Keystone Bacteria Research Articles

Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome.

Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities. Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences. In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.

Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron.

Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques-a known mucin degrader that has been implicated in inflammatory bowel diseases (IBDs)-degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong α-L-fucosidase, sialidase and β1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which might contribute to its association with IBD.IMPORTANCEAn important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade the various components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate species associated with bacterial mucus damage and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another species of gut bacteria, Bacteroides thetaiotaomicron. Our findings underscore the importance of understanding mucin degradation mechanisms in different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately affect mucus damage and could therefore be key players in effects that result from reductions in mucus integrity.

Ciprofloxacin affects nutrient removal in manganese ore-based constructed wetlands: Adaptive responses of macrophytes and microbes

Ciprofloxacin (CIP) has received considerable attention in recent decades due to its high ecological risk. However, little is known about the potential response of macrophytes and microbes to varying levels of CIP exposure in constructed wetlands. Therefore, lab-scale manganese ore-based tidal flow constructed wetlands (MO-TFCWs) were operated to evaluate the responses of macrophytes and microbes to CIP over the long term. The results indicated that total nitrogen removal improved from 79.93% to 87.06% as CIP rose from 0 to 4 mg L−1. The chlorophyll content and antioxidant enzyme activities in macrophytes were enhanced under CIP exposure, but plant growth was not inhibited. Importantly, CIP exposure caused a marked evolution of the substrate microbial community, with increased microbial diversity, expanded niche breadth and enhanced cooperation among the top 50 genera, compared to the control (no CIP). Co-occurrence network also indicated that microorganisms may be more inclined to co-operate than compete. The abundance of the keystone bacterium (involved in nitrogen transformation) norank_f__A0839 increased from 0.746% to 3.405%. The null model revealed drift processes (83.33%) dominated the community assembly with no CIP and 4 mg L−1 CIP. Functional predictions indicated that microbial carbon metabolism, electron transfer and ATP metabolism activities were enhanced under prolonged CIP exposure, which may contribute to nitrogen removal. This study provides valuable insights that will help achieve stable nitrogen removal from wastewater containing antibiotic in MO-TFCWs.

Arbuscular mycorrhizal fungi and Streptomyces: brothers in arms to shape the structure and function of the hyphosphere microbiome in the early stage of interaction

BackgroundFungi and bacteria coexist in a wide variety of environments, and their interactions are now recognized as the norm in most agroecosystems. These microbial communities harbor keystone taxa, which facilitate connectivity between fungal and bacterial communities, influencing their composition and functions. The roots of most plants are associated with arbuscular mycorrhizal (AM) fungi, which develop dense networks of hyphae in the soil. The surface of these hyphae (called the hyphosphere) is the region where multiple interactions with microbial communities can occur, e.g., exchanging or responding to each other’s metabolites. However, the presence and importance of keystone taxa in the AM fungal hyphosphere remain largely unknown.ResultsHere, we used in vitro and pot cultivation systems of AM fungi to investigate whether certain keystone bacteria were able to shape the microbial communities growing in the hyphosphere and potentially improved the fitness of the AM fungal host. Based on various AM fungi, soil leachates, and synthetic microbial communities, we found that under organic phosphorus (P) conditions, AM fungi could selectively recruit bacteria that enhanced their P nutrition and competed with less P-mobilizing bacteria. Specifically, we observed a privileged interaction between the isolate Streptomyces sp. D1 and AM fungi of the genus Rhizophagus, where (1) the carbon compounds exuded by the fungus were acquired by the bacterium which could mineralize organic P and (2) the in vitro culturable bacterial community residing on the surface of hyphae was in part regulated by Streptomyces sp. D1, primarily by inhibiting the bacteria with weak P-mineralizing ability, thereby enhancing AM fungi to acquire P.ConclusionsThis work highlights the multi-functionality of the keystone bacteria Streptomyces sp. D1 in fungal-bacteria and bacterial-bacterial interactions at the hyphal surface of AM fungi.3XiVYVBxkNucerLC-WX6ofVideo

Heritable microbiome variation is correlated with source environment in locally adapted maize varieties.

Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.

Cracking the code of seasonal seawater biofouling: enhanced biofouling control with quorum sensing inhibitor-functionalized membranes

Membrane biofouling poses an ongoing challenge in seawater reverse osmosis (SWRO) desalination. Here we delved into the impact of seasonal variations in microbial communities on membrane biofouling and innovatively fabricated quorum sensing inhibitors (acylase (AC) and methyl anthranilate (MA))-modified membranes to combat it. Results indicated that Proteobacteria dominated in seawater and membrane biofilm across all seasons, while other phyla varied seasonally. At the class level, the two leading bacteria on the membrane were Gamma- and Alphaproteobacteria, constituting 14–48% and 4–27%, respectively. Genera like Arcobacter, Vibrio, and Rhodobacteraceae were identified as keystone species that exhibited a significant positive correlation with extracellular polymeric substance (EPS) and biofilm formation, leading to a substantive reduction in membrane flux by 70 to 77%. The introduction of AC and MA inhibitors on the membrane suppressed keystone bacteria Rhodobacteraceae and Arcobacter and affected their metabolism, thereby significantly reducing EPS by 65–69% and 55–59%, respectively, and alleviating membrane flux decline by 30–32% and 18–22%, respectively, compared to the pristine membrane. These findings shed new light on the seasonal patterns of membrane biofouling and provide valuable insights into anti-biofouling strategies based on QS inhibition for collaborative biofilm formation.

Investigating Local Delivery of Mesenchymal Stromal Cell Extracellular Vesicles for Treatment-resistant Periodontitis: A Hypothesis

Background: One of the main reasons for tooth loss and functional incompatibility of dentition is periodontitis which is a multi-factorial disease. Among the main reasons for periodontitis is inflammation. Hypothesis: Some keystone bacteria, such as Prophyromonas gingivalis with a notable number of virulence factors could activate and modify inflammatory pathways in gingiva. A well-established therapy for this disease is topical antibiotics; however, these treatments have side effects and could promote antibiotic-resistant infections as well. Such antibiotic-resistant infections are a group of periodontitis with a severely complicated treatment approach that could fail. Thus, new strategies need to be developed for treatment-resistant (antibiotic-resistant) periodontitis. In the past decades, many randomized controlled clinical trials have shown that mesenchymal stromal cells (MSCs) could treat inflammatory-dependent diseases or disorders. In addition to MSCs, the anti-inflammatory effects of their extracellular vesicles (EVs) have also been studied in the clinic. Results: Considering the anti-inflammatory potential of MSCs-derived EVs, it could be hypothesized that local delivery of these EVs could be an effective method for periodontal treatment due to the accessible location of the periodontium. Conclusion: This study suggests further in vivo studies and randomized clinical trials on the potential effects of MSCs-derived EVs on periodontal disease treatment.

Indirect regulation of topsoil nutrient cycling by groundwater depth: impacts on sand-fixing vegetation and rhizosphere bacterial communities.

The impact of groundwater table depth (GTD) on bacterial communities and soil nutrition in revegetated areas remains unclear. We investigated the impacts of plant growth and soil physicochemical factors on rhizosphere bacterial communities under different GTD. The four plant growth indices (Pielou, Margalef, Simpson, and Shannon-Wiener indices) and soil water content (SWC) at the Artem and Salix sites all showed a decreasing trend with increasing GTD. Salix had a higher nutrient content than Artem. The response of plant rhizosphere bacterial communities to GTD changes were as follows. Rhizosphere bacteria at the Artem and Salix sites exhibited higher relative abundance and alpha diversity in SW (GTD < 5 m) compared than in DW (GTD > 5 m). Functional microbial predictions indicated that the rhizosphere bacterial communities of Artem and Salix promoted carbon metabolism in the SW. In contrast, Artem facilitated nitrogen cycling, whereas Salix enhanced both nitrogen cycling and phototrophic metabolism in the DW. Mantel test analysis revealed that in the SW of Artem sites, SWC primarily governed the diversity of rhizosphere and functional bacteria involved in the nitrogen cycle by affecting plant growth. In DW, functional bacteria increase soil organic carbon (SOC) to meet nutrient demands. However, higher carbon and nitrogen availability in the rhizosphere soil was observed in the SW of the Salix sites, whereas in DW, carbon nutrient availability correlated with keystone bacteria, and changes in nitrogen content could be attributed to nitrogen mineralization. This indicates that fluctuations in the groundwater table play a role in regulating microbes and the distribution of soil carbon and nitrogen nutrients in arid environments.

Integrating variation in bacterial‐fungal co‐occurrence network with soil carbon dynamics

Abstract Bacteria and fungi are core microorganisms in diverse ecosystems, and their cross‐kingdom interactions are considered key determinants of microbiome structure and ecosystem functioning. However, how bacterial‐fungal interactions mediate soil organic carbon (SOC) dynamics remains largely unexplored in the context of artificial forest ecosystems. Here, we characterised soil bacterial and fungal communities in four successive planting of Eucalyptus and compared them to a neighbouring evergreen broadleaf forest. Carbon (C) mineralisation combined with five C‐degrading enzymatic activities was investigated to determine the effects of successive planting of Eucalyptus on SOC dynamics. Our results indicated that successive planting of Eucalyptus significantly altered the diversity and structure of soil bacterial and fungal communities and increased the negative bacterial‐fungal associations. The bacterial diversity significantly decreased in all Eucalyptus plantations compared to the evergreen forest, while the fungal diversity showed the opposite trend. The ratio of negative bacterial‐fungal associations increased with successive planting of Eucalyptus due to the decrease in SOC, ammonia nitrogen (NH4+‐N), nitrate nitrogen (NO3−‐N) and available phosphorus (AP). Structural equation modelling indicated that the potential cross‐kingdom competition, based on the ratio of negative bacterial‐fungal correlations, was significantly negatively associated with the diversity of total bacteria and keystone bacteria, thereby increasing C‐degrading enzymatic activities and C mineralisation. Synthesis and applications: Our results highlight the regulatory role of the negative bacterial‐fungal association in enhancing the correlation between bacterial diversity and C mineralisation. This suggests that promoting short‐term successive planting in the management of Eucalyptus plantations can mitigate the impact of this association on SOC decomposition. Taken together, our study advances the understanding of bacterial‐fungal negative associations to mediate carbon mineralisation in Eucalyptus plantations, giving us a new insight into SOC cycling dynamics in artificial forests.

Bacterial community diversity and co-occurrence networks in biochar as a sustainable soil amendment material for apple orchards

Biochar amended soils are considered to be a novel concept to improve soil health by providing favorable habitats for microbial activity. This study carried out field experiments to assess the diversity, composition, and co-occurrence networks of soil bacterial communities in the presence of biochar, in order to validate the optimal amount of biochar addition for the practical application of soil improvement in apple orchards in terms of bacterial interactions. The application of appropriate biochar increased bacterial diversity and the prominent presence of copiotroph bacteria was Proteobacteria, and improved the network complexity and cooperative mutualism of the bacterial ecological networks with enhanced stability and environmental resistance. Biochar addition shifts keystone bacteria from anaerobic and cellulose-degrading bacteria to aerobic and nitrogen cycling-related bacteria. Obtained 2 kg/m2 of biochar-amended soil favors micro-environment optimization with the strongest resource utilization and adaptability of the bacterial community. Biochar as a sustainable soil amendment material and 2 kg/m2 biochar addition has the potential to be a viable approach for soil health improvement in apple orchards.

Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats

BackgroundThe increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period.ResultsBased on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats’ growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats’ growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%).ConclusionsThis study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants.CFkFrpUn9s69m82LGb2Mf6Video

Effects of different soil water holding capacities on vegetable residue return and its microbiological mechanism.

With the gradual expansion of the protected vegetable planting area, dense planting stubbles and increasing labor cost, the treatment of vegetable residues has become an urgent problem to be solved. Soil bacterial community structure plays an important role in vegetable residue return and is susceptible to environmental changes. Therefore, understanding the influences of different soil water holding capacities on plant residue decomposition and soil bacterial communities is important for biodegradation. During the whole incubation period, the weight loss ratio of plant residue with 100% water holding capacity was 69.60 to 75.27%, which was significantly higher than that with 60% water holding capacity in clay and sandy soil, indicating that high water holding capacity promoted the decomposition of plant residue. The degradation of lignin and cellulose was also promoted within 14 days. Furthermore, with the increase in soil water holding capacity, the contents of NH4+ increased to 5.36 and 4.54 times the initial value in the clay and sandy soil, respectively. The increase in napA and nrfA resulted in the conversion of NO3- into NH4+. The increase in water holding capacity made the bacterial network structure more compact and changed the keystone bacteria. The increase in water holding capacity also increased the relative abundance of Firmicutes at the phylum level and Symbiobacterium, Clostridium at the genus level, which are all involved in lignin and cellulose degradation and might promote their degradation. Overall, these findings provide new insight into the effects of different soil water holding capacities on the degradation of plant residues in situ and the corresponding bacterial mechanisms.

Heavy metal pollution triggers a shift from bacteria-based to fungi-based soil micro-food web: Evidence from an abandoned mining-smelting area

Heavy metals pose significant threats to soil biota, ultimately disrupting soil micro-food web. However, no studies have yet elucidated the impact of heavy metals on soil micro-food web. In this study, we explored the response of bacteria, fungi, nematodes, and soil micro-food web along a gradient of heavy metals in an abandoned smelting-mining area. We found that bacteria responded strongly to heavy metals, whereas fungi showed greater resistance and tolerance. Nematodes responses were less apparent. With the increasing levels of heavy metal pollution, the importance of heavy metal-tolerant organisms in micro-food webs increased significantly. For instance, the keystone bacteria in soil micro-food web shifted from copiotrophic to oligotrophic types, while the keystone nematodes shifted from to bacterial-feeding (e.g., Eucephalobus) to fungal-feeding species (e.g., Ditylenchus). Additionally, elevated heavy metal concentrations increased the proportion of fungi (e.g., Mortierellomycota), intensifying their interactions with bacteria and nematodes and causing a shift from bacteria-based to fungi-based soil micro-food web. Furthermore, heavy metal contamination induced a more complex and stable soil micro-food web. Overall, we highlight the changes in soil micro-food web as a mechanism for coping with heavy metal stress. Our study provides valuable insights into how heavy metal pollution can cause shifts in soil micro-food webs and has critical implications for enhancing our understanding of the ecological consequences of environmental pollution at the ecosystem level.

Keystone bacteria in a thiosulfate-driven autotrophic denitrification microbial community

Keystone bacteria associated with a thiosulfate-driven autotrophic denitrification microbial community for treating high nitrate concentration wastewater were identified in this study. Five laboratory-scale anoxic bioreactors, designated as S0-S4, were fed with synthetic wastewater containing 120 mg NO– 3-N/L. Meanwhile, thiosulfate was used as the sole electron donor and provided varying ratios to these bioreactors, resulting in (S/N ratios of 0, 0.7, 2.4, 4.0, and 5.7), respectively. These bioreactors were run in a 104-day period, which was composed of eight operational cycles. Overall, bioreactors S1-4 could achieve 14.0, 56.5, 88.9, and 85.0 % nitrate removal rates, respectively. Approximately 30% of the electrons from thiosulfate were estimated to be directed to autotrophic denitrification across the bioreactors. The microbial ecology analysis revealed that Proteobacteria (42–66%), Bacteriodetes (15–30%), and Firmicutes (15–28%) were the major phyla residing in the bioreactors. Thiobacillus, Pseudomonas, Arenimonas, and Thauera were identified as predominant genera shared across the bioreactors. Thiobacillus was the dominant genus in thiosulfate-driven autotrophic denitrification, and contributed 42% to community in S4 reactor. Functional genes analysis further showed that only Thiobacillus and Thauera contained the complete nitrate reduction pathway. Higher S/N ratios directly promoted the oxidation of thiosulfate to sulfate by the sulfur oxidation (SOX) system. Due to Thiobacillus was absence of SoxCD for catalysis from SoxYZ-S-SH to SoxYZ-S-SO3, Thiobacillus and Thauera could work collaboratively on the SOX pathway as the keystone bacteria to achieve thiosulfate oxidation. But such collaboration might have led to extracellular electron transportation and casused low electron utilization for the autotrophic denitrification process.

The Impact of Long-Term Macrolide Exposure on the Gut Microbiome and Its Implications for Metabolic Control.

Long-term low-dose macrolide therapy is now widely used in the treatment of chronic respiratory diseases for its immune-modulating effects, although the antimicrobial properties of macrolides can also have collateral impacts on the gut microbiome. We investigated whether such treatment altered intestinal commensal microbiology and whether any such changes affected systemic immune and metabolic regulation. In healthy adults exposed to 4 weeks of low-dose erythromycin or azithromycin, as used clinically, we observed consistent shifts in gut microbiome composition, with a reduction in microbial capacity related to carbohydrate metabolism and short-chain fatty acid biosynthesis. These changes were accompanied by alterations in systemic biomarkers relating to immune (interleukin 5 [IL-5], IL-10, monocyte chemoattractant protein 1 [MCP-1]) and metabolic (serotonin [5-HT], C-peptide) homeostasis. Transplantation of erythromycin-exposed murine microbiota into germ-free mice demonstrated that changes in metabolic homeostasis and gastrointestinal motility, but not systemic immune regulation, resulted from changes in intestinal microbiology caused by macrolide treatment. Our findings highlight the potential for long-term low-dose macrolide therapy to influence host physiology via alteration of the gut microbiome. IMPORTANCE Long-term macrolide therapy is widely used in chronic respiratory diseases although its antibacterial activity can also affect the gut microbiota, a key regulator of host physiology. Macrolide-associated studies on the gut microbiota have been limited to short antibiotic courses and have not examined its consequences for host immune and metabolic regulation. This study revealed that long-term macrolides depleted keystone bacteria and impacted host regulation, mediated directly by macrolide activity or indirectly by alterations to the gut microbiota. Understanding these macrolide-associated mechanisms will contribute to identifying the risk of long-term exposure and highlights the importance of targeted therapy for maintenance of the gut microbiota.

Positive interactions among Corynebacterium glutamicum and keystone bacteria producing SCFAs benefited T2D mice to rebuild gut eubiosis

Accumulating evidences strongly support the correlations between the compositions of gut microbiome and therapeutic effects on Type 2 diabetes (T2D). Notably, gut microbes such as Akkermansia muciniphila are found able to regulate microecological balance and alleviate dysmetabolism of mice bearing T2D. In order to search out similarly functional bacteria, bacteriophage MS2 with a good specificity to bacteria carrying fertility (F) factor were used to treat T2D mice. Based on multi-omics analysis of microbiome and global metabolism of mice, we observed that gavage of bacteriophage MS2 and metformin led to a significant increase in the abundance of Corynebacterium glutamicum and A. muciniphila, respectively. Consequently, the gut microbiota were remodeled, leading to variations in metabolites and a substantial increase in short-chain fatty acids (SCFAs). In which, the amount of acetate, propionate, and butyrate presented negative correlations to that of proinflammatory cytokines, which was beneficial to repairing the intestinal barriers and improving their functions. Moreover, main short fatty acid (SCFA) producers exhibited positive interactions, further facilitating the restoration of gut eubiosis. These findings revealed that C. glutamicum and its metabolites may be potential dietary supplements for the treatment of T2D. Moreover, our research contributes to a novel understanding of the underlying mechanism by which functional foods exert their anti-diabetic effects.

Soil bacterial communities associated with multi-nutrient cycling under long-term warming in the alpine meadow.

The functions of terrestrial ecosystems are mainly maintained by bacteria, as a key component of microorganisms, which actively participate in the nutrient cycling of ecosystems. Currently, there are few studies have been carried out on the bacteria contributing to the soil multi-nutrient cycling in responding to climate warming, which hampers our obtainment of a comprehensive understanding of the ecological function of ecosystems as a whole. In this study, the main bacteria taxa contributing to the soil multi-nutrient cycling under the long-term warming in an alpine meadow was determined based onphysichemical properties measurement and high-throughput sequencing, and the potential reasons that warming altered the main bacteria contributing to the soil multi-nutrient cycling were further analyzed. The results confirmed that the bacterial β-diversity was crucial to the soil multi-nutrient cycling. Furthermore, Gemmatimonadetes, Actinobacteria, and Proteobacteria were the main contributors to the soil multi-nutrient cycling, and played pivotal roles as keystone nodes and biomarkers throughout the entire soil profile. This suggested that warming altered and shifted the main bacteria contributing to the soil multi-nutrient cycling toward keystone taxa. Meanwhile, their relative abundance was higher, which could make them have the advantage of seizing resources in the face of environmental pressures. In summary, the results demonstrated the crucial role of keystone bacteria in the multi-nutrient cycling under the climate warming in the alpine meadow. This has important implications for understanding and exploring the multi-nutrient cycling of alpine ecosystems under the global climate warming.

A Placebo-Controlled Trial to Evaluate Two Locally Delivered Antibiotic Gels (Piperacillin Plus Tazobactam vs. Doxycycline) in Stage III-IV Periodontitis Patients.

Background and objectives: this study aims to evaluate the clinical and microbiological effects of a single subgingival administration of a locally delivered antibiotic gel containing piperacillin plus tazobactam and compare it with a slow-release doxycycline (14%) gel and a placebo gel, following subgingival instrumentation (SI) in patients with severe periodontitis. Materials and methods: sixty-four patients diagnosed with stage III-IV periodontitis were enrolled, were randomly assigned into three groups, and were treated additionally with a single subgingival administration of piperacillin plus tazobactam gel (group A); doxycycline gel (group B); and placebo gel (group C). The primary outcome variable was the change in mean probing pocket depth (PPD) 6 months after the intervention. Secondary outcome variables were changes in mean full-mouth bleeding score (FMBS); full-mouth plaque score (FMPS); overall bleeding index (BOP); pocket closure; and clinical attachment level (CAL), along with changes in the numbers of five keystone bacteria: Aggregatibacter actinomycetemcomitans (A.a.), Porphyromonas gingivalis (P.g.), Prevotella intermedia (P.i.), Tannerella forsythia (T.f.), and Treponema denticola (T.d.). Intergroup and intragroup differences were evaluated at 3 and 6 months. Results: at baseline, the three groups were comparable. An improvement in clinical parameters such as PPD, CAL, and BOP between groups was observed at 3 and 6 months, but without statistical significance (p > 0.05). At 6 months, the intragroup analysis showed a significant reduction in clinical parameters. Even though the piperacillin plus tazobactam group showed slightly higher PPD reduction, this was not statistically significant when compared to both control groups. Conclusions: The groups had similar results, and subgingival instrumentation can be executed without adjunctive antimicrobials, reducing the costs for the patient and the working time/load of the professional.

Dynamic network modeling of gut microbiota during Alzheimer’s disease progression in mice

ABSTRACT The intimate association between the gut microbiota (GM) and the central nervous system points to potential intervention strategies for neurological diseases. Nevertheless, there is currently no theoretical framework for selecting the window period and target bacteria for GM interventions owing to the complexity of the gut microecosystem. In this study, we constructed a complex network-based modeling approach to evaluate the topological features of the GM and infer the window period and bacterial candidates for GM interventions. We used Alzheimer’s disease (AD) as an example and traced the GM dynamic changes in AD and wild-type mice at one, two, three, six, and nine months of age. The results revealed alterations of the topological features of the GM from a scale-free network into a random network during AD progression, indicating severe GM disequilibrium at the late stage of AD. Through stability and vulnerability assessments of the GM networks, we identified the third month after birth as the optimal window period for GM interventions in AD mice. Further computational simulations and robustness evaluations determined that the hub bacteria were potential candidates for GM interventions. Moreover, our GM functional analysis suggested that Lachnospiraceae UCG-001 – the hub and enriched bacterium in AD mice – was the keystone bacterium for GM interventions owing to its contributions to quinolinic acid synthesis. In conclusion, this study established a complex network-based modeling approach as a practical strategy for disease interventions from the perspective of the gut microecosystem.

Functional bacterial consortium responses to biochar and implications for BDE-47 transformation: Performance, metabolism, community assembly and microbial interaction

The influence of biochar on the biodegradation of persistent organic pollutants (POPs) has been extensively studied. However, the underlying mechanisms behind the response of functional microbial consortia to biochar remain poorly understood. Herein, we systematically explored the effect of biochar on 2,2′,4,4′-tetrabrominated ether (BDE-47) biodegradation, and investigated the interaction and assembly mechanism of the functional bacterial consortium QY2. The results revealed that the biodegradation efficiency of QY2 for BDE-47 increased from 53.85% to 94.11% after the addition of biochar. Fluorescence excitation-emission matrix and electrochemical analysis showed that biochar-attached biofilms were rich in redox-active extracellular polymeric substances (EPS, 3.03-fold higher than free cell), whose strong interaction with biochar facilitated the electron transfer of the biofilm, thus enhancing the debromination degradation of BDE-47. Meanwhile, the assembly model and molecular ecological networks analysis indicated that bacterial community assembly in biofilms was more driven by deterministic processes (environmental selection >75.00%) upon biochar stimulation and exhibited closer interspecific cooperative interactions, leading to higher biodiversity and broader habitat niche breadth for QY2 in response to BDE-47 disturbance. Potential degraders (Methylobacterium, Sphingomonas, Microbacterium) and electrochemical bacteria (Ochrobactrum) were selectively enriched, whose role as keystone bacteria may be participated in biofilm formation and redox-active EPS secretion (r > 0.5, P < 0.05). These findings deepen the understanding of the mechanisms by which biochar promotes microbial degradation of PBDEs and provided a theoretical basis for better regulation of functional bacterial communities during environmental remediation.