SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Bacterial community diversity and variation in spray water sources and the tomato phyllosphere

Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato phyllosphere and the water sources commonly used in commercial vegetable production.    The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The phyllosphere bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both phyllosphere environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant.    Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato phyllosphere. This study has provided the first next-generation sequencing database describing the bacterial communities living in the phyllosphere of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.

Biome: root:Engineered:Food production
A longitudinal study of the feline faecal microbiome identifies changes into early adulthood irrespective of sexual development

Companion animals provide an excellent model for studies of the gut microbiome because potential confounders such as diet and environment can be more readily controlled for than in humans. Additionally, domestic cats and dogs are typically neutered early in life, enabling an investigation into the potential effect of sex hormones on the microbiome. In a longitudinal study to investigate the potential effects of neutering, neutering age and gender on the gut microbiome during growth, the faeces of kittens (16 male, 14 female) were sampled at 18, 30 and 42 weeks of age. DNA was shotgun sequenced on the Illumina platform and sequence reads were annotated for taxonomy and function by comparison to a database of protein coding genes. In a statistical analysis of diversity, taxonomy and functional potential of the microbiomes, age was revealed as the only factor with significant effects on the variation observed. No significant effects were detected for gender, neutering, or age when neutered (19 or 31 weeks). At 18 weeks of age the microbiome was dominated by the genera Lactobacillus and Bifidobacterium (35% and 20% average abundance). Structural and functional diversity was significantly increased by week 30 but there was no further significant increase. At 42 weeks of age the most abundant genera were Bacteroides (16%), Prevotella (14%) and Megasphaera (8%). Significant differences in functional potential included an enrichment for genes in energy metabolism (carbon metabolism and oxidative phosphorylation) and depletion in cell motility (flagella and chemotaxis). We conclude that the feline faecal microbiome is predominantly determined by age when diet and environment are controlled for. We suggest this finding may also be informative for studies of the human microbiome, where control over such factors is usually limited.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Experimental challenge of poultry feces

Poultry feces have been spiked with known concentration of bacteria and stored at different times and temperatures before DNA extraction

Biome: root:Host-associated:Birds:Digestive system:Fecal
Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidifications on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 µatm) and those exposed to present day CO2 conditions.

Biome: root:Environmental:Aquatic:Marine:Coastal
Semi-synthetic marine metagenomes for metagenomic pipeline assessment

As part of ELIXIR project, six different semi-synthetic marine metagenomes were created to analyse and evaluate the available metagenomic tools/pipelines.

Biome: root:Engineered:Modeled
Handley et al. demonstrate that vaccination against SIV infection in Rhesus macaques prevents alterations in the gastrointestinal virome and bacterial microbiome that are typically associated with poor disease outcome.

Pathogenic simian immunodeficiency virus (SIV) infection is associated with AIDS, expansion of the eukaryotic enteric virome, consequent intestinal epithelial damage, translocation of viral and bacterial components into the circulation and systemic immune activation. Here we characterized changes in the enteric virome and bacterial microbiome during pathogenic SIV infection, and determined whether vaccine-mediated protection altered these disease manifestations. Vaccine-associated protection against SIV infection prevented expansion of the enteric virome. Overall gastrointestinal bacterial community structure was indistinguishable in protected and unprotected animals, however, animals that ultimately succumb to AIDS related disease had altered levels of several bacterial taxa including an increased abundance of many disease-associated bacteria. These data suggest that immune control of SIV-induced immunodeficiency aids in the maintenance of a normal fecal microbiome and ameliorates SIV-associated systemic inflammation.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Sialylated milk glycans promote growth in gnotobiotic mice and pigs with a stunted Malawian infant gut microbiota

Identifying interventions that more effectively promote healthy growth of children with undernutrition is a pressing global health goal. Analysis of human milk oligosaccharides (HMOs) from 6-month postpartum mothers in two Malawian birth-cohorts revealed that sialylated HMOs are significantly less abundant in mothers with severely stunted infants. To explore this association, we colonized young germ-free mice with a consortium of bacterial strains cultured from the fecal microbiota of a 6-month old stunted Malawian infant and fed recipient animals a prototypic Malawian diet with or without purified sialylated bovine milk oligosaccharides (S-BMO). S-BMO produced a microbiota-dependent augmentation of lean body mass gain, changed bone morphology and altered liver, muscle and brain metabolism in ways indicative of a greater ability to utilize nutrients for anabolism. These effects were also documented in gnotobiotic piglets using the same consortium and Malawian diet. These preclinical models establish a causal microbiota-dependent relationship between S-BMO and growth promotion.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Arsenophonus and Sodalis Symbionts in Louse Flies: an Analogy to the Wigglesworthia and Sodalis System in Tsetse Flies

Symbiosis between insects and bacteria result in a variety of arrangements, genomic modifications, and metabolic interconnections. Here, we present genomic, phylogenetic, and morphological characteristics of a symbiotic system associated with Melophagus ovinus, a member of the blood-feeding family Hippoboscidae. The system comprises four unrelated bacteria representing different stages in symbiosis evolution, from typical obligate mutualists inhabiting bacteriomes to freely associated commensals and parasites. Interestingly, the whole system provides a remarkable analogy to the association between Glossina and its symbiotic bacteria. In both, the symbiotic systems are composed of an obligate symbiont and two facultative intracellular associates, Sodalis and Wolbachia. In addition, extracellular Bartonella resides in the gut of Melophagus. However, the phylogenetic origins of the two obligate mutualist symbionts differ. In Glossina, the mutualistic Wigglesworthia appears to be a relatively isolated symbiotic lineage, whereas in Melophagus, the obligate symbiont originated within the widely distributed Arsenophonus cluster. Although phylogenetically distant, the two obligate symbionts display several remarkably similar traits (e.g., transmission via the host's “milk glands” or similar pattern of genome reduction). To obtain better insight into the biology and possible role of the M. ovinus obligate symbiont, “Candidatus Arsenophonus melophagi,” we performed several comparisons of its gene content based on assignments of the Cluster of Orthologous Genes (COG). Using this criterion, we show that within a set of 44 primary and secondary symbionts, “Ca. Arsenophonus” is most similar to Wigglesworthia. On the other hand, these two bacteria also display interesting differences, such as absence of flagellar genes in Arsenophonus and their presence in Wigglesworthia. This finding implies that a flagellum is not essential for bacterial transmission via milk glands.

Biome: root:Host-associated:Insecta:Digestive system
Temporal dynamics of the toxic cyanobacterial community composition and toxin presence in two South German lakes

Bacterioplankton plays an essential role in aquatic ecosystems, and cyanobacteria are an influential part of the microbiome in many water bodies. In freshwaters used for recreational activities or drinking water, toxic cyanobacteria cause concerns due to the risk of intoxication with cyanotoxins, such as microcystins. In this study, we aimed to unmask relationships between toxicity, cyanobacterial community composition, and environmental factors. At the same time, we assessed the suitability of a genetic marker to serve as toxicity proxy and aimed to expose the main microcystin producer bacterium. We used Illumina MiSeq sequencing to assess bacterioplankton and perform an in depth analysis of the cyanobacterial community composition in two recreational lakes in South Germany during the cyanobacterial bloom period. We quantified a microcystin biosynthesis gene (mcyB) using qPCR and linked this information with microcystin concentration using HPLC and ELISA to assess toxicity. Microcystin biosynthesis gene (mcyE)-clone libraries were used to determine the origin of toxicity genes. Both lakes displayed distinct bacterial community compositions during the sampling period despite sharing a large fraction of their microbiome (about three quarters of all bacterial OTUs). Proteobacteria, Actinobacteria, and Cyanobacteria dominated Lake Klostersee while Cyanobacteria prevailed in Lake Bergknappweiher. The cyanobacterial community composition was highly dynamic in both lakes, and temporal variations were most evident at the lowest taxonomic level. In both lakes, we witnessed a diversification of dominant cyanobacterial genera. Microcystin concentration correlated positively with total phosphorus and mcyB copy number. However, mcyB copy number was not a reliable signal for bloom toxicity. We identified low abundant Microcystis sp. as the only microcystin producer in both lakes. Therefore, risk assessment efforts need to take into account the fact that dominant cyanobacterial taxa did not contribute to the microcystin contamination of the blooms observed.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Microbiota of caloric restricted mice by WMGS

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

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Whole shotgun metagenome sequencing of AD micro biome

The microbial community responsible for the biogas-producing anaerobic digestion (AD) process used to recover energy from waste is poorly characterised and likely contains many organisms not required for gas generation. Metagenomics approaches offer insights into AD communities that could potentially be exploited to improve the conversion of biomass to biogas, but distinguishing between the biological and technical variability of samples from different sources makes generalisation of results challenging. To determine how different DNA extraction methodologies and sequencing approaches influence the perceived microbiome, we analysed technical replicates of 16S rRNA amplicons and whole shotgun metagenomes from different AD systems. Here we show that diversity measurements of the microbiome in AD samples were strongly influenced by extraction regimes and analysis methodology. 16S rRNA amplification resulted in over- and under-estimation of several taxonomic phyla compared to a PCR-free metagenomics approach. Samples extracted using mechanical methods displayed significantly lower diversity and fewer observed phylotypes than samples extracted by chemical and thermal lysis, which produced higher molecular weight DNA and showed the greatest diversity in community profiles. Our results highlight that the most commonly used extraction and analysis protocols provide a skewed view of the diversity and species richness of the AD microbiome which is likely to extent to other samples. We suggest that methodological differences could be a significant source of variability among AD, and other, metagenomics studies.

Biome: root:Engineered:Biogas plant:Wet fermentation
16S and 18S amplicon sequencing of compost wheat straw composting microbial community

This study investigated the microbial community structure  of wheat straw derived composting microbial community using 16S and 18S amplicon sequencing.

Biome: root:Engineered:Solid waste:Composting
Detection of bacterial pathogens from broncho-alveolar lavage by next-generation sequencing

The application of culture-free methods, notably whole-metagenome shotgun (WMGS) sequencing, in routine clinical analysis is still limited although they have some advantage over culture-based approach. A combination of an appropriate DNA extraction procedure, sequencing and bioinformatics tools is essential for removal of human DNA and improved bacterial species identification. We tackled these issues by applying a specifically-designed clinical metagenomics pipeline, from DNA extraction to bioinformatics methods, on a broncho-alveolar lavage (BAL) sample from a severely immunocompromised patient who developed an atypical nosocomial pneumonia.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system
Microbiome of anaerobic digesters in municipal wastewater treatment plants

Anaerobic digestion (AD) is a promising biotechnology that simultaneously achieves waste treatment and energy recovery simultaneously. For the purpose of improving operation performance, previous researches have attempted to define the core microbiota of AD, but due to the complexity of the microbial ecology and limited sampling size of the diverse type of digesters, our understanding remains insufficient. In this study, we performed a comprehensive microbial community survey by using 16S rRNA gene-based sequencing of 148 digester sludge samples from 90 full-scale digesters at 51 municipal wastewater treatment plants from North America, Europe, and East Asia. Among the samples, eight different types of community structures were identified, among which the largest one could serve as a model structure of digester microbiome. Relatively mild community changes were induced by moderate temperature fluctuation, while drastic community changes were caused by pretreatment, high salinity and high temperature. Within each type, we identified the signature microbial populations that were associated with the operating conditions. By performing pairwise comparisons between the microbiomes in the feed to and within the digesters, microbial populations that were likely resides as result of incomplete digestion were identified. Overall, this study elucidates of microbial ecology in AD and provides a basis for further investigations into the functions of poorly defied microorganisms, which could ultimately enable improvement of digestion performance.

Biome: root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
Extraction and sequencing methodology affects perceived microbiome

The microbial community responsible for the biogas-producing anaerobic digestion (AD) process used to recover energy from waste is poorly characterised and likely contains many organisms not required for gas generation. Metagenomics approaches offer insights into AD communities that could potentially be exploited to improve the conversion of biomass to biogas, but distinguishing between the biological and technical variability of samples from different sources makes generalisation of results challenging. To determine how different DNA extraction methodologies and sequencing approaches influence the perceived microbiome, we analysed technical replicates of 16S rRNA amplicons and whole shotgun metagenomes from different AD systems. Here we show that diversity measurements of the microbiome in AD samples were strongly influenced by extraction regimes and analysis methodology. 16S rRNA amplification resulted in over- and under-estimation of several taxonomic phyla compared to a PCR-free metagenomics approach. Samples extracted using mechanical methods displayed significantly lower diversity and fewer observed phylotypes than samples extracted by chemical and thermal lysis, which produced higher molecular weight DNA and showed the greatest diversity in community profiles. Our results highlight that the most commonly used extraction and analysis protocols provide a skewed view of the diversity and species richness of the AD microbiome which is likely to extent to other samples. We suggest that methodological differences could be a significant source of variability among AD, and other, metagenomics studies.

Biome: root:Engineered:Biogas plant:Wet fermentation
discovery of GH genes using metatranscriptomic approach

discovery of GH genes from enrichment culture using metatranscriptomic approach

Biome: root:Engineered:Solid waste:Composting
Microbial diversity in high-nitrate wastewater bioreactor

Denitrification of high concentration of nitrate wastewater was investigated in expanded granular sludge bed (EGSB) reactor with sodium acetate as the carbon source. The optimal parameters were achieved with C/N mole ratio of 2.0, liquid up-flow velocity (Vup) of 3.0 m/h and pH of 6.2–8.2. Complete denitrification can be achieved even with nitrate nitrogen concentration as high as 14000 mg/L. Furthermore, 454-pyrosequencing technology was used to analyze bacterial diversity. Results showed that a total of 5573 sequences were obtained which could be affiliated to 6 phylogenetic groups, including Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Chloroflexi and unclassified phylum. Proteobacteria (84.53%) was the dominant microbial population, followed by Firmicutes (13.24%) and Actinobacteria (0.38%). The dominate phylum was different from that in other anaerobic system.

Biome: root:Engineered:Wastewater:Water and sludge
ECOLOGICAL AND MOLECULAR ASPECTS OF LIGNOCELLULOSE DIGESTION IN NEOTROPICAL HIGHER TERMITES

Due to their ability in digesting lignocellulose, termites are key organisms in the ecosystems that maintain carbon balance and incorporate organic matter into the soil. They are also considered the world's smallest bioreactors. The evolution of termites was marked by modifications on symbiont composition and acquisition of new feeding strategies that improved the digestion of lignocellulose resulting in the diversification of food sources. Nevertheless, some aspects of lignocellulose digestion in neotropical species are poorly known and studies are necessary to further comprehend their impact on the environment and their potential in the new bioeconomy. The aim of this proposal will be to study the digestion of lignocellulose and the community structure of the symbiotic microbiota in six species of neotropical higher termites by integrating ecological and molecular analyses. We will first compare microbiota functions of Cornitermes cumulans based on metagenomics and metatranscriptomic analyses. Then we will evaluate the activity of lignocellulases and the microbial community composition by six species of higher termites with different feeding strategies using enzymatic assays and 16S and ITS sequencing. We suggest that C. cumulans stores food in order to facilitate the digestion of lignocellulose by soil microorganisms before ingestion. In addition, both lignocellulose digestion and microbiota functional composition will be different according to termite feeding specialization. The results of this study will be significant to further understand the symbiotic relationship between the microbiota and termites.

Biome: root:Host-associated:Insecta