SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
metataxonomics analysis of fungal populations in Vitis vinifera L. cv. Corvina grapes and musts

The fungal populations present in Vitis vinifera L. cv. Corvina grapes and musts were compared in two different years vintages. The comparison was carried out through ITS1-5.8S-ITS2 454-pyrosequencing. Grapes were collected from a recent vineyard located in the Italian winery region called "Valpolicella" (Sant"Ambrogio, Verona, Italy). After the harvesting, grapes were subjected to withering in a dedicated warehouse located a few kilometers far from the vineyars (<5Km). The warehouse is supplemented with automatic systems able to control and modify the internal temperature and humidity. The duration of grape withering was defined according to the regional rules for Amarone production (Paronetto and Dellaglio, 2011), which define the time in which the grapes for Amarone vinification can be mashed. The comparison of the fungal populations present in these samples sheds lights on the Amarone production, allowing the identification of the persistent fungal genera and on genera varying as suffering from seasonal environmental changes.

Biome: root:Host-associated:Plants
16s rRNA gene amplicon sequencing of 50 week-old mouse gut microbiota as performed on Illumina MiSeq and Oxford Nanopore MinION sequencer.

Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples. Sci Rep. 2016 Jul 14;6:29681. doi: 10.1038/srep29681.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Soil microcosms amended with 13C wheat Targeted Locus

To identify soil bacteria assimilating carbon from whole plants, we incubated soil from (cattle) pasture and natural beech forest with 13C-labelled wheat roots in microcosms for 72 hours. The degradation of the plant material was followed by measuring total CO2 and 13CO2. Pyrosequencing of density-resolved 16S rRNA identified soil bacteria involved in the assimilation of carbon from wheat residues.

Biome: root:Environmental:Terrestrial:Soil:Crop:Agricultural land
16S rRNA amplicons for dugout DNA samples - primers removed.

Three methods to profile a microbial community are compared.  These samples are 16S rRNA amplicons from a single DNA sample

Biome: root:Environmental:Aquatic:Freshwater
Modulation of the infant gut microbiota by a starter infant formula containing a synbiotic of bovine milk-derived oligosaccharides and Bifidobacterium animalis subsp. lactis CNCM I-3446

NCT01983072

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
The Effect of High Oxalate Exposure on the Gut Microbiota of Neotoma albigula

The mammalian gut microbiota is a complex ecosystem with hundreds to thousands of interacting species and numerous ecological niches, in a nearly closed off system primarily shaped by host physiology and diet.  Given the complexity of this system, it is difficult to elucidate specific interactions that shape the gut microbiota and its response to a dietary challenge. Oxalate, a simple organic acid widely distributed among plants, is a carbon and energy source for some gut bacteria that cannot be metabolized by mammalian enzymes.  Therefore, this compound can be used to identify fundamental ecological interactions between diet and the gut microbiota without confounding factors associated with other dietary components or host physiology.  We examined interactions between oxalate and the gut microbiota of the mammalian herbivore Neotoma albigula, which consumes a high oxalate diet in the wild.   By comparing the relative abundance of genes and metabolic pathways in the gut microbiota after exposure to 0.2% oxalate or 6% oxalate, we will elucidate those pathways that are enriched or inhibited by high oxalate exposure.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Soil samples collected for whole-genome shotgun sequencing.

Soil samples collected for whole-genome shotgun sequencing.

Biome: root:Environmental:Terrestrial:Soil
Managing human microbiomes: Explaining heterogeneous responses in butyrate to dietary supplementation with resistant starch

Colonic bacteria produce the health-promoting metabolite butyrate. We sought to influence butyrate production in 20 healthy adults by supplementing their diet with resistant starch (RS). While average fecal butyrate increased from 8 to 12 mmol/kg wet feces, responses varied widely between individuals. Three types of responses were categorized: enhanced, high, and low (n = 11, 3, and 6 respectively). Fecal butyrate increased by 87% in the enhanced group, while it remained =12 mmol/kg in the high group and =8 mmol/kg in the low group. Microbiome analyses revealed that RS-degrading organisms increased from ~ 2 to 10% in the enhanced and high groups, but remained at ~ 2% in the low group. This lack of increase in RS-degrading microbes is likely why individuals in the low group do not benefit in butyrate with RS. This study underscores the importance of understanding inter-individual variability in managing ecosystem services from microbiomes.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Phage therapy in Bangladeshi children hospitalized with acute bacterial diarrhea

NCT00937274

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenomics of laying hens

To study the effect on the microbiota of laying hens, dietary treatments were established supplementing a basal diet with prebiotic whey at 6% and probiotic Pediococcus acidilactici. Metagenomic sequences were obtained after DNA isolation from caecal samples

Biome: root:Host-associated:Birds:Digestive system:Ceca
Viral metagenome of Lake Soyang

This is a viral metagenome study of an oligotrophic freshwater lake, Lake Soyang, located in South Korea. The samples were collected from the surface of the lake.

Biome: N/A
Microbiomes from different citrus rootstock genotypes

This project is devote to study the citrus microbiome of two rootstock genotypes grown in different environments.

Biome: root:Host-associated:Plants:Rhizosphere
Plastic Metagenome Study

Plastic associated metagenomes from LMFS.

Biome: root:Engineered
The rumen microbial network is key to understanding how the mode of action of yeast and bicarbonate differs.

The rumen microbiota plays an essential role in maintaining an optimal fermentation pattern to satisfy the energy and protein requirement of the host. In this study, the effect of 2 additives (live yeast: YD and sodium bicarbonate: SBD) on the rumen microbial network structure was investigated in dairy cattle fed highly fermentable diets. Both YD and SBD were able to restore rumen fermentation, probably mediated through a stabilisation of the pH, however there seemed to be differences in the way this was actually achieved. Lactate concentration decreased and higher NDF digestibility was recorded with YD compared to either SBD or control. These changes were associated with different shifts in the bacterial population: higher bacterial richness in the solid fraction, decrease in Ruminobacter and increase in Megasphaera with YD, increase in Fibrobacter and Ruminococcus and decrease in Prevotella with both YD and SBD. Bacterial network and canonical correspondence analysis revealed the presence of 2 major bacterial consortiums (mutualistic groups composed of 6 and 4 genera respectively) negatively correlated with each other and having an opposite effects on VFA and acetate production. The use of network and interaction plots has shed new light on the mode of action, of apparently similar additives, on the rumen microbiota.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Faecal microbiome of Simmental calves determined by 16S rRNA gene amplicon sequencing

Calves undergo several changes of basic nutrition during early development from birth to weaning accompanied by pivotal changes of anatomy and physiology of the gastrointestinal tract. These changes go along with concomitant changes of the gastrointestinal tract microbiota. Therefore the aim of our study was to examine the fecal microbiota of six Simmental dairy calves during early development in a longitudinal study by using 16S rRNA gene amplicon pyrosequencing. Animals were followed up from birth to the time after weaning - calves were sampled six times according to critical timepoints during physiologic development. Overall, after quality control 253,528 reads (from 35 samples) were obtained. Reads were classified into 5,410 operational taxonomic units based on 0.03 16S rRNA distance with Bacteroidetes, Firmicutes and Proteobacteria being the most abundant phyla. The calves showed a high inter-individual variation in the composition of their fecal microbiota, although some tendencies could be seen: (i) an increasing diversity and species richness of the fecal bacterial community with increasing age and (ii) an increasing within-age-group similarity and distinct bacterial communities in early timepoints (from birth to the middle of the milk feeding period) compared to the timepoints around weaning.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
The influence of chitin addition on the lettuce rhizosphere microbiome

Within this study we used chitin as a soil amendment to influence plant growth, disease resistance and the rhizosphere microbiome. Lettuce plants were grown in potting soil for eight weeks or in potting soil amended with 2% chitin. The effect of the chitin addition was observed at the end of the experiment. Using amplicon sequencing, we already reported some first results, which can be found in: Debode et al. (2016) Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology. Frontiers in Microbiology 7.

Biome: root:Host-associated:Plants:Rhizosphere
Biofilm sloughing in integrated fixed-film activated sludge (IFAS) systems

Biofilm sloughing is an integral aspect, and a dynamic activity of biofilm development. This study focused on biofilm sloughing on carriers in integrated fixed-film activated sludge (IFAS) systems in both laboratory (LS; synthetic feed) and full-scale (FS; municipal) systems. During biofilm development in the LS system the relative hydrophobicity of flocs and biofilm increased with an increase in carrier bound biomass. There was a decline in relative hydrophobicity of the flocs and attached biomass upon sloughing. The protein to polysaccharide ratio in the extracted EPS of the suspended biomass (flocs and sloughed biomass) and biofilms decreased and increased, respectively, which corresponds to confocal imaging showing that micro-colonies with polysaccharide rich content sloughing from the biofilms. Sloughed biomass rapidly associated with flocs to form large and compact structures that led to a decrease in SVI from 60-70 ml/L to 34 ml/L. The α and β diversities determined by 16S rRNA gene sequencing (Illumina) of FS samples revealed greater diversity of the biofilm community compared to flocs. The α diversity of biofilms and suspended solids decreased and increased, respectively, during sloughing. The shift in community structure was in part due to the loss of Comamonadacae from the biofilm. At the class level, after biofilm sloughing, Alphaproteobacteria, Gammaproteobacteria, Flavobacteria, and Acidobacteria-6 dominated on the remaining biofilm. The relative abundance of Rhodocyclacae decreased in biofilms and flocs, after biofilm sloughing. Live-dead staining revealed areas of the biofilm where viability of biomass is an additional factor in sloughing.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
Novel immunomodulatory flagellin-like protein FlaC in Campylobacter jejuni and other Campylobacterales

The human diarrheal pathogens Campylobacter jejuni and Campylobacter coli interfere with host innate immune signalling by different means, and their flagellins, FlaA and FlaB, have a low intrinsic property to activate the innate immune receptor TLR5. We have investigated here the hypothesis that the unusual secreted, flagellin-like molecule FlaC present in C. jejuni, C. coli and other Campylobacterales might activate cells via TLR5 and interact with TLR5. FlaC shows a striking sequence identity in its D1 domains to TLR5-activating flagellins of other bacteria such as Salmonella, in contrast to non-stimulating Campylobacter flagellins. We overexpressed and purified FlaC, and tested its immunostimulatory properties on cells of human and chicken origin. Treatment of cells with highly purified FlaC resulted in p38 activation. FlaC directly interacted with TLR5. Preincubation with FlaC decreased the responsiveness of chicken and human macrophages towards the bacterial TLR4 agonist LPS, suggesting that FlaC mediates crosstolerance. C. jejuni flaC mutants induced an increase of cell responses in comparison to the wild type, which was suppressed by genetic complementation. Supplementing excess purified FlaC likewise reduced the cellular response to C. jejuni. In vivo, the administration of ultapure FlaC led to a decrease in caecal IL-1beta expression and a significant change of the caecal microbiota in chickens. We propose that Campylobacter spp. have evolved a novel type of immunostimulatory flagellin-like secreted effector in order to specifically modulate host responses, for example towards other PRR ligands such as LPS.

Biome: root:Host-associated:Birds:Digestive system:Fecal
Intestinal microbiota composition of interleukin-10 deficient C57BL/6J mice and susceptibility to Helicobacter hepaticus-induced colitis

The mouse pathobiont, Helicobacter hepaticus, can induce typhlocolitis in interleukin-10 deficient mice, and H. hepaticus infection of immunodeficient mice is widely used as a model to study the role of pathogens and commensal bacteria in the pathogenesis of inflammatory bowel disease. C57BL/6J Il10-/- mice kept under specific pathogen-free conditions in two different facilities (MHH and MIT), displayed strong differences with respect to their susceptibilities to H. hepaticus-induced intestinal pathology. Mice at MIT developed robust typhlocolitis after infection with H. hepaticus, while mice at MHH developed no significant pathology after infection with the same H. hepaticus strain. We hypothesized that the intestinal microbiota might be responsible for these differences and therefore performed high resolution analysis of the intestinal microbiota composition in uninfected mice from the two facilities by deep sequencing of partial 16S rRNA amplicons. The microbiota composition differed markedly between mice from both facilities. Significant differences were also detected between two groups of MHH mice born in different years. Of the 119 operational taxonomic units (OTUs) that occurred in at least half the cecum or colon samples of at least one mouse group, 24 were only found in MIT mice, and another 13 OTUs could only be found in MHH samples. While most of the MHH-specific OTUs could only be identified to class or family level, the MIT-specific set contained OTUs identified to genus or species level, including the opportunistic pathogen, Bilophila wadsworthia. The susceptibility to H. hepaticus-induced colitis differed considerably between Il10-/- mice originating from the two institutions. This was associated with significant differences in microbiota composition, highlighting the importance of characterizing the intestinal microbiome when studying murine models of IBD.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Ontogeny of the gut microbiota in the cockroach Blattella germanica

Bacterial symbionts of insects have many metabolic activities that are absent in their hosts, and vice versa.  Blattabacterium lives inside the fat body cells of most of the cockroaches and plays an important role in nitrogen recycling. These insects also carry a variety of exosymbionts attached to the gastrointestinal walls, which collaborate in digestion and act as a barrier against colonization by pathogens, among other functions. For this work, the cockroach Blattella germanica was chosen in part by its importance as an indoor pest and also, because of its experimental convenience due to its short life cycle. The mode of acquisition of the gut exosymbionts is unknown, as well as the dynamics of their ecological succession across the life cycle of the insect. We have characterized the intestinal flora by different approaches. First, electron scanning microscopy confirmed the presence of a bacterial biofilm exclusively in the hindgut. qPCR revealed that the bacterial load in the gut increases with age. Pyrosequencing the hyper-variable regions V1-V3 of the 16S rRNA genes present in the guts of all the nymphal instars and adults of B. germanica revealed that the microbial composition is stage-specific through the development of the insect. Last, analysis of the embryos demonstrated that Blattabacterium is the only symbiont inherited maternally via the eggs, running out to elucidate the mode of adquisition of the intestinal microbiota.

Biome: root:Host-associated:Insecta:Digestive system
Interactions between gut microbiota, host genetics and diet in the development of metabolic syndrome

Obesity, diabetes and metabolic syndrome are the results of complex interactions between genetic and environmental factors, including the gut microbiota. To dissect interactions between the gut microbiota, diet and genetic background, we utilized three inbred strains of mice, which differ in development of obesity and metabolic syndrome, plus three derivative lines generated by breeding these strains in a common environment. Analysis of metabolic parameters and gut microbiota in the inbred strains and their environmentally normalized derivatives revealed strong interactions between the microbiota, diet, environmental history and metabolic phenotypes. Some phenotypes could be transferred to germ-free recipient animals by fecal transplant. Strong strain-dependent and strain-independent correlations were found between specific microbes and metabolic phenotypes. Environmental reprogramming of the microbiota resulted in one obesity-prone strain becoming obesity-resistant. Thus, in mice, development of obesity/metabolic syndrome is the result of strong interactions between the gut microbiota, host genetics and diet. In permissive genetic backgrounds, environmental reprograming of the microbiota can ameliorate development of metabolic syndrome.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Fecal transplants modulate a high-fat diet-related alterations of gut microbiota in mice

Background. The intestinal microbiota is altered in obese human subjects and in animal models of obesity. Transplantation of feces from lean, healthy donors to obese recipients has been shown to improve peripheral insulin sensitivity in subjects with metabolic syndrome.
Aim. We examined the gut microbiota in mice after administering a long-term, high-fat diet (HFD) supplemented with feces from lean mice
Methods. Forty-eight C57BL6/W mice were allowed to adapt to a non-specific pathogen free (SFP) environment for 2 weeks before being divided into three groups of 16 animals. Animals in each group were fed for 28 weeks with a normal diet (ND), HFD, or HFD supplemented  with feces from ND-fed mice (HFDS). The composition of colonizing bacteria was evaluated in mice droppings collected under SPF conditions at the beginning of the study (week 0) and at 12 and 28 weeks using an Ion 16S Metagenomics Kit on an Ion Torrent PGM

Biome: root:Host-associated:Mammals:Digestive system:Fecal
All 16S rRNA amplicon sequences for dugout DNA samples

Three methods to profile microbial community are compared. These samples are 16S rRNA amplicon sequencing of a single DNA sample.

Biome: root:Environmental:Aquatic:Freshwater
Hellbender cutaneous microbiomes

Characterization of microbial communities has become useful in studying the ties between organismal health and the host microbiome. Pathogens currently threaten the existence of many amphibian species, and some studies have characterized the amphibian cutaneous microbiome. Hellbender salamanders (Cryptobranchus alleganiensis) provide an ideal system to explore the relationship between microbiome and disease due to differences in health between the two hellbender subspecies. The Ozark hellbender subspecies (C. a. bishopi) currently exhibits chronic wounds believed to be caused by bacterial infections, whereas the eastern hellbender (C. a. alleganiensis) does not. Through bacterial 16s rRNA amplicon sequencing, we detected more than 8,000 distinct operational taxonomic units in the cutaneous and environmental microbiome. We found differences in the bacterial communities between the two subspecies, while but there were no differences between the Ozark wound and healthy samples nor between respective subspecies environment samples. Several opportunistic pathogens were found to have an association with Ozark hellbenders. These findings suggest that wounds present only in the Ozark hellbenders may be due to a reduced immunocompetence relative to eastern hellbenders. Using next generation sequencing allowed for an in-depth exploration of the distribution and abundance of bacteria between two threatened amphibian subspecies.

Biome: root:Host-associated:Amphibia
pig microbiota

pig gut microbiota

Biome: root:Host-associated:Mammals:Digestive system:Fecal
The Pig's other genome: a reference gene catalogue of the gut microbiome

Pig is a main species for livestock and biomedicine. The pig genome sequence was recently reported. To boost research, we established a catalogue of the genes of the gut microbiome based on faecal samples of 287 pigs from France, Denmark and China. More than 7.6 million non-redundant genes representing 719 metagenomic species were identified by deep metagenome sequencing, highlighting more similarities with the human than with the mouse catalogue. The pig and human catalogues share only 12.6 and 9.3 % of their genes, respectively, but 70 and 95% of their functional pathways. The pig gut microbiota is influenced by gender, age and breed. Analysis of the prevalence of antibiotics resistance genes (ARGs) reflected antibiotics supplementation in each farm system, and revealed that non-antibiotics-fed animals still harbour ARGs. The pig catalogue creates a resource for whole metagenomics-based studies, highly valuable for research in biomedicine and for sustainable knowledge-based pig farming.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Amplicon study from BBSRC-DBT project

Metagenomic analysis of caecum in Global Commercial Broilers and Kadaknath using 16sRNA V3-V4 primers.

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum