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opencc-by-4.0Feb 2018View details →

The molecular investigation of Blood cockles (Anadara granosa) associated bacterial communities using 16S rRNA sequencing

This data on the bacterial communities and its diversity associated with Anadara granosa. The Anadara granosa samples were obtained from two major estuaries in Penang, Malaysia using a culture dependent and 16S rRNA sequencing approach.

opencc-by-4.0Aug 2024View details →

Impact of transgenic maize Ruifeng125 on diversity and dy-namics of bacterial community in rhizosphere soil

With the development of commercialized planting of genetically modified crops, their ecological security risks remain a hot topic of public concern. Insect-resistant genetically modified maize Ruifeng125 which expressing a fusion Bt protein (Cry1Ab-Cry2Aj) has obtained the application safety certificate issued by the Chinese government. To determine the effects of Ruifeng125 on the diversity and dynamics of bacterial communities, the accumulation and degradation pattern of the fusion Bt protein in the rhizosphere soil of transgenic maize were detected firstly. Results showed that the contents of Bt protein varied significantly at different developmental stages, but after straw returning to the field, over 97% of Bt proteins has been degraded quickly at the early stages (≤ 10 d) and then they were degraded at a relative slow rate. In addition, the variations of bacterial community diversity in the rhizosphere soil were detected by 16S ribosomal RNA (Rrna) high-throughput sequencing technology. A total of 44 phyla, 435 families and 842 genera were obtained by 16S rRNA sequencing, among which Proteobacteria, Actinobacia, Acidobacter Acidobacterium and Chloroflexi were the dominant taxa. At the same developmental stage, no significant differences in soil bacterial diversity were detected between Ruifeng125 and its non-transgenic control variety. Further analysis revealed that developmental stage, rather than the transgenic event, made the greatest contribution for the changes in soil microbial diversity. This research provides important information for evaluating the impacts of Bt crops on the soil microbiome and establish a theoretical foundation for their environmental safety assessment.

opencc-by-4.0Dec 2025View details →

Relative abundance tables for bacterial species, pathways, ARGs, and VFGs in "Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Insights from Metagenomic Sequencing"

Dyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. In this study, we analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and resistome in 1384 participants (895 with dyslipidemia cases and 489 controls) using shotgun metagenomic sequencing. Our results revealed that Bacteroides caccae was enriched in dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism, while Coprococcus eutactus and Coprococcus catus, known producers of short-chain fatty acids (SCFAs) in lipid regulation, and Blautia obeum, known to be positively impacted by SCFAs, were more abundant in controls. We also identified an enrichment of the dTDP-beta-D-fucofuranose biosynthesis pathway gene family, which is linked to bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris contributing strongly. Dyslipidemia cases exhibited depleted glycogen and peptidoglycan biosynthesis pathways, potentially impairing energy storage and immune function, alongside distinct metabolic profiles, including decreased pseudouridine, which may affect RNA metabolism. Furthermore, we observed a higher abundance of antibiotic-resistance genes, particularly tetQ, in dyslipidemia cases, suggesting a link between gut resistome and metabolic disorders. These findings provide new insights into how dysbiosis of the gut microbiota may contribute to the pathophysiology of dyslipidemia, offering potential avenues for microbiome-based interventions in personalized medicine.

opencc-zeroDec 2010View details →

Data from: Ecological drift and local exposures drive gastrointestinal bacterial community differences among Galápagos iguana populations

Diet strongly influences the intestinal microbial communities through species sorting. Alternatively, these communicates may differ because of chance variation in local microbial exposures or species losses among allopatric host populations (i.e. ecological drift). We investigated how these forces shape enteric communities of Galápagos marine and land iguanas. Geographically proximate populations shared more similar communities within a host ecotype, suggesting a role for ecological drift during host colonization of the islands. Additionally, evidence of taxa sharing between proximate heterospecific host populations suggests that contemporary local exposures also influence the gut community assembly. While selective forces such as host-bacterial interactions or dietary differences are dominant drivers of intestinal community differences among hosts, historical and contemporary processes of ecological drift may lead to differences in bacterial composition within a host species. Whether such differences in community structure translate into geographic variation in benefits derived from these intimate microbial communities remains to be explored.

opencc-zeroDec 2012View details →

Data from: Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment

The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila–associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

opencc-zeroDec 2013View details →

Data from: Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge

We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobac- teria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus–Thermus. Statisti- cally significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, avail- able energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities.

opencc-by-4.0Apr 2021View details →

Gut bacterial communities of Lymantria xylina and their associations with host development and diets

The gut microbiota of insects has a wide range of effects on host nutrition, physiology, and behavior. The structure of gut microbiota may also be shaped by their environment, causing them to adjust to their hosts; thus, the objective of this study was to examine variations in the morphological traits and gut microbiota of Lymantria xylina in response to natural and artificial diets using high-throughput sequencing. Regarding morphology, the head widths for larvae fed on a sterilized artificial diet were smaller than for larvae fed on a non-sterilized host-plant diet in the early instars. The gut microbiota diversity of L. xylina fed on different diets varied significantly, but did not change during different development periods. This seemed to indicate that vertical inheritance occurred in L. xylina mutualistic symbionts. Acinetobacter and Enterococcus were dominant in/on eggs. In the first instar larvae, Acinetobacter accounted for 33.52% of the sterilized artificial diet treatment, while Enterococcus (67.88%) was the predominant bacteria for the non-sterilized host-plant diet treatment. Gut microbe structures were adapted to both diets through vertical inheritance and self-regulation. This study clarified the impacts of microbial symbiosis on L. xylina and might provide new possibilities for improving the control of these bacteria.

opencc-zeroJan 2023View details →

A cryopreservation method to recover laboratory- and field-derived bacterial communities from mosquito larval habitats

Mosquitoes develop in a wide range of aquatic habitats containing highly diverse and variable bacterial communities that shape both larval and adult traits, including the capacity of adult females of some mosquito species to vector disease-causing organisms to humans. However, while most mosquito studies control for host genotype and environmental conditions, the impact of microbiota variation on phenotypic outcomes of mosquitoes is often unaccounted for. The inability to conduct reproducible intra- and inter-laboratory studies of mosquito-microbiota interactions has also greatly limited our ability to identify microbial targets for mosquito-borne disease control. Here, we developed an approach to isolate and cryopreserve bacterial communities derived from lab- and field-based larval-rearing environments of the yellow fever mosquito Aedes aegypti–a primary vector of dengue, Zika, and chikungunya viruses. We then validated the use of our approach to generate experimental microcosms colonized by standardized lab- and field-derived bacterial communities. Our results overall reveal minimal effects of cryopreservation on the recovery of both lab- and field-derived bacteria when directly compared with isolation from non-cryopreserved fresh material. Our results also reveal improved reproducibility of bacterial communities in replicate microcosms generated using cryopreserved stocks over fresh material. Communities in replicate microcosms further captured the majority of total bacterial diversity present in both lab- and field-based larval environments, although the relative richness of recovered taxa as compared to non-recovered taxa was substantially lower in microcosms containing field-derived bacteria. Altogether, these results provide a critical next step toward the standardization of mosquito studies to include larval-rearing environments colonized by defined microbial communities. They also lay the foundation for long-term studies of mosquito-microbe interactions and the identification and manipulation of taxa with potential to reduce mosquito vectorial capacity.

opencc-zeroDec 2021View details →

Bacterial communities in carnivorous pitcher plants colonize and persist in inquiline mosquitoes

Background The leaves of carnivorous pitcher plants harbor diverse communities of inquiline species, including bacteria and larvae of the pitcher plant mosquito (Wyeomyia smithii), which aid the plant by processing captured prey. Despite the growing appreciation for this microecosystem as a tractable model in which to study food web dynamics and the moniker of W. smithii as a 'keystone predator', very little is known about microbiota acquisition and assembly in W. smithii mosquitoes or the impacts of W. smithii-mcirobiota interactions on mosquito and/or plant fitness. Results In this study, we used high throughput sequencing of bacterial 16S rRNA gene amplicons to characterize and compare microbiota diversity in field- and laboratory-derived W. smithii larvae. We then conducted controlled experiments in the laboratory to better understand the factors shaping microbiota acquisition and persistence across W. smithii life history. Methods were also developed to produce axenic (microbiota-free) W. smithii larvae that can be selectively recolonized with one or more known bacterial species in order to study microbiota function. Our results support a dominant role for the pitcher environment in shaping microbiota diversity in W. smithii larvae, while also indicating that pitcher-associated microbiota can persist and be dispersed by adult W. smithii mosquitoes. We also demonstrate the successful generation of axenic W. smithii larvae and report variable fitness outcomes in gnotobiotic larvae monocolonized by individual bacterial isolates during from naturally occurring pitchers in the field. Conclusions This study provides the first information on microbiota acquisition and assembly in W. smithii mosquitoes. This stusy also provides the first evidence for successful microbiota manipulation in this species. Altogether, our results highlight the value of such methods for studying host-microbiota interactions and lay the foundation for future studies to understand how W. smithii-microbiota interactions shape the structure and stablity of this important model ecosystem.

opencc-by-4.0Aug 2022View details →

Viral Regulation of Bacterial Metabolism and Community Composition across Trophic Status in Marine Environments

Table 1: Details and microbial abundances during the incubation at the three stations. Table 2: Details and parameters at the end of the incubation.

opencc-zeroJun 2023View details →

Data from: Classifying interactions in a synthetic bacterial community is hindered by inhibitory growth medium

Predicting the fate of a microbial community and its member species relies on understanding the nature of their interactions. However, designing simple assays that distinguish between interaction types can be challenging. Here, we performed spent media assays based on the predictions of a mathematical model to decipher the interactions between four bacterial species: Agrobacterium tumefaciens (At), Comamonas testosteroni (Ct), Microbacterium saperdae (Ms) and Ochrobactrum anthropi (Oa). While most experimental results matched model predictions, the behavior of Ct did not: its lag phase was reduced in the pure spent media of At and Ms, but prolonged again when we replenished with our growth medium. Further experiments showed that the growth medium actually delayed the growth of Ct, leading us to suspect that At and Ms could alleviate this inhibitory effect. There was, however, no evidence supporting such "cross-detoxification" and instead, we identified metabolites secreted by At and Ms that were then consumed or "cross-fed" by Ct, shortening its lag phase. Our results highlight that even simple, defined growth media can have inhibitory effects on some species and that such negative effects need to be included in our models. Based on this, we present new guidelines to correctly distinguish between different interaction types, such as cross-detoxification and cross-feeding.

opencc-by-4.0Aug 2023View details →

Dataset of manuscript "Divergent responses of soil bacterial and fungal communities to climate warming in an alpine tundra ecosystem"

Our study conducts a translocation experiment in the alpine tundra of the Changbai Mountains to explore how climate warming will affect soil bacterial and fungal communities in the alpine tundra and what are the underlying ecological mechanisms for their potential community changes. Soil samples (n = 24) were respectively collected during the early growing season (June 5, EGS), peak growing season (July 30, PGS), and late growing season (September 20, LGS) of 2021.  The uploaded data contains the soil properties and  OTU abundance measurements for these soil samples, as well as air and soil temperature from  June 1, 2020 to  September 15, 2021.

opencc-by-4.0Sep 2023View details →

Soil fauna-microbial interactions complexity triggers shifts in both fungal and bacterial communities under a contamination disturbance

meta.otu.june2020.txt : Willow morphological data, data related to qPCR of PAH-RHD genes and phenanthrene amounts found by GC-MS in soil, associated to the paper entitled: Soil fauna-microbial interactions complexity triggers shifts in both fungal and bacterial communities under a contamination disturbance. Files starting by 16s, its, gn and gp are data tables of bioinformatically processed amplicon sequencing data containing filtered  and rarefied counts corresponding to 4 set of genes (16S rRNA gene, fungal ITS, PAH-RHD Gram Negative and Gram Positive bacteria) and corresponding taxonomy.

Efficacy and Safety Study of Oral Solithromycin (CEM-101) Compared to Oral Moxifloxacin in Treatment of Patients With Community-Acquired Bacterial Pneumonia

ClinicalTrials.gov study NCT01756339. IPD Sharing: Not stated. Countries: 17. Publications: 1.

Safety and Efficacy Study of Ceftaroline Versus a Comparator in Pediatric Subjects With Community Acquired Bacterial Pneumonia (CABP)

ClinicalTrials.gov study NCT01530763. IPD Sharing: Not stated. Countries: 9. Publications: 1.

closedIPD-NOFeb 2026View details →

Efficacy and Safety of Faropenem in Bangladeshi Adult Patients With Community-Acquired Bacterial Pneumonia (CABP)

ClinicalTrials.gov study NCT06804096. IPD Sharing: NO. Countries: 1. Publications: 9.

closedIPD-NOFeb 2026View details →

Determining Bacterial Communities in the Lungs of HIV-infected Individuals With COPD in Uganda.

ClinicalTrials.gov study NCT04070248. IPD Sharing: NO. Countries: 1. Publications: 13.

Efficacy Study of Community-Based Treatment of Serious Bacterial Infections in Young Infants

ClinicalTrials.gov study NCT00189384. IPD Sharing: Not stated. Countries: 1. Publications: 3.

Efficacy and Safety Study of Oral CEM-101 Compared to Oral Levofloxacin in Treatment of Patients With Community-Acquired Bacterial Pneumonia

ClinicalTrials.gov study NCT01168713. IPD Sharing: Not stated. Countries: 2. Publications: 1.

Efficacy and Safety Study of Intravenous to Oral Solithromycin (CEM-101) Compared to Intravenous to Oral Moxifloxacin in Treatment of Patients With Community-Acquired Bacterial Pneumonia

ClinicalTrials.gov study NCT01968733. IPD Sharing: Not stated. Countries: 26. Publications: 1.