SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Dynamics tracheal intubation airway microbiota of ventilated patients at continuous time points via metagenomic sequencing

Abstract  Background: The use of an endotracheal tube may influence the tracheal  microbiota compositions of ventilator patients which may be the leading cause of mortality in hospital intensive care units. Our primary objective is totrack the diversity and dynamics of bacterial communities within or between the patients, and to determine whether antibiotic therapy and adrenal corticosteroids treatment might influence the harbor of human bacterial pathogens..  Methods: The samples were obtained from eight patients of ventilator with endotracheal tube from Peking University People's Hospital in Respiratory Intensive Care Unit (RICU) during a period of 15 days. The microbiota of tracheal aspirates samples from day0, 1, 3, 5,7,10 and 14 were analyzed using 454 pyrosequencing. The primers: 341F and 805R, complemented with 454 adapters and sample specific barcodes were used for PCR amplification of the 16S rRNA genes.   Results: Analysis of 736,495 high-quality sequences (92,061 reads per patient) revealed a wide range of aerobic, anaerobic, pathogenic, opportunistic, novel and uncultivable bacterial species. The composition of microbiota species were significantly distinguished between the day0 and the day14 of tracheal aspirate samples (Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Streptococcus pneumoniae). On the individual basis, the microbiota was, however, relatively stable over time. Treatment with antibiotics and adrenal corticosteroids indeed influenced the global composition of the microbiota. CONCLUSION: These results support the phenomenon of dynamics diversification of airway microbiota  in ventilated patients with tracheal intubation. Antibiotics and adrenal corticosteroids therapy may contribute to the alternation of microbiota.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system
co-fermentation of straw and swine manure with cattle swine-seeded inoculum

The spatial and temporal dynamics of microbial community in the straw and sludge, and their correlations to bioreactor performance remain to be unveiled. To address these questions, we investigated the microbial compositions and the dynamics of microbiota associated to straw and sludge during co-fermentation of straw and swine manure with cattle swine-seeded inoculum by using 16S rRNA amplicon pyrosequencing technique. There are 18 samples in total, including 9 and 9 independent samples associated with straw and sludge, respectively. each of straw or sludge associated samples includes 3 sampling time point representing different fermentation process.

Biome: root:Engineered:Bioreactor
anaerobic co-fermentation of straw and swine manure

The spatial and temporal dynamics of microbial community in the straw and sludge, and their correlations to bioreactor performance remain to be unveiled. To address these questions, we investigated the microbial compositions and the dynamics of microbiota associated to straw and sludge during co-fermentation of straw and swine manure using 16S rRNA amplicon pyrosequencing technique. There are 17 samples in total, including 9 and 8 associated with straw and sludge, respectively. each of straw or sludge associated samples includes 3 sampling time point representing different fermentation process.

Biome: root:Engineered:Bioreactor
Biofilm-forming microbiota of a full-scale biogas reactor

Biogas is a flexible carrier of renewable energy, since methane can partly substitute fossil fuels for both heat and power generation and as fuel. Anaerobic digestion of biowastes in a full-scale biogas reactor was improved by the addition of straw, while the organic loading rate (OLR) could be increased in order to gain higher methane production. The composition of microbial community on straw as biofilm carrier and in fluid reactor content was analyzed by a 16S rDNA 454 pyrosequencing. The microorganisms Candidatus Cloacomonas acidaminovorans and the methanogenic archaeum Methanoculleus dominated the biofilm on straw. Most likely a syntrophic interaction between C. acidaminovorans and the hydrogenotrophic Methanoculleus is responsible for the achievable higher biogas yield after straw addition.

Biome: root:Engineered:Biogas plant
Anaerobic enrichment culture affected by heat shock

Sludge from anaerobic digester in municipal wastewater treatment process was enriched with benzoate for over three years. This methanogenic enrichment culture was exposed to different levels of heat shock (temperature and duration). Distinct methane production profiles and microbial community structures were observed after heat shock.

Biome: root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
Electricity generation from rice bran in microbial fuel cells

Laboratory-scale single-chamber microbial fuel cells (MFCs) were inoculated with paddy-field soil and supplied with rice bran for electricity generation. Power outputs and microbiome compositions were compared between MFCs containing pure water as the liquid phase (MFC-W) and those containing mineral solution (MFC-M).

Biome: root:Engineered:Lab enrichment:Defined media
16S rRNA pyrosequencing of bacterial community associated with lightly pickled vegetables

16S rRNA pyrosequencing of bacterial community associated with lightly pickled vegetables was performed to determine the effect of the revision of prerequisite program for those minimally-processed fresh produce.

Biome: root:Engineered:Food production:Fermented vegetables
Bacterial community of Korean fish sauce

The metagenome data of Korean fish sauce were obtained by the 454 GS FLX Titanium. This metagenome data contains 19,420,342 bp. Detailed genomic analysis will give further information and insight for bacterial community of Korean fish sauce.

Biome: root:Engineered:Food production:Fermented seafood
prokaryotic community and assembly in fermentation pit muds

The raw sequences, obtained from illumina MiSeq sequencing, were processed (e.g. trimming, denoising, chimeras removing, etc.). A total of 170098 effective sequences from all (fermentation pit mud) FPM samples remained and the number of reads per sample ranged from 13613 to 14653. Based on 97% similarity of 16S rRNA gene sequences, they distributed into 4927 OTUs and each sample contained 774 to 1453 OTUs. Moreover, the coverage of effective reads per sample was higher than 94% (ranged from 94.3% to 96.4%).For the general phylogenetic composition of FPM community, a total of 33 phyla including 31 bacterial and 2 archaeal phyla, with relative abundance per sample ranged from 90.96-98.44%, were observed. Among them, 20 phyla were commonly shared by all of the FPMs, with abundances accounted for 89.21-98.34%. The dominant phyla (>10%, of total effective sequences) were Firmicutes (58%), Euryarchaeota (19%) and Bacteroidetes (11%).

Biome: root:Engineered:Solid waste:Solid animal waste
Phylogenetic identification of a hydrogel complex composed of microbially reduced graphene oxide and sewage sludge

Graphene oxide (GO) was recently shown to be an excellent anode substrate for exoelectrogens, such as Geobacter species. The enrichment of exoelectrogenic bacteria can be achieved on GO by using an electron acceptor, together with the acetate oxidization, which leads to the formation of a self-aggregated hydrogel anode with the microbially reduced GO (rGO). We investigated the applicability of GO as the anode for electricity recovery from sewage wastewaters. The project investigated prokaryotic composition of the electrically polarized two different anode-microbes complexes. i.e. rGO-micobes complex and graphite felt-microbes complexes.

Biome: root:Engineered:Lab enrichment
Phylogenetic identification of GO-reducing bacteria enriched from freshwater environments

This project conducted the phylogenetic identification of bacteria capable of respiration with an extracellular electron acceptor, graphene oxide (GO). GO is the oxidized form of graphene, a 2D honeycomb lattice of carbon. GO can be reduced to the reduced GO (rGO) by bacteria via extracellular electron transferring. Ant the rGO can facilitate the recovering electricity from bacteria. A variety of microorganisms potentially ability to reduce GO, while the reduction of GO was demonstrated by only Schewanella spp. This study enriched GO respiring bacteria from fresh water environments, and identified the enriched GO respiring bacteria by pyrosequencing targeting V4 region of 16SrRNA gene.

Biome: root:Engineered:Lab enrichment
Microbial community analysis of methanogenic enrichments

To define syntrophy-associated microbial communities, this study enriched methanogenic communities with propionate, butyrate, benzoate, acetate, formate, and H2 from two different inocula.

Biome: root:Engineered:Lab enrichment:Defined media
An innovative bioelectrochemical-anaerobic digestion-coupled system for counteracting ammonia toxicity by in-situ ammonia recovery: process performance and microbial ecology

The bacterial and archaeal communities in a bioelectrochemical-anaerobic diegstion-coupled system were sequenced by Ion Torrent Personal Genome Machine

Biome: root:Engineered:Biotransformation
Protist community structure in several habitats of the Central Arctic Ocean in summer 2011 and 2012

Protists form a major part of the Arctic ecosystem and are of great importance for biodiversity and productivity of the Central Arctic Ocean (CAO). The sea ice is considered as one of the main factors that influence protist communities. Current changes in sea ice conditions are assumed to alter protist community biodiversity and composition in ice-influenced habitats with further implications for the overall productivity of the CAO and carbon sequestration to the deep sea. We investigated the environmental factors driving protist community structure and the potential consequences of sea ice retreat on protists in the CAO. Samples were collected from the deep-chlorophyll maximum water and sea ice during August and September in 2011 and 2012. In addition, we sampled melt pond water and under-ice water during record sea ice minimum in 2012 to analyze the exchange of protist communities (i.e. number of shared operational taxonomic units, OTUs) between the different habitats under several sea ice conditions.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Impact of the Mk VI SkinSuit on skin microbiota of terrestrial volunteers and an International Space Station-bound astronaut

Microgravity induces physiological deconditioning due to the absence of gravity loading, resulting in bone mineral density loss, atrophy of lower limb skeletal and postural muscles, and lengthening of the spine. SkinSuit is a lightweight compression suit designed to provide head-to-foot (axial) loading to counteract spinal elongation during spaceflight. As synthetic garments may impact negatively on the skin microbiome, we used 16S ribosomal RNA (rRNA) gene amplicon procedures to define bacterial skin communities at sebaceous and moist body sites of five healthy male volunteers undergoing SkinSuit evaluation. Each volunteer displayed a diverse, distinct bacterial population at each skin site. Short (8 h) periods of dry hyper-buoyancy flotation wearing either gym kit or SkinSuit elicited changes in the composition of the skin microbiota at the genus level but had little or no impact on community structure at the phylum level or the richness and diversity of the bacterial population. We also determined the composition of the skin microbiota of an astronaut during pre-flight training, during an eight-day visit to the International Space Station involving two 8 h periods of SkinSuit wear, and for one month after return. Changes in composition of bacterial skin communities at five body sites were strongly linked to changes in geographical location. A distinct ISS microbiome signature was found which reversed to a pre-flight profile on return. No changes in microbiome complexity or diversity were noted, with little evidence for colonisation by potentially pathogenic bacteria. We conclude that short periods of SkinSuit wear do not compromise the healthy skin microbiome.

Biome: root:Host-associated:Human:Skin
Microbiota of caloric restricted mice by 16S

We explored the effect of caloric restriction on fecal and cecal microbiota in mice.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Characterization of tissue microbiota using the Illumina MiSeq sequencing technology after pipeline validation on Mock communities

Characterization of tissue microbiota using 16S metagenomic sequencing by Illumina MiSeq of:  - feces  - ileum  - adipose tissue   - heart  - liver  - brain  - muscle The validation of the sequencing pipeline was also assessed using Mock communities.

Biome: root:Host-associated:Mammals
metabarcoding data from marine samples

The data regards the study of polluted samples from the Mediterranean sea. The bacterial community of the samples were analysed by a 454 pyrotag experiment targetting the 16S rRNA gene partial sequences (length >100 nucleotides). The of the study was to unravel, categorize, and catalogue the diversity and ecology of microorganisms thriving in four major oil refinery polluted sites on the coastlines of Morocco, Tunisia, Egypt and Greece and three Northern polluted sites at Gulf of Genoa, strait of Messina and Syracuse.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
Role of Tissue-specific Microbiota in Initial Establishment Success of Pacific oysters (Crassostrea gigas)

We transplanted oysters from two invasive, genetically distinct invasive populations of the Wadden sea (Texel, Netherlands and Sylt, Germany, and monitored the short term microbiota shifts and colonization in different tissues during the initial phases of establishment in the new habitat. To manipulate the microbiome mismatch we treated half of the oyster with antibiotics in order to minimize the interactions between resident microbiota and new colonizers, while the other half was transplanted with their natural resident microbiome. We followed oyster survival and changes in diversity, composition and abundance of oyster-associated bacterial communities as a whole and Vibrionaceae and Arcobacter in particular, over the first five days in the new habitat. In this way, we could estimate how the composition and diversity of microbiota in different tissues contribute to success of oyster establishment in the new environment.

Biome: root:Host-associated:Mollusca
Randomized controlled trial on the impact of early live intervention with bifidobacteria on the healthy infant fecal microbiota and metabolite profile

Background: Early life colonization of the intestinal tract is a dynamic process influenced by numerous factors. The impact of probiotic-supplemented infant formula on the composition and function of the infant gut microbiota is not well defined. Objective:To determine the effect of a bifidobacteria-containing formula on the healthy human intestinal microbiome during the first year of life.Design: Double-blinded, randomized and placebo-controlled study with newborn infants assigned to a standard whey-based formula containing a total of 10(8) cfu/g of Bifidobacterium bifidum, B. breve, B. longum, B. longum subsp. infantis (intervention), or to control formula without bifidobacteria (placebo). Breast-fed controls were included. Diversity and composition of fecal microbiota were determined by 16S rRNA gene amplicon sequencing and metabolite profiles were analysed by UHP-LC mass spectrometry over a period of two years. Results: One hundred six infants were randomized to the interventional (n=48) or placebo (n=49) group; 9 infants were solely breast-fed throughout the entire intervention period of 12 months. Infants exposed to bifidobacteria-supplemented formula showed decreased occurrence of Bacteroides and Blautia spp. associated  with changes in lipids and unknown metabolites at month 1. Microbiota and metabolite profiles converged during the intervention period and long-term colonization (24 months) of the supplemented Bifidobacterium strains was not detected. Significant differences in microbiota and metabolites were detected between infants fed by breast or formula (p<0.005) and between infants born by vaginal and caesarean birth (p<0.005). No significant differences were observed between infant feeding groups regarding growth, antibiotic uptake, or other health variables (p>0.05).Conclusions: The supplementation of bifidobacteria to infant diet can modulate the occurrence of specific bacteria and metabolites during early life with no detectable long-term effects.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Microbial community of PM microbiome

We investigate the community of the PM using MiSeq-sequencing of 16S rDNA and rRNA

Biome: root:Engineered:Solid waste:Composting
Tropical urban market crop waste composting in Uganda

n a composting study as a management option for urban market crop wastes in Uganda, the population of microorganisms involved in composting were evaluated. The study covered bacteria and fungi. Bacteria were studied by means of pyrosequencing of SSU rDNA and fungi by ITS rDNA.

Biome: root:Engineered:Solid waste:Composting
Appraisal of the important PAO and GAO communities of fullscale EBPR wastewater treatment systems

The current study collectively assessed the abundance and diversity of all proposed PAO and GAO in 18 Danish fullscale wastewater treatment  plants with biological nutrient removal over a period of 9 years using 16S rRNA gene amplicon sequencing. The microbial community structure in all plants exhibited a large temporal stability during this period. Evidence for the role of the proposed PAO and GAO in EBPR varies and is critically assessed, in light of their calculated amplicon abundances, to indicate which of these are important in full-scale systems.

Biome: root:Engineered:Wastewater:Nutrient removal:Biological phosphorus removal:Bioreactor
Low FODMAP diet and probiotics in irritable bowel syndrome: a 2x2 factorial design, randomised, placebo-controlled trial

Background and aims: Feeding studies demonstrate the clinical potential of restriction of fermentable carbohydrates (low FODMAP diet, LFD) in irritable bowel syndrome (IBS). However, a placebo-controlled dietary advice study has not been conducted and the diet leads to a potentially detrimental shift in microbiota composition.Methods: A 2x2 factorial trial was undertaken in the tertiary care setting. Patients aged 18-65 years with Rome III IBS were recruited. Patients were randomised 1:1 for four weeks to a diet (sham diet vs LFD) and supplement (placebo vs probiotic), resulting in four different groups. The sham diet was equivalent in dietary restriction compared with LFD. The probiotic was multistrain (VSL#3). Patients were masked to the interventions. The primary endpoints were adequate relief of symptoms and stool Bifidobacteria abundance at four weeks. Results: 104 patients were randomised. 27 were allocated to sham diet/placebo, 26 to sham diet/probiotic, 24 to LFD/placebo and 27 to LFD/probiotic. There was no interaction between the interventions. In the intention-to-treat analysis, adequate symptom relief was higher for LFD (57%) versus sham (38%), although did not reach statistical significance (p=0.051), whereas in the per protocol analysis the higher proportion for LFD (61%) versus sham (39%) was statistically significant (p=0.043). Bifidobacteria were lower after LFD versus sham (8.8 vs 9.2 16S rRNA genes/g, p=0.008) and higher after probiotic versus placebo (p=0.019). There was no effect of LFD on microbiota diversity.Conclusions: This is the first placebo-controlled study of LFD advice in IBS, reporting adequate symptom relief that approached significance together with significantly reduced symptom scores compared with placebo.  Probiotic co-administration ameliorated the diet-induced decline in Bifidobacteria abundance.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Phloroglucinol degradation in the rumen promotes the redirection of hydrogen when methanogenesis is suppressed

Strategies to manage metabolic hydrogen ([H]) in the rumen should be considered when reducing ruminant methane emissions. However, little is known about the use of dietary treatments to stimulate rumen microorganisms capable of capturing the [H] available when methane is inhibited in vivo. The effects of a phenolic compound (phloroglucinol) on methane production, [H] flows and subsequent responses in rumen fermentation and microbial community composition when methanogenesis is inhibited were investigated in cattle. Eight rumen fistulated Brahman steers fed ad libitum with a ratio 60:40 forage:concentrate were randomly allocated in two groups receiving chloroform as antimethanogenic compound for 21 days. Following that period one group received the chloroform + phloroglucinol, whilst the other group just received the chloroform for 16 days. The chloroform treatment resulted in an increase in H2 expelled as methane production decreased with a shift in rumen fermentation towards propionate and formate at day 21 of treatment. Also OTUs assigned to Prevotella were promoted whilst archaea OTUs were decreased with the chloroform treatment as expected. The addition of phloroglucinol in the rumen resulted in a decrease of H2 expelled (g) per kg of DMI and moles of H2 expelled per mol of methane decrease compared with the chloroform only-treated animals. A shift towards acetate and a decrease in formate were observed on the phloroglucinol-treated animals. These changes in the rumen fermentation were accompanied by an increase of OTUs assigned to Coprococcus spp., which could suggest the genus is a significant contributor to the metabolism of this phenolic compound in the rumen. This study demonstrates for the first time in vivo that under methanogenesis inhibition, H2 gas accumulation can be reduced by redirecting [H] towards alternative sinks through the nutritional stimulation of microbial groups that generates metabolites of value to the host and also it might help to decrease the partial pressure of H2 in the methane-inhibited rumen.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Metagenomic analysis sweet wort

Metagenomic analysis of ivorian sweet wort(tchapalo processing)

Biome: root:Engineered:Food production:Fermented beverages
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

The gastrointestinal tracts of mammalians are sterile in utero and colonized by microorganisms immediately after delivery. The subsequent development of the infant gut microbiota involves a complex succession of microbes, driven by factors such as gestational age, mode of delivery, antibiotic use, hygiene, geographical zone and type of feeding.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon