Bacterial Taxonomic Diversity Research Articles

Exploring the biosynthesis potential of permafrost microbiomes

BackgroundPermafrost microbiomes are of paramount importance for the biogeochemistry of high latitude soils and while endemic biosynthetic domain sequences involved in secondary metabolism have been found in polar surface soils, the biosynthetic potential of permafrost microbiomes remains unexplored. Moreover, the nature of these ecosystems facilitates the unique opportunity to study the distribution and diversity of biosynthetic genes in relic DNA from ancient microbiomes. To explore the biosynthesis potential in permafrost, we used adenylation (AD) domain sequencing to evaluate non-ribosomal peptide (NRP) production in permafrost cores housing microbiomes separated at kilometer and kiloyear scales.ResultsPermafrost microbiomes represented NRP repertoires significantly different from that of temperate soil microbiomes, but as for temperate soils, the estimated domain richness and diversity was strongly correlated to the bacterial taxonomic diversity across locations. Furthermore, we found significant differences in both community composition and AD domain composition across geographical and temporal distances. Overall, the vast majority of biosynthetic domains showed below 90% amino acid similarity to characterized BGCs, confirming the high degree of novelty of NRPs inherent to permafrost microbiomes. Using available metagenomic sequences, we further identified a high biosynthetic diversity beyond NRPs throughout arctic surface soils down to deep and ancient (megayear old) permafrost microbiomes.ConclusionWe have shown that arctic permafrost microbiomes harbor a unique biosynthetic repertoire rich in hitherto undescribed NRPs. This diversity is driven by geographic separation across kilometer scales and by the bacterial taxonomic diversity between microbiomes confined in separate permafrost layers. Hence the permafrost biome represents a unique resource for studying secondary metabolism, and potentially for the discovery of novel drug leads.

Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient

Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.

Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea

BackgroundCorals are the foundational species of coral reefs and coralligenous ecosystems. Their success has been linked to symbioses with microorganisms, and a coral host and its symbionts are therefore considered a single entity, called the holobiont. This suggests that there may be evolutionary links between corals and their microbiomes. While there is evidence of phylosymbiosis in scleractinian hexacorals, little is known about the holobionts of Alcyonacean octocorals.Results16S rRNA gene amplicon sequencing revealed differences in the diversity and composition of bacterial communities associated with octocorals collected from the mesophotic zones of the Mediterranean and Red Seas. The low diversity and consistent dominance of Endozoicomonadaceae and/or Spirochaetaceae in the bacterial communities of Mediterranean octocorals suggest that these corals may have a shared evolutionary history with their microbiota. Phylosymbiotic signals were indeed detected and cophylogeny in associations between several bacterial strains, particularly those belonging to Endozoicomonadaceae or Spirochaetaceae, and coral species were identified. Conversely, phylosymbiotic patterns were not evident in Red Sea octocorals, likely due to the high bacterial taxonomic diversity in their microbiota, but cophylogeny in associations between certain coral and bacterial species was observed. Noteworthy were the associations with Endozoicomonadaceae, suggesting a plausible evolutionary link that warrants further investigations to uncover potential underlying patterns.ConclusionsOverall, our findings emphasize the importance of Endozoicomonadaceae and Spirochaetaceae in coral symbiosis and the significance of exploring host-microbiome interactions in mesophotic ecosystems for a comprehensive understanding of coral-microbiome evolutionary history.

Amplicon metagenome comparison of Tandag River, Surigao del Sur, Philippines, based on high-throughput parallel DNA sequencing analysis of bacterial communities

Abstract. Eupeña-Caray RG, Ramos GB, Panduyos JB, Bacquial LS, Tabugo SRM. 2024. Amplicon metagenome comparison of Tandag River, Surigao del Sur, Philippines, based on high-throughput parallel DNA sequencing analysis of bacterial communities. Biodiversitas 25: 3464-3472. Rivers serve as a vital freshwater reservoir for the environment and human consumption. Biomonitoring based on eDNA is essential for aquatic ecosystems. The present study investigates the bacterial taxonomic diversity of this ecosystem using the V1-V3 16S rRNA regions obtained from paired-end Illumina MiSeq reads. A total of nine amplicon libraries (U1, U2, U3, M1, M2, M3, D1, D2, D3) were constructed corresponding to the sites (U-upstream, M-midstream, D-downstream) of the Tandag River. After post-quality control and processing, there were 608,099 amplicon sequence variants (ASVs), representing 1194 families and 2090 genera. Results showed that the most abundant ASVs were affiliated with genera Bacillus, Pseudomonas, Ralstonia, Alcaligenes, and Pseudarcicella, along with unclassified bacteria derived from Gammaproteobacteria, Alphaproteobacteria, Verrucomicrobia subdivision, Flavobacteria, and Pseudomonadaceae. The bacterial alpha diversity was ranked upstream>midstream>downstream. An increase in the abundance of Bacillus (Firmicutes) and Gammaproteobacteria in an urbanized zone indicated a high level of human activity and an important threat to public health. Noteworthy is that the alkaline environment characterized by increased pH levels favors the occurrence of alkaliphilic bacteria. Microbial community structure was influenced by anthropogenic interference and selective pressure from loads of urban discharge in the area. The functional prediction of bacterial communities by Parallel-Meta Suite (PMS) using the PICRUSt algorithm suggests functions related to metabolism and environment information processing. The presence of xenobiotic biodegradation bacteria highlights future possible applications. Findings contribute to understanding microbial communities in response to rapid urbanization. This is the first account of high-throughput sequencing analysis of bacterial communities in an urban river under anthropogenic stress in the Philippines.

Further reduction in soil bacterial diversity under severe acidification in European temperate forests.

Despite a decrease in industrial nitrogen and sulfur deposition over recent decades, soil acidification remains a persistent challenge to European forest health, especially in regions of intense agriculture and urbanisation. Using topsoil eDNA metabarcoding and functional annotations from a sample of 49 plots (each 30 × 30 m) located in The Netherlands and Germany, we investigated the effect of severe acidification on bacterial taxonomic diversity under different forest types and explored potential functional implications for nutrient cycling. Furthermore, we assessed which soil parameters known to influence soil bacterial communities affect these acidophilic communities. Here, we are the first to demonstrate under natural conditions that soil bacterial diversity in extremely acidic soils (pH <4.5) continues to decline similarly across forest types as pH further decreases under intensifying human activity. Our results confirmed pH as the key driver of soil bacterial communities, even in extremely acidic soils. Ongoing severe acidification continues to reduce bacterial communities, favouring taxa adapted to extreme acidity and primarily involved in recalcitrant carbon-degradation compounds (e.g. cellulolysis potential = 0.78%-9.99%) while simultaneously diminishing taxa associated with nitrogen cycling (e.g. fixation potential = 6.72%-0.00%). Altogether, our findings indicate a further decline in bacterial diversity in already extremely acidic soils, likely disrupting nutrient cycling through changes in immobilisation and mineralisation processes. Our study highlights the continuous acidification of European temperate forests to extremely low pH levels, further disrupting forest ecosystem functioning. The significant reduction in bacterial diversity under such a severe acidification gradient, as demonstrated here, underscores the necessity to include severely acidified forests in conservation programmes and monitoring to prevent further degradation of European soils beyond repair.

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

P334 The longitudinal analysis of fecal microbiota in response to ustekinumab treatment in patients with Crohn’s disease

Abstract Background Emerging evidence supports that treatment of Crohn’s disease (CD) can alter the intestinal microbiota, which can play a significant role in the pathogenesis and therapeutic outcomes of CD. Ustekinumab (UST) has also been reported to modify the intestinal microbiota during a short-term treatment period. However, the long-term impact of UST treatment on the intestinal microbiota has rarely been studied. Methods We prospectively enrolled patients with CD who were planning to start UST treatment and collected fecal samples before (baseline) and after UST administration at week 20 and week 52. Fecal bacterial taxonomic diversity and composition were analyzed through 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing. The difference in the intestinal microbiota between clinical remitters and non-remitters defined by Crohn’s disease activity index (CDAI) was investigated, along with the longitudinal changes in the intestinal microbiota. Results A total of 124 fecal samples acquired from 43 patients were analyzed (median age 30 years, male 76.7%, median CDAI at baseline 183.2). Clinical remission was observed in 34.9% (n=15/43), 61.0% (n=25/41), and 60.0% (n=24/40) at baseline, week 20, and week 52, respectively. Shannon’s alpha diversity index increased significantly at week 20 and week 52 compared to baseline (both P&amp;lt;0.001). Compared to non-remitters, a significant increase of Shannon’s alpha diversity index was also observed among remitters (P=0.044) across all time points, while no significant difference was noted at each time point. The beta diversity analysis based on the Bray-Curtis distance revealed a significant difference among remitters at week 20 (P=0.027), however, there were no significant differences at other time points. Compared to the baseline, the abundance of the Firmicutes phylum was higher at week 20 (P=0.048) and 52 (P=0.019). The Lactobacillus genus (P=0.042), and Lactobacillus gasseri group (P=0.016) were significantly less abundant in remitters, while the Lachnospiraceae family (P=0.017) was more abundant in remitters. At week 20, Bifidobacterium genus (P=0.027) and Bifidobacterium pseudolongum group (P=0.040) were significantly more abundant in remitter while the Lactobacillus genus was less abundant (P=0.009) in remitter (Figure 1). Conclusion The alteration of fecal microbiota after UST treatment may have the potential to serve as a biomarker for predicting clinical remission. Financial Support This study was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2021R1A2C2095096), the grant (2020IT0012) from the Asan Institute for Life Sciences, Seoul, Korea and the grant (CR 2017-4) from CELLTRION PHARM, Inc., Chungcheongbuk-do, Korea.

Droplet microfluidic system for high throughput and passive selection of bacteria producing biosurfactants.

Traditional methods for the enrichment of microorganisms rely on growth in a selective liquid medium or on an agar plate, followed by tedious characterization. Droplet microfluidic techniques have been recently used to cultivate microorganisms and preserve enriched bacterial taxonomic diversity. However, new methods are needed to select droplets comprising not only growing microorganisms but also those exhibiting specific properties, such as the production of value-added compounds. We describe here a droplet microfluidic screening technique for the functional selection of biosurfactant-producing microorganisms, which are of great interest in the bioremediation and biotechnology industries. Single bacterial cells are first encapsulated into picoliter droplets for clonal cultivation and then passively sorted at high throughput based on changes in interfacial tension in individual droplets. Our method expands droplet-based microbial enrichment with a novel approach that reduces the time and resources needed for the selection of surfactant-producing bacteria.

Effects of planting year of alfalfa on rhizosphere bacterial structure and function

In many areas across the world, alfalfa is still cultivated in the same place over many years, leading to gradually deplete the soil nutrients and increase plant disease and consequent decreases in the yield and quality. Agricultural management practices have been proved to affect largely soil microbial community structure and functions in many reports, but it remains unclear how planting year effects extend to the rhizosphere under a long-term cultivation practices of alfalfa. Exploring such impacts is of great importance to understand and develop plant-microorganism interactions for agricultural sustainability. A long-term field experiment was set up at Linze research station of Lanzhou University in Gansu province, where alfalfa was continuously planted for four years (Y4) and six years (Y6). Rhizosphere soils from two different planting years were collected to examine differences in the bacterial diversity, composition and co-occurrence patterns using 16S rRNA gene sequencing technologies as well as in functional profiles involved in nitrogen cycling predicted by FAPROTAX. We found that soil nutrients including soil organic carbon (SOC), AP (available phosphorus) and nitrate nitrogen (NO3−-N) differed significantly between planting years. Bacterial taxonomic diversity, composition and the relative abundance of functional groups involved in nitrogen cycling were significantly affected by planting years, sampling time and their interactions. Co-occurrence network analysis showed that keystone taxa in both planting years were affiliated to Proteobacteria and bacteria taxa had less complexity and more negative correlations in Y6 than in Y4. NO3−-N was a major factor affecting bacterial community diversity and composition across planting years. Together, our findings suggest that planting years of alfalfa can lead to large variations in soil nutrients and rhizosphere microbial community patterns. These results implies that in agricultural management practices, planting year effects can even extend to microorganisms in association with plant roots, which may affect crop growth given close linkages between rhizosphere processes and plant nutrition availability.

Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi

The immunogenicity and effectiveness of oral rotavirus vaccines (ORVs) against severe rotavirus-associated gastroenteritis are impaired in low- and middle-income countries (LMICs) where the burden of disease is highest. Determining risk factors for impaired ORV response may help identify strategies to enhance vaccine effectiveness. In this study, we use metagenomic sequencing to provide a high-resolution taxonomic analysis of stool samples collected at 6 weeks of age (coinciding with the first ORV dose) during a prospective study of ORV immunogenicity in India and Malawi. We then analyse the functional capacity of the developing microbiome in these cohorts. Microbiome composition differed significantly between countries, although functional capacity was more similar than taxonomic composition. Our results confirm previously reported findings that the developing microbiome is more diverse in taxonomic composition in ORV non-seroconverters compared with seroconverters, and we additionally demonstrate a similar pattern in functional capacity. Although taxonomic or functional feature abundances are poor predictors of ORV response, we show that skews in the direction of associations within these microbiome data can be used to identify consistent markers of ORV response across LMIC infant cohorts. We also highlight the systemic under-representation of reference genes from LMICs that limit functional annotation in our study (7% and 13% annotation at pathway and enzyme commission level, respectively). Overall, higher microbiome diversity in early life may act as marker for impaired ORV response in India and Malawi, whilst a holistic perspective of functional capacity may be hidden in the “dark matter” of the microbiome.

Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.

Uncovering the Resistome of a Peruvian City through a Metagenomic Analysis of Sewage Samples

Background: Antibiotic resistance is a major public health concern globally. In this study, we aimed to evaluate the abundance and diversity of antibiotic resistance genes (ARGs) in sewage water samples from two hospitals and an adjacent community or urban setting in Huanuco, a Peruvian city located in the highlands. Methods: We collected samples from the community wastewater system and from sewage pipes from the two hospitals in Huanuco. DNA was extracted from 250 mL of sewage water samples (n = 6) and subjected to microbiome profiling using 16S rRNA short amplicon sequencing and shotgun metagenomics. We analyzed the taxonomic and functional content in all samples, including alpha and beta diversity metrics, and searched for ARGs. Results: Our results showed that samples taken from the community wastewater system were compositionally different and harbored greater bacterial taxonomic and functional diversity compared to samples collected from the hospitals’ wastewater system. We found a high abundance of bacteria associated with resistance to beta-lactams, macrolides, aminoglycosides, fluoroquinolones, and tetracyclines in all samples. However, there were no significant differences in the abundance or composition of ARGs between the community wastewater samples and those taken from the two hospitals. Conclusions: Our findings suggest that metagenomics analyses in wastewater sewage could be a useful tool for monitoring antibiotic resistance in urban settings. These data could be used to develop local public health policies, particularly in cities or countries with limited resources to establish large-scale One Health projects.

Effect of Lactobacillus buchneri and sodium benzoate on the fermentative profile, bacterial taxonomic diversity, and aerobic stability of sorghum silages at different fermentation times

Effect of Lactobacillus buchneri and sodium benzoate on the fermentative profile, bacterial taxonomic diversity, and aerobic stability of sorghum silages at different fermentation times

Plant neopolyploidy and genetic background differentiate the microbiome of duckweed across a variety of natural freshwater sources.

Whole-genome duplication has long been appreciated for its role in driving phenotypic novelty in plants, often altering the way organisms interface with the abiotic environment. Only recently, however, have we begun to investigate how polyploidy influences interactions of plants with other species, despite the biotic niche being predicted as one of the main determinants of polyploid establishment. Nevertheless, we lack information about how polyploidy affects the diversity and composition of the microbial taxa that colonize plants, and whether this is genotype-dependent and repeatable across natural environments. This information is a first step towards understanding whether the microbiome contributes to polyploid establishment. We, thus, tested the immediate effect of polyploidy on the diversity and composition of the bacterial microbiome of the aquatic plant Spirodela polyrhiza using four pairs of diploids and synthetic autotetraploids. Under controlled conditions, axenic plants were inoculated with pond waters collected from 10 field sites across a broad environmental gradient. Autotetraploids hosted 4%-11% greater bacterial taxonomic and phylogenetic diversity than their diploid progenitors. Polyploidy, along with its interactions with the inoculum source and genetic lineage, collectively explained 7% of the total variation in microbiome composition. Furthermore, polyploidy broadened the core microbiome, with autotetraploids having 15 unique bacterial taxa in addition to the 55 they shared with diploids. Our results show that whole-genome duplication directly leads to novelty in the plant microbiome and importantly that the effect is dependent on the genetic ancestry of the polyploid and generalizable over many environmental contexts.

Endophytic bacterial taxonomic and functional diversity in the seeds of wheat genotypes from different agroecologies

ABSTRACT Plant genotype and agroecology influence the composition and functionality of seed endophytic bacterial communities. Taxonomic analysis of 123 wheat seeds endophytic bacteria classified these into 23 genera predominantly under Firmicutes followed by Actinobacteria and Proteobacteria. Genus Bacillus was most abundant (30.7%) followed by Streptomyces (18.4%) with other representative genera such as Stenotrophomonas, Paenibacillus, Mixta, Enterobacter, Micrococcus, Pantoea, Alkalihalobacillus, Cortiobacterium, and more. Across agroecologies, the core microbiota of seeds consists of Bacillus, Streptomyces, Paenibacillus, and Stenotrophomonas, with maximum diversity and abundance observed in seeds of the North Western Plain Zone of India. Seed endophytic bacteria had PGP traits; nitrogen fixation (n = 101), production of IAA (n = 65), siderophores (n = 43), ammonia (n = 82) and solubilization of phosphate (n = 47), potassium (n = 37), and zinc (n = 8). The isolates produced HCN and hydrolytic enzymes and displayed antagonism against fungal pathogens. Overall, the information generated on wheat seeds’ endophytic bacterial taxonomy and beneficial traits may pave the path for the development of novel bioinoculants. Key message Wheat seeds from various agro-ecologies of India harbor diverse endophytic bacteria. Firmicutes were dominant followed by Actinobacteria and Proteobacteria. Genus Bacillus, Stenotrophomonas, Streptomyces, and Paenibacillus were core endophytic bacteria in different agro-ecologies. The endophytic bacterial strains were displaying diverse functional traits.

Small Spatial Scale Drivers of Secondary Metabolite Biosynthetic Diversity in Environmental Microbiomes.

In the search for novel drug candidates, diverse environmental microbiomes have been surveyed for their secondary metabolite biosynthesis potential, yet little is known about the biosynthetic diversity encoded by divergent microbiomes from different ecosystems, and the environmental parameters driving this diversity. Here, we used targeted amplicon sequencing of adenylation (AD) and ketosynthase (KS) domains along with 16S sequencing to delineate the unique biosynthetic potential of microbiomes from three separate habitats (soil, water, and sediments) exhibiting unique small spatial scale physicochemical gradients. The estimated richness of AD domains was highest in marine sediments with 656 ± 58 operational biosynthetic units (OBUs), while the KS domain richness was highest in soil microbiomes with 388 ± 67 OBUs. Microbiomes with rich and diverse bacterial communities displayed the highest PK potential across all ecosystems, and on a small spatial scale, pH and salinity were significantly, positively correlated to KS domain richness in soil and aquatic systems, respectively. Integrating our findings, we were able to predict the KS domain richness with a RMSE of 31 OBUs and a R2 of 0.91, and by the use of publicly available information on bacterial richness and diversity, we identified grassland biomes as being particularly promising sites for the discovery of novel polyketides. Furthermore, a focus on acidobacterial taxa is likely to be fruitful, as these were responsible for most of the variation in biosynthetic diversity. Overall, our results highlight the importance of sampling diverse environments with high taxonomic diversity in the pursuit for novel secondary metabolites. IMPORTANCE To counteract the antibiotic resistance crisis, novel anti-infective agents need to be discovered and brought to market. Microbial secondary metabolites have been important sources of inspiration for small-molecule therapeutics. However, the isolation of novel antibiotics is difficult, and the risk of rediscovery is high. With the overarching purpose of identifying promising microbiomes for discovery of novel bioactivity, we mapped out the most significant drivers of biosynthetic diversity across divergent microbiomes. We found the biosynthetic potential to be unique to individual ecosystems, and to depend on bacterial taxonomic diversity. Within systems, and on small spatial scales, pH and salinity correlated positively to the biosynthetic richness of the microbiomes, Acidobacteria representing the taxa most highly associated with biosynthetic diversity. Ultimately, understanding the key drivers of the biosynthesis potential of environmental microbiomes will allow us to focus bioprospecting efforts and facilitate the discovery of novel therapeutics.

P710 Changes of gut microbiome after anti-TNF-α therapy and the prediction of clinical remission in patients with active ulcerative colitis

Abstract Background The aims of this study are to explore the changes of gut microbiome after anti-TNF-α therapy (adalimumab; ADA) and to identify biomarkers to predict clinical remission to ADA in patients with active ulcerative colitis (UC). Methods Fecal samples were taken before (baseline) and after ADA administration at weeks 8 and 56 in patients with active UC. Fecal bacterial taxonomic composition and diversity were investigated by 16S sequencing and analyzed by divisive amplicon denoising algorithm version 2 (DADA2) at the level of amplicon sequence variant (ASV). The table was imported into R 4.0.2 to analyze for richness, diversity, heatmap and ordination plot . The linear discriminant analysis effect size (LEfSe) was used for statistical analysis. Clinical remission was assessed using the Mayo score. Results 260 fecal samples from 146 patients with UC administering ADA and 40 fecal samples of healthy controls (HC) were analyzed. The mean age of the participants was 44 ±14.8 years, and 60.7% were male (patients 64.9%, healthy control 42.5%). Overall communities (β-diversity) of gut microbiota in HC clearly differed from those before, after 8 weeks, and after 56 weeks of ADA treatment in patients with UC regardless of remission. The compositions of microbiota were affected by the disease severity and extent. ADA treatment significantly reduced the dissimilarity among samples in remitters at both 8 and 56 weeks, which were not observed in non-remitters. In remitters, the abundance of genus Staphylococcus was significantly decreased and genera Bifidobacterium and Dorea were significantly increased during ADA treatment period. The baseline samples of remitter at week 8 showed a higher abundance of 40 ASVs, including Sporosarcina (ASV2803), Bacteroides sp. (ASV1298, ASV1490), and Enterobacter (ASV9330, ASV9332) compared to baseline of non-remitters. Given that the 48 ASVs increased or decreased in baseline samples of remitters at week 8, the best log ratio of average relative abundance of increased ASVs/decreased ASVs to predict remission for ADA treatment was 0.07459, with 72.4% sensitivity and 84.3% specificity on the receiver operating curve (area under the curve, 0.855). Conclusion The composition of gut microbiota varies depending on the status of the disease and the effectiveness of the ADA treatment. Relative abundance of s fecal bacteria before treatment can be a biomarker for predicting efficacy of ADA in patients with UC.

A deep continental aquifer downhole sampler for microbiological studies.

To be effective, microbiological studies of deep aquifers must be free from surface microbial contaminants and from infrastructures allowing access to formation water (wellheads, well completions). Many microbiological studies are based on water samples obtained after rinsing a well without guaranteeing the absence of contaminants from the biofilm development in the pipes. The protocol described in this paper presents the adaptation, preparation, sterilization and deployment of a commercial downhole sampler (PDSshort, Leutert, Germany) for the microbiological studying of deep aquifers. The ATEX sampler (i.e., explosive atmospheres) can be deployed for geological gas storage (methane, hydrogen). To validate our procedure and confirm the need to use such a device, cell counting and bacterial taxonomic diversity based on high-throughput sequencing for different water samples taken at the wellhead or at depth using the downhole sampler were compared and discussed. The results show that even after extensive rinsing (7 bore volumes), the water collected at the wellhead was not free of microbial contaminants, as shown by beta-diversity analysis. The downhole sampler procedure was the only way to ensure the purity of the formation water samples from the microbiological point of view. In addition, the downhole sampler allowed the formation water and the autochthonous microbial community to be maintained at in situ pressure for laboratory analysis. The prevention of the contamination of the sample and the preservation of its representativeness are key to guaranteeing the best interpretations and understanding of the functioning of the deep biosphere.

Eco-evolutionary implications of helminth microbiomes.

The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host-parasite interactions in light of new technological developments.

Impacts of high-quality coal mine drainage recycling for replenishment of aquatic ecosystems in arid regions of China: Bacterial community responses

Coal mine water is usually recycled as supplementary water for aquatic ecosystems in arid and semiarid mining regions of China. To ensure ecosystem health, the coal mine water is rigorously treated using several processes, including reverse osmosis, to meet surface water quality standards. However, the potential environmental impacts of this management pattern on the ecological function of receiving water bodies are unclear. In this study, we built several microcosm water ecosystems to simulate the receiving water bodies. High-quality treated coal mine drainage was mixed into the model water bodies at different concentrations, and the sediment bacterial community response and functional changes were systematically investigated. The results showed that the high-quality coal mine drainage could still shape bacterial taxonomic diversity, community composition and structure, with a concentration threshold of approximately 50%. Moreover, both the Mantel test and the structural equation model indicated that the salinity fluctuation caused by the receiving of coal mine drainage was the primary factor shaping the bacterial communities. 10 core taxa in the molecular ecological network influenced by coal mine drainage were identified, with the most critical taxa being patescibacteria and g_Geothermobacter. Furthermore, the pathway of carbohydrate metabolism as well as signaling molecules and interactions was up-regulated, whereas amino acid metabolism showed the opposite trend. All results suggested that the complex physical-chemical and biochemical processes in water ecosystems may be affected by the coal mine drainage. The bacterial community response and underlying functional changes may accelerate internal nutrient cycling, which may have a potential impact on algal bloom outbreaks.