SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Topical antimicrobial treatments elicit shifts to resident skin bacterial communities and reduce colonization by Staphylococcus aureus competitors

The skin microbiome is a complex ecosystem with important implications for cutaneous health and disease. This includes its ability to educate the immune system and promote key epidermal barrier functions during infection. Despite their widespread use, the effects of topical antibiotics and antiseptics on these communities have been largely understudied. Instead the majority of work has focused on their effect in pathogenic bacteria, with little regard for their influence on broader communities. Here, we report the longitudinal impact of topical antibiotics and antiseptics on skin bacterial communities. In response to antibiotics, cutaneous populations exhibited an immediate and long-term shift in bacterial residents. By contrast, antiseptics elicited only minor changes to underlying communities. Upon deeper analysis, we detected a conserved decrease in Staphylococcus residents, a group which varied greatly in response to both antimicrobial and environmental pressures. These particular inhabitants were also shown to compete with Staphylococcus aureus for colonization at the skin surface, a stable effect which extended to multiple resident Staphylococcus species. This study demonstrates that antimicrobial drugs have distinct and durable effects on skin bacterial residents, and that these alterations have important ramifications for infection by pathogenic bacteria such as S. aureus.

Biome: root:Host-associated:Mammals:Skin
The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut

16S rRNA gene amplicon libraries generated from jejunal contents, ileal contents, ileal contents, and feces ofmice housed in static or ventilated housing, with aspen or paperchip bedding, and with one of three commercially available rodentchows, for thirteen weeks, in a fully crossed study design

Biome: root:Host-associated:Mammals:Digestive system
16S amplicons New Zealand agricultural soils

This study consists of soil samples collected from pastures under a range of land uses and across three time points (May 2014, Nov 2014, May 2015

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Perth Otitis Media Microbiome (biOMe) Study (16S rRNA amplicon data)

Recurrent acute otitis media (rAOM; recurrent ear infections) is a common disease in childhood. We characterised the microbiome of rAOM-prone and rAOM-resistant children to identify novel pathogens and potentially protective commensal bacteria, which may guide the development of more effective therapies.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
manure metagenome Targeted loci environmental

Spontaneous foaming in deep-pit swine manure storage accumulates methane and is a threat to the welfare of both human and animal in pork production industry. To understand the microbial drivers behind the foaming manure methane accumulation, we collected pit manure samples from barns across Iowa for 13 months. We integrated swine feed information, manure characteristics, bacterial community (16S rRNA gene amplicon sequencing), and methanogen communities (mcrA gene amplicon sequencing to identify the key characteristics and microbial organisms that were unique in foaming and non-foaming pit-manure. By using correlation analysis, we identified the potential microbial organisms that could influence the pit-manure community structures and potentially be used in foaming manure mitigation.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
METSIM gut microbiome

The gut microbiome is complex and metabolically active community that directly influences host phenotype. In this study, we profiled gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finnish men collected from the population-based Metabolic Syndrome In Men (METSIM) study.

Biome: root:Host-associated:Human:Digestive system
Patterns in the skin microbiota differ in children and teenagers between rural and urban environments

The skin protects from outer threats and this function is supported by commensal microbes. Alterations in skin microbiota are linked with common dermatological diseases. Thus, it is central to understand what drives these alterations. We show that the age and the living environment are associated with the composition of individual skin microbiota. The effect of living environment seems to be strongest in young children, which is notable as the first years of life are most chritical for immune system development in cross-talk with microbiota. Age-related skin physiology and lifestyle also importantly shape microbiota. In conclusion, children growing-up in contrasting environments are exposed to different microbial environment, which may influence their future health through the altered development of microbiota.

Biome: root:Host-associated:Human:Skin
Unraveling the faecal microbiota and functional capacity associated with feed efficiency in pigs

The data is used for unraveling the faecal microbiota and functional capacity associated with feed efficiency in pigs

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Response of soil bacteria to anthropogenic soil variables at large spatial scales

We sought to determine the relative influences of spatial and environmental factors on entire bacterial communities and individual taxa, in both natural and human-impacted soils in the upper North Island of New Zealand. We conducted 16S rRNA (v3-v4 region) amplicon sequencing on soil samples from 110 native forests, plantation forest, horticultural or pastoral sites, which constitute the dominant land uses within temperate climate zones. These sites were located between 5 m and 300 km apart. This bacterial data was paired with extensive site metadata to determine which environmental variables were correlated with changes in bacterial community composition as a whole, as well as with changes in the abundance of specific taxa.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Microbiome of high and low methane-emitting sheep (3633 progeny)

Bacterial 16S rRNA genes were amplified from sheep rumen contents to study heritability of the rumen microbiome in regards to host genotype and methane phenotype.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Genetic associaiton with vaginal microbiome in Korean twins

We characterized the vaginal microbiome from 542 females including 222 monozygotic and 56 dizygotic twins aged 29-58 years and investigated the genetic contribution on the vaginal microbiome.

Biome: root:Host-associated:Human:Reproductive system:Vagina
Rumen contents Targeted Locus (Loci)

Rumen microbial communities of sheep fed different diets

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
DIPP Stool Metagenome

16S rRNA and metagenomes DIPP microbiome study

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Drinking water distribution system biofilm samples Metagenome

This project reveals the community structure and composition of biofilms from an urban drinking water distribution system across two years.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
Metcalf_Mouse_Decomp_Forensics_2011_18S

Establishing the time since death or postmortem interval (PMI) is critical in the initial stages of death investigations, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess PMI, but errors can range on the scale of days, weeks or season depending on the scenario1. Limitations of forensic entomology include uncertainty in the interval between death and initial egg deposition2, lack of insects during particular weather events or seasons3, and regionally specific blowfly larval growth curves and insect communities4. Microbes may provide a novel method for estimating PMI that might avoid many of these limitations, because microbes are ubiquitous in the environment, located on humans before death, and can be reliably quantified using high-throughput DNA sequencing. However, the feasibility of using microbes forensically has yet to be rigorously tested, and we must determine whether microbial community change is sufficiently measurable and directional during decomposition to allow accurate predictions. Here, we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing estimates of PMI to within ~3 days over 48 days, and provide insight into the ecological factors underlying succession of bacteria and microbial eukaryotes within the decomposing corpse system. Our results suggest that microbial community data can be developed into a forensic tool for estimating PMI.

Biome: root:Host-associated:Mammals
Global patterns of microbial diversity associated with eelgrass, Zostera marina

Plant-associated microorganisms are essential for their hosts'' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. We focus on the microbial communities associated with Zostera marina, a marine foundation species found throughout the Northern Hemisphere, by sampling microbial communities present on the leaf and root surfaces of 129 eelgrass individuals and sequencing amplified fragments of the V4 region of the 16S rRNA gene on an Illumina MiSeq. Additionally, we sampled microbial communities from adjacent water and sediments to highlight important differences in the communities compared to those associated with plants. This study will allow us to compare global differences and detect assembly mechanisms of the microbial communities associated with roots.

Biome: root:Host-associated:Plants:Root
Gut microbiota community and functions of mouse exposed to single As, single Fe, and combined As and Fe

Mice were fed with pure water, 3mg/L As, 5mg/L Fe, and  3mg/L As + 5mg/L Fe for 90 days. Then, the fecal samples were collected, and genomic DNA was extracted  by FastDNA SPIN Kit for Soil (Qiagen, CA). Genomic DNA was amplified with a set of primers targeting the hypervairable V3 and V4 regions of 16S rRNA gene. The PCR products were quantified using Nanodrop and was sent out for pyrosequencing on the Roche 454 FLX Titanium platform. High-throughput sequencing for mouse fecal genomic DNA using Illumina Hiseq 2000 was performed to identify the function genes of gut microbiota.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
bovine gut metagenome Metagenome

In this study, we hypothesized that specific bacterial features influence feed efficiency phenotype of beef cattle. Rumen bacterial community composition from two cohorts of animals (heifers and steers) was determined through 16S rRNA gene sequencing to identify differentially abundant bacterial groups across varying feed efficiency phenotypes. Based on the differential abundant bacterial groups, models were built and tested to explain the variation in feed efficiency traits (average daily gain, average daily dry matter intake, and gain-to-feed efficiency).

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Saliva microbiome of pig in Japan

Metagenomic sequences of microbiome obtained from pig saliva in Japan

Biome: root:Host-associated:Mammals:Digestive system:Oral cavity:Buccal mucosa
Preparing for the manned Mars journey: Microbiome dynamics in the confined MARS 500 habitat during simulated Mars flight and landing

The MARS 500 project was the first full duration simulation of a manned flight to Mars. For 520 days, a six-man crew lived like astronauts in a specifically designed and hermetically sealed spacecraft-like environment. The MICHAm (MIcrobial ecology of Confined Habitats and humAn health, modified) study aimed to survey the microbial distribution and its community structure within the facility from the start to the end of the simulation study, and to investigate the impact of confinement. Therefore, the microbial load and biodiversity in the air and on surfaces as well as their changes over time were monitored.The cultivation approach showed that the overall microbial inventory in the air and on different surfaces was moderate compared to other non-confined rooms (air: 0 to 716 CFU/m3; average=86 CFU/m3; surface: 0 to 29,760 CFU/10 m2; average=675 CFU/10 m2). Despite the detection of fluctuations in microbial load over time and places, microbial hotspots were identified. Phylogenetic investigations revealed a higher diversity on surfaces than in air indicating the dominance of human-associated microorganisms (e.g. staphylococci). Besides cultivation-based analyses, the microbial community was also studied on the molecular level via PhyloChip analysis and next generation sequencing. The whole microbiome structure exhibited a significant change in structure and decrease in diversity over time, but potentially pathogenic microorganisms containing mobile elements increased during the confinement. Additionally, significantly different microbiome structures were identified for investigated modules.Since the majority of microorganisms were not harmful there was no alert and health concern due to potential danger caused by microorganisms. The scientific information obtained by our study is essential to evaluate biosafety risks, predict and mitigate the possible occurrence of biocorrosion, and improve the sanitary and hygienic quality of life for the crew inside closed habitats.

Biome: root:Engineered:Built environment
EMG produced TPA metagenomics assembly of the Skin metagenomes (human skin metagenome) data set.

The human skin metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA281366.  This project includes samples from the following biomes: Host-associated, Human, Skin.

Biome: root:Host-associated:Human:Skin
Characterization and Analysis of Skin- and Intestine-associated Microbiomes of Fish in the Lower Northwest Passage of Nunavut, Canada (2019)

The Towards a Sustainable Fishery for Nunavummiut (TSFN) Project seeks to increase our understanding of the fisheries resources in the lower Northwest Passage in partnership with Nunavummiut communities. Our goal is to use genomic, demographic, physiological and microbial analysis to inform strategies to retain genetically-diverse and healthy stocks for the sustainable supply of high quality fish to Inuit communities. Genetic analysis will allow the identification of fish populations, but it is also important to assess the health of this resource. We are therefore characterizing fish with respect to their microbial consortia.

Biome: root:Host-associated:Fish
Microbiota associated with Daphnia exhibiting genetic variation in behavior

In many organisms, host-associated microbial communities are acquired horizontally after birth. This process is believed to be shaped by a combination of environmental and host genetic factors. We examined whether genetic variation in animal behavior could affect the composition of the animals microbiota in different environments. The freshwater crustacean Daphnia magna is primarily planktonic, but exhibits variation in the degree to which it browses in benthic sediments. We performed an experiment with clonal lines of D. magna showing different levels of sediment-browsing intensity exposed to either bacteria-rich or bacteria-poor sediment or whose access to sediments was prevented. We find that the bacterial composition of the environment and genotype-specific browsing intensity together influence the composition of the Daphnia-associated bacterial community. Exposure to more diverse bacteria did not lead to a more diverse microbiome, but greater abundances of environment-specific bacteria were found associated with host genotypes that exhibited greater browsing behavior. Our results indicate that, although there is a great deal of variation between individuals, behavior can mediate genotype-by-environment interaction effects on microbiome composition.

Biome: root:Host-associated:Animal
Selective maternal seeding and rearing environment shape the colonization and development of the piglet gut microbiome from birth to weaning

The early-life gut microbiome establishment has long-term implications for neonate health and immune system development. However, the acquisition patterns of the early-life microbiome in piglet gut is largely unknown. Here, microbiota of 1119 samples were characterized to longitudinally assess the transmission contribution of the maternal and environmental microbiota on the colonization and development from birth through weaning. Source tracking analysis revealed that the contribution of various microbial sources on the microbiome of was gradually changed over time. The neonatal microbiota was sparsely populated and predominantly comprised of maternal vaginal microbiota that increased gradually from day 0 to day 3, and decreased till day 28. However, with the increasing piglet age, the microbiome were more associated with the floor and sows feces. Additionally, the intestinal microbial diversity, composition and function significantly changed with the age of piglets. 30 age-discriminatory bacterial taxa were identified with distinctive time-dependent changes in their relative abundance, which reflected probable selection within or adaptations of piglet gut microbiota to maternal and environmental sources. Our results demonstrated that the sow vagina, feces and floor are the primary bacterial sources for the early gut microbiota colonization in piglets, which highlights the importance of the health of sows rearing environment especially the floor to the development of the piglet gut microbiome.

Biome: root:Host-associated:Mammals:Digestive system
Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa

Linear growth delay (stunting) affects roughly 155 million children under the age of five worldwide. Treatment has been limited by a lack of understanding of the underlying pathophysiological mechanisms. Stunting is most likely associated with changes in the microbial community of the small intestine, a compartment vital for digestion and nutrient absorption. Efforts to better understand the pathophysiology have been hampered by difficulty of access to small intestinal fluids. Here, we describe for the first time the microbial community found in the upper gastrointestinal tract of stunted children. We studied 46 duodenal and 57 gastric samples from stunted children as well as 404 fecal samples from stunted and non-stunted children aged 2-5 years living in Bangui, Central African Republic and in Antananarivo, Madagascar, using 16S Illumina Amplicon sequencing and semi-quantitative culture methods. The vast majority of the stunted children showed small intestinal bacterial overgrowth dominated by bacteria that normally reside in the oropharyngeal cavity. There was an overrepresentation of oral bacteria in fecal samples of stunted children opening the way for developing non-invasive diagnostic markers. In addition, E. coli/Shigella sp. and Campylobacter sp. were found to be more prevalent in stunted children, while Clostridia, well-known butyrate producers, were reduced. Our data suggest that stunting is associated with a microbiome decompartmentalization of the gastrointestinal tract characterized by an increased presence of oropharyngeal bacteria from the stomach to the colon, hence challenging the current view of stunting arising solely as a consequence of small intestine overstimulation through recurrent infections by enteric pathogens.

Biome: root:Host-associated:Human:Digestive system
Sheep feces, epithelial and maternal samples Raw sequence reads

Development of micro biome of lambs

Biome: root:Host-associated:Mammals
Cell phone and shoe swabs across the USA Raw sequence reads

These are raw sequence reads from Illumina 16S sequencing of swabs collected from cell phones and shoes across the USA.

Biome: root:Mixed
Seasonal changes of the nasal microbial diversity of pig farmers

Background: Prior studies have demonstrated an influence of the environment on the human nasal microbiota, particularly in the case of pig farming. However, very little is known about the impact of season on the dynamics of the microbiota in a pig farm setting. Methods: We performed a longitudinal study, investigating the changes in the nasal microbiota of different samples collected in the four seasons (winter, spring, summer and fall). We collected samples from 30 pig farms in Switzerland in each season from 2014-2015. This included nasal swabs from pigs (n=225), air samples taken in the pig confinement building (n=105), and nasal swabs from pig farmers working in these pig farms (n=154 from 48 pig farmers). As controls, nasal swabs from cow farmers (n=56 from 18 cow farmers) and individuals with no contact with farm animals (n=69 from 24 non-exposed individuals) were collected. Analysis of the microbiota was performed based on 16S rRNA high-throughput sequencing utilizing the Illumina MiSeq platform and the recently developed DADA2 pipeline. Results: Alpha-diversity values were generally higher in samples received in winter with the exception of samples from the non-exposed controls which displayed low alpha-diversity values throughout the seasons with no significant differences. The microbial structure of pig farmers, cow farmers and non-exposed individuals was significantly influenced by season. Also, the farm where the samples were taken from influenced the nasal microbiota of pig and cow farmers. There was a stronger similarity for samples that originated from the same farm as compared to samples from different farms in winter and this farm-specificity was partially or completely lost in spring, summer and fall.Conclusions: Nasal microbiota of pig farmers is affected by the regular exposure to pigs throughout the year. However, season has a very strong effect on the nasal microbiota of pig farmers, pigs, and cow farmers, as well as the airborne bacterial composition. This seasonal effect is much weaker in individuals without any contact with farm animals.

Biome: root:Mixed
Linking microbiomes of soils and foliar feeding insects

We studied the legacy effects of plants on fungal and bacterial communities in soils, roots, leaves and caterpillars.

Biome: root:Mixed
Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota

The effect of injectable antimicrobials on the NP and gut microbiota of beef cattle after feedlot placement was determined.

Biome: root:Host-associated:Mammals
Longitudinal microbiome analyses of acute myelogenous leukemia patients during induction chemotherapy


Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Chemotherapy Induced Oral Mucositis and Microbiome


Biome: root:Host-associated:Human:Digestive system:Oral
Microbiome Quality Control Project - 16S

The MBQC is a collaborative effort to comprehensively evaluate methods for measuring the human microbiome. This pilot phase includes 16S rDNA amplicon based surveys of the human microbiome.

Biome: root:Host-associated:Human:Digestive system
Hong Kong Residences Raw sequence reads

16S rRNA sequencing reads from samples of household surfaces, residents'' skin and household air in Hong Kong residences.

Biome: root:Mixed
Microbial analysis is challenged by immigration

High throughput characterisation of microbial communities is widely used as a source of information to develop strategies for improved biological processes in humans, animals and engineered systems. However, the introduction of organisms that do not contribute or grow in the system can ruin conclusions derived from the composition. In this study we sequenced samples from digesters and their influent streams to evaluate which organisms were truly growing and which were probably just continuously fed into the system.

Biome: root:Mixed