Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

The microbiota-derived bile acid taurodeoxycholic acid improves hepatic cholesterol levels in mice with cancer cachexia

Alterations in bile acid profile and pathways contribute to hepatic inflammation in cancer cachexia, a syndrome worsening the prognosis of cancer patients. As the gut microbiota impinges on host metabolism through bile acids, the current study aimed to explore the functional contribution of gut microbial dysbiosis to bile acid dysmetabolism and associated disorders in cancer cachexia. Using three mouse models of cancer cachexia (the C26, MC38 and HCT116 models), we evidenced a reduction in the hepatic levels of several secondary bile acids, mainly taurodeoxycholic (TDCA). This reduction in hepatic TDCA occurred before the appearance of cachexia. Longitudinal analysis of the gut microbiota pinpointed an ASV, identified as Xylanibacter rodentium, as a bacterium potentially involved in the reduced production of TDCA. Coherently, stable isotope-based experiments highlighted a robust decrease in the microbial 7α-dehydroxylation (7α-DH) activity with no changes in the bile salt hydrolase (BSH) activity in cachectic mice. This approach also highlighted a reduced microbial 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 12α-hydroxysteroid dehydrogenase (12α-HSDH) activities in these mice. The contribution of the lower production of TDCA to cancer cachexia was explored in vitro and in vivo. In vitro, TDCA prevented myotube atrophy, whereas in vivo hepatic whole transcriptome analysis revealed that TDCA administration to cachectic mice improved the unfolded protein response and cholesterol homeostasis pathways. Coherently, TDCA administration reversed hepatic cholesterol accumulation in these mice. Altogether, this work highlights the contribution of the gut microbiota to bile acid dysmetabolism and the therapeutic interest of the secondary bile acid TDCA for hepatic cholesterol homeostasis in the context of cancer cachexia. Such discovery may prove instrumental in the understanding of other metabolic diseases characterized by microbial dysbiosis. More broadly, our work demonstrates the interest and relevance of microbial activity measurements using stable isotopes, an approach currently underused in the microbiome field.

Combined tumor-associated microbiome and immune gene expression profiling predict response to neoadjuvant chemo-radiotherapy in locally advanced rectal cancer

Locally advanced rectal cancer (LARC) is treated with neoadjuvant chemo-radiotherapy (nCRT) followed by surgery. A minority of patients show complete response (CR) to nCRT and may avoid surgery and its functional consequences. Instead, most patients show non-complete response (non-CR) and may benefit from additional treatments to increase CR rates. Reliable predictive markers are lacking. Aim of this study was to identify novel signatures predicting nCRT responsiveness. We performed a combined analysis of tumor-associated microbiome and immune gene expression profiling of diagnostic biopsies from 70 patients undergoing nCRT followed by rectal resection, including 16 with CR and 54 with non-CR. Findings were validated by an independent cohort of 49 patients, including 7 with CR and 42 with non-CR. Intratumoral microbiota significantly differed between CR and non-CR groups at genus and species level. Colonization by bacterial species of Ruminococcus genera was consistently associated with CR, whereas abundance of Fusobacterium, Porhpyromonas, and Oscillibacter species predicted non-CR. Immune gene profiling revealed a panel of 59 differentially expressed genes and significant upregulation of IFN-gamma and -alpha response in patients with CR. Integrated microbiome and immune gene profiling analysis unraveled clustering of microbial taxa with each other and with immune cell-related genes and allowed the identification of a combined signature correctly identifying non-CRS in both cohorts. Thus, combined intratumoral microbiome-immune profiling improves the prediction of response to nCRT. Correct identification of unresponsive patients and of bacteria promoting responsiveness might lead to innovative therapeutic approaches based on gut microbiota pre-conditioning to increase nCRT effectiveness in LARC.

Single-cell microbiota phenotyping reveals distinct disease and therapy-associated signatures in Crohn's disease

IgA-coated fractions of the intestinal microbiota of Crohn's disease (CD) patients have been shown to contain taxa that hallmark the compositional dysbiosis in CD microbiomes. However, the correlation between other cellular properties of intestinal bacteria and disease has not been explored further, especially for features that are not directly driven by the host immune-system, e.g. the expression of surface sugars by bacteria. By sorting and sequencing IgA-coated and lectin-stained fractions from CD patients microbiota and healthy controls, we found that lectin-stained bacteria were distinct from IgA-coated bacteria, but still displayed specific differences between CD and healthy controls. To exploit the discriminatory potential of both, immunoglobulin coated bacteria and the altered surface sugar expression of bacteria in CD, we developed a multiplexed single cell-based analysis approach for intestinal microbiota. By multi-parameter microbiota flow cytometry (mMFC) we characterized the intestinal microbiota of 55 CD patients and 44 healthy controls for 11-parameters in total, comprising host-immunoglobulin coating and the presence of distinct surface sugar moieties. The data were analyzed by machine-learning to assess disease-specific marker patterns in the microbiota phenotype. mMFC captured detailed characteristics of CD microbiota and identified patterns to classify CD patients. In addition, we identified phenotypic signatures in the CD microbiota which not only reflected remission after 6 weeks of anti-TNF treatment, but were also able to predict remission before the start of an adalimumab treatment course in a pilot study. We here present the proof-of-concept demonstrating that multi-parameter single-cell bacterial phenotyping by mMFC could be a novel tool with high translational potential to expand current microbiome investigations by phenotyping of bacteria to identify disease- and therapy-associated cellular alterations and to reveal novel target properties of bacteria for functional assays and therapeutic approaches.

Mucosal washes are useful for sampling intestinal mucus-associated microbiota despite low biomass

Understanding the dynamic relationship between mucus-associated microbiota and host health is critical. However, studies predominantly using stool samples may not accurately represent these bacterial communities. Here, we investigated the mucus-associated microbiota in the gastrointestinal tract of mice and the terminal ileum of humans using different sample types: mucosal washes, brushes, scrapings, and intestinal contents in mice and biopsies, brushes and mucosal washes in humans. We used DNA quantification and 16S rRNA amplicon sequencing to evaluate the comparability of the information yielded from the different sample types under a controlled benchmark. In mice, mucosal washes and brushes had comparative bacterial DNA and host DNA contamination than scraping samples. Similarly, in humans, washes outperformed biopsies in bacterial DNA content. Read counts and microbiota alpha diversity remained remarkably similar in mice and between brushes and washes in humans. The composition of the microbiota varied based on the subsegment and sample type in mice and sample type in humans. We conclude that washes and brushes reduce host contamination without inducing substantial compositional bias when sampling mucosal microbiota. Our findings suggest that mucosal washes and brushes are a viable alternative to biopsies in humans and scrapings in mice, thereby improving the transferability of results across hosts. Our study highlights the importance of focusing on mucus-associated microbiota to better capture host-microbiome interactions at their closer interface.

Effect of intestinal microbiota on adaptation to overcrowding stress in grouper (Epinephelus fuscoguttatus♀×E. lanceolatus♂)

Density is an important aquaculture parameter. When the pearl gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) is farmed intensively, it could lead to a degradation in genetic resources and an increase in disease outbreaks. The composition of the intestinal microbiota plays a key role in creating a specific intestinal microecosystem, which is essential for the survival, growth, and immune response of the host under environmental stress like overcrowding. This study utilized 16S rRNA sequencing and metabolomics analysis techniques to investigate the differences in intestinal microbial community stability of grouper under different stocking time and density pressure conditions. The research results showed that compared to the low-density group, the high-density group of groupers experienced an increase in mortality rate and feed coefficient in the early stages of culture, while the weight gain rate decreased. Differential analysis of intestinal microbial communities revealed significant differences in the gut microbiota of grouper between different density groups after 10 days of culture, but no significant differences were observed after 20 days of culture. At the same time, intestinal histopathology showed that the high-density group of groupers exhibited a reduction in intestinal villi length and thickness of the intestinal wall after 10 days of culture. However, the intergroup differences had reduced after 20 days of culture. Furthermore, high density cultivation upregulated the expression of inflammatory factors like IL-1β, TNF-α, IL-8, and IL-6 in the intestinal tract of groupers after 10 days of culture. However, after 20 days of culture, the expression levels of intestinal inflammatory factors in both the high-density and low-density groups of groupers were significantly reduced, and the differences between the intergroup diminished. Through correlation analysis of differential metabolites and species in the intestine, multiple metabolites significantly upregulated and associated with the upregulation of the Staphylococcus genus were identified in the intestinal tract of groupers after 20 days of high-density cultivation. The selected four associated metabolites (including creatine, fosinopril, 4-aminobutyric acid, and guanidinopropanoic acid) were validated to significantly reduce the expression of cellular inflammatory factors using the self-established grouper head kidney (HK) cell line. In conclusion, density pressure in the early culture period could affect the stability of the intestinal microbial environment of grouper. As aquaculture time increases, the intestinal microbial community of grouper drives the body's anti-inflammatory response and enhanced its adaptation to density pressure by regulating own structure and secretion of metabolites.

The Cry2Aa protein is not enough to pose a threat to Pardosa astrigera

The widespread commercialization of genetically modified (GM) crops makes it important to assess the potential impact of Bacillus thuringiensis (Bt) on non-target organisms. Pardosa astrigera is an important predator in agroforestry ecosystems, and female and male spiders may react differently to Bt toxins due to their different activity habits and nutritional requirements. In this study, we found that exposure to Cry2Aa protein did not affect the survival and body weight of P. astrigera during growth and development. However, according to 16S rRNA sequencing results of the P. astrigera adults, Cry2Aa protein not only changed the diversity of symbiont bacteria, but also changed its symbiont composition. During feeding on prey without Bt artificial feed, the dominant communities in female and male adults were Actinobacteria and Corynebacterium-1, respectively. Feeding on prey containing Cry2Aa protein, Firmicutes were the dominant phyla. At the genus level, Cry2Aa protein significantly increased the relative abundance of Enterococcus and became the dominant genus in females only. In addition, Bacillus, Weissella and other symbiotic bacteria had significant changes in females. In terms of species composition, sex differences resulted in the absence of different types of symbiotic bacteria. Functional analysis of enrichment pathways showed significant changes in various metabolic pathways such as "Carbohydrate metabolism" and "Nucleotide metabolism", and there are differences between the sexes. These findings provide new data information and support for revealing the different strategies of spiders to cope with Cry2Aa protein based on sex differences, and also provide new data information and support for environmental safety assessment of GM crops.

Bacterial and fungal diversity and species interactions inversely affect ecosystem functions under drought in a semi-arid grassland

Extreme climatic events, such as drought, can significantly alter belowground microbial diversity and species interactions, leading to unknown consequences for ecosystem functioning. Here, we simulated a drought gradient by removing 30 %, 50 %, and 70 % of precipitation in a semi-arid grassland over five years. We assessed the effects of drought on bacterial and fungal diversity, as well as on their species interactions. We also evaluated the impact of drought on ecosystem individual functions (e.g., plant biomass and microbial activity), and on multifunctionality (EMF). Finally, we linked the drought-induced changes in microbial communities with the variations in EMF. Drought significantly increased fungal diversity and intensified species interactions, but it decreased bacterial diversity and species interactions. Both plant and microbial biomass significantly decreased with increasing drought severity, while microbial activity showed the opposite trend. Only the -50 % rainfall treatment notably reduced EMF. Bacterial diversity and species interactions positively correlated with most ecosystem functions. However, fungal parameters were negatively associated with these functions. Structural equation modeling indicated that bacterial diversity had a strong direct positive effect on EMF (standardized path coefficient: 0.52), and that bacterial diversity was indirectly suppressed by drought through decreasing soil water content and bacterial phospholipid fatty acids (PLFAs). In contrast, fungal species interactions had a significant direct negative effect on EMF with the highest standardized path coefficient (-0.6) and were directly enhanced by fungal diversity. Drought had indirect positive effects on fungal diversity by decreasing soil water content and stimulating fungal PLFAs. Our results highlight the importance of considering soil microbial species interactions when evaluating the ecological impacts of drought. Furthermore, the divergent regulatory pathways of bacterial and fungal communities to EMF suggest that improving ecosystem functionality may be achieved by enhancing bacterial diversity while mitigating fungal species interactions through reducing fungal diversity.

Tracking the nitrogen transformation in saline wastewater by marine anammox bacteria-based Fe(II)-driven autotrophic denitratation and anammox

Marine anammox bacteria-based Fe(II)-driven autotrophic denitratation and anammox (MFeADA) was investigated for nitrogen removal from saline wastewater for the first time. The study demonstrated that varying influent doses of Fe(II), which participate in the Fe cycle, significantly influenced nitrogen removal performance by altering the fate of nitrite. When 50 mg/L Fe(II) was added, the nitrogen removal was mainly performed by the anammox and Fe(II)-driven autotrophic denitratation (FeAD). As the Fe(II) rose to 100-150 mg/L, the anammox, FeAD and Feammox mainly occurred. Optimal nitrogen removal efficiency, reaching 93 %, was achieved at an influent Fe(II) concentration of 150 mg/L. As the Fe(II) reached 250 mg/L, however, nitrate was directly reduced to dinitrogen gas by the excessive Fe(II) through the Fe(II)-driven autotrophic denitrification (FeADN). Candidatus Scalindua (4.1 %), Marinicella (5.3 %) and SM1A02 (31.8 %) were the dominant functional microbes. In addition, the normalized nitrate reductase abundance was about 3.1 times that of nitrite reductase, leading to the occurrence of FeAD, which achieved a stable nitrite supply for marine anammox bacteria. This novel study can promote the practical implementation of the MFeADA process in nitrogen-laden saline wastewater treatment.

Porous polyurethane biocarriers could enhance system nitrification resilience under high organic loading by retaining key functional bacteria

Resilience to increasing organic loading rates (OLRs) is the key to maintaining stable performance in treating industrial wastewater. First, this study compared the stability, particularly the nitrification performance, of two lab-scale moving bed biofilm reactors (MBBRs) filled with porous polyurethane biocarriers with two conventional activated sludge reactors (ASRs) in the treatment of synthetic coking wastewater under OLRs increasing from 0.3 kg to 1.5 kg COD m-3 day-1. In comparison with the ASRs, which could only achieve complete nitrification (99.31 % ± 0.43 %) at an OLR of 0.7 kg COD m-3 day-1, the MBBRs could achieve efficient NH4+-N removal (99.45 % ± 0.21 %) at an OLR as high as 1.3 kg COD m-3 day-1. Even at an OLR of 1.5 kg COD m-3 day-1 where nitrification was inhibited, the porous polyurethane biocarriers in the MBBRs still maintained a highly diversified bacterial community (Shannon index, 4.34 ± 0.31) by retaining the slow-growing nitrifying bacteria and phenol-degrading bacteria, including Methyloversatilis and Acinetobacter, whose phenol degradation functions were confirmed by metagenome-assembled genome extraction and analysis, while the ASRs lost diversity (Shannon index, 1.41 ± 0.45) due to the sequential occurrence of filamentous and viscous sludge bulking. The advantage of the MBBR was further verified in a full-scale coking wastewater treatment system, where a reactor series filled with 4.35 % porous polyurethane biocarriers exhibited better NH4+-N removal of 99.57 % ± 0.34 % compared to 96.85 % ± 2.56 % for a conventional one under an OLR of 0.54 ± 0.12 kg COD m-3 day-1. The results could contribute to the development of more effective and resilient treatment systems for industrial wastewater.

Investigating the gut microbiome in schizophrenia cases versus controls: South Africa's version

Schizophrenia (SCZ) is a chronic and severe mental disorder with a complex molecular aetiology. Emerging evidence indicates a potential association between the gut microbiome and the development of SCZ. Considering the under-representation of African populations in SCZ research, this study aimed to explore the association between the gut microbiome and SCZ within a South African cohort. Gut microbial DNA was obtained from 89 participants (n = 41 SCZ cases; n = 48 controls) and underwent 16S rRNA (V4) sequencing. Data preparation and taxa classification were performed with the DADA2 pipeline in R studio followed by diversity analysis using QIIME2. Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) was utilised to identify differentially abundant taxa. No statistically significant differences were observed between SCZ patients and controls in terms of alpha-diversity (Shannon q = 0.09; Simpson q = 0.174) or beta-diversity (p = 0.547). Five taxa, namely Prevotella (p = 0.037), Faecalibacterium (p = 0.032), Phascolarctobacterium (p = 0.002), Dialister (p = 0.043), and SMB53 (p = 0.012), were differentially abundant in cases compared to controls, but this observation did not survive correction for multiple testing. This exploratory study suggests a potential association between the relative abundance of Prevotella, Faecalibacterium, Phascolarctobacterium, Dialister, and SMB53 with SCZ case-control status. Given the lack of significance after correcting for multiple testing, these results should be interpreted with caution. Mechanistic studies in larger samples are warranted to confirm these findings and better understand the association between the gut microbiome and SCZ.

Variation and assembly mechanisms of Rhinolophus ferrumequinum skin and cave environmental fungal communities during hibernation periods

Animal skin acts as the barrier against invasion by pathogens and microbial colonizers. Environmental microbiota plays a significant role in shaping these microbial communities, which, in turn, have profound implications for host health. Previous research has focused on characterizing microorganisms on bats' skin and in their roosting environments, particularly bacterial communities. The emergence of white-nose syndrome, caused by the fungal-pathogen Pseudogymnoascus destructans, highlights the importance of understanding fungal dynamics in cave ecosystems and on bats' skin. In this study, we employed ITS amplicon sequencing to investigate the fungal community associated with the skin of Rhinolophus ferrumequinum and surfaces within hibernacula. In addition, we utilized neutral community and null models to assess the relative importance of stochastic and deterministic processes in fungal community assembly. The infection status of P. destructans did not significantly impact fungal community composition either on bat skin or cave environments. However, fungal diversity was significantly higher in cave environments compared to bat skin. Notably, potentially inhibitory genera of fungal pathogens were present in both bats and cave environments during hibernation. Furthermore, the composition and structure of fungal communities on both bat skin and cave environments varied across hibernation periods. Our findings suggest neutral processes primarily drive the assembly of fungal communities associated with hibernating R. ferrumequinum and cave environments, with dispersal limitation exerting a significant influence. This study provides insights into the fungal communities associated with hibernating R. ferrumequinum and cave environments.IMPORTANCEAnimal habitats provide sources and reservoirs for host microorganisms, making it critical to understand changes in microbial communities between habitats and hosts. While most studies have focused on bacterial microorganisms, research on fungal communities is lacking. This study investigated how community dynamics and assembly processes differ between the skin of hibernating Rhinolophus ferrumequinum and the cave environments under pathogen stress. We found significant differences in the composition and structure of the fungal communities between bat skin and roosting cave environments. Fungal genera with potential inhibitory effects on pathogens were found in all bat skin and cave environments. In addition, dispersal limitations during stochastic processes were a key factor in the formation of environmental fungal communities on bat skin and in caves. These findings offer new insights for exploring pathogen-host-environment-microbe interactions.

Gut microbiome and plasma metabolome alterations in ileostomy and after closure of ileostomy

A temporary loop ileostomy is a routine procedure for protecting the anastomosis in patients undergoing radical resection of rectal cancer. Fecal diversion by a diverting ileostomy may induce microbiota dysbiosis in the defunctioned colon; however, data on temporal and spatial microbiome and metabolome changes in these patients are sparse. Thirty patients who underwent ileostomy closure were enrolled. Fecal and plasma samples were collected successively before ileostomy closure, at the first postoperative defecation, and 1 month postoperatively. The 16S rRNA gene sequencing was used to assess changes in gut microbes, and metabolic components in the plasma were analyzed using global untargeted metabolomics. Advanced data analysis methods were used to examine the differences and correlations between flora and metabolites. The gut microbiota in the ileostomy effluent and defunctioned colon had lesser species diversity and richness, with an abundance of aerobic, gram-negative, and potentially pathogenic bacteria. After the intestinal continuity was restored with routine meal feeding, the gut microbes recovered to a standard composition within 1 month. Moreover, xanthine, traumatic acid, L-glutamine, and norepinephrine levels increased markedly in patients with ileostoma. The ileostomy closure reversed the ileostomy-associated metabolic alterations, including an increased abundance of L-leucine, creatine, and 2-ketobutyric acid. Furthermore, Agathobacter and Peptostreptococcus were most closely associated with the reconstruction of postoperative gut microbes. We described a spatiotemporal map of the intestinal microbial ecological reconstruction and metabolic recovery before and after ileostomy reversal for perioperative intervention in patients with ileostomy closure surgery.

IMPORTANCE

In this paper, the changes in the intestinal microbiome and plasma metabolome before and after temporary ileostomy were reported for the first time, and the dynamic changes in intestinal contents were described. At the same time, the key bacterial genera involved in the reestablishment of microflora after the restoration of intestinal continuity were found, and the key relationship between them and plasma metabolites was also found. More importantly, we found that patients with ileal fistula may be at risk of metabolic imbalance and that this particular metabolic state may potentially affect the course of tumor treatment. Finally, the samples in this study were obtained in their natural state and can be easily applied to the clinic to avoid unnecessary invasive examinations.

Gut Microecology of Four Sympatric Desert Rodents Varies by Diet

The gut microbiome can be one pathway by which a host rapidly acclimates and adapts to its ecological environment. Exploring how the microbiome has evolved to differ between hosts with different diets provides insights into the profound interactions between hosts and microbes within these systems. In this study, we used DNA metabarcoding techniques and macrogenomic prediction techniques to study the gut microbes of four desert rodent species with different feeding strategies in the same habitat. One species is herbivorous (Spermophilus alashanicu)s, one is granivorous (Phodopus roborovskii), another is omnivorous (Dipus sagitta), and the last (Orientallactaga sibirica) has a diet with a relatively high proportion of insects. Diets rich in plants and insects can be challenging to digest due to the abundance of indigestible fiber and stable chitin, respectively. Out of the species studied, the herbivorous Spermophilus alashanicus has the highest density of UCG-005 genes and the highest predicted abundance of genes related to digestive complexity. The composition of Phodopus roborovskii's microbiome has the highest variation between individuals, yet Phodopus roborovskii has the highest predicted abundance of genes associated with simple sugars-reflecting this species' potential adaptability to the starch within plant seeds and its constraints brought about by its smaller body size. The most insectivorous species, Orientallactaga sibirica, exhibits the highest predicted abundance of genes related to chitin degradation. This study has enhanced our understanding of the gut microbiota in the intestines of rodents as they adapt to various dietary strategies.

Biochemical study and digestion profile of olive oil by LipBK: Revealing the potential applications of a new acid/broad thermal range true lipase

This study characterized a novel bacterial lipase with high biotechnological potential, focusing on industrial and environmental applications. Bacterial isolates were screened using olive oil as a substrate, and the strain with the highest hydrolytic halo was identified as Burkholderia sp. via 16S rRNA analysis. The secreted lipase was purified and exhibited high hydrolytic activity, specifically targeting long-chain fatty acids. Gas chromatography analyses confirmed its ability to hydrolyze fatty acids present in olive oil, while kinetic parameters and substrate preferences were assessed using synthetic substrates. Optimal activity was observed at pH 4.5 and temperatures between 40 and 60 °C. The enzyme demonstrated remarkable thermal stability, retaining over 78 % residual activity after 24 h at 30, 40, 60, and even 70 °C. It also displayed broad pH stability, with increased relative activity at pH 6.5 over time. LipBK showed resilience in the presence of metallic ions, salts, EDTA, and non-ionic detergents, with enhanced activity in the presence of additives like KCl, CaCl₂, and Triton X-100. These properties highlight its robustness and suitability for applications in acidic and thermally variable environments, such as biodiesel production, waste treatment, and sustainable industrial processes, contributing to global sustainability goals.

Assemblage of root-associated microbiome contributes to disparate performance of two rice genotypes under aluminum stress

Aluminum (Al) toxicity severely inhibits rice growth under acidic soils, posing a significant threat to food security. The assemblies of root-associated microbiomes throughout the lifecycle of rice are hypothesized to furnish a resilient reservoir of ecological functions for rice growth performance under Al stresses. However, the mechanisms that drive the assembly of root-associated microbiomes of rice are largely unknown. In this study, we chose two rice genotypes (including aluminum-tolerant (Al-T) and aluminum-sensitive (Al-S)) as model plants to investigate the microbial assemblage of root-associated microbiome and their potential roles on the plant growth performance under Al stress. The microbial community diversity (Shannon) and evenness (Chao1) in the endosphere of the Al-T genotype gradually decreased, converging towards levels observed in the Al-S genotype. In addition, the rhizosphere and endosphere microbiomes of Al-T genotype are primarily influenced by deterministic processes, while those of Al-S genotype are more influenced by stochastic processes. Compared to Al-S genotype, Al-T genotype exhibited higher complexity and stability in its rhizosphere and endosphere microbiomes, while the rhizoplane microbiome showed the opposite trend. In the rhizosphere microbiome of the Al-T genotype, we identified Gallionellales, Rhodobacterales, and Rhizobiales as keystone taxa. Their abundance was closely associated with microbial functions, including indole-3-acetic acid (IAA) synthesis, phosphorus solubilization, glutathione (GSH) metabolism, and 1-aminocyclopropane-1-carboxylate (ACC) metabolism. In the Al-S genotype, the keystone taxa included Actinomycetales and Burkholderiales. This study offers new insights into plant adaptation to abiotic stress and underscores the significance of the assemblage of root-associated microbiome in this process.

Responses of microbial communities in coastal sediments exposed to triclocarban and triclosan

Triclocarban (TCC) and triclosan (TCS) are applied in a wide range of pharmaceutical and personal care products to prevent or reduce bacterial growth. Due to their extensive application, they are frequently detected in marine environments. In this study, marine sediment systems exposed to different concentrations of TCC and TCS were established to evaluate their effects on microbial communities. It was found that TCC and TCS increased catalase and protease activities on Day 1, but inhibited after 15 days. Microbial activity, as indicated by increased dehydrogenase activity and polysaccharide production, should be enhanced after a 15-day adaptation period. High-throughput sequencing revealed resilient α-diversity but significant shifts in community structures were observed, particularly on Day 15. Function prediction analysis confirmed that most functional profiles remained stable, and network analysis indicated that TCC and TCS enhanced the complexity of the microbial community. This study provides new insights into the impacts and risks of TCC and TCS on the marine environment.

Biochar-based organic fertilizer application promotes the alleviation of tobacco (Nicotiana tabacum L.) continuous cropping obstacles by improving soil chemical properties and microbial community structure

BACKGROUND

Intensive monoculture poses a serious threat to agricultural sustainable development due to the phenomenon of continuous cropping obstacles. Although organic amendment has been considered an efficient and environmentally friendly solution to mitigate this tough issue, the associated mechanisms remain poorly understood. Here, a two-year field experiment was conducted with the application of four fertilizers, wood, rice straw, compound biochar-based organic fertilizers (WBF, RBF, CBF) and chemical fertilizer (CF) under tobacco rotation with broad bean and oilseed rape, respectively. This work aims to determine how BFs application alleviates tobacco CCO and to further reveal the underlying action mechanisms primarily focusing on the change of soil micro-ecology environments.

RESULTS

The results depicted that BFs addition decreased tobacco morbidity (by 15.7-85.0%), heavy metals (Cd, V, Cu, Zn) contents in tobacco, and improved tobacco leaf production yield (by 4.5-20.5%), economic value (by 14.6-34.4%) and chemical quality compared with CF. Rhizosphere soil chemical properties and the structure and diversity of microbial communities were enhanced under BFs treatments, reflecting in the growth of bacterial OTUs number, microbial alpha-diversity, the abundances of some beneficial genera (Arthrobacter, Pseudomonas, Gemmatimonas, Trichoderma, Mortierella, Penicillium, Chaetomium, etc.), and the reduction of the numbers of detrimental microbes (Alternaria, Phytophthora nicotianae and Fusarium oxysporum). Moreover, CBF amendment improved the stability and complexity of microbial co-occurrence networks. Soil total carbon, microbial structure, and diversity were the most important explanatory factors for the increase of tobacco leaf yield and economic value.

CONCLUSIONS

Collectively, BFs application under rotation regime showed the great potential as a practical and environmentally friendly strategy to alleviate tobacco CCO by providing an optimized soil environment.

Reduced content of gamma-aminobutyric acid enhances resistance to bacterial wilt disease in tomato

Bacteria within the Ralstonia solanacearum species complex cause devastating diseases in numerous crops, causing important losses in food production and industrial supply. Despite extensive efforts to enhance plant tolerance to disease caused by Ralstonia, efficient and sustainable approaches are still missing. Before, we found that Ralstonia promotes the production of gamma-aminobutyric acid (GABA) in plant cells; GABA can be used as a nutrient by Ralstonia to sustain the massive bacterial replication during plant colonization. In this work, we used CRISPR-Cas9-mediated genome editing to mutate SlGAD2, which encodes the major glutamate decarboxylase responsible for GABA production in tomato, a major crop affected by Ralstonia. The resulting Slgad2 mutant plants show reduced GABA content, and enhanced tolerance to bacterial wilt disease upon Ralstonia inoculation. Slgad2 mutant plants did not show altered susceptibility to other tested biotic and abiotic stresses, including drought and heat. Interestingly, Slgad2 mutant plants showed altered microbiome composition in roots and soil. We reveal a strategy to enhance plant resistance to Ralstonia by the manipulation of plant metabolism leading to an impairment of bacterial fitness. This approach could be particularly efficient in combination with other strategies based on the manipulation of the plant immune system, paving the way to a sustainable solution to Ralstonia in agricultural systems.

Tenuifilum osseticum sp. nov., a novel thermophilic hydrolytic bacterium within the Tenuifilaceae isolated from a North Ossetian thermal spring, and emended description of the genus Tenuifilum

A novel anaerobic moderately thermophilic bacterium, strain 4138-strT, was isolated from a thermal spring of North Ossetia (Russian Federation). Gram-negative cells were non-sporeforming, straight or curved filamentous rods, occasionally forming rosettes. The strain grew at 30-55 °C, pH range of 6.1-8.7, NaCl range of 0-4 %, with an optimum at 50 °C, pH 7.1-7.5 and 0.2-0.4 % NaCl. It was a chemoorganoheterotroph, growing on simple sugars (glucose, maltose, cellobiose, etc.) and carbohydrates (starch, pullulan, laminarin, xylan, lichenan, curdlan, pachyman) or proteinaceous substrates (peptone, tryptone, gelatin, casein). Sulfur was used as electron acceptor. Major products of glucose fermentation were acetate, hydrogen, and carbon dioxide. Major cellular fatty acids were iso-C15:0 and anteiso-C15:0. The quinone was MK-7. The size of the whole genome of strain 4138-strT was 3.275 Mbp; DNA G + C content was 42.1 %. Genome analysis allowed to identify genes encoding carbohydrate-active enzymes and extracellular proteases. In addition, central metabolism and fermentation pathways of strain 4138-strT were reconstructed. According to both phylogenetic analyses, based on 16S rRNA gene sequences and conserved protein sequences, as well as genome-based comparisons, strain 4138-strT formed a species-level lineage within Tenuifilum genus of Tenuifilaceae family (phylum Bacteroidota). Here we propose a novel species Tenuifilum osseticum sp. nov. with type strain 4138-strT(=KCTC 25386T = VKM B-3628T = UQM 41477T).

Watershed urbanization alters aquatic plant mycobiomes through the loss of rare taxa

Urban expansion, projected to triple globally from 2000 to 2030, significantly impacts biodiversity and ecosystem processes, including those of microbial communities. Microbes are key drivers of many ecosystem processes and affect the fitness and resilience of plants and animals, but research on the biotic effects of urbanization has focused primarily on macroorganisms. This study investigates host-associated fungal communities in the pollution-tolerant aquatic plant Ranunculus aquatilis along an urbanization gradient in the Provo River, Utah, USA, a rapidly urbanizing region. We collected plant and adjacent water samples from 10 locations along the river, spanning from rural to urbanized areas within a single watershed, and conducted DNA amplicon sequencing to characterize fungal community composition. Our results show a significant decline in fungal alpha diversity correlated with increased urbanization metrics such as impervious surface area and developed land cover. Specifically, fungal richness and Shannon diversity decreased as urbanization intensified, driven primarily by a reduction in rare taxa. Despite a stable core microbiome dominated by a few taxa, the overall community structure varied significantly along the urbanization gradient, with notable shifts in dominant fungal taxa. Contrary to expectations, no detectable levels of heavy metals were found in water samples at any location, suggesting that other urbanization-related factors, potentially including organic pollutants or plant stress responses, influence fungal endophyte communities. Our findings underscore the need for further investigation into the mechanisms driving these patterns, particularly the roles of organic pollution, nutrient loads, and plant stress. As global urbanized watershed area grows, the fate of aquatic plant life is tied to their fungal community. Understanding these interactions is crucial for predicting the impacts of continued urbanization on freshwater ecosystems.

Impact of gender and reproductive states on diets and intestinal microbiota in Pratt's leaf-nosed bats (Hipposideros pratti)

Lactation represents a critical evolutionary adaptation in mammals, imposing heightened nutritional demands that drive shifts in foraging behavior and intestinal microbiota to optimize nutrient acquisition. In the sexually dimorphic Pratt's leaf-nosed bat (Hipposideros pratti), males exhibit enlarged transverse lobes posterior to the nasal leaf, a morphological trait may influence echolocation dynamics and dietary niche partitioning. This provides an opportunity to examine dietary and microbiota differences between genders and across various reproductive states. Using high-throughput sequencing of fecal samples from male (HPM), non-lactating female (HPF), and lactating female (HPFL) H. pratti collected in late June, we identified gender- and physiology-linked ecological strategies. While dietary diversity indices showed no significant intergroup differences, compositional analysis revealed distinct prey preferences: both HPM and HPFL predominantly consumed Coleoptera, whereas HPF favored Diptera. Coleoptera's larger size and nutrient profile-rich in leucine, isoleucine, and chitin-likely optimize energy efficiency for HPFL, reducing foraging effort while supplying amino acids critical for mammary gland function and immunity. Gender-based differences were observed in intestinal microbiota diversity, with females demonstrating higher diversity indices compared to males. Males showed a notable abundance of Clostridium sensu stricto 1, a proteolytic genus associated with Coleoptera digestion but linked to inflammatory risks via pathogenic strains. The HPFL group exhibited microbiota enriched in Lactococcus (chitinolytic taxa) and lactation-adapted symbionts: Lachnoclostridium may suppress pro-inflammatory responses via acetate production, while Pseudonocardia may enhance calcium homeostasis and antimicrobial defense. This study advances understanding of host-microbe coadaptation in mitigating life-history trade-offs and highlights ecological drivers of microbiota plasticity in insectivorous bats.

Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model

The human microbiome is the collection of microorganisms living on and inside of our bodies. A major aim of microbiome research is understanding the role microbial communities play in human health with the goal of designing personalized interventions that modulate the microbiome to treat or prevent disease. Microbiome data are challenging to analyze due to their high-dimensionality, overdispersion, and zero-inflation. Analysis is further complicated by the steps taken to collect and process microbiome samples. For example, sequencing instruments have a fixed capacity for the total number of reads delivered. It is therefore essential to treat microbial samples as compositional. Another complicating factor of modeling microbiome data is that taxa counts are subject to measurement error introduced at various stages of the measurement protocol. Advances in sequencing technology and preprocessing pipelines coupled with our growing knowledge of the human microbiome have reduced, but not eliminated, measurement error. Ignoring measurement error during analysis, though common in practice, can then lead to biased inference and curb reproducibility. We propose a Dirichlet-multinomial modeling framework for microbiome data with excess zeros and potential taxonomic misclassification. We demonstrate how accommodating taxonomic misclassification improves estimation performance and investigate differences in gut microbial composition between healthy and obese children.

Enhanced resilience to oxygen exposure and toxicity of chlorinated solvents in immobilized Dehalococcoides mccartyi

Members of Dehalococcoides mccartyi (Dhc) are strictly anaerobic and play crucial roles in the restoration of many industrial sites impacted by chlorinated solvents, such as tetrachloroethene (PCE) and trichloroethene (TCE). In situ bioremediation with Dhc involves intricate procedures intended to minimize oxygen intrusion, and achieving optimal dechlorination performance in aquifers near the dense non-aqueous phase liquids source zone is challenging. Here, we respectively embedded Dhc strain 195 and the biomass of a Dhc-containing, PCE-dechlorinating consortium in poly(vinyl alcohol)-alginate hydrogel beads. The ethene-forming potential was well-retained in immobilized Dhc following a prolonged oxygen exposure spanning from 12 hours to 7 days, with dechlorination rates ranging from 54.6 ± 4.2-101.9 ± 13.5 µM Cl- released day-1. In contrast, suspended strain 195 and the Dhc-containing biomass exposed to oxygen for a shorter duration were completely deactivated, or suffered a substantial reduction in dechlorination potential. Cell immobilization also significantly improved the ability of Dhc to tolerate the toxic effects of chlorinated solvents. When exposed to 300 mg L-1 TCE or free-phase PCE, an immobilized Dhc inoculum enabled more rapid recovery of dechlorination activity with shorter lag phases and up to 2.1-fold higher dechlorination rate compared to the use of their suspended counterparts. Our results demonstrate the effectiveness of cell immobilization for shielding Dhc from various environmental stresses (e.g., oxygen exposure).

Gut Microbiota-Butyrate-PPARγ Axis Modulates Adipose Regulatory T Cell Population

Gut microbiota is essential for the function of peripherally-induced regulatory T (pTreg) cells. However, how commensal bacteria affect thymically derived fat-resident Treg cells that harbor a unique expression of peroxisome proliferator-activated receptor (PPAR)-γ and suppress inflammation in visceral adipose tissue (VAT), is not well defined. Here it is revealed that microbiota depletion causes a drastic decline in Treg cell population in VAT, particularly those expressing ST2 (ST2+ Treg), which are largely restored after gut microbiome reconstruction. Mechanistically, gut microbiota-derived butyrate increases VAT ST2+ Treg cells through binding PPARγ. Butyrate supplementation and high fiber diet increase VAT ST2+ Treg population in obese mice, and ameliorated glucose tolerance and visceral inflammation. Furthermore, human omental adipose Treg cells show positive correlation with fecal butyrate and certain butyrate-producing microbes. This study identifies the critical role of gut microbiota-butyrate-PPARγ axis in maintaining VAT Treg population, pinpointing a potential approach to augment VAT Treg population and ameliorate inflammation.

Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples

Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets Atopobium (Fannyhessea) vaginae, Megasphaera-1, and Bacterial Vaginosis Associated Bacterium (BVAB)-2. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (P < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct Lactobacilli, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.

The impact of ibezapolstat and other Clostridioides difficile infection-relevant antibiotics on the microbiome of humanized mice

Ibezapolstat (IBZ) is a competitive inhibitor of the bacterial Pol IIIC enzyme in clinical development for the treatment of Clostridioides difficile infection (CDI). Previous studies demonstrated that IBZ carries a favorable microbiome diversity profile compared to vancomycin (VAN). However, head-to-head comparisons with other CDI antibiotics have not been done. The purpose of this study was to compare microbiome changes associated with IBZ to other clinically used CDI antibiotics. Groups of germ-free (GF) mice received a fecal microbiota transplant from one of two healthy human donors and were subsequently exposed to either IBZ, VAN, fidaxomicin (FDX), metronidazole (MET), or no antibiotic (control). 16S rRNA encoding gene sequencing of temporally collected stool samples was used to compare the gut microbiome perturbations between treatment and no-drug control groups. Among the tested antibiotics, the most significant change in microbiome diversity was observed in MET-treated mice. Each antibiotic had a unique effect, but changes in alpha and beta diversities following FDX- and IBZ-treated groups were less pronounced than those observed in VAN- or MET-treated groups. By the end of therapy, both IBZ and FDZ increased the relative abundance of Bacteroidota (phylum), with IBZ additionally increasing the relative abundance of Actinomycetota (phylum). In microbiome-humanized mice, IBZ and FDX had smaller effects on gut microbiome diversity than VAN and MET. Notable differences were observed between the microbiome of IBZ- and FDX-treated groups, which may allow for differentiation of these two antibiotics in future studies.

Biogeography and genetic diversity of freshwater diatoms: The potential of large combined rbcL metabarcoding datasets

Aiming to gain a general picture of rbcL diversity within freshwater diatom species, this study assembles and analyzes multiple metabarcoding datasets spanning various geographical regions. From these datasets, we inferred >10,000 amplicon sequence variants (ASVs) of 263-bp length. More than half of the 1000 most abundant ASVs were recorded in both Eurasia and N America and there was only limited evidence for continent-specific lineages. The geographical range was extended for some species, illustrating the potential of metabarcoding datasets for such checks. For detailed analysis of intraspecific diversity, 73 freshwater species were selected, corresponding to 360 ASVs assigned phylogenetically. We found notable variation, some species being represented by only one or a few ASVs, while others were represented by a higher number. Furthermore, within species, ASVs exhibited different dominance and distribution patterns, in some cases with a head-tail pattern, in others a more equal spread of abundance or unresolved reticulate relationships. Except for Ulnaria ulna, no geographical structure among species' ASVs was detectable in haplotype networks using the 263-bp rbcL marker. Observed heterogeneity within species was categorized by computing several metrics of genetic variation and classified into three groups, reflecting optimal sampling strategies based on the patterns of intraspecific variation in the 73 target species There was a significant relationship between intraspecific diversity and the traditional separation between 'centric' and 'pennate' diatoms, with centric species exhibiting significantly fewer variants than pennates, possibly because of different plastid inheritance patterns.

Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere

Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (Zostera marina and Phyllospadix iwatensis). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.

The association of gut microbiome composition with musculoskeletal features in middle-aged and older adults: a two-cohort joint study

Background

Bones and muscles are connected anatomically, and functionally. Preliminary evidence has shown the gut microbiome influences the aging process of bone and muscle in animal studies. However, such evidence in humans is still scarce. This study aimed to assess the microbiome-bone and microbiome-muscle associations in two cohorts of community-dwelling older adults.

Methods

We leveraged information from two large population-based cohorts, i.e., the Rotterdam Study (mean age 62.7 ± 5.6 years; n=1,249) and the Framingham Heart Study (mean age 55.2 ± 9.1 years; n=1,227). For individuals included in this study, gut microbiome 16S rRNA sequencing, musculoskeletal phenotyping derived from DXA images, lifestyle and socioeconomic data, and medication records were available. Per cohort, the 16S rRNA sequencing data, derived from stool, were processed with the DADA2 pipeline and taxonomies were assigned using the SILVA reference database. In addition, the microbiome functional potential was obtained with PICRUSt2. Further, we investigated the association between the human gut microbiome (alpha diversity, genera and predicted functional pathways) and appendicular lean mass (ALM), femoral neck bone mineral density (FN-BMD) and trabecular bone score (TBS) using multilinear regression models controlling for multiple confounders, and performed a joint analysis from both cohorts. Sex-stratified analyses were also conducted.

Results

The gut microbiome alpha diversity was not associated with either tested phenotype after accounting for multiple-testing (P>1.67e-02). In the joint analysis, lower abundance of Oscillibacter (beta= -.51, 95%CI [-0.74, -.29]), Anaerotruncus (beta=-0.41, 95%CI [-0.61, - 0.21]), Eisenbergiella (beta=-0.39, 95%CI [-0.59, -.19]) and higher abundance of Agathobacter (beta=0.40, 95%CI [0.20, 0.60]) were associated with higher ALM (P<2.0e-04). Lower abundance of Anaerotruncus (beta=-0.32, 95%CI [-0.45, -.19]), Hungatella (beta=-0.26, 95%CI [-0.38, -.15]) and Clostridiales bacterium DTU089 (beta=-0.37, 95%CI [-0.55, -.19]) was associated with higher ALM only in females (P< 2.0e-04). Moreover, the biotin biosynthesis II pathway was positively associated with ALM (beta=0.44, 95% CI [0.24, 0.64]) (P<1.90e-04) in females while no associations were observed in males. We did not observe any robust association of bone traits with gut microbiome features.

Conclusion

Our results indicate that specific genera are associated with ALM in middle-aged and older adults and these associations can present in a sex-specific manner. Overall, our study suggests that the gut microbiome is linked to muscle aging in middle-aged and older adults. However, larger sample sizes are still needed to underpin the specific microbiome features involved.

Influence of biochar-based microbial agents on post-consumption food waste composting

Recycling nutrients by post-consumption food waste (PCFW) composting is impeded by the slow composting process because of the high perishability and moisture content of PCFW. Concerning this issue, a biochar-based microbial agent with trehalose as a protectant was developed, and was evaluated as inoculum in PCFW composting. Inoculation effectively ameliorated acidic conditions, accelerated organics degradation resulting in quick temperature rising, shortened maturation from 28 to 14 days, and altered the succession of the bacterial community structure. The combination of microbial consortium and biochar effectively inhibited the acid-producing bacteria Weissella and increased Bacillus, which contributed to a better condition for indigenous microbes by ameliorating the acidic condition of PCFW. This further expedited temperature rising that selectively enriched Firmicutes (Bacillus, Compostibacillus, Novibacillus) and Actinobacteria (Pseudonocardia) at the thermophilic stage. Moreover, carbon cycle was strengthened by chemoheterotrophy and aerobic chemoheterotrophy, while fermentation was inhibited, which was in favor of organic material degradation. The addition of 5% trehalose further enhanced the effect, and increased germination index to 152% at day 14. This study suggested that a biochar-based microbial agent was an efficient inoculant specifically for PCFW composting.

A secondary metabolite of Limosilactobacillusreuteri R2lc drives strain-specific pathology in a spontaneous mouse model of multiple sclerosis

Limosilactobacillus reuteri is an immunomodulatory bacterium enriched in non-industrialized microbiomes, making it a therapeutic candidate for chronic diseases. However, effects of L. reuteri strains in mouse models of multiple sclerosis have been contradictory. Here, we show that treatment of spontaneous relapsing-remitting experimental autoimmune encephalomyelitis (EAE) mice with L. reuteri R2lc, a strain that activates the aryl hydrocarbon receptor (AhR) through the pks gene cluster, resulted in severe pathology. In contrast, a pks mutant and a pks-negative strain (PB-W1) failed to exacerbate EAE and exhibited reduced pathology compared to R2lc despite earlier disease onset in PB-W1 mice. Differences in pathology occurred in parallel with a pks-dependent downregulation of AhR-related genes, reduced occludin expression in the forebrain, and altered concentrations of immune cells. This work establishes a molecular foundation for strain-specific effects on autoimmunity, which has implications for our understanding of how microbes contribute to chronic conditions and the selection of microbial therapeutics.

Within-project and cross-project defect prediction based on model averaging

Software defect prediction has an important impact on the national economy and financial service industry. Discovering defective modules in the early stage of software development has great significance. This paper proposes a within-project and cross-project defect prediction technology based on model averaging, which uses XGBoost and LightGBM algorithms in machine learning as candidate models and introduces model averaging theory to improve performance. First, two candidate models are used for probability prediction, and then each group is used as a test dataset to evaluate the model by the cross-validation method. Then, the model weight is determined by minimizing the sum of the squared prediction errors of all groups, and finally, the predicted probability of model averaging is obtained. Four typical public software defect datasets (NASA, AEEEM, ReLink, SoftLab) are used as test datasets, and the four indicators, precision, recall, F1 and AUC are used as evaluation criteria. For within-project defect prediction, compared with the XGBoost and LightGBM algorithms, the prediction results of the model averaging method on the four datasets are slightly better than the XGBoost and LightGBM algorithms, which also corresponds with the ensemble learning idea of model averaging theory. Compared with the seven traditional machine learning algorithms, the model average prediction method performed best on most of the data. For cross-project defect prediction, compared with the four benchmark methods, the model averaging method performs better overall. The experimental results show that the model averaging prediction method achieves good prediction results in both the within-project and cross-project defect scenarios.

Sex-specific effects of gastrointestinal microbiome disruptions on Helicobacter pylori-induced gastric carcinogenesis in INS-GAS mice

BACKGROUND

Accumulating evidence indicates that the dysbiosis of gastrointestinal microbiota is associated with the development of gastric carcinogenesis. However, the sex-specific traits of gastrointestinal microbiota and their correlation with the sexually dimorphic response to gastric cancer remain poorly understood.

METHODS

Male and female transgenic FVB/N insulin-gastrin (INS-GAS) mice as a model of gastric cancer were randomly administered Brucella Broth or Helicobacter pylori (H. pylori). Stomachs were evaluated by histopathology. The gastric inflammation was examined by immunohistochemical and immunofluorescence staining. Gastric mucosal and fecal samples were collected for microbiota analysis using 16S rRNA gene sequencing.

RESULTS

Following H. pylori infection, male mice showed heightened inflammatory infiltration and notably greater intestinal metaplasia compared to female mice. The structure of gastrointestinal microbiota was different between male and female mice, with relative higher diversity in females than males. Notably, we found gender disparities in the alterations of gastric and intestinal microbiota in mice post H. pylori infection. While the enrichment of Bifidobacterium and Lachnospiraceae was observed in female mice, Escherichia_Shigella and Akkermansia were more abundant in males. Furthermore, the microbial profile was distinct in estrogen-deficient ovariectomized (OVX) mice, including the overgrowth of Akkermansia and the loss of Butyricicoccus. Infected OVX females developed significantly more severe gastric lesions, which was normalized through co-housing with intact females.

CONCLUSIONS

We have identified a novel microbiome-based mechanism that provides insight into the sexual dimorphism in the development of H. pylori-associated gastric cancer.

Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting

k-mer frequency information in biological sequences is used for a wide range of applications, including taxonomy classification, sequence similarity estimation, and supervised learning. However, in spite of its widespread utility, k-mer counting has been largely neglected for diversity estimation. This work examines the application of k-mer counting for alpha and beta diversity as well as supervised classification from microbiome marker-gene sequencing data sets (16S rRNA gene and full-length fungal internal transcribed spacer [ITS] sequences). Results demonstrate a close correspondence with phylogenetically aware diversity metrics, and advantages for using k-mer-based metrics for measuring microbial biodiversity in microbiome sequencing surveys. k-mer counting appears to be a suitable and efficient strategy for feature processing prior to diversity estimation as well as supervised learning in microbiome surveys. This allows the incorporation of subsequence-level information into diversity estimation without the computational cost of pairwise sequence alignment. k-mer counting is proposed as a complementary approach for feature processing prior to diversity estimation and supervised learning analyses, enabling large-scale reference-free profiling of microbiomes in biogeography, ecology, and biomedical data. A method for k-mer counting from marker-gene sequence data is implemented in the QIIME 2 plugin q2-kmerizer (https://github.com/bokulich-lab/q2-kmerizer).

IMPORTANCE

k-mers are all of the subsequences of length k that comprise a sequence. Comparing the frequency of k-mers in DNA sequences yields valuable information about the composition of these sequences and their similarity. This work demonstrates that k-mer frequencies from marker-gene sequence surveys can be used to inform diversity estimates and machine learning predictions that incorporate sequence composition information. Alpha and beta diversity estimates based on k-mer frequencies closely correspond to phylogenetically aware diversity metrics, suggesting that k-mer-based diversity estimates are useful proxy measurements especially when reliable phylogenies are not available, as is often the case for some DNA sequence targets such as for internal transcribed spacer sequences.

Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA

The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.

Structural characteristics of intestinal microbiota of domestic ducks with different body sizes

Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.

The Fungal and Protist Community as Affected by Tillage, Crop Residue Burning and N Fertilizer Application

The bacterial community in soil is often affected by agricultural practices, but how they affect protists and fungi is less documented. Soil from treatments that combined different N fertilizer application rates, tillage and crop residue management was sampled from a field trial started by the International Maize and Wheat Improvement Center (CIMMYT) at the 'Campo Experimental Norman E. Borlaug' (CENEB) in the Yaqui Valley in the northwest of Mexico in the early 1990s, and the fungal and protist community determined. Tillage, residue burning, and N fertilizer application had no significant effect on the fungal and protists alpha diversity expressed as Hill numbers and no significant effect on the fungal and protist community structure considering all species. The relative abundance of plant pathogens and undefined saprotrophs as determined with FUNGuildR increased significantly with tillage, while that of dung-plant and dung-soil saprotroph, and plant pathogens by burning (P < 0.05). It was found that the protists and fungal community structures were not altered by different agricultural practices, but some fungal guilds were, i.e., plant pathogens and saprotrophs, which might affect soil organic matter decomposition, nutrient cycling and crop growth.

Escherichia abundance and metabolism align with vitiligo disease activity

Vitiligo is a cutaneous autoimmune disorder characterized by progressive depigmentation due to melanocyte destruction by cytotoxic T cells. Genetic factors predispose patients to the disease, supported by environmental factors often initiating new disease episodes. We questioned whether disease outcomes are partially defined by pathogenic microbes driving nutrient deficiencies and inflammation. Our study presents results from research on the diet and gut microbiome composition of vitiligo patients and healthy controls from Kazakhstan and the USA. Dietary nutrient intake was assessed using NIH-generated Diet History Questionnaires. Vitiligo patients with active disease exhibited limited intake of specific fatty acids, amino acids, and zinc. Disease activity was further characterized by an abundance of Odoribacter and Escherichia genera in the gut. Metabolic pathway analysis supported a role for the Escherichia genus in disease activity by limiting energy metabolism and amino acid biosynthetic pathways. Disease activity also aligned with elevated circulating pro-inflammatory cytokines. These findings suggest that nutritional limitations are not compensated by metabolites from the gut microbiome in active disease, potentially leaving room for inflammation and exacerbating vitiligo. The intricate relationship between diet, gut microbiome composition, and disease progression in vitiligo highlights potential avenues for targeted interventions to reduce autoimmune activity and improve patient outcomes.

Deciphering Planktonic Bacterial Community Assembly in the Storage Reservoir of the Long-Distance Water Diversion Project

Storage reservoirs are crucial components of long-distance water diversion projects, where water diversion may lead to changes in microbial diversity and community structure. Seasonal variations also drive alterations in microbial communities. However, the way that microbes assemble under the combined effects of water diversion and seasonal variations in the storage reservoir has not been extensively studied. Jihongtan Reservoir is the terminal storage reservoir of the Yellow River to Qingdao Water Diversion Project (YQWD), which had an average annual water diversion period exceeding 290 days in recent years. In this study, 16S rDNA amplicon sequencing was used to investigate the seasonal dynamics and assembly of planktonic bacterial communities during the water diversion period in Jihongtan Reservoir. The results indicate that planktonic bacteria were able to maintain stable diversity across all four seasons, while the community structure underwent significant seasonal succession. Water temperature (WT) was found to be the primary driving environmental factor influencing the seasonal dynamic of planktonic bacterial communities. Co-occurrence network patterns of planktonic bacterial communities varied across different seasons, particularly in spring and winter. The spring network displayed the most complexity, showcasing the highest connectivity and greater stability. In contrast, the winter network was simpler, exhibiting lower local connectivity but higher global connectivity and lower stability. The analysis of the neutral community model and null model revealed that the relative importance of deterministic and stochastic processes in governing planktonic bacterial community assembly varies seasonally. Stochastic processes (dispersal limitation) are more prominent in spring, summer, and autumn, while deterministic processes (heterogeneous selection) play a greater role in winter. This study is essential for gaining a comprehensive understanding of the effects of water diversion projects and offers valuable references for the assessment of other similar projects.

Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition

Microbiome analysis has become a crucial tool for basic and translational research due to its potential for translation into clinical practice. However, there is ongoing controversy regarding the comparability of different bioinformatic analysis platforms and a lack of recognized standards, which might have an impact on the translational potential of results. This study investigates how the performance of different microbiome analysis platforms impacts the final results of mucosal microbiome signatures. Across five independent research groups, we compared three distinct and frequently used microbiome analysis bioinformatic packages (DADA2, MOTHUR, and QIIME2) on the same subset of fastQ files. The source data set encompassed 16S rRNA gene raw sequencing data (V1-V2) from gastric biopsy samples of clinically well-defined gastric cancer (GC) patients (n = 40; with and without Helicobacter pylori [H. pylori] infection) and controls (n = 39, with and without H. pylori infection). Independent of the applied protocol, H. pylori status, microbial diversity and relative bacterial abundance were reproducible across all platforms, although differences in performance were detected. Furthermore, alignment of the filtered sequences to the old and new taxonomic databases (i.e., Ribosomal Database Project, Greengenes, and SILVA) had only a limited impact on the taxonomic assignment and thus on global analytical outcomes. Taken together, our results clearly demonstrate that different microbiome analysis approaches from independent expert groups generate comparable results when applied to the same data set. This is crucial for interpreting respective studies and underscores the broader applicability of microbiome analysis in clinical research, provided that robust pipelines are utilized and thoroughly documented to ensure reproducibility.IMPORTANCEMicrobiome analysis is one of the most important tools for basic and translational research due to its potential for translation into clinical practice. However, there is an ongoing controversy about the comparability of different bioinformatic analysis platforms and a lack of recognized standards. In this study, we investigate how the performance of different microbiome analysis platforms affects the final results of mucosal microbiome signatures. Five independent research groups used three different and commonly used bioinformatics packages for microbiome analysis on the same data set and compared the results. This data set included microbiome sequencing data from gastric biopsy samples of GC patients. Regardless of the protocol used, Helicobacter pylori status, microbial diversity, and relative bacterial abundance were reproducible across all platforms. The results show that different microbiome analysis approaches provide comparable results. This is crucial for the interpretation of corresponding studies and underlines the broader applicability of microbiome analysis.

Relic DNA obscures bacterial diversity and interactions in ballast tank sediment

The dark and anoxic environment of ballast tank sediment (BTS) harbors substantial amounts of relic DNA, yet its impact on microbial diversity estimates in BTS management remains poorly understood. This study employed propidium monoazide (PMA) treatment to eliminate relic DNA and used 16S amplicon high-throughput sequencing to characterize both total and viable bacteria. Our findings revealed that relic DNA is abundant in BTS. When removed, it led to variable reductions in species richness, which fluctuated from a 3.15% increase to a 37.52% decrease. Additionally, 6.27%-15.79% of OTUs were absent in the PMA-treated samples. These findings indicate that relic DNA has diverse effects on microbial diversity estimates. Moreover, relic DNA removal altered the relative abundances of a wide range of taxa, thereby facilitating the detection of rare taxa. Furthermore, the absence of relic DNA resulted in an overestimation of co-occurrence network size, complexity, and competitiveness, which could lead to misinterpretations of community assembly processes. In conclusion, our findings indicate that relic DNA obscures microbial diversity estimates and risk assessments in BTS, highlighting the critical need for monitoring viable bacteria in ballast sediment management.

Source-oriented risks of heavy metals and their effects on resistance genes in natural biofilms

Heavy metal (HM) introduction from various land-use patterns can be a major source of metal resistance genes (MRGs) entering river environments. This influx can trigger the occurrence of other resistomes, such as antibiotic resistance genes (ARGs), by improving co-resistant conjugative transfer. Biofilms, which form at water-solid interfaces, could serve as potential hotspots for HMs and resistance genes. However, the enrichment of HMs from various sources within biofilms and their effect on resistomes remain undocumented. This study aims to investigate the physicochemical properties of biofilm samples collected from the Heihui River, a tributary of the Lancang River, and to analyze the concentrations of nine HMs (As, Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) within these biofilms. The 16S rRNA gene and metagenomic high-throughput sequencing techniques were integrated to uncover the association between HM accumulation levels in biofilms and ecological and health risks, considering the presence of two resistance genes. Natural sources (Co, Cr), industrial (As, Cu, V), agricultural (Cd, Ni), and transportation activities (Pb, Zn) markedly contributed to HM presence within biofilms, with industrial activities posing higher noncarcinogenic and carcinogenic risks than other sources. The network-correlation analyses revealed higher levels of ARG-MRG coexistence in biofilms, with the ecological and health risk index of HMs in biofilms closely associated with the abundance of both resistance genes. Furthermore, the biofilm As concentration markedly affected the abundance and expression of ARGs and MRGs, with elevated As levels within biofilms significantly and positively influencing all four functional categories of MRGs. Water pH also indirectly impacted these functional types by modulating the ionic form of HMs within the biofilm matrix. Our findings underscore the significance of integrating biofilms into environmental management practices and standards for assessing environmental quality.

Treatment of Acute Ulcerative Colitis with Zinc Hyaluronate in Mice

Ulcerative colitis (UC) is a type of inflammatory bowel disease arising from numerous factors, while UC patients face insufficient treatment options and a high incidence of adverse reactions to the current therapies. As a functional food additive, hyaluronic acid plays a certain role in intestinal repair. In this study, we constructed a mouse model of dextran sulfate sodium (DSS)-induced UC to examine the effects and underlying mechanisms of action of zinc hyaluronate (ZnHA) on the pathogenesis of UC. ZnHA effectively alleviated key clinical UC symptoms, such as weight loss, loose stools, and bloody stools. Mechanistically, ZnHA attenuated the expression of inflammatory factors, such as tumor necrosis factor-α, interleukin (IL)-6, and myeloperoxidase while upregulating the expression of IL-10. Furthermore, through intestinal flora and short-chain fatty acid analyses, ZnHA was found to promote propionic acid production by enriching beneficial bacteria. ZnHA simultaneously enhanced the expression of tight junction proteins, specifically ZO-1 and occludin, thereby restoring intestinal barrier function. Overall, our findings elucidate the therapeutic potential of ZnHA in treating acute UC by inhibiting intestinal inflammation and regulating flora, while also providing further theoretical support for development of hyaluronic acid to treat this disease.

Virus-induced perturbations in the mouse microbiome are impacted by microbial experience

The bacterial microbiome has a major impact on health and can shape metabolism, host tolerance, immune responses, and the outcome of future infections. The bacterial microbiome is highly variable between individuals. Specific pathogen-free animals have reduced microbiome diversity, making it difficult to evaluate the impact of infection-induced microbiome disruption that would be observed in free-living animals, including people. Mice are commonly used as a preclinical model but unfortunately often fail to predict translation success or failure, particularly for immune and infectious disease-targeting therapies. Here, we utilize pet store mouse cohoused "dirty" mice with diverse microbial experience to explore how host variability and infection may be interacting to drive unique microbiome changes. We found that cohoused animals had significantly increased bacterial diversity in the small intestine and cecum but not in the large intestine. There were differentially abundant taxa between clean and dirty animals in all three tissues. After infection with influenza A virus, samples clustered by both housing condition and infection status in the cecum and large intestine, while small intestine samples clustered predominantly by infection. Altogether, these results highlight the differential impact of housing, infection, and interaction between the two in dictating community composition across the gastrointestinal microbiome.IMPORTANCETraditionally housed pathogen-free mouse models do not fully capture the natural variability observed among human microbiomes, which may underlie their poor translationally predictive value. Understanding the difference between pathogen-induced shifts in the bacterial microbiome and natural microbiome variance is a major hurdle to determining bacterial biomarkers of disease. It is also critical to understand how diverse baseline microbiomes may be differentially impacted by infection and contribute to disease. Pet store cohoused "dirty" mice have diverse microbial experiences and microbiomes, allowing us to evaluate how baseline variation, infection, and interaction between the two impact the microbiome.

Spartina alterniflora invasion significantly alters the assembly and structure of soil bacterial communities in the Yellow River Delta

Soil microbial communities are integral to almost all terrestrial biogeochemical cycles, which are essential to coastal wetland functioning. However, how soil bacterial community assembly, composition, and structure respond to native and non-native plant invasions in coastal wetlands remains unclear. In this study of the coastal wetlands of the Yellow River Delta in China, the assembly, community composition, and diversity of soil bacterial communities associated with four wetland plant species (Phragmites australis, Spartina alterniflora, Suaeda salsa, and Tamarix chinensis) and four soil depths (0-10 cm, 10-20 cm, 20-30 cm, and 30-40 cm) were characterized using high-throughput sequencing. Plant species identity, as well as environmental factors, rather than soil depth, was found to play predominant roles in shaping the diversity and structure of wetland soil bacterial communities. S. alterniflora invasion altered bacterial community structure and increased bacterial diversity. Phragmites australis-associated bacterial communities were enriched with sulfate-reducing bacteria such as Desulfurivibrio and Desulfuromonas. In comparison, S. alterniflora-associated bacterial communities were enriched with both sulfate-reducing bacteria (SEEP-SRB1) and sulfate-oxidizing bacteria (Sulfurimonas), which maintained a dynamic balance in the local sulfur-cycle, and thereby enhanced S. alterniflora growth. In addition, stochastic processes dominated the assembly of soil bacterial communities associated with all four plant species, but were most important for the S. alterniflora community. The S. alterniflora-associated bacterial community also showed stronger interactions and more extensive connections among bacterial taxa; a co-occurrence network for this community had the greatest average clustering coefficient, average degree, modularity, and number of links and nodes, but the lowest average path length. Altogether, individual plant species had distinct effects on soil bacterial community assembly and structure, with the invasive species having the strongest impact. These results provide insights into microbial ecology and inform management strategies for coastal wetland restoration.

Single, but not mixed dietary fibers suppress body weight gain and adiposity in high fat-fed mice

Dietary fiber can suppress excess adipose tissue and weight gain in rodents and humans when fed high fat diets. The gut microbiome is thought to have a key role, although exactly how remains unclear. In a tightly controlled murine study, we explored how different types of dietary fiber and doses affect the gut microbiota and gut epithelial gene expression. We show that 10% pectin and 10% FOS suppress high fat diet (HFD)-induced weight gain, effects not seen at 2% doses. Furthermore, 2 and 10% mixtures of dietary fiber were also without effect. Each fiber treatment stimulated a distinct gut microbiota profile at the family and operational taxonomic unit (OTU) level. Mechanistically it is likely that the single 10% fiber dose shifted selected bacteria above some threshold abundance, required to suppress body weight, which was not achieved by the 10% Mix, composed of 4 fibers each at 2.5%. Plasma levels of the gut hormone PYY were elevated by 10% pectin and FOS, but not 10% mixed fibers, and similarly RNA seq revealed some distinct effects of the 10% single fibers on gut epithelial gene expression. These data show how the ability of dietary fiber to suppress HFD-induced weight gain is dependent upon both fiber type and dose. It also shows that the microbial response to dietary fiber is distinct and that there is not a single microbial response associated with the inhibition of adiposity and weight gain. PYY seems key to the latter response, although the role of other factors such as Reg3γ and CCK needs to be explored.

Different lysine-to-methionine ratios in a low-protein diet affect the microbiome and metabolome, influencing the jejunal barrier function in Tibetan sheep

Introduction

The objective of this study was to evaluate the effects of the dietary lysine (Lys)/ methionine (Met) ratio in a low-protein diet on short-chain fatty acid (SCFA) profiles, villus morphology, antioxidant capacity, and immune status of the jejunum in Tibetan sheep.

Methods

A total of 90 weaned Tibetan sheep, each 2 months old with an initial weight of 15.37 ± 0.92 kg, were randomly divided into three treatment groups. These groups were supplemented with different Lys/Met ratios of 3 [low protein-high methionine (LP-H)], 2 [low protein-medium methionine (LP-M)], and 1 [low protein-low methionine (LP-L)] in the basal diet (10% crude protein). The feeding trial lasted 100 days, including a 10-day acclimation period and a 90-day experimental period.

Results

The hematoxylin-eosin (H&E) sections showed that the LP-L group had a significantly increased villus height compared to the LP-M and LP-H groups (p < 0.05). In addition, the LP-L group showed higher levels of Superoxide dismutase (SOD) activity and Total Antioxidant Capacity (T-AOC) concentrations (p < 0.05). A lower concentration of Interleukin-1 beta (IL-1β) was observed in the LP-H group (p < 0.05). The activities of α-amylase, chymotrypsin, and lipase were higher in the LP-L group compared to the LP-H group (p < 0.05). Bacterial sequencing showed that both Chao1 and ACE richness were significantly increased in the LP-L group (p < 0.05), suggesting that the species richness in the jejunum is connected to the ratio of dietary Lys/Met. Furthermore, lowering the dietary Lys/ Met ratio significantly increased the abundance of Romboutsia, the Ruminococcus gauvreauii group, the Lachnospiraceae NK3A20 group, Ruminococcus 2, and the Christensenellaceae R-7 group (p < 0.05) while decreasing the abundance of Methanobrevibacter (p < 0.05). Several differential metabolites, including beta-alanine, pantothenate, pantothenic acid, phosphoenolpyruvate, cysteine, adenosine 5'-diphosphate, isodeoxycholic acid, glutamate conjugated cholic acid, and 3-dehydrocholic acid, were significantly increased in the LP-L group (p < 0.05). The functional analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations indicated that these metabolites were mainly involved in pantothenate and CoA biosynthesis, ferroptosis, and the tricarboxylic acid cycle. Several genes related to barrier function, such as Occludin and Muc- 2, were upregulated in the LP-L group (p < 0.05), while IL-6 and TNF-α were downregulated (p < 0.05).

Discussion

Collectively, our results suggest that the dietary Met/ Lys ratio could affect the jejunal SCFA concentration by modulating the microbial community and regulating metabolism, thereby contributing to jejunal barrier function. Our findings provide a theoretical basis for the application of Lys/Met diet supplementation in the nutritional management of Tibetan sheep, particularly when reducing the dietary crude protein (CP) level.

Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms

Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications.IMPORTANCEAlthough soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction-less than 1%-can be cultured under specific media and cultivation conditions. This indicates that there are ample opportunities in harvesting the diverse environmental microorganisms if isolating and recovering these uncultured microorganisms are possible. This paper presents a new cultivation technique composed of isolating single-soil microorganism cell from an in situ soil microorganism community in microfluidic droplets and conducting in-droplet cultivation in media supplemented by soil extract or soil metabolites. This method enables the recovery of a broader diversity of the original microorganism community, laying the groundwork for a high-throughput phenotyping of these diverse microorganisms from their natural habitats.

Compositional shifts and co-occurrence patterns of topsoil bacteria and micro-eukaryotes across a permafrost thaw gradient in alpine meadows of the Qilian Mountains, China

Soil microorganisms play a pivotal role in the biogeochemical cycles of alpine meadow ecosystems, especially in the context of permafrost thaw. However, the mechanisms driving microbial community responses to environmental changes, such as variations in active layer thickness (ALT) of permafrost, remain poorly understood. This study utilized next-generation sequencing to explore the composition and co-occurrence patterns of soil microbial communities, focusing on bacteria and micro-eukaryotes along a permafrost thaw gradient. The results showed a decline in bacterial alpha diversity with increasing permafrost thaw, whereas micro-eukaryotic diversity exhibited an opposite trend. Although changes in microbial community composition were observed in permafrost and seasonally frozen soils, these shifts were not statistically significant. Bacterial communities exhibited a greater differentiation between frozen and seasonally frozen soils, a pattern not mirrored in eukaryotic communities. Linear discriminant analysis effect size analysis revealed a higher number of potential biomarkers in bacterial communities compared with micro-eukaryotes. Bacterial co-occurrence networks were more complex, with more nodes, edges, and positive linkages than those of micro-eukaryotes. Key factors such as soil texture, ALT, and bulk density significantly influenced bacterial community structures, particularly affecting the relative abundances of the Acidobacteria, Proteobacteria, and Actinobacteria phyla. In contrast, fungal communities (e.g., Nucletmycea, Rhizaria, Chloroplastida, and Discosea groups) were more affected by electrical conductivity, vegetation coverage, and ALT. This study highlights the distinct responses of soil bacteria and micro-eukaryotes to permafrost thaw, offering insights into microbial community stability under global climate change.IMPORTANCEThis study sheds light on how permafrost thaw affects microbial life in the soil, with broader implications for understanding climate change impacts. As permafrost degrades, it alters the types and numbers of microbes in the soil. These microbes play essential roles in environmental processes, such as nutrient cycling and greenhouse gas emissions. By observing shifts from bacteria-dominated to fungi-dominated communities as permafrost thaws, the study highlights potential changes in these processes. Importantly, this research suggests that the stability of microbial networks decreases with permafrost degradation, potentially disrupting the delicate balance of these ecosystems. The findings not only deepen our understanding of microbial responses to changing climates but also support the development of strategies to monitor and potentially mitigate the effects of climate change on fragile high-altitude ecosystems.

Amplicon sequences of sourdough starter cultures treated with varying levels of water chlorination

Here, we present amplicon sequences from sourdough starter cultures that have been treated with a chlorine concentration gradient mirroring public water distribution systems. Data derived present insights into the effect of important environmental factors that may influence the formation of microbial communities in food biomes.