases developing large extracellular cysts (bacterial aggregates), infecting primarily gill and digestive gland, have been historically reported in a wide diversity of economically important mollusk species worldwide, sometimes associated with severe lesions and mass mortality events. As an effort to characterize those organisms, traditionally named as Rickettsia or Chlamydia-like organisms, 1950 specimens comprising 22 mollusk species were collected over 10 countries and after histology examination, a selection of 99 samples involving 20 species were subjected to 16S rRNA gene amplicon sequencing. Phylogenetic analysis showed Endozoicomonadaceae sequences in all the mollusk species analyzed. Geographical differences in the distribution of Operational Taxonomic Units (OTUs) and a particular OTU associated with pathology in king scallop (OTU_2) were observed. The presence of Endozoicomonadaceae sequences in the IMC was visually confirmed by in situ hybridization (ISH) in eight selected samples. Sequencing data also indicated other symbiotic bacteria. Subsequent phylogenetic analysis of those OTUs revealed a novel microbial diversity associated with molluskan IMC infection distributed among different taxa, including the phylum Spirochetes, the families Anaplasmataceae and Simkaniaceae, the genera Mycoplasma and Francisella, and sulfur-oxidizing endosymbionts. Sequences like Francisella halioticida/philomiragia and Candidatus Brownia rhizoecola were also obtained, however, in the absence of ISH studies, the association between those organisms and the IMCs were not confirmed. The sequences identified in this study will allow for further molecular characterization of the microbial community associated with IMC infection in marine mollusks and their correlation with severity of the lesions to clarify their role as endosymbionts, commensals or true pathogens.

Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems.

Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems. Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers. Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq). The R package ‘picante’ and FUNGuild were used to analyse fungal community composition and trophic mode, respectively. Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota (14) and to the Glomeromycota (1). Fungal communities from conventional farming sites are phylogenetically more related than expected by chance. Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU’s abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised. The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming. Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices. Although it is not fully clear which factors determine the fungal communities, our findings suggest that organic farming systems have a positive effect on fungal communities in winter wheat crops.

Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers

The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ13C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic 15N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.

Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease.

Alterations in the urinary microbiome have been associated with urological diseases. The microbiome of patients with urethral stricture disease (USD) remains unknown. Our objective is to examine the microbiome of USD with a focus on inflammatory USD caused by lichen sclerosus (LS). We collected mid-stream urine samples from men with LS-USD (cases; n = 22) and non-LS USD (controls; n = 76). DNA extraction, PCR amplification of the V4 hypervariable region of the 16S rRNA gene, and sequencing was done on the samples. Operational taxonomic units (OTUs) were defined using a > 97% sequence similarity threshold. Alpha diversity measurements of diversity, including microbiome richness (number of different OTUs) and evenness (distribution of OTUs) were calculated and compared. Microbiome beta diversity (difference between microbial communities) relationships with cases and controls were also assessed. Fifty specimens (13 cases and 37 controls) produced a 16S rRNA amplicon. Mean sample richness was 25.9 vs. 16.8 (p = 0.076) for LS-USD vs. non-LS USD, respectively. LS-USD had a unique profile of bacteria by taxonomic order including Bacillales, Bacteroidales and Pasteurellales enriched urine. The beta variation of observed bacterial communities was best explained by the richness. Men with LS-USD may have a unique microbiologic richness, specifically inclusive of Bacillales, Bacteroidales and Pasteurellales enriched urine compared to those with non-LS USD. Further work will be required to elucidate the clinical relevance of these variations in the urinary microbiome.

Normal gut microbiome in NMDA receptor encephalitis.

ObjectiveTo determine whether the gut microbiota shows overabundance of commensal bacteria species in patients with anti-NMDA receptor (NMDAR) encephalitis, similar to patients with MS or neuromyelitis optica where they potentially balance pro- and anti-inflammatory immune responses or participate in disease pathogenesis by molecular mimicry.MethodsIntestinal microbiota was characterized in patients with NMDAR encephalitis (n = 23, mean age: 34 ± 12.7 years; 21 females) and age/sex/environment-matched healthy controls (n = 24, 40 ± 14.2 years; 22 females) using stool bacteria 16S rDNA sequencing and classification in operational taxonomic units (OTUs). Statistical analyses focused on intraindividual and interindividual bacterial diversity and identification of differentially abundant taxa.ResultsPatients with NMDAR encephalitis and controls had similar microbiome profiles of the gut microbiota regarding intraindividual bacterial diversity, OTU distribution, ratio between regional and local species diversity when testing all OTUs, and genera with a relative abundance greater than 0.5%. Similarly, the subgroup of NMDAR encephalitis patients with an ovarian teratoma (n = 3) showed no differences in microbiome variation compared with controls. Patients in the acute encephalitis stage (n = 8) showed significant differences in the numbers of Clostridium XVIII, Clostridium IV, Oscillibacter, Prevotella, and Blautia; however, significance was lost after correction for multiple testing.ConclusionPatients with NMDAR encephalitis and controls both had a normal gut microbiome. The lack of overabundance of certain bacterial species in patients suggests that microbiome changes are no major contributors to the pathogenesis, disease course, or prognosis in NMDAR encephalitis. Despite the small sample size and heterogeneous groups, findings indicate differences to other neuroimmunologic diseases.

Neutral models predict biogeographical patterns of soil microbes at a local scale in Mediterranean heathlands, South Africa

The South African Fynbos is the smallest floristic kingdom with high levels of endemism and where fire dominates the landscape. However, drivers of soil microbial distribution and diversity are still poorly understood. This study aims to highlight the biogeographical patterns of bacterial and fungal communities and elucidate the mechanisms that mediate their distribution. Soil samples were collected from four Fynbos vegetation types and microbial dynamics were examined using Illumina sequencing of the 16S rRNA bacterial gene and fungal ITS region. Bacterial alpha diversity significantly varied across all Fynbos vegetation types, whilst only the fungal community structure was significantly influenced by vegetation types and environmental variables. The relative abundance of major phyla was similar across all Fynbos types with the exception of Gemmatimonadetes, Cyanobacteria, Ascomycota and Zygomycota. Lastly, neutral models were the best predictor of the abundance and distribution of operational taxonomic units (OTUs) across all Fynbos vegetation types, suggesting that during the winter months dispersal limitations play a role in microbial community assembly. Overall, taken together with previous studies from the region, this study provides novel insight into the processes that modulate the biogeographical patterns of soil microbes and contributes to our knowledge of factors that mediate microbial ecology in diverse ecosystems.

Carbon: Nitrogen (C:N) ratio level variation influences microbial community of the system and growth as well as immunity of shrimp (Litopenaeus vannamei) in biofloc based culture system

Biofloc technology (BFT) is a novel modern aquaculture farming technique used to reduce toxic nitrogen concentration, act as in situ food source and eradicate pollutants using carbon and therefore to control C:N ratio in an aquaculture system. In this study, effect of different C:N ratios of a biofloc based system on water quality such as the level of Total ammonia nitrogen (TAN) nitrite-nitrogen (NO2−–N) and nitrate nitrogen (NO3−–N) were explored. Further, the growth and immunity status of shrimp L. vannamei under the influence of different C:N ratios were evaluated. Two of the C:N ratios (15 and 20) could significantly (P < 0.05) reduce TAN, NO2-N and NO3-N levels (0.456 ± 0.01, 0.145 ± 0.09, and 0.102 ± 0.02 ppm) compared to control (1.45 ± 0.1, 0.749 ± 0.14 and 0.675 ± 0.16 ppm). Large variations in the frequency distribution of operational taxonomic units (OTUs) for the bacterial community in water with different C:N ration (BFT) and control were observed. Vibrios often considered as opportunistic pathogens, where the most dominant bacterial flora of water in control (79%) and C:N5 (37%) group. In C:N10, Thauera (62%) was most represented genus. Similarly, Attheyaceae (56%), followed by Peridiniaceae (30%) were the most dominant groups in C:N15 treatment. The diversity of bacterial flora was more spread in C:N20 treatments with Psychrobacter (26%), Proteobacteria (25%) and Peridiniaceae (20%) as the major groups. The trend of Vibrio dominance decreased with the increase in C:N ratios and thus confirming the dominance of heterotrophic bacteria in high C:N ratio groups. Upon challenge with pathogens, shrimps from C:N10, C:N15 and C:N20 groups showed significantly higher survival (P < 0.05) compared to the C:N5 and control group. Similarly, better growth rate was also observed in BFT tanks compared to control both during the culture and at harvest. Comparatively higher expression of four immune-related genes (ras-related nuclear gene (RAN), serine proteinase gene (SP), prophenoloxidase activating enzyme (PPAE), and crustin were observed in different C:N ratio ponds than control and these were in increasing trend with the C:N ratio. Gene expression analysis showed that the transcripts of those immune genes were significantly increased among all C:N treatments than that of control. Overall, these findings demonstrated that with optimum C:N ratio, BFT can be used to optimize the bacterial community composition for both optimal water quality and optimal shrimp health. This study thus indicates the possibility of obtaining better performance of L. vannamei culture with proper adjustment of C:N ratio in a biofloc based system.

A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics.

Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction. The maps were scanned to highlight the distribution of bacteria commonly claimed as probiotics, such as bifidobacteria and lactobacilli, and of butyrate-producing colon bacteria, such as Eubacterium spp. and Faecalibacterium prausnitzii. The analyses highlighted 24 OTUs eligible as putative probiotics. Eleven and nine species were prevalently associated with the GM of CF and HC subjects, respectively. Their KEGG prediction provided differential CF and HC pathways, indeed associated with health-promoting biochemical activities in the latter case. GM profiling and KEGG biomarkers concurred in the evaluation of nine bacterial species as novel putative probiotics that could be investigated for the nutritional management of CF patients.

Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea.

AIMTo investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea.METHODSFollowing 2 d of adaptive feeding, 12 specific pathogen-free Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics (23.33 mL·kg-1·d-1) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units (OTUs) was carried out after amplification and sequencing.RESULTSOTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups (P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively.CONCLUSIONAntibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.

Heart failure is associated with depletion of core intestinal microbiota.

AimsIn spite of current medical treatment approaches, mortality of chronic heart failure (HF) remains high and novel treatment modalities are thus urgently needed. A recent theory proposes a possible impact of the intestinal microbiome on the incidence and clinical course of heart failure. This study sought to systematically investigate, if there are specific changes of the intestinal microbiome in heart failure patients.Methods and resultsThe intestinal microbiome of 20 patients with heart failure with reduced ejection fraction due to ischemic or dilated cardiomyopathy was investigated by applying high‐throughput sequencing of the bacterial 16S rRNA gene. Microbial profiles were compared to those of matched controls in which heart failure was ruled out by clinical assessment and NT‐proBNP serum levels (n = 20). According to the Shannon diversity index (which measures the intra‐individual alpha‐diversity) based on the distribution of operational taxonomic units (OTUs), HF cases showed a nominally significantly lower diversity index compared to controls (P nom. = 0.01), and testing for genera abundance showed a tendency towards a decreased alpha diversity of HF patients. Beta‐diversity measures (inter‐individual diversity) revealed a highly significant separation of HF cases and controls, (e.g. P weighted UniFracv = 0.004). Assessing the individual abundance of core measurable microbiota (CMM), a significant decrease of Coriobacteriaceae, Erysipelotrichaceae and Ruminococcaceae was observed on the family level. In line with that, Blautia, Collinsella, uncl. Erysipelotrichaceae and uncl. Ruminococcaceae showed a significant decrease in HF cases compared to controls on the genus level.ConclusionsHeart failure patients showed a significantly decreased diversity of the intestinal microbiome as well as a downregulation of key intestinal bacterial groups. Our data point to an altered intestinal microbiome as a potential player in the pathogenesis and progression of heart failure.

Responses of soil inhabiting nitrogen-cycling microbial communities to wetland degradation on the Zoige Plateau, China

The wetlands on the Zoige Plateau have experienced serious degradation, with most of the original marsh being converted to marsh meadow or meadow. Based on the 3 wetland degradation stages, we determined the effects of wetland degradation on the structure and relative abundance of nitrogen-cycling (nitrogen-fixing, ammonia-oxidizing, and denitrifying) microbial communities in 3 soil types (intact wetland: marsh soil; early degrading wetland: marsh meadow soil; and degraded wetland: meadow soil) using 454-pyrosequencing. The structure and relative abundance of nitrogen-cycling microbial communities differed in the 3 soil types. Proteobacteria was the predominant phylum in most soil samples but the most abundant soil nitrogen-fixing and denitrifying microbial bacteria differed at the class, order, family, and genus levels among the 3 soil types. At the genus level, the majority of nitrogen-fixing bacterium sequences related to Bradyrhizobium were from marsh and marsh meadow soils; whereas those related to Geobacter originated from meadow soil. The majority of ammonia-oxidizing bacterium sequences related to Nitrosospira were from marsh (except for the 40-60 cm layer), marsh meadow and meadow soils; whereas those related to Candidatus Solibacter originated from 40-60 cm layer of marsh soil. The majority of denitrifying bacterium sequences related to Candidatus Solibacter and Anaeromyxobacter were from marsh and meadow soils; whereas those related to Herbaspirillum originated from meadow soil. The distribution of operational taxonomic units (OTUs) and species were correlated with soil type based upon Venn and Principal Coordinates Analysis (PCoA). Changes in soil type, caused by different water regimes were the most important factors influencing compositional changes in the nitrogen-fixing, ammonia-oxidizing, and denitrifying microbial communities.

Abstract 13745: Heart Failure is Associated With Depletion of Core Intestinal Microbiota

Introduction: Despite current medical treatment approaches, mortality of chronic heart failure (HF) remains high. Novel treatment modalities are thus urgently needed. A recent theory proposes a possible impact of the intestinal microbiome on the incidence and clinical course of HF. This study sought to investigate, if there are specific changes of the intestinal microbiome in HF patients. Methods and Results: The intestinal microbiome of 20 patients with HF with reduced ejection fraction due to ischemic or dilated cardiomyopathy was investigated applying high-throughput sequencing of the bacterial 16S rRNA gene. Microbial profiles were compared to those of healthy matched controls (n=20). According to the Shannon diversity index (measuring the intra-individual alpha-diversity) based on the distribution of operational taxonomic units, HF cases showed a nominally significantly lower diversity index compared to controls (P nom. =0.01), testing for genera abundance showed a tendency towards a decreased alpha diversity of HF patients. Beta-diversity measures (inter-individual diversity) revealed a significant separation of HF cases and controls, (e.g. P weighted UniFrac =0.004). Assessing the individual abundance of core measurable microbiota, a significant decrease of Coriobacteriaceae , Erysipelotrichaceae and Ruminococcaceae was observed on the family level. In line, Blautia , Collinsella , Erysipelotrichaceae and Ruminococcaceae showed a significant decrease in HF cases on the genus level. Conclusions: HF patients showed a significantly decreased diversity of the intestinal microbiome as well as a downregulation of key intestinal bacterial groups. Our data point to an altered intestinal microbiome as a potential target in the pathogenesis and progression of HF. Figure: Differences of taxonomic groups between HF pat. and controls. ns: not significant (p&gt;0.05), *: p&lt;0.05, **: p&lt;0.01, ***: p&lt;0.001. before/after correction for multiple testing.

Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system.

BackgroundBiofloc technology (BFT), a rearing method with little or no water exchange, is gaining popularity in aquaculture. In the water column, such systems develop conglomerates of microbes, algae and protozoa, together with detritus and dead organic particles. The intensive microbial community presents in these systems can be used as a pond water quality treatment system, and the microbial protein can serve as a feed additive. The current problem with BFT is the difficulty of controlling its bacterial community composition for both optimal water quality and optimal shrimp health. The main objective of the present study was to investigate microbial diversity of samples obtained from different culture environments (Biofloc technology and clear seawater) as well as from the intestines of shrimp reared in both environments through high-throughput sequencing technology.ResultsAnalyses of the bacterial community identified in water from BFT and “clear seawater” (CW) systems (control) containing the shrimp Litopenaeus stylirostris revealed large differences in the frequency distribution of operational taxonomic units (OTUs). Four out of the five most dominant bacterial communities were different in both culture methods. Bacteria found in great abundance in BFT have two principal characteristics: the need for an organic substrate or nitrogen sources to grow and the capacity to attach to surfaces and co-aggregate. A correlation was found between bacteria groups and physicochemical and biological parameters measured in rearing tanks. Moreover, rearing-water bacterial communities influenced the microbiota of shrimp. Indeed, the biofloc environment modified the shrimp intestine microbiota, as the low level (27 %) of similarity between intestinal bacterial communities from the two treatments.ConclusionThis study provides the first information describing the complex biofloc microbial community, which can help to understand the environment-microbiota-host relationship in this rearing system.

Elevation gradient of soil bacterial communities in bamboo plantations.

BackgroundElevation trends of macro organisms have long been well studied. However, whether microbes also exhibit such patterns of elevation change is unknown. Here, we investigated the changes in bamboo forest soil bacterial communities along six elevation gradients, from 600 to 1800 m a.s.l. in Mt. Da-an, a subtropical montane area in Nantou county at central Taiwan.ResultsData from 16S rRNA gene clone libraries revealed that more than 70 % of the six communities contained Acidobacteria and Proteobacteria, although the relative abundance differed. Nonmetric multidimensional scaling analysis of the distribution of operational taxonomic units showed differences in bamboo soil bacterial communities across gradients. The bacterial communities at 1000 and 1200 m showed greater diversity than the communities at both lower (600 and 800 m) and higher (1400 and 1800 m) elevations. In contrast to the bacterial community trend, soil C and N and microbial biomass properties increased linearly with elevation.ConclusionThe bamboo soil bacterial community could interact with multiple factors such as soil organic matter content and temperature, for differences in composition and diversity with change in elevation.

Metals other than uranium affected microbial community composition in a historical uranium-mining site.

To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

한국 남부 지역별 돼지 장내 미생물생태 비교분석

Since the banning of antibiotic growth promoters (AGPs), the death of livestock has been increased, thus there is a strong demand for AGP-alternatives. Modulation of gut microbiota has been reported to affect host physiological functions and suggested to be a novel approach for developing AGP-alternatives. However, little has been understood about livestock gut microbiota compared to that of humans. We conducted preliminary study provide fundamental information regarding to regional differences in swine gut microbiota. Swine fecal samples were obtained from farms in Jeju (n=40), Gwangju (n=28), and Haenam (n=30). MiSeq was used to sequence 16S rRNA V4 region, and Mothur pipeline (Schloss et al., 2009) was used for data processing. A total of 5,642,125 reads were obtained and 3,868,143 reads were remained after removing erroneous reads. Analysis of taxonomic composition at the phylum level indicated greater abundance of Firmicutes among Jeju swine, and cluster analysis of distribution of operational taxonomic units also showed regional differences among swine gut microbiota. In addition, correlation analysis between non-metric multidimensional scaling and abundance of phyla suggested that the phyla Actinobacter, Verrucomicrobia, Firmicutes, and Fibrobacteres were driving factors for the regional differences. Livestock gut microbiota may be affected by diet and practices in farms. Our results indicated significant regional differences in swine gut microbiota, suggesting that future livestock gut microbiota studies should be designed with the regional differences in mind.

High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities.

Viruses in the order Picornavirales infect eukaryotes, and are widely distributed in coastal waters. Amplicon deep-sequencing of the RNA dependent RNA polymerase (RdRp) revealed diverse and highly uneven communities of picorna-like viruses in the coastal waters of British Columbia (BC), Canada. Almost 300 000 pyrosequence reads revealed 145 operational taxonomic units (OTUs) based on 95% sequence similarity at the amino-acid level. Each sample had between 24 and 71 OTUs and there was little overlap among samples. Phylogenetic analysis revealed that some clades of OTUs were only found at one site; whereas, other clades included OTUs from all sites. Since most of these OTUs are likely from viruses that infect eukaryotic phytoplankton, and viral isolates infecting phytoplankton are strain-specific; each OTU probably arose from the lysis of a specific phytoplankton taxon. Moreover, the patchiness in OTU distribution, and the high turnover of viruses in the mixed layer, implies continuous infection and lysis by RNA viruses of a diverse array of eukaryotic phytoplankton taxa. Hence, these viruses are likely important elements structuring the phytoplankton community, and play a significant role in nutrient cycling and energy transfer.