Bacterial Taxonomic Composition Research Articles

Gastrointestinal-inert prebiotic micro-composites improve the growth and community diversity of mucosal-associated bacteria.

The process of microencapsulation and the development of microparticle-based drug formulations have gained increased pharmaceutical interest, particularly for drug delivery and bacterial-encapsulation purposes for probiotic delivery. Existing studies have examined microcomposite (MC) responses to gastrointestinal (GI) conditions with the aim of controlling disintegration, and thus release, across the small and large bowel. However, the delivery of MCs which remain intact, without degrading, could act as bacterial growth scaffolds or materials providing a prebiotic support, conferring potentially beneficial GI health properties. This present study employs prilling as a method to produce a portfolio of MCs using a variety of biopolymers (alginate, chitosan, pectin and gellan gum) with a range of MC diameters and density compositions. Fluorescent probes are co-encapsulated within each MC to enable flow-cytometry directed release profile assessments following exposure to chemical simulated gastric and intestinal digestion conditions. We observe that MC size, gel-strength, density, and biopolymer material all influence response to gastric and intestinal conditions. Gellan gum (GG) MCs demonstrated complete resistance to disintegration throughout GI-simulation in the stomach and small intestine. Considering these MCs could reach the colon intact, we then examined how such MCs, doped with prebiotic growth supporting carboxymethyl cellulose (CMC) polymers, could impact microbial communities using a bioreactor model of the colonic microbiome. Following supplementation with GGCMC MCs, mucosal bacterial diversity (using 16 s rRNA sequencing and Shannon entropy and observed feature diversity metrics) and taxonomic composition changes were observed. Concentrations of short chain fatty acid (SCFA) metabolites were also found to be altered. This is the first study to comprehensivelyexamine how MC physicochemistry can be manipulated to tailor MCs to have the desired GI release performance and subsequently, how GI-resistant MCs could have influential microbial altering properties and be adopted in novel prebiotic strategies.

Effect of Mineral Fertilizers and Pesticides Application on Bacterial Community and Antibiotic-Resistance Genes Distribution in Agricultural Soils

Soils are a hotspot for the emergence and spread of antibiotic resistance. The effects of agrochemical treatments on the bacterial community of agricultural soils and the content of antibiotic-resistance genes (ARGs) were studied. Treatments included the following: control, mineral fertilizers (NPKs), pesticides, and the combined treatment of soils under soya (Glycine max), sunflower (Helianthus annuus L.), and wheat (Triticum aestivum). Bacterial community taxonomic composition was studied using 16S rRNA gene sequencing. The content of 10 ARGs and 3 integron genes (intI1, intI2, intI3) was determined using quantitative real-time PCR. The results showed that the treatments had little effect on the taxonomic composition and diversity of the soil bacterial community. The most significant factors determining differences in the microbial community were sampling time and soil physico-chemical parameters. A significant role of the bacterial community in ARG distribution in soils was demonstrated. Representatives of the Pseudomonas, Bacillus, Sphingomonas, Arthrobacter genera, and the Nocardioidaceae and Micrococcaceae families were likely ARG hosts. The presence of integron genes of all three classes was detected, the most numerous being intI3. This work provides important information on the role of agricultural soils in ARG transfer, and the findings may be useful for sustainable and safe agricultural development.

Bacterial community shifts occur primarily through rhizosphere expansion in response to subsoil amendments.

To comprehensively evaluate the impact of agricultural management practices on soil productivity, it is imperative to conduct a thorough analysis of soil bacterial ecology. Deep-banding nutrient-rich amendments is a soil management practice that aims to improve plant growth and soil structure by addressing the plant-growth constraints posed by dense-clay subsoils. However, the response of bacterial communities to deep-banded amendments has not been thoroughly studied. To address this knowledge gap, we conducted a controlled-environment column experiment to examine the effects of different types of soil amendments (poultry litter, wheat straw + chemical fertiliser and chemical fertiliser alone) on bacterial taxonomic composition in simulated dense-clay subsoils. We evaluated the bacterial taxonomic and ecological group composition in soils beside and below the amendment using 16S rRNA amplicon sequencing and robust statistical methods. Our results indicate that deep-banded amendments alter bacterial communities through direct and indirect mechanisms. All amendments directly facilitated a shift in bacterial communities in the absence of growing wheat. However, a combination of amendments with growing wheat led to a more pronounced bacterial community shift which was distinct from and eclipsed the direct impact of the amendments and plants alone. This indirect mechanism was evidenced to be mediated primarily by plant growth and hypothesised to result from an enhancement in wheat root distribution, density and rhizodeposition changes. Therefore, we propose that subsoil amendments regardless of type facilitated an expansion in the rhizosphere which engineered a substantial plant-mediated bacterial community response within the simulated dense-clay subsoils. Overall, our findings highlight the importance of considering the complex and synergistic interactions between soil physicochemical properties, plant growth and bacterial communities when assessing agricultural management strategies for improving soil and plant productivity.

Oral Microbiome Stamp in Alzheimer's Disease.

Recent studies have suggested that periodontal disease and alterations in the oral microbiome may be associated with cognitive decline and Alzheimer's disease (AD) development. Here, we report a case-control study of oral microbiota diversity in AD patients compared to healthy seniors from Central Asia. We have characterized the bacterial taxonomic composition of the oral microbiome from AD patients (n = 64) compared to the healthy group (n = 71) using 16S ribosomal RNA sequencing. According to our results, the oral microbiome of AD has a higher microbial diversity, with an increase in Firmicutes and a decrease in Bacteroidetes in the AD group. LEfSe analysis showed specific differences at the genus level in both study groups. A region-based analysis of the oral microbiome compartment in AD was also performed, and specific differences were identified, along with the absence of differences in bacterial richness and on the functional side. Noteworthy findings demonstrated the decrease in periodontitis-associated bacteria in the AD group. Distinct differences were revealed in the distribution of metabolic pathways between the two study groups. Our study confirms that the oral microbiome is altered in AD. However, a comprehensive picture of the complete composition of the oral microbiome in patients with AD requires further investigation.

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<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.

Unraveling the role of bacterial communities in mangrove habitats under the urban influence, using a next-generation sequencing approach

Mangrove ecosystems are vital coastal habitats with rich biodiversity and play a significant role in carbon sequestration, these habitats are facing mounting threats from rapid urbanization. This study delves into assessing the sediment bacterial communities from the urban mangrove habitats of Campal and Panaji, within the Mandovi estuarine environment of Goa, to understand the intricate interplay between urbanization and bacterial dynamics in the mangrove habitats. We used a combined approach of 16S amplicon and shotgun sequencing methodologies to understand the bacterial taxonomic composition and functional profiles. The community structure revealed the dominance of bacterial groups from phylum Proteobacteria, Chloroflexi and Actinobacteria at both locations. The impact of urbanization was evident from the increased abundance of pathogenic groups at class and genus levels in this region. The core microbiome analysis showed the presence of Shewanella, Pseudomonas and Clostridium which are mostly pathogenic, anaerobic taxa Woeseia, Rheinheimera, like genera that are involved in the organic matter cycling and unclassified bacteria. Though increased pathogenic forms are reported, it is evident that the dominant taxa also included groups that contributed to the biogeochemical cycling of organic matter in sediment from these locations. Functional diversity elucidated through shotgun metagenomics analysis showcased the predominance of carbohydrate metabolism and the presence of glycoside hydrolases degrading plant-based starch, pectin and cellulosic organic matter. The occurrence of xenobiotic biodegradation pathways is an indication of the presence of xenobiotic degrading microbes as a natural means of degrading high amounts of pollutants at this location. Comparative analysis of the metagenomes from this study with similar earlier studies at Ribandar, Mandovi and Cortalim, Zuari mangrove habitats of Goa with varying pollution levels also reiterates the terrestrial influence on the microbial community in these habitats. It showed that Panaji and Campal locations had the presence of dominant pathogenic forms which was absent in the other two locations. The Ribandar and Coratlim location which is reported to have a comparatively lesser impact due to anthropogenic activity had an increased abundance of distinct genera which are predominant heterotrophic forms involved in remineralization and reduced levels of pathogens. Our findings highlight the profound influence of urbanization on the sediment mangrove bacterial communities and spotlight the resilience and adaptability of these microorganisms. This calls for immediate action and preventive measures to restore their functional potential in maintaining the health of these ecosystems amidst expanding urban landscapes.

Analysis of oral microbiome diversity in Alzheimer’s disease patients from Kazakhstan

AbstractBackgroundRecent studies have suggested that periodontal disease and alterations in the oral microbiome may be associated with cognitive decline and the development of Alzheimer’s disease (AD). Here, we report a pilot case‐control study of oral microbiota diversity in AD patients in comparison with healthy seniors from the Central Asian region.MethodWe have characterized the bacterial taxonomic composition of the oral microbiome from AD patients (n = 69) compared to the healthy group (n = 72) using 16S ribosomal RNA sequencing.ResultOur analysis showed that the oral microbiome of AD has a higher microbial diversity. More importantly, differences across taxonomic groups are distinguished by the diversity of opportunistic flora in the AD group. We identified differences between phyla and genera in bacterial abundance, including a decrease in the Firmicutes/Bacteroidetes ratio in the microbiome of AD participants. LEfSe allowed determining an enrichment at the Genus Pseudomonas, Prevotella_9, UCG_002, Esherichia_Shigella, Mogibacterium, Ralstonia, and Bergeyella in the AD group. A significant increase in the genus Mogibacterium, which is also associated with an aggressive form of periodontitis and type 2 diabetes mellitus, was revealed. The genus Ralstonia are commensal representatives of the oral microbiome, but with a reduced immune system they exhibit pathogenic properties and are associated with a higher risk of mortality in hematological malignancies and hereditary disorders of hematopoiesis. One of the least studied Bergeyella spp, which is a representative of the oral microbiome of dogs, cats, and pigs, therefore, it is isolated on contact and is associated with the risk of preterm birth, as well as the development of endocarditis in a weakened body.ConclusionOur results confirm that the oral microbiome is a potential target for therapeutic intervention in AD. However, a comprehensive picture of the full composition of the oral microbiome in patients with AD requires further investigation.

Soil bacterial habitat generalists strengthen depth-dependent organic carbon accrual in coastal reclaimed lands after afforestation

The microbially driven soil organic carbon (SOC) turnover and accrual at the aggregate scale are crucial to reveal potential SOC sequestration and stabilization. However, information about how afforestation in reclaimed lands influences the bacterial contribution to SOC within soil aggregates remains unclear. Here, we investigated the bacterial taxonomic and functional composition and habitat associations of species (i.e., generalists and specialists) in different aggregates. Soil aggregates were isolated using an optimal soil moisture method. Bacterial taxonomic and functional composition were determined using high-throughput sequencing and PICRUSt2, respectively. We evaluated the effect of bacterial traits on SOC accrual within aggregates along the soil profile in unreclaimed tideland and two poplar plantations at different stages of reclamation (i.e., reclaimed 24 and 64 years prior to data collection) in East China. The bacterial traits and SOC concentration did not differ significantly among different-sized aggregates and that bacterial alpha diversity and SOC within aggregates increased with reclamation time, but this was only pronounced in surface soil. The relative abundance of generalists increased, specialists decreased in the soil profile with reclamation time, and the magnitude of variation declined with soil depth. The random forest model and variation partitioning analysis confirmed that generalists and specialists dominated the variation in SOC. Moreover, some subgroups from Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi phyla were rich in generalists and may play crucial roles in SOC accrual. These findings suggest that the bacterial traits and SOC in coastal coarse-textured soil were not affected by aggregate sizes and might rely on other aggregate attributes (e.g., stability). Furthermore, SOC accrual was strongly affected by an increase in habitat generalists. We provide new insights into the variation pattern in SOC and bacterial traits at the aggregate scale and illustrate that bacterial generalists have the greatest impact on SOC accrual in coastal reclaimed lands after afforestation.

Soil Bacterial Communities Across Seven Rhizoma Peanut Cultivars (Arachis glabrata Benth.) Respond to Seasonal Variation.

Soil microorganisms play key roles in soil nutrient transformations and have a notable effect on plant growth and health. Different plant genotypes can shape soil microbial patterns via the secretion of root exudates and volatiles, but it is uncertain how a difference in soil microorganisms induced by crop cultivars will respond to short-term seasonal variations. A field experiment was conducted to assess the changes in soil bacterial communities of seven rhizoma peanut (Arachis glabrata Benth, RP) cultivars across two growing seasons, April (Spring season) and October (Fall season). Soils' bacterial communities were targeted using 16S rRNA gene amplicon sequencing. Bacterial community diversity and taxonomic composition among rhizoma peanut cultivars were significantly affected by seasons, cultivars, and their interactions (p < 0.05). Alpha diversity, as estimated by the OTU richness and Simpson index, was around onefold decrease in October than in April across most of the RP cultivars, while the soils from Arblick and Latitude had around one time higher alpha diversity in both seasons compared with other cultivars. Beta diversity differed significantly in April (R = 0.073, p < 0.01) and October (R = 0.084, p < 0.01) across seven cultivars. Bacterial dominant taxa (at phylum and genus level) were strongly affected by seasons and varied towards more dominant groups that have functional potentials involved in nutrient cycling from April to October. A large shift in water availability induced by season variations in addition to host cultivar's effects can explain the observed patterns in diversity, composition, and co-occurrence of bacterial taxa. Overall, our results demonstrate an overriding effect of short-term seasonal variations on soil bacterial communities associated with different crop cultivars. The findings suggest that season-induced shifts in environmental conditions could exert stronger impacts on soil microorganisms than the finer-scale rhizosphere effect from crop cultivars, and consequently influence largely microbe-mediated soil processes and crop health in agricultural ecosystems.

Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems.

The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.

Topsoil and subsoil bacterial community assemblies across different drainage conditions in a mountain environment

BackgroundHigh mountainous environments are of particular interest as they play an essential role for life and human societies, while being environments which are highly vulnerable to climate change and land use intensification. Despite this, our knowledge of high mountain soils in South America and their microbial community structure is strikingly scarce, which is of more concern considering the large population that depends on the ecosystem services provided by these areas. Conversely, the Central Andes, located in the Mediterranean region of Chile, has long been studied for its singular flora, whose diversity and endemism has been attributed to the particular geological history and pronounced environmental gradients in short distances. Here, we explore soil properties and microbial community structure depending on drainage class in a well-preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S. This presents an opportunity to determine changes in the overall bacterial community structure across different types of soils and their distinct layers in a soil depth profile of a highly heterogeneous environment.MethodsFive sites closely located (<1.5 km) and distributed in a well preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S were selected based on a pedological approach taking into account soil types, drainage classes and horizons. We analyzed 113 soil samples using high-throughput sequencing of the 16S rRNA gene to describe bacterial abundance, taxonomic composition, and co-occurrence networks.ResultsAlmost 18,427 Amplicon Sequence Variant (ASVs) affiliated to 55 phyla were detected. The bacterial community structure within the same horizons were very similar validating the pedological sampling approach. Bray-Curtis dissimilarity analysis revealed that the structure of bacterial communities in superficial horizons (topsoil) differed from those found in deep horizons (subsoil) in a site-specific manner. However, an overall closer relationship was observed between topsoil as opposed to between subsoil microbial communities. Alpha diversity of soil bacterial communities was higher in topsoil, which also showed more bacterial members interacting and with higher average connectivity compared to subsoils. Finally, abundances of specific taxa could be considered as biological markers in the transition from topsoil to subsoil horizons, like Fibrobacterota, Proteobacteria, Bacteroidota for shallower soils and Chloroflexi, Latescibacterota and Nitrospirota for deeper soils.ConclusionsThe results indicate the importance of the soil drainage conditions for the bacterial community composition, suggesting that information of both structure and their possible ecological relationships, might be useful in clarifying the location of the edge of the topsoil-subsoil transition in mountainous environments.

Effects of sample collection and storage methods on fecal bacterial diversity in California ground squirrels (Otospermophilus beecheyi)

Abstract Measures of fecal bacterial abundance and taxonomic composition are commonly used as proxies for gut microbial diversity in studies of free-living mammals. Because methods of sample collection and storage may affect measures of bacterial diversity, we evaluated the effects of several procedures on fecal bacterial diversity in a free-living population of California ground squirrels (Otospermophilus beecheyi). Replicate fecal samples from 12 adult female squirrels were collected either from the soil beneath traps in which individuals had been captured or from tubs placed under squirrels during handling. Samples were then either frozen immediately in liquid nitrogen or stored on ice for several hours before being transferred to a −80°C freezer. Sequencing of the bacterial 16s RNA gene revealed no differences among methods with regard to sequence read depth (number of sequences recovered per animal) or alpha (within-individual) diversity of bacterial taxa. While our collection-storage procedures had a significant effect on one of the metrics of beta (among-individual) bacterial diversity examined, this effect was small compared to that of individual identity. Date of sample collection affected alpha and beta diversity; samples collected only 1 week apart differed significantly in bacterial diversity. Overall, these findings suggest that the collection and storage methods employed yield generally comparable information and are capable of capturing potentially important patterns of fecal bacterial composition and diversity in free-living mammals.

Landscape in the gallbladder mycobiome and bacteriome of patients undergoing cholelithiasis with chronic cholecystitis.

Gallstone disease (GSD) is associated with changes in the gut and gallbladder bacterial composition, but there is limited information on the role of the fungal community (mycobiome) in disease development. This study aimed to characterize the gallbladder mycobiome profiles and their interactions with bacteriome in GSD. A total of 136 bile and gallstone samples (34 paired for bacteriome, and 33 paired and extra 2 bile samples for mycobiome) were obtained from calculi patients with chronic cholecystitis. Bile and gallstone bacteriome and mycobiome were profiled by 16S and internal transcribed spacer (ITS) rRNA gene sequencing, respectively. Gallbladder bacteriome, mycobiome, and interkingdom and intrakingdom interactions were compared between bile and gallstone. In general, microbial diversity was higher in bile than in gallstone, and distinct microbial community structures were observed among them. Deep Sea Euryarchaeotic Group, Rhodobacteraceae, and Rhodobacterales were microbial biomarkers of bile, while Clostridiales and Eubacterium coprostanoligenes were biomarkers of gallstone. Five fungal taxa, including Colletotrichum, Colletotrichum sublineola, and Epicoccum, were enriched in gallstone. Further ecologic analyses revealed that intensive transkingdom correlations between fungi and bacteria and intrakingdom correlations within them observed in gallstone were significantly decreased in bile. Large and complex fungal communities inhabit the gallbladder of patients with GSD. Gallstone, compared with bile, is characterized by significantly altered bacterial taxonomic composition and strengthened bacterial-bacterial, fungal-fungal, and bacterial-fungal correlations in the gallbladder of patients with GSD.

Effects of Adding Lean Red Meat to a U.S.-Style Healthy Vegetarian Dietary Pattern on Gut Microbiota and Cardiovascular Risk Factors in Young Adults: a Crossover Randomized Controlled Trial

BackgroundLimited research evidence exists on the effects of red meat on gut microbiota in human adults. ObjectiveWe aim to assess the effects of consuming a Healthy U.S.-Style Dietary Pattern (HDP), without or with unprocessed or processed lean red meats, on gut microbiota and fecal short-chain fatty acid (SCFA) levels in healthy young adults. Secondary outcomes are cardiovascular disease risk factors. MethodsWe conducted a randomized, controlled, crossover trial with 3 3-wk dietary interventions, each separated by a 5-wk washout period with habitual dietary intake. Nineteen participants (8 females, age 26 ± 4 y old, BMI 23 ± 3 kg/m2) consumed 3 study diets in random order: 1) healthy lacto-ovo vegetarian diet (LOV); 2) LOV plus 3 ounces/d of cooked unprocessed lean red meat (URM); and 3) LOV plus 3 ounces/d of cooked processed lean red meat (PRM). Fecal and fasting blood samples were collected before and during the last 2 wk of each intervention. We measured fecal bacterial community structure using 16S rRNA amplicon sequencing (V4 region, primers 515F-806R). Community diversity, structure, and taxonomic composition were computed using Mothur v.1.44.3. ResultsThe addition of unprocessed or processed lean red meats to a LOV HDP did not influence short-term changes in bacterial taxonomic composition. Independent of red meat intake, the HDP led to changes in 23 bacteria; reductions in serum total cholesterol (TC) and LDL-C concentrations; but no changes in fecal SCFA, serum triglycerides, HDL-C concentrations, TC/HDL-C ratio, or blood pressures. With data from all 3 diet interventions combined, changes in some bacteria were associated with improvements in TC, LDL-C, triglycerides, and HDL-C concentrations, and TC/HDL-C ratio. ConclusionsHealthy young adults who adopt an HDP that may be vegetarian or omnivorous, including lean red meat, experience short-term changes in gut microbial composition, which associate with improvements in multiple lipid-related cardiovascular risk factors.NCT03885544, https://clinicaltrials.gov/ct2/show/NCT03885544?cond=NCT03885544&draw=2&rank=1

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.

The rhizosphere Microbiome of Malus sieversii (Ldb.) Roem. in the geographic and environmental gradients of China's Xinjiang

Malus sieversii (Ldb.) Roem. is the original species of modern cultivated apple and a key national essential conservation plant in China. In recent years, degradation and death of wild apple has been exacerbated by imbalances in the rhizosphere micro-ecosystems of wild apple forests due to soil nutrient loss, grazing, climate change and pest and disease outbreaks. However, the structure, diversity and response to environmental factors of wild apple rhizosphere microbial communities are so far unclear. In this study, the rhizosphere bacterial and eukaryotic communities of M. sieversii (Ldb.) Roem. in eight regions of the Yili River were analyzed using 16S/18S rDNA high-throughput sequencing technology. The results indicated that the bacterial operational taxonomic units (OTUs), Shannon index, and community composition were significantly lower in regions A, E, and F than in other regions. By contrast, the dominant eukaryotic communities in all regions were relatively similar in composition and differed less than the relative abundance of bacterial communities. Geographical and climatic distance were found to be key factors influencing the composition and diversity of wild apple rhizosphere microbial communities through mantel analysis. Moreover, these factors above were more correlated with bacterial diversity than with eukaryotes. This study identified the structure of wild apple rhizosphere microbial communities in Xinjiang and their interaction mechanisms under geographical and environmental gradients. It provides guidance for the sustainable management and ecological construction of wild apple forests in China.

The Development of the Bacterial Community of Brown Trout (Salmo trutta) during Ontogeny.

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish's bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.

Investigation of Surface Bacterial Diversities and Compositions in the Global Subway Facilities

Indoor microbes are a key component of air contamination that causes human health risks. However, compared with the aquatic and soil environment, microbial diversity and taxonomic structure and composition in subway facility are not well characterized. This study tries to explore surface bacterial communities by using swabs collected from four global subway facilities, such as Busan, Boston, Mexico City, and Moscow using 16S rRNA gene amplicon sequencing. The alpha-diversities on bacterial communities were significantly different between Moscow and other samples, despite the different sample characteristics among Busan, Boston, Mexico City samples. For bacterial taxonomic composition, three phyla such as Actinobacteria (41.1%), Proteobacteria (27.7%), and Firmicutes (18.9%), were most dominant among all samples, indicating that there was no significance (p &gt; 0.05). The subway station surface samples were mostly dominated by Gram-positive bacteria, including genera Corynebacterium, Staphylococcus, and Streptococcus. PCoA analysis also revealed that the Moscow bacterial communities were clearly separated from others. In addition, core genera were only shared 75 genera among all samples, but 486 genera were shared with three global stations, such as Busan, Boston and Mexico City. These results suggested that the human activity and geographical environment potentially affect the establishment of the bacterial community. Although this study provided basic information on surface bacterial communities in the subway system, there is a remaining unknown microbiome in the indoor air environment. Therefore, we consistently try to understand the indoor environment’s microbial ecology in the subway system.

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.

Different maturation of gut microbiome in Korean children.

Gut microbiome plays a crucial role in maintaining human health and is influenced by food intake, age, and other factors. In this study based in Korea, we examined the bacterial taxonomic composition of the gut microbiota in infants (≤ 1 year), toddlers (1-<4 years), and school-aged children (4-13 years) and compared them with those of healthy adults to investigate the microbiota changes in early life and their association with the resistome. We used whole metagenome sequences obtained by Illumina HiSeq sequencing and clinical information of 53 healthy children, and sequence data of 61 adults from our previous study. Our results indicate that the bacterial proportion of the gut in the population ranging from infants to adults forms three clusters: the Ruminococcus-Eubacterium (G1), Bifidobacterium-Escherichia (G2), and Bacteroides-Faecalibacterium (G3) groups. The gut microbiota of infants and toddlers (100% of infants and 85% of toddlers) constituted mostly of G2 and G3 groups, whereas 90% of adults showed G1-type gut microbiota. School-aged children showed a transitional gut microbiota composition of both infants and adults (31%, 38%, and 31% in G1, G2, and G3, respectively). Notably, the three clusters of microbiota showed significantly different patterns of bacterial diversity (p < 0.001): G2 showed the lowest Shannon index, followed by G3 and G1 (1.41, 2.08, and 2.48, respectively; median Shannon index). When combined with the adult group, alpha diversity showed a positive correlation with age (R2 = 0.3). Furthermore, clustering the composition of antibiotic resistance genes (ARG) identified two clusters (A1 and A2), and most of G1 (95%) and G3 (80%) belonged to A1. However, G2 showed the least diversity and the highest abundance of ARGs. Nine ARG families showed a significant difference among age groups; three tetracycline resistance genes, tet32, tetO, and tetW, showed a positive correlation, and six other genes, ampC, TEM, ileS, bacA, pmr transferase, and cepA, showed a negative correlation with age. In conclusion, our results highlighted that a delayed persistence of the Bifidobacterium-dominant enterotype with a lower bacterial diversity was observed in Korean children up to 13 years of age, which suggests a different maturation process with a delayed maturation time.