Bacterial Beta Diversity Research Articles

Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.

Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections among men who have sex with men and transgender women. Although poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from the DoxyPEP trial, a randomized clinical trial comparing doxy-PEP use, a one-time doxycycline 200-mg dose taken after condomless sex (DP arm, n = 100), to standard of care (SOC arm, n = 50) among men who have sex with men and transgender women. From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data were analyzable from 127 samples derived from 89 participants, and RNA-seq data were analyzable from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time. The median number of doxycycline doses taken since enrollment by participants with DNA-seq data was zero (interquartile range (IQR): 0-7 doses) for the SOC arm and 42 (IQR: 27-64 doses) for the DP arm. Tetracycline ARGs were detected in all day-0 DNA-seq samples and in 85% of day-0 RNA-seq samples. The proportional mass of tetracycline ARGs in the resistome increased between day-0 and month-6 in DP participants from 46% to 51% in the metagenome (P = 2.3 × 10-2) and from 4% to 15% in the metatranscriptome (P = 4.5 × 10-6), but no statistically significant increases in other ARG classes were observed. Exposure to a higher number of doxycycline doses correlated with proportional enrichment of tetracycline ARGs in the metagenome (Spearman's ρ = 0.23, P = 9.0 × 10-3) and metatranscriptome (Spearman's ρ = 0.55, P = 3.7 × 10-8). Bacterial microbiome alpha diversity, beta diversity and total bacterial mass did not differ between day-0 and month-6 samples from DP participants when assessed by either DNA-seq or RNA-seq. In an abundance-based correlation analysis, we observed an increase over time in the strength of the correlation between tetracycline ARGs and specific bacterial taxa, including some common human pathogens. In sum, doxy-PEP use over a 6-month period was associated with an increase in the proportion of tetracycline ARGs comprising the gut resistome and an increase in the expression of tetracycline ARGs. At 6 months of doxy-PEP use, no residual differences were observed in alpha and beta diversity or taxonomic composition of the gut microbiome. As doxy-PEP is implemented as a public health strategy, further studies and population-level surveillance of doxycycline-resistant pathogens are needed to understand the implications of these findings. ClinicalTrials.gov registration number: NCT03980223 .

Biotic Interactions Shape Soil Bacterial Beta Diversity Patterns along an Altitudinal Gradient during Invasion

Invasive plants have already been observed in the understory of mountain forests, which are often considered a safe shelter for most native plants. Microorganisms might be drivers of plant invasions. Nevertheless, the mechanisms determining variations in microbial community composition (beta diversity) during invasion along altitudinal gradients remain to be elucidated. Here, the elevational patterns and the driving ecological processes (e.g., environmental filtering, co-occurrence patterns, and community assembly processes) of soil bacterial beta diversity were compared between invasive and native plants on the Qinling Mountains. The species turnover dominated bacterial compositional dissimilarities in both invasive and native communities, and its contribution to total beta diversity decreased during invasion. Total soil bacterial dissimilarities and turnover exhibited significant binominal patterns over an altitudinal gradient, with a tipping point of 1413 m. Further analysis showed that the contributions of assembly processes decreased in parallel with an increase in contributions of co-occurrence patterns during the invasion process, indicating that species interdependence rather than niche partitioning is strongly correlated with the bacterial biogeography of invasive communities. Plant invasion affects the relative contributions of stochastic processes and co-occurrence interactions through the regulation of the physiochemical characteristics of soil, and ultimately determines compositional dissimilarities and the components of the bacterial community along altitudinal gradients.

PSIX-10 Effects of Bacillus subtilis ATCC PTA-122264 on macronutrient digestibility and fecal characteristics, metabolites, and microbiota of healthy adult dogs subjected to an abrupt diet change

Abstract Probiotic use in dogs is increasing, with spore-forming Bacillus species gaining interest due to their viability during processing, storage, and in the gastrointestinal tract. B. subtilis is known for its adaptable metabolism that may be useful in pets subjected to abrupt dietary changes. The objective of this study was to determine dietary apparent total tract macronutrient digestibility (ATTD) and fecal characteristics, metabolites, and microbiota of healthy adult dogs supplemented with B. subtilis ATCC PTA-122264. All procedures were approved by the University of Illinois IACUC prior to experimentation. Dogs [n = 12; 6 ± 1 yr; 8.71 ± 0.91 kg body weight (BW)] were used in a replicated 3x3 Latin square design (n = 12/group) and fed to maintain BW. In each 42-d experimental period, dogs were allotted to one of three treatments: Control (kibble diet only), Low [kibble diet + 1×109 colony-forming units (CFU) of B. subtilis], and High (kibble diet + 5×109 CFU of B. subtilis). After a 22-d adaptation phase, a 5-d fecal collection phase was followed by a blood collection phase. On d 28, dogs were abruptly changed to a canned diet and fed for 14 d, with fecal samples collected on d 30 (2 d post change), 34 (6 d post change), 38 (10 d post change), and 42 (14 d post change). Fecal microbiota data were evaluated using QIIME2. All other data were analyzed using the Mixed Models procedure of SAS, with P < 0.05 being considered significant. B. subtilis supplementation of the kibble diet did not influence food or energy intake, fecal output, ATTD, most serum metabolites, hematology, fecal characteristics, fecal bacterial alpha and beta diversity indices, and dysbiosis index, demonstrating the safety of the strain in dogs. However, fecal Streptococcus and Blautia abundances were higher in High dogs than Low or Control dogs, while E. coli abundance was less in Low dogs than High and Control dogs. The abrupt change to a canned diet led to significant alterations in fecal characteristics, dysbiosis index, and bacterial abundances, which were not influenced by B. subtilis supplementation. Bacterial alpha diversity measures were affected, with observed ASV (amplicon sequence variants) and the Fisher Index reducing, and the Shannon Index increasing by dietary change. The abrupt dietary change caused a distinct shift in microbial communities, as evidenced by principal coordinates analysis plots. The relative abundances of various fecal bacterial taxa, including Bifidobacterium, Faecalibaculum, Turicibacter, and Lactobacillus were decreased, while Collinsella, Ruminococcus gnavus group, and Escherichia-Shigella were increased with the dietary change. Our data support the notion that daily supplementation of 1 – 5×109 CFU of B. subtilis ATCC PTA-122264 in healthy dogs is safe and does not affect markers of general health and fecal characteristics, warranting further exploration.

Seasonal variation in the stomach microbiota of two sympatrically breeding Pygoscelis penguin species at Signy Island, South Orkney Islands.

The gut microbiomes of Antarctic penguins are important for the fitness of the host birds and their chicks. The compositions of microbial communities in Antarctic penguin guts are strongly associated with the birds' diet, physiological adaptation and phylogeny. Whilst seasonal changes in food resources, distribution and population parameters of Antarctic penguins have been well addressed, little research is available on the stability or variability of penguin stomach microbiomes over time. Here, we focused on two Pygoscelis penguin species breeding sympatrically in the maritime Antarctic and analysed their stomach contents to assess whether penguin gut microbiota differed over three austral summer breeding seasons. We used a high-throughput DNA sequencing approach to study bacterial diversity in stomach regurgitates of Adélie (Pygoscelis adeliae) and chinstrap (Pygoscelis antarctica) penguins that have a similar foraging regime on Signy Island (South Orkney Islands). Our data revealed significant differences in bacterial alpha and beta diversity between the study seasons. We also identified bacterial genera that were significantly associated with specific breeding seasons, diet compositions, chick-rearing stages and sampling events. This study provides a baseline for establishing future monitoring of penguin gut microbiomes in a rapidly changing environment.

Impacts of Whole-Grain Soft Red, Whole-Grain Soft White, and Refined Soft White Wheat Flour Crackers on Gastrointestinal Inflammation and the Gut Microbiota of Adult Humans.

Consumption of whole-grain wheat has been associated with positive health outcomes, but it remains unclear whether different types of wheat elicit varying effects on the gut microbiome and intestinal inflammation. The objectives of this research were to investigate the effect of two whole-grain wheat flours versus refined wheat flour on the diversity of the human gut microbiota, as well as on butyrate production capacity and gastrointestinal inflammation, using one-week dietary interventions. For this study, 28 participants were recruited, with ages ranging from 18 to 55 years and a mean BMI of 26.0 kg/m2. For four weeks, participants were provided 80 g daily servings of different wheat crackers: Week A was a run-in period of crackers made from soft white wheat flour, Week B crackers were whole-grain soft white wheat flour, Week C crackers were a wash-out period identical to Week A, and Week D crackers were whole-grain soft red wheat flour. At the end of each week, participants provided fecal samples that were analyzed for markers of intestinal inflammation, including lipocalin and calprotectin, using enzyme-linked immunosorbent assays and quantitative real-time PCR. The primary outcome, gut bacterial community alpha and beta diversity, was similar across timepoints. Three taxa significantly differed in abundance following both whole-grain wheat flour interventions: Escherichia/Shigella and Acidaminococcus were significantly depleted, and Lachnospiraceae NK4A136 group was enriched. Secondary outcomes determined that protein markers of intestinal inflammation and genes related to putative butyrate production capacity were similar throughout the study period, with no significant changes. Lipocalin concentrations ranged from 14.8 to 22.6 ng/mL while calprotectin ranged from 33.2 to 62.5 ng/mL across all 4 weeks. The addition of wheat crackers to the adult human subjects' usual diet had a minimal impact on their gastrointestinal inflammation or the gut microbiota.

Beta diversity patterns and driving mechanisms of stream bacteria and fungi on Mt. Kilimanjaro

Aquatic microbes, which are highly diverse in freshwater biofilms, play a vital role in shaping the structure and functioning of ecosystems. Nevertheless, the influence of environmental factors on aquatic microbes in different biogeographic ecosystems, especially in tropical mountains, is relatively unexplored. Here, we examined the relative influence of climate and physicochemical factors on beta diversity of stream bacteria and fungi using 16S rRNA amplicon sequencing at 40 sites on Mt. Kilimanjaro. Towards larger elevational distance, the total beta diversity and turnover of bacteria and fungi increased significantly, while nestedness decreased. The beta diversity of fungi showed greater spatial variation than that of bacteria, while the local contribution to beta diversity (LCBD) showed U-shaped elevational pattern for both taxa. Bacteria and fungi had strong positive relationships regarding the total beta diversity, LCBD and their components, except for nestedness, indicating similar environmental preferences and resource overlap. Among environmental variables, mean annual temperature, water depth and elevation predicted microbial beta diversity, while water depth, mean annual temperature and precipitation primarily affected LCBD. Overall, climate-related variables were the dominant factors for beta diversity and their effects were more pronounced for fungi than bacteria. The contrasting patterns of bacterial and fungal beta diversity and their ecological interactions in tropical aquatic ecosystems provide a rare dataset for assessing ecological functions in understudied aquatic ecosystems and predicting the impact of global change on microorganisms.

Nonbiodegradable microplastic types determine the diversity and structure of soil microbial communities: A meta-analysis

As an emerging contaminant, microplastics (MPs) have received considerable attention for their potential threat to the soil environment. However, the response of soil bacterial and fungal communities to MPs exposure remains unclear. In this study, we conducted a global meta-analysis of 95 publications and 2317 observations to assess the effects of nonbiodegradable MP properties and exposure conditions on soil microbial biomass, alpha and beta diversity, and community structure. Our results indicate that MPs increased (p < 0.05) soil active microbial biomass by 42%, with the effect varying with MPs type, exposure concentration, exposure time and soil pH. MPs concentration was identified as the most important factor controlling the response of soil microbial biomass to MPs. MPs addition decreased (p < 0.05) the soil bacterial Shannon and Chao1 indices by 2% and 3%, respectively, but had limited effects (p > 0.05) on soil fungal Shannon and Chao1 indices. The type of MPs and exposure time determined the effects of MPs on bacterial Shannon and Chao1 indices, while the type of MPs and soil pH controlled the response ratios of fungal Shannon and Chao1 indices to MPs. Specifically, soil organic carbon (SOC) was the major factor regulating the response ratio of bacterial alpha diversity index to MPs. The presence of MPs did not affect soil bacterial community structure and beta diversity. Our results highlight that MPs reduced bacterial diversity and richness but increased the soil active microbial biomass, suggesting that MPs could disrupt biogeochemical cycles by promoting the growth of specific microorganisms.

Genome-wide association study identifies host genetic variants influencing oral microbiota diversity and metabolic health

The microbial communities of the oral cavity are important elements of oral and systemic health. With emerging evidence highlighting the heritability of oral bacterial microbiota, this study aimed to identify host genome variants that influence oral microbial traits. Using data from 16S rRNA gene amplicon sequencing, we performed genome-wide association studies with univariate and multivariate traits of the salivary microbiota from 610 unrelated adults from the Danish ADDITION-PRO cohort. We identified six single nucleotide polymorphisms (SNPs) in human genomes that showed associations with abundance of bacterial taxa at different taxonomical tiers (P < 5 × 10–8). Notably, SNP rs17793860 surpassed our study-wide significance threshold (P < 1.19 × 10–9). Additionally, rs4530093 was linked to bacterial beta diversity (P < 5 × 10–8). Out of these seven SNPs identified, six exerted effects on metabolic traits, including glycated hemoglobin A1c, triglyceride and high-density lipoprotein cholesterol levels, the risk of type 2 diabetes and stroke. Our findings highlight the impact of specific host SNPs on the composition and diversity of the oral bacterial community. Importantly, our results indicate an intricate interplay between host genetics, the oral microbiota, and metabolic health. We emphasize the need for integrative approaches considering genetic, microbial, and metabolic factors.

Altitude Distribution Characteristics of Farmland Soil Bacteria in Loess Hilly Region of Ningxia

It is of great significance for the conservation of biodiversity in farmland ecosystems to study the diversity, structure, functions, and biogeographical distribution of soil microbes in farmland and their influencing factors. High-throughput sequencing technology was used to analyze the distribution characteristics of soil bacterial diversity, community structure, and metabolic function along elevation and their responses to soil physicochemical properties in farmland in the loess hilly areas of Ningxia. The results showed that:① The Alpha diversity index of soil bacterial was significantly negatively correlated with elevation (P &lt; 0.05) and showed a trend of decreasing and then slightly increasing along the elevation. ② Seven phyla, including Proteobacteria, Actinobacteria, and Acidobacteria, were the dominant groups, and five of them showed highly significant differences between altitudes (P &lt; 0.01). ③ At the secondary classification level, there were 36 metabolic functions of bacteria, including membrane transport, carbohydrate metabolism, and amino acid metabolism, of which 22 showed significant differences, and 12 showed extremely significant differences among different altitudes. ④ Pearson correlation analysis showed that soil water content, bulk density, pH, and carbon-nitrogen ratio had the most significant effects on bacterial Alpha diversity, whereas soil nutrients such as total organic carbon, total nitrogen, and total phosphorus had significant effects on bacterial Beta diversity. ⑤ Mantel test analysis showed that the soil water content, total organic carbon, and carbon-nitrogen ratio affected bacterial community structure at the phylum level, and soil pH, total organic carbon, total nitrogen, total phosphorus, and carbon-nitrogen ratio were significantly correlated with bacterial metabolic function. Variance partitioning analysis showed that soil water content had the highest explanation for the community structure of soil bacteria, whereas soil pH had the highest explanation for metabolic function. In conclusion, soil water content and pH were the main factors affecting the diversity, community composition, and metabolic function of soil bacteria in farmland in the loess hilly region of Ningxia.

Microbiome and floral associations of a wild bee using biodiversity survey collections.

The health of bees can be assessed through their microbiome, which serves as a biomarker indicating the presence of both beneficial and harmful microorganisms within a bee community. This study presents the characterisation of the bacterial, fungal, and plant composition on the cuticle of adult bicoloured sweat bees (Agapostemon virescens). These bees were collected using various methods such as pan traps, blue vane traps and sweep netting across the northern extent of their habitat range. Non-destructive methods were employed to extract DNA from the whole pinned specimens of these wild bees. Metabarcoding of the 16S rRNA, ITS and rbcL regions was then performed. The study found that the method of collection influenced the detection of certain microbial and plant taxa. Among the collection methods, sweep net samples showed the lowest fungal alpha diversity. However, minor differences in bacterial or fungal beta diversity suggest that no single method is significantly superior to others. Therefore, a combination of techniques can cater to a broader spectrum of microbial detection. The study also revealed regional variations in bacterial, fungal and plant diversity. The core microbiome of A. virescens comprises two bacteria, three fungi and a plant association, all of which are commonly detected in other wild bees. These core microbes remained consistent across different collection methods and locations. Further extensive studies of wild bee microbiomes across various species and landscapes will help uncover crucial relationships between pollinator health and their environment.

Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing

This study aimed to evaluate the blood bacterial microbiota in healthy and febrile cats. High-quality sequencing reads from the 16S rRNA gene variable region V3-V4 were obtained from genomic blood DNA belonging to 145 healthy cats, and 140 febrile cats. Comparisons between the blood microbiota of healthy and febrile cats revealed dominant presence of Actinobacteria, followed by Firmicutes and Proteobacteria, and a lower relative abundance of Bacteroidetes. Upon lower taxonomic levels, the bacterial composition was significantly different between healthy and febrile cats. The families Faecalibacterium and Kineothrix (Firmicutes), and Phyllobacterium (Proteobacteria) experienced increased abundance in febrile samples. Whereas Thioprofundum (Proteobacteria) demonstrated a significant decrease in abundance in febrile. The bacterial composition and beta diversity within febrile cats was different according to the affected body system (Oral/GI, systemic, skin, and respiratory) at both family and genus levels. Sex and age were not significant factors affecting the blood microbiota of febrile cats nor healthy ones. Age was different between young adult and mature adult healthy cats. Alpha diversity was unaffected by any factors. Overall, the findings suggest that age, health status and nature of disease are significant factors affecting blood microbiota diversity and composition in cats, but sex is not.

Contour prairie strips alter microbial communities and functioning both below and in adjacent cropland soils

Prairie strips are narrow strips of native, perennial vegetation (10–40 m width) integrated within cropped fields to provide benefits for water quality and biodiversity. However, the impact of prairie strips on soil microbial communities and function, both underneath the prairie strips and in the adjacent cropland, is not known. We assessed the effect of restoring native perennial vegetation on soil C and N, potential enzyme activities (PEA), and microbial community composition in the soil directly underneath and cropland adjacent (0.1 to 9 m) to 12-year-old prairie strips integrated within row crop fields. We found that prairie strips consistently increased soil microbial biomass carbon (>56 %) and altered PEA in complex ways. Generally, prairie strips increased hydrolase and decreased oxidoreductase PEA. Prairie strips also changed the soil microbial community directly under prairie vegetation, and, contrary to the expectation that greater plant diversity leads to greater soil microbial diversity, prairie strips reduced bacterial and fungal diversity. The prairie strip's effect on adjacent cropland soils depended on year, but it was strong when it occurred and was typically independent of distance from the prairie strip. Prairie strips increased PEA in adjacent soils (<9 m) by as much as 38 % and shifted bacterial and fungal beta diversity, but neither showed patterns with distance from the prairie strip, indicating that prairie strips cause field-scale shifts in soil biota and functioning, and these effects are not mediated by proximity to the prairie strip. Understanding the mechanisms underlying prairie strips' impact on soil biota, both underneath and adjacent to the prairie, is key to optimize their agroecosystem benefits.

Bacterial community analysis of the skin microbiota of cultured Chinese giant salamander infected with Ranavirus.

Skin microorganisms are an important component of host innate immunity and serve as the first line of defense against pathogenic infections. The relative abundance of bacterial species, microbial community assembly, and secretion of specific bacterial metabolites are closely associated with host health. In this study, we investigated the association between the skin microbiome and Ranavirus, and compared the bacterial community assemblage, alpha and beta diversity, and functional predictions of the skin bacterial assemblage in cultured healthy Chinese giant salamanders (Andrias davidianus) and individuals infected with Chinese giant salamander iridovirus (GSIV or ADRV). To achieve this, we employed 16S rRNA amplicon sequencing. The results identified Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota as the dominant phyla in the diseased and healthy groups. Alpha diversity analysis indicated that the skin bacterial community in the diseased group exhibited no significant differences in bacterial species diversity and lower species richness compared to the healthy group. Beta diversity suggested that the two group bacterial community was quite different. Kyoto encyclopedia of genes and genomes (KEGG) pathway analyze and clusters of orthologous groups of proteins (COG) function predictions revealed that changes and variations occurred in the metabolic pathways and function distribution of skin bacterial communities in two groups.

Rare subcommunity maintains the stability of ecosystem multifunctionality by deterministic assembly processes in subtropical estuaries.

Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of the links between ecosystem multifunctionality (EMF) and the diversity of rare bacterial taxa in estuary ecosystems remains limited. Employing high-throughput sequencing and a variety of statistical methods, we assessed the diversities and assembly process of abundant and rare bacterioplankton and their contributions to EMF in a subtropical estuary. Taxonomic analysis revealed Proteobacteria as the predominant phylum among both abundant and rare bacterial taxa. Notably, rare taxa demonstrated significantly higher taxonomic diversity and a larger species pool than abundant taxa. Additionally, our findings highlighted that deterministic assembly processes predominantly shape microbial communities, with heterogeneous selection exerting a stronger influence on rare taxa. Further analysis reveals that rare bacterial beta-diversity significantly impacts to EMF, whereas alpha diversity did not. The partial least squares path modeling (PLS-PM) analysis demonstrated that the beta diversity of abundant and rare taxa, as the main biotic factor, directly affected EMF, while temperature and total organic carbon (TOC) were additional key factors to determine the relationship between beta diversity and EMF. These findings advance our understanding of the distribution features and ecological knowledge of the abundant and rare taxa in EMF in subtropical estuaries, and provide a reference for exploring the multifunctionality of different biospheres in aquatic environments.

Biochar dose-dependent impacts on soil bacterial and fungal diversity across the globe

Biochar, a widely used material for soil amendment, has been found to offer numerous advantages in improving soil properties and the habitats for soil microorganisms. However, there is still a lack of global perspectives on the influence of various levels of biochar addition on soil microbial diversity and primary components. Thus, in our study, we performed a global meta-analysis of studies to determine how different doses of biochar affect soil total carbon (C), nitrogen (N), pH, alpha- and beta-diversity, and the major phyla of both bacterial and fungal communities. Our results revealed that biochar significantly increased soil pH by 4 %, soil total C and N by 68 % and 22 %, respectively, in which the positive effects increased with biochar doses. Moreover, biochar promoted soil bacterial richness and evenness by 3–8 % at the biochar concentrations of 1–5 % (w/w), while dramatically shifting bacterial beta-diversity at the doses of >2 % (w/w). Specifically, biochar exhibited significantly positive effects on bacterial phyla of Acidobacteria, Bacteroidetes, Gemmatimonadetes, and Proteobacteria, especially Deltaproteobacteria and Gammaproteobacteria, by 4–10 % depending on the concentrations. On the contrary, the bacterial phylum of Verrucomicrobia and fungal phylum of Basidiomycota showed significant negative responses to biochar by −8 % and −24 %, respectively. Therefore, our meta-analysis provides theoretical support for the development of optimized agricultural management practices by emphasizing biochar application dosing.

Phosphorus addition increases stability and complexity of co-occurrence network of soil microbes in an artificial Leymus chinensis grassland.

Understanding the response of cross-domain co-occurrence networks of soil microorganisms to phosphorus stability and the resulting impacts is critical in ecosystems, but the underlying mechanism is unclear in artificial grassland ecosystems. In this study, the effects of four phosphorus concentrations, P0 (0 kg P ha-1), P1 (15.3 kg P ha-1), P2 (30.6 kg P ha-1), and P3 (45.9 kg P ha-1), on the cross-domain co-occurrence network of bacteria and fungi were investigated in an artificial Leymus chinensis grassland in an arid region. The results of the present study showed that phosphorus addition significantly altered the stem number, biomass and plant height of the Leymus chinensis but had no significant effect on the soil bacterial or fungal alpha (ACE) diversity or beta diversity. The phosphorus treatments all increased the cross-domain co-occurrence network edge, node, proportion of positively correlated edges, edge density, average degree, proximity to centrality, and robustness and increased the complexity and stability of the bacterial-fungal cross-domain co-occurrence network after 3 years of continuous phosphorus addition. Among them, fungi (Ascomycota, Basidiomycota, Mortierellomycota and Glomeromycota) play important roles as keystone species in the co-occurrence network, and they are significantly associated with soil AN, AK and EC. Finally, the growth of Leymus chinensis was mainly due to the influence of the soil phosphorus content and AN. This study revealed the factors affecting the growth of Leymus chinense in artificial grasslands in arid areas and provided a theoretical basis for the construction of artificial grasslands.

Synthetic and natural rubber associated chemicals drive functional and structural changes as well as adaptations to antibiotics in in vitro marine microbiomes

The leaching of additives from plastics and elastomers (rubbers) has raised concerns due to their potential negative impacts on the environment and the development of antibiotic resistance. In this study, we investigated the effects of chemicals extracted from two types of rubber on microbiomes derived from a benthic sea urchin and two pelagic fish species. Additionally, we examined whether bacterial communities preconditioned with rubber-associated chemicals displayed adaptations to antibiotics. At the highest tested concentrations of chemicals, we observed reduced maximum growth rates and yields, prolonged lag phases, and increased alpha diversity. While the effects on alpha and beta diversity were not always conclusive, several bacterial genera were significantly influenced by chemicals from the two rubber sources. Subsequent exposure of sea urchin microbiomes preconditioned with rubber chemicals to the antibiotic ciprofloxacin resulted in decreased maximum growth rates. This indicates a more sensitive microbiome to ciprofloxacin when preconditioned with rubber chemicals. Although no significant interaction effects between rubber chemicals and ciprofloxacin exposure were observed in bacterial alpha and beta diversity, we observed log-fold changes in two bacterial genera in response to ciprofloxacin exposure. These findings highlight the structural and functional alterations in microbiomes originating from various marine species when exposed to rubber-associated chemicals and underscore the potential risks posed to marine life.

Microbial butyrate capacity is reduced in inflamed mucosa in patients with ulcerative colitis

Reduced butyrate-production capacity has been reported in fecal microbial communities in patients with active ulcerative colitis. However, the butyrate-production capacity of the mucosal microbiome from active vs quiescent mucosa in ulcerative colitis has been unexplored. We sought to determine the diversity and relative abundance of mucosal bacterial and fungal communities from endoscopically active vs quiescent mucosa in patients with UC, and aimed to predict contributions of mucosal microbial communities to butyrate synthesis. Systematic, segmental right- and left-sided biopsies were obtained from endoscopically active (n = 13) or quiescent (n = 17) colonic mucosa, among 15 patients with pan-colonic ulcerative colitis. Dietary fiber intake of patients was performed using the validated five-item FiberScreen questionnaire. Amplicon sequencing of mucosal bacteria and fungi was performed. The diversity and relative abundance of mucosal bacterial and fungal taxa were quantified, and predicted contributions to butyrate synthesis were ascertained. Bacterial alpha and beta diversity were similar between active vs quiescent mucosa. Butyrogenic taxa were significantly increased in quiescence, including Butyricimonas, Subdoligranulum, and Alistipes. Predicted butyrate kinase activity was significantly and concomitantly increased in quiescent mucosa. Fiber intake was positively correlated with butyrogenic microbes. Compared to mucosal bacterial prevalence, mucosal fungi were detected in low prevalence. Butyrogenic microbes are relatively increased in quiescent mucosa in ulcerative colitis, and may be related to increased fiber intake during quiescence. Manipulation of the mucosal microbiome towards butyrate-producing bacteria may be associated with endoscopic quiescence.

Microbial ensemble in the hives: deciphering the intricate gut ecosystem of hive and forager bees of Apis mellifera.

The gut microbiome of honey bees significantly influences vital traits and metabolic processes, including digestion, detoxification, nutrient provision, development, and immunity. However, there is a limited information is available on the gut bacterial diversity of western honey bee populations in India. This study addresses the critical knowledge gap and outcome of which would benefit the beekeepers in India. This study investigates the gut bacterial diversity in forager and hive bees of Indian Apis mellifera, employing both culture-based and culture-independent methods. In the culturable study, a distinct difference in gut bacterial alpha and beta diversity between forager and hive bees emerges. Firmicutes, Proteobacteria, and Actinobacteria dominate, with hive bees exhibiting a Firmicutes-rich gut (65%), while foragers showcase a higher proportion of Proteobacteria (37%). Lactobacillus in the hive bee foregut aligns with the findings by other researchers. Bacterial amplicon sequencing analysisreveals a more intricate bacterial composition with 18 identified phyla, expanding our understanding compared to culturable methods. Hive bees exhibit higher community richness and diversity, likely due to diverse diets and increased social interactions. The core microbiota includes Snodgrassella alvi, Gilliamella apicola, and Bombilactobacillus mellis and Lactobacillus helsingborgensis, crucial for digestion, metabolism, and pathogen resistance. The study emphasises bacteria's role in pollen and nectar digestion, with specific groups like Lactobacillus and Bifidobobacterium spp. associated with carbohydrate metabolism and polysaccharide breakdown. These microbes aid in starch and sucrose digestion, releasing beneficial short-chain fatty acids. This research highlights the intricate relationship between honey bees and their gut microbiota, showcasing how the diverse and complex microbiome helps bees overcome dietary challenges and enhances overall host health. Understanding these interactions contributes to bee ecology knowledge and has implications for honey bee health management, emphasising the need for further exploration and conservation efforts.

Common vetch intercropping with reduced irrigation ensures potato production by optimizing microbial interactions

ContextInner Mongolia is a major potato-producing region in China. Soil quality degradation and water deficiency limit the local potato industry. Legumes can improve soil fertility and moisture, an intercropping system of common vetch with reduced irrigation was established to achieve potato production and soil restoration considering the annual cultivation system in Inner Mongolia. MethodsA two-factor field experiment design was then used. The first factor was the plant pattern with two levels, namely, potato monoculture (M) and potato-common vetch intercropping (I). The second factor was the irrigation amount with two levels, namely, reduced irrigation (R) and conventional irrigation (C). qPCR and high-throughput sequencing were used to determine soil microbial abundances and communities. ResultsAfter two years of field experiments, reduced irrigation significantly (p < 0.05) reduced the aboveground biomass of common vetch by 36.06%. Reduced irrigation reduced potato quality by 11.87–31.37%, but intercropping compensated for this shortcoming. Compared with potato monoculture, common vetch incorporation into the soil significantly (p < 0.05) increased the soil water content and available nutrients, by 10.98% and 13.75–55.08%, respectively. Although intercropping significantly (p < 0.05) increased the abundance of bacteria and fungi, it did not change (p > 0.05) the abundance of protists. The Beta-diversity of fungi and protists were also affected (p < 0.05) by intercropping and irrigation, whereas the bacterial Beta-diversity did not change (p > 0.05). The network complexity and connection between protists and fungi under the IR treatment were higher than those under the MC treatment. Soil available nutrients and network topological indices such as edges linking protists to fungi were significantly positively correlated with potato production. Conclusions or significanceCommon vetch intercropping with reduced irrigation could ensure potato tuber yield and quality, and improve soil quality, our research provides a sustainable cropping system suitable for potato cultivation in Inner Mongolia.