SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Total RNA-Seq on sputum samples from patients with active tuberculosis

Total RNA from sputum collected from patients with active tuberculosis (TB) was analysed by RNA sequencing. The transcription phenotype of Mycobacterium tuberculosis (Mtb) was found to resemble that of actively replicating bacteria in laboratory culture. Transcription profiling of commensal bacteria in the sputum provided further provide details in of the sputum environment. Understanding of the microbiology and microbial ecology of Mtb after release from tuberculous lesions may reveal novel opportunities to modulate the efficiency of disease transmission.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Microbial community composition in the sediment at naturally CO2-rich sites and its implications for ocean acidification research

Microbial processes are fundamental in nutrient cycling and remineralization in marine sediments. To understand how ocean acidification (OA) may influence sediment microbial diversity and activity, naturally CO2-rich sites are increasingly being used. However, the characterization of naturally CO2-rich sites is often limited to OA-related variables, neglecting additional variables that may obscure OA effects, especially when the CO2 increase is caused by geological processes. Here, we reevaluated the factors affecting changes in microbial communities at volcanic CO2 seeps in Papua New Guinea based on a comprehensive characterization of the conditions in the sediment. Microbial community composition was assessed using molecular fingerprinting and amplicon sequencing. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. In-situ microprofiles and trace element concentrations further showed a variation in the strength of the hydrothermal signature of the sediment at similar pH allowing the identification of sites which may better represent future OA than others. At these sites, changes in the microbial community may have implications for element cycling in the sediment. We recommend focusing on a detailed environmental characterization in future OA research, to ensure better comparability between studies and a more reliable selection of naturally CO2-rich sites.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Wastewater metagenomics.

Wastewater metagenomics.

Biome: root:Engineered:Wastewater
Metagenomics - bat faecal metagenome

Metagenomics - Sierre Leone bat faecal metagenome

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Marine Microbes pilot study

Pilot study for the Australian Marine Microbes project.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Transcriptome analysis of the Root, rhizosphere and soil of Oilseed rape lines that showed, high or low malate exudation.

RNA was extracted and sequenced from the root, rhizosphere and bulk soil of 7 pooled Oilseed rape genotypes, that showed; high and low malate exudation.

Biome: root:Host-associated:Plants:Rhizosphere
Annotation of Fusobacterium

Analysis of genome of the strain

Biome: root:Host-associated:Mammals:Circulatory system:Blood
Microbial Dysbiosis in gut of Acutely and Chronically SIV Infected macaques

Microbial dysbiosis has been linked to systemic immune activation and accelerated disease progression from acute HIV-1 infection to the end stage disease AIDS.  HIV-1 infection leads to a massive depletion of CD4 T cells within the gut associated lymphoid tissue.  As a part of this depletion CD4 Th17 cells are selectively killed and the mechanisms protecting the body against microbial translocation break down.  The loss of immune regulation and systemic immune activation can lead to changes in the gut microbial community.  These changes can manifest themselves as microbial dysbiosis and microbial translocation, which are believed to be key contributors to systemic immune activation and chronic inflammation.  Chronic inflammation persists in patients treated for HIV-1 and likely contributes to the high incidence of age-related diseases seen in these patients.  Using SIV as a model for HIV-1 transmission and pathogenesis; a study was conducted to determine the changes in the gut microbiota composition through cross-sectional samples of infected individuals. Rhesus Macaque fecal samples were collected from the Jejunum and Rectum and characterized by 16S rRNA Illumina Mi-Seq paired-end sequencing.  A longitudinal study was then performed using 6 infected individuals sampled across different time points of infection.  We were able to  draw important conclusions about how SIV induced changes in the immune system can impact the make-up of gut microbiota, and how the changes in microbiota could possibly impact microbial translocation and chronic inflammation.  Specifically we were able to observe increases in inflammation tolerant taxa, increases in motile taxa, and the loss of taxa important for metabolism related to immune regulation.  The data obtained could be beneficial in providing alternative or complementary treatment options and a better understanding of HIV-1 transmission and pathogenesis.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Effect of DNA extraction methods on the determination of the structure of microbial communities in the phosphogypsum waste heap soil

The aim of this project is to compare the structure of bacterial communities, created by using different DNA extraction protocols, from soil samples of the phosphogypsum waste heap in Wislinka, (Poland, Pomeranian district). The selection of proper methods is of a high importance in every research, due to its influence on the obtained results and theirs interpretation. Therefore, in this project we want to verify, whether the DNA extraction methods have a significant impact on the proper recognition of the final structure of bacterial communities. During this study, we want to determine whether the results are strongly influenced by choice of DNA extraction protocols or significant changes in experimentally estimated structure of community cannot be observed. Several evaluation studies have been performed in order to compare DNA extraction methods from soil samples. However, these studies have never compared the diversity of obtained sequences by high-throughput sequencing. In this project we want to compare not only yield and purity of extracted DNA using different isolation protocols, but also the results of the sequencing, and their impact on recognized complexity of microbial community structure estimated on their basis.  In this study we collected soil samples from the phosphogypsum waste heap in Wislinka, (Pomerania district). The heap was created from production wastes, mainly phosphogypsum and due to that fact it may be attractive place to study biodiversity of microorganisms. This study can be a valuable source of rare and unique types of bacteria living in very unique environmental conditions.

Biome: root:Environmental:Terrestrial:Soil:Mine
A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds

Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring. Here, we present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We show that metagenomics outperform traditional MIC and CFU counting in terms of predicting expected resistance based on antimicrobial consumption and demonstrate that composite pen floor samples are suited to approximate the in-animal resistomes. Finally, we show the method is sensitive enough to detect subtle differences in antimicrobial-induced resistome changes and can identify genes whose abundances are affected by antimicrobial usage. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programs and potentially of integrated One Health monitoring in all reservoirs.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Whole genome sequencing of metagenomes extracted from palms of two individuals

Whole genome sequencing of metagenomes extracted from palms of two individuals

Biome: root:Host-associated:Human:Skin
Study of the abundance of bacteria from human samples

this study contains 12 samples for the analysis of abundance of bacterial communities on human residues farm derived samples

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Dysbiosis of the fecal microbiota in the TNBS-induced Crohn?s disease mouse model

Crohn?s disease (CD) is characterized by chronic transmural inflammation. The symptom of the mice model induced by 2, 4, 6-Trinitrobenzenesulfonic acid (TNBS) is closed to human under CD condition, so this kind of animal is widely used in the related researches. Although the dysbiosis of the fecal microbiota have been proved to play an important role in the patients with CD, the composition of the gastrointestinal microbiota in the mouse model under disease condition is still unclear. In the current study, male seven-weeks BALB/c mice were anesthetized and intrarectal administrated by ethanol (ET group), TNBS in ethanol (TN group) and phosphate buffered saline (PBS) (CK group) as control. The symptoms of individuals under the CD condition were observed, and the changes of the bacterial taxonomic structure and functional composition were revealed by NGS 16S sequencing. The BALB/c mice in TN group demonstrated CD-like symptoms and the damages in the intestinal tract. The NGS 16S results exhibited that the diversity and microbial composition under CD condition are significantly different with those in ET group. The KO profile were generated from PICRUSt, and function modules such as methanogenesis (M00347) and microcin C transport system (M00349) were found enriched in the individuals in the TN group. This study proved that mouse model induced by TNBS could develop the similar symptom to CD patient, and we firstly showed the significant intestinal microbes changes both on taxonomic structure and functional composition in this mouse model.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Artic fresh water viromes (1)

Recent metagenomic studies have shown that our knowledge about viruses in nature is very scarce. We aimed to augment such knowledge by analyzing newly sequenced polar freshwater viral metagenomes (both arctic and antarctic). Previously unexplored arctic viromes were dominated by ssDNA viruses with no known relatives in the databases. Arctic and antarctic viromes were shown to differ at the fine grain level, yet we were able to find a circular contig in both environments with very high similarity.

Biome: root:Environmental:Aquatic:Freshwater
Rainforest Soil

Many natural ecosystems are efficiently degrading lignocellulose and harbor enzymes that could potentially be harnessed for the production of next generation biofuels from plant biomass. We have used shotgun metagenome sequencing to provide a survey of the microbial community and potential metabolic pathways present in the tropical rain forest soil of Puerto Rico. Wet tropical forest soils are some of the most productive and diverse terrestrial ecosystems on earth. These soils are characterized by high iron concentrations and regular fluctuations between oxic and anoxic conditions on a scale of days to weeks. These dynamic conditions suggest that bacterial and archaeal processes are more important in this type of environment than in other ecosystems.

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
A core gut microbiome in obese and lean twins

We have characterized the fecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers. The results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiologic states (obese versus lean)

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Glacier Metagenome

The largest part of the Earth's microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic potential and phylogenetic diversity of a microbial assemblage present in glacial ice is presented. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. Pyrosequencing of this DNA yielded 1,076,539 reads (239.7 Mbp). The phylogenetic composition of the prokaryotic community was assessed by evaluation of a pyrosequencing-derived data set and sequencing of 16S rRNA genes. The Proteobacteria (mainly Betaproteobacteria), Bacteroidetes, and Actinobacteria  were the predominant phylogenetic groups. In addition, isolation  of psychrophilic microorganisms was performed, and 13 different  bacterial isolates were recovered. Analysis of the 16S rRNA gene sequences of the isolates revealed that all were affiliated to the predominant groups. As expected for microorganisms residing in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected by analysis of the pyrosequencing-derived data set. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance  with the results of the phylogenetic samples, in which mainly  aerobic and facultative aerobic bacteria were detected, genes  typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected. Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
Wheat Rhizosphere, John Innes Centre

The interaction between microbes and plants in the region around plant roots (rhizosphere) is a key determinant of plant productivity. Here we use meta-transcriptomic sequences of mRNA extracted from 4 pooled 1g wheat rhizosphere soil samples to map metabolic interactions in the rhizosphere.

Biome: root:Environmental:Terrestrial:Soil
Windshield splatter

How many species inhabit our immediate surrounding? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. Combined with next-generation sequencing this approach allows for species identification. Here we describe an application of this methodology to two geographic locations within the Northeastern United States. We identified 61 arthropod and 39 plant species, seven of which showed significant difference in the relative abundance between the two localities. Importantly, we developed a novel robust computational framework for the comparison of relative species abundances between geographic locations, which can be used in other read-count-based applications of next-generation sequencing, such as comparison of expression levels. 
The main aim of our study was to contrast eukaryotic species differences between two distinct geographical location in northeastern United States. DNA, isolated from the material stuck to the tapped front bumper of a car driven in these locations, was sequenced using 454 (Roche) FLX pyrosequencing technology.

Biome: root:Environmental:Air
The Metagenome of the deep chlorophyll maximum in the Mediterranean studied by direct and fosmid library 454 pyrosequencing

The Deep Chlorophyll Maximum (DCM) is a zone of maximal photosynthetic activity, generally located towards the base of the photic zone in lakes and oceans. The DCM in the Mediterranean is a seasonal phenomenon. The metagenome from a single sample of a mature Mediterranean DCM community has been 454 pyrosequenced both directly and after cloning in fosmids. The comparison between the two approaches revealed a bias in the fosmid libraries against low GC DNA and specifically against the two most dominant members of the community, Candidatus Pelagibacter and Prochlorococcus marinus subsp. pastoris, thus unexpectedly providing a feasible method to obtain large genomic fragments from other less prevalent members of this community. This study is the first to be carried out at this sequencing depth (ca. 600 Mbp combining direct and fosmid sequencing) at any DCM. Our results indicate a microbial community massively dominated by the high-light adapted P. marinus subsp. pastoris, Synechococcus sp. and the heterotroph Candidatus Pelagibacter. The sequences retrieved were remarkably similar to the existing genome of P. marinus subsp. pastoris with a nucleotide identity over 98%. Besides, we found a large number of cyanophages that could prey on this microbe although sequence conservation was much lower. The high abundance of phage sequences in the cellular size fraction indicated a remarkably high proportion of cells suffering phage lytic attack. In addition, several fosmids clearly belonging to Group II Euryarchaeota were retrieved and recruited many fragments from the total DNA sequencing suggesting that this group might be quite abundant in this habitat.
We have extracted metagenomic DNA from the pico-planktonic 5-0.2 μm size fraction (mostly prokaryotic cells) from a single sample obtained in mid October at 50 m depth and analyzed the DNA from this sample (without cloning or amplification) by 454 pyrosequencing (hereafter referred to as Direct Sequencing, DS). We also used 454 to sequence ca. 1152 randomly selected fosmid clones from a metagenomic fosmid library constructed from the same DNA sample. Here we compare the output from both methods and the picture of the microbial community that they provide.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Kimchi metagenome

Kimchi, the Korean culture's traditional food, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation. Metagenomic DNA was extracted from kimchi samples obtained periodically and followed by sequencing using a 454 GS-FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera; Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of MG-RAST revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophage during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.
We have extracted metagenomic DNA from fermented food kimchi and sequenced the DNA from this sample by 454 GS-FLX titanium without cloning or amplification. Here we analyze changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation using metagenomic approaches.

Biome: root:Engineered:Food production:Fermented vegetables
Human Gut Microbiome in Crohn's Disease

Inflammatory bowel diseases (IBD), such as Crohn’s disease, are chronic, immunologically mediated disorders that have severe medical consequences. The current hypothesis is that these diseases are due to an overly aggressive immune response to a subset of commensal enteric bacteria. Studies to date on IBD have suggested that the disorder may be caused by a combination of bacteria and host susceptibility; however the etiologies of these diseases remain an enigma. 
In this application, we propose to develop and demonstrate the ability to profile Crohn’s disease at an unprecedented molecular level by elucidation of specific biomarkers (bacterial strains, genes, or proteins) that correlate to disease symptoms. To achieve this goal, we will employ a multidisciplinary approach based on metagenomic and metaproteomic molecular tools to elucidate the composition of the commensal microbiota in monozygotic twins that are either healthy or exhibit Crohn’s disease (for concordant, both are diseased; for discordant, one is healthy and one is diseased). 
The central hypotheses of this proposal are (1) that specific members and/or functional activities of the gastrointestinal (GI) microbiota differ in patients with Crohn’s disease as compared to healthy individuals, and (2) that it will be possible to elucidate microbial signatures which correlate with the occurrence and progression of this disease by integration of data obtained from 16S rRNA-based molecular fingerprinting, metagenomics, and metaproteomics approaches. To address these hypotheses, three specific aims are proposed: 1) Obtain data on community gene content (metagenome) in a subset of healthy twins and twins with Crohn’s Disease to assess potential differences in the metabolic capabilities of the gut microbiota associated with CD, 2) Obtain data on community protein content (metaproteome) in a subset of healthy twins and twins with Crohn’s Disease to assess the state of expressed proteins associated with CD, 3) Apply various statistical clustering and classification methods to correlate/associate microbial community composition, gene and protein content with patient metadata, including metabolite profiles and clinical phenotype. 
The ultimate goal of these efforts is to identify novel biomarkers for non-invasive diagnostics of CD and to eventually identify drug targets (i.e. bacterial strains) for cure or suppression of disease symptoms. 
PUBLIC HEALTH RELEVANCE: This study aims to unravel the contribution of the bacteria that normally inhabit the human gastrointestinal tract to Crohn’s disease by using a multidisciplinary approach to study changes in the structure and function of gut microbial communities in three sets of patient cohorts who have Crohn’s disease. These results will be compared with those obtained from the study of healthy individuals and have the potential to identify new biomarkers of disease severity, location, and progression.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal