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Drought is one of the most serious abiotic stresses, and emerging evidence suggest plant microbiome affects plant drought tolerance. However, there is a lack of genetic evidence regarding whether and how plants orchestrate the dynamic assembly of the microbiome upon drought. By utilizing mutants with enhanced or decreased root hair densities, we find that root hair regulators also affect drought induced root microbiome changes. Rhizobiaceae is a key biomarker taxa affected by root hair related mutants. We isolated and sequenced 1479 root associated microbes, and confirmed that several Rhizobium strains presented stress-alleviating activities. Metagenome, root transcriptome and root metabolome studies further reveal the multi-omic changes upon drought stress. We knocked out an ornithine cyclodeaminase (ocd) gene in Rhizobium sp. 4F10, which significantly dampens its stress alleviating ability. Our genetic and integrated multi-omics studies confirm the involvement of host genetic effects in reshaping a stress-alleviating root microbiome during drought, and provide mechanistic insights into Rhizobiaceae mediated abiotic stress protection., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Microbiota that originate in the seed can have consequences for the education of the plant immune system, competitive exclusion of pathogens from the host tissue, and host access to critical nutrients. Our research objective was to investigate the consequences of the environmental conditions of the parent plant for bacterial seed microbiome assembly and transmission across plant generations. Using a fully factorial, three-generational experimental design, we investigated endophytic seed bacterial communities of common bean lines ( Phaseolus vulgaris L.) grown in the growth chamber and exposed to either control conditions, drought, or excess nutrients at each generation. We applied 16S rRNA microbiome profiling to the seed endophytes and measured plant health outcomes. We discovered stable transmission of 22 bacterial members, regardless of the parental plant condition. This study shows the maintenance of bacterial members of the plant microbiome across generations, even under environmental stress. Overall, this work provides insights into the ability of plants to safeguard microbiome members, which has implications for crop microbiome management in the face of climate change.IMPORTANCESeed microbiomes initiate plant microbiome assembly and thus have critical implications for the healthy development and performance of crops. However, the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown, but this is critical information, given the intensifying stressors that crops face as the climate crisis accelerates. This study provides insights into the maintenance of plant microbiomes across generations, with implications for durable plant microbiome maintenance in agriculture on the changing planet., Competing Interests: The authors declare no conflict of interest.

This study characterized and compared the fecal and oral microbiota from women with early-stage breast cancer (BC), women with ductal carcinoma in situ (DCIS), and healthy women. Fecal and oral samples were collected from newly diagnosed patients prior to any therapy and characterized using 16S rRNA sequencing. Measures of gut microbial alpha diversity were significantly lower in the BC vs healthy cohort. Beta diversity differed significantly between the BC or DCIS and healthy groups, and several differentially abundant taxa were identified. Clustering (non-negative matrix factorization) of the gut microbiota identified five bacterial guilds dominated by Prevotella , Enterobacteriaceae, Akkermansia , Clostridiales, or Bacteroides . The Bacteroides and Enterobacteriaceae guilds were significantly more abundant in the BC cohort compared to healthy controls, whereas the Clostridiales guild was more abundant in the healthy group. Finally, prediction of functional pathways identified 23 pathways that differed between the BC and healthy gut microbiota including lipopolysaccharide biosynthesis, glycan biosynthesis and metabolism, lipid metabolism, and sphingolipid metabolism. In contrast to the gut microbiomes, there were no significant differences in alpha or beta diversity in the oral microbiomes, and very few differentially abundant taxa were observed. Non-negative matrix factorization analysis of the oral microbiota samples identified seven guilds dominated by Veillonella , Prevotella , Gemellaceae, Haemophilus , Neisseria , Propionibacterium , and Streptococcus ; however, none of these guilds were differentially associated with the different cohorts. Our results suggest that alterations in the gut microbiota may provide the basis for interventions targeting the gut microbiome to improve treatment outcomes and long-term prognosis., Importance: Emerging evidence suggests that the gut microbiota may play a role in breast cancer. Few studies have evaluated both the gut and oral microbiomes in women with breast cancer (BC), and none have characterized these microbiomes in women with ductal carcinoma in situ (DCIS). We surveyed the gut and oral microbiomes from women with BC or DCIS and healthy women and identified compositional and functional features of the gut microbiota that differed between these cohorts. In contrast, very few differential features were identified in the oral microbiota. Understanding the role of gut bacteria in BC and DCIS may open up new opportunities for the development of novel markers for early detection (or markers of susceptibility) as well as new strategies for prevention and/or treatment., Competing Interests: The authors declare no conflict of interest.

High molecular weight (HMW; >1 kDa) carbohydrates are a major component of dissolved organic matter (DOM) released by benthic primary producers. Despite shifts from coral to algae dominance on many reefs, little is known about the effects of exuded carbohydrates on bacterioplankton communities in reef waters. We compared the monosaccharide composition of HMW carbohydrates exuded by hard corals and brown macroalgae and investigated the response of the bacterioplankton community of an algae-dominated Caribbean reef to the respective HMW fractions. HMW coral exudates were compositionally distinct from the ambient, algae-dominated reef waters and similar to coral mucus (high in arabinose). They further selected for opportunistic bacterioplankton taxa commonly associated with coral stress (i.e., Rhodobacteraceae , Phycisphaeraceae , Vibrionaceae , and Flavobacteriales ) and significantly increased the predicted energy-, amino acid-, and carbohydrate-metabolism by 28%, 44%, and 111%, respectively. In contrast, HMW carbohydrates exuded by algae were similar to those in algae tissue extracts and reef water (high in fucose) and did not significantly alter the composition and predicted metabolism of the bacterioplankton community. These results confirm earlier findings of coral exudates supporting efficient trophic transfer, while algae exudates may have stimulated microbial respiration instead of biomass production, thereby supporting the microbialization of reefs. In contrast to previous studies, HMW coral and not algal exudates selected for opportunistic microbes, suggesting that a shift in the prevalent DOM composition and not the exudate type (i.e., coral vs algae) per se , may induce the rise of opportunistic microbial taxa., Importance: Dissolved organic matter (DOM) released by benthic primary producers fuels coral reef food webs. Anthropogenic stressors cause shifts from coral to algae dominance on many reefs, and resulting alterations in the DOM pool can promote opportunistic microbes and potential coral pathogens in reef water. To better understand these DOM-induced effects on bacterioplankton communities, we compared the carbohydrate composition of coral- and macroalgae-DOM and analyzed the response of bacterioplankton from an algae-dominated reef to these DOM types. In line with the proposed microbialization of reefs, coral-DOM was efficiently utilized, promoting energy transfer to higher trophic levels, whereas macroalgae-DOM likely stimulated microbial respiration over biomass production. Contrary to earlier findings, coral- and not algal-DOM selected for opportunistic microbial taxa, indicating that a change in the prevalent DOM composition, and not DOM type, may promote the rise of opportunistic microbes. Presented results may also apply to other coastal marine ecosystems undergoing benthic community shifts., Competing Interests: The authors declare no conflict of interest.

In plant environments, there exist heterogeneous microbial communities, referred to as the plant microbiota, which are recruited by plants and play crucial roles in promoting plant growth, aiding in resistance against pathogens and environmental stresses, thereby maintaining plant health. These microorganisms, along with their genomes, collectively form the plant microbiome. Research on the plant microbiome can help unravel the intricate interactions between plants and microbes, providing a theoretical foundation to reduce pesticide use, enhance agricultural productivity, and promote environmental sustainability. Despite significant progress in the field of research, unresolved challenges persist due to ongoing technological limitations and the complexities inherent in studying microorganisms at small scales. Recently, synthetic community (SynCom) has emerged as a novel technique for microbiome research, showing promising prospects for applications in the plant microbiome field. This article systematically introduces the origin and distribution of plant microbiota, the processes of their recruitment and colonization, and the mechanisms underlying their beneficial functions for plants, from the aspects of composition, assembly, and function. Furthermore, we discuss the principles, applications, challenges, and prospects of SynCom for promoting plant health., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Previous work shows that a host's resident microbial community can provide resistance against an invading pathogen. However, this community is continuously changing over time due to adaptive mutations, and how these changes affect the invasion resistance of these communities remains poorly understood. To address this knowledge gap, we used an experimental evolution approach in synthetic communities of Escherichia coli and Salmonella Typhimurium to investigate how the invasion resistance of this community against a bacterium expressing a virulent phenotype, i.e., colicin secretion, changes over time. We show that evolved communities accumulate mutations in genes involved in carbon metabolism and motility, while simultaneously becoming less resistant to invasion. By investigating two-species competitions and generating a three-species competition model, we show that this outcome is dependent on the strength of interspecies interactions. Our study demonstrates how adaptive changes in microbial communities can make them more prone to the detrimental effects of an invading species., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Muzafar et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The profound impact of the microbiota on the initiation and progression of cancer has been a focus of attention. In recent years, many studies have shown that microbial metabolites serve as key hubs that connect the microbiome and cancer progression, but the underlying molecular mechanisms have not been fully elucidated. Multiple mechanisms that influence tumour development and therapy resistance, including disrupting cellular signalling pathways, triggering oxidative stress, inducing metabolic reprogramming and reshaping tumour immune microenvironment, are reviewed. Focusing on recent advancements in this field, this review also summarises the methodological framework of studies regarding microbial metabolites. In this review, we outline the current state of research on tumour-associated microbial metabolites and describe the challenges in future scientific research and clinical applications. KEY POINTS: Metabolites derived from both gut and intratumoural microbiota play important roles in cancer initiation and progression. The dual roles of microbial metabolites pose an obstacle for clinical translations. Absolute quantification and tracing techniques of microbial metabolites are essential for addressing the gaps in studies on microbial metabolites. Integrating microbial metabolomics with multi-omics transcends current research paradigms., (© 2024 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.)

Over the last two decades, advancements in sequencing technologies have significantly deepened our understanding of the human microbiome's complexity, leading to increased concerns about the detrimental effects of antibiotics on these intricate microbial ecosystems. Concurrently, the rise in antimicrobial resistance has intensified the focus on how beneficial microbes can be harnessed to treat diseases and improve health and offer potentially promising alternatives to traditional antibiotic treatments. Here, we provide a comprehensive overview of both established and emerging microbe-centric therapies, from probiotics to advanced microbial ecosystem therapeutics, examine the sophisticated ways in which microbes are used medicinally, and consider their impacts on microbiome homeostasis and health outcomes through a microbial ecology lens. In addition, we explore the concept of rewilding the human microbiome by reintroducing "missing microbes" from nonindustrialized societies and personalizing microbiome modulation to fit individual microbial profiles-highlighting several promising directions for future research. Ultimately, the advancements in sequencing technologies combined with innovative microbial therapies and personalized approaches herald a new era in medicine poised to address antibiotic resistance and improve health outcomes through targeted microbiome management., (© 2024 The Author(s). Annals of the New York Academy of Sciences published by Wiley Periodicals LLC on behalf of The New York Academy of Sciences.)

The efficient co-production of H 2 and CH 4 via anaerobic digestion (AD) requires separate stages, as it cannot yet be achieved in one step. Lactic acid bacteria (LAB) (Limosilactobacillus) release H 2 and acetate by enhancing hydrolysis, potentially increasing CH 4 production with simultaneous H 2 accumulation. This study investigated the enhanced effect of one-step co-production of H 2 and CH 4 in AD by LAB and elucidated its enhancement mechanisms. The results showed that 236.3 times increase in H 2 production and 7.1 times increase in CH 4 production are achieved, resulting in profits of 469.39 USD. Model substrates lignocellulosic straw, sodium acetate, and H 2 confirmes LAB work on the hydrolysis stage and subsequent sustainable volatile fatty acid production during the first 6 days of AD. In this stage, the enrichment of Limosilactobacillus carrying bglB and xynB, the glycolysis pathway, and the high activity of protease, acetate kinase, and [FeFe] hydrogenase, jointly achieved rapid acetate and H 2 accumulation, driving hydrogenotrophic methanogenesis dominated. From day 7 to 24, with enriched Methanosarcina, and increased methenyltetrahydromethanopterin hydrogenase activity, continuously produced acetate led to the mainly acetoclastic methanogenesis shift from hydrogenotrophic methanogenesis. The power generation capacity of LAB-enhanced AD is 333.33 times that of China's 24,000 m 3 biogas plant., (© 2024 The Author(s). Advanced Science published by Wiley‐VCH GmbH.)

Temperature is the critical factor affecting the efficiency and cost of anaerobic digestion (AD). The current work develops a shift-temperature AD (STAD) between 35 °C and 55 °C, intending to optimise microbial community and promote substrate conversion. The experimental results showed that severe inhibition of biogas production occurred when the temperature was firstly increased stepwise from 35 °C to 50 °C, whereas no inhibition was observed at the second warming cycle. When the organic load rate was increased to 6.37 g VS/L/d, the biogas yield of the STAD reached about 400 mL/g VS, nearly double that of the constant-temperature AD (CTAD). STAD promoted the proliferation of Methanosarcina (up to 57.32 %), while severely suppressed hydrogenophilic methanogens. However, when the temperature was shifted to 35 °C, most suppressed species recovered quickly and the excess propionic acid was quickly consumed. Metagenomic analysis showed that STAD also promoted gene enrichment related to pathways metabolism, membrane functions, and methyl-based methanogenesis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Anaerobic electrochemical digestion (AED) is an effective system for recovering biogas from organic wastes. However, the effects of different anode potentials on anaerobic activated sludge remain unclear. This study confirmed that biofilms exhibited the best electroactivity at -0.2 V (vs. Ag/AgCl) compared to -0.4 V and 0 V. Gas was further regulated, with the highest hydrogen content (47 ± 7 %) observed at -0.2 V. The 0 V system produced the largest amount of methane (70 ± 8 %) and exhibited the greatest presence of hydrogen-utilizing microorganisms. The gas yield at -0.4 V was the lowest, with no hydrogen detected. Excess bioelectrohydrogen at -0.2 V and 0 V caused the co-enrichment of Methanobacterium and Acetoanaerobium, establishing a thermodynamically feasible current-acetate-hydrogen electron cycle to improve electrogenesis. These results provide insights into the regulatory strategies of MEC technology during anaerobic digestion, which play a decisive role in determining the composition of biogas., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Purpose of Review: The existence of urinary microbiome in healthy individuals is now widely accepted as the longstanding belief in urinary tract sterility was disproved over a decade ago. The urinary microbiome has since been implicated in multiple urologic conditions including urinary tract infection (UTI), urinary incontinence, and bladder cancer. This review relays new findings of urinary microbiome compositional changes associated with aging and UTI susceptibility., Recent Findings: Recent advancements have established how the urinary microbiome changes over the lifespan. Studies finding distinct urinary microbiomes in prepubescent, reproductive age, and postmenopausal females have identified sex hormones as potential modulators of urinary microbiome composition and have identified prevalent species that may be markers of dysbiosis. Research in male children finds a cultivable urinary microbiota that varies with age or urologic history but not delivery mode. Emerging research also addresses the function of the urinary microbiota, including genetic factors associated with urinary tract colonization and interactions with uropathogens., Summary: The urinary microbiome is a promising therapeutic target for urologic disease. However, a more functional understanding is necessary for the development of microbiome-based therapies. Future research should develop accurate animal models and explore functional relationships between the urinary microbiome and the host environment., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Many genitourinary tract disorders could be attributed partly to the microbiota. This study sought to conduct a systematic review of the role of the microbiota in urinary chronic pelvic pain syndrome (UCPPS)., Methods: We searched Embase, Scopus, Web of Science, and PubMed with no time, language, or study type restrictions until December 1, 2023. The JBI Appraisal Tool was used to assess the quality of the studies. Study selection followed the PRISMA statement. Studies addressing microbiome variations among patients suffering from interstitial cystitis/bladder pain syndrome (IC/BPS) or chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and a control group were considered eligible., Results: A total of 21 studies (1 UCPPS, 12 IC/BPS, and 8 CP/CPPS) comprising 1125 patients were enrolled in our final data synthesis. It has been shown that the reduced diversity and discrepant composition of the gut microbiota may partly be attributed to the UCPPS pathogenesis. In terms of urine microbiota, some operational taxonomic units were shown to be elevated, while others became less abundant. Furthermore, various bacteria and fungi are linked to specific clinical features. Few investigations denied UCPPS as a dysbiotic condition., Conclusions: Urinary and intestinal microbiota appear to be linked with UCPPS, comprising IC/BPS and CP/CPPS. However, given the substantial disparity of published studies, a battery of prospective trials is required to corroborate these findings., (© 2024 Wiley Periodicals LLC.)

Hadal trenches represent the deepest oceanic realm and were once considered to be deprived of life. However, trenches act as important depocenters for organic matter with highly elevated microbial activity. In this forum, we discuss the biogeochemistry of the hadal realm and its microbial communities thriving at extreme hydrostatic pressure., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Anaerobic digestion (AD) has been proven to be an effective green technology for producing biomethane while reducing environmental pollution. The interspecies electron transfer (IET) processes in AD are critical for acetogenesis and methanogenesis, and these IET processes are carried out via mediated interspecies electron transfer (MIET) and direct interspecies electron transfer (DIET). The latter has recently become a topic of significant interest, considering its potential to allow diffusion-free electron transfer during the AD process steps. To date, different multi-heme c-type cytochromes, electrically conductive pili (e-pili), and other relevant accessories during DIET between microorganisms of different natures have been reported. Additionally, several studies have been carried out on metagenomics and metatranscriptomics for better detection of DIET, the role of DIET's stimulation in alleviating stressed conditions, such as high organic loading rates (OLR) and low pH, and the stimulation mechanisms of DIET in mixed cultures and co-cultures by various conductive materials. Keeping in view this significant research progress, this study provides in-depth insights into the DIET-active microbial community, DIET mechanisms of different species, utilization of various approaches for stimulating DIET, characterization approaches for effectively detecting DIET, and potential future research directions. This study can help accelerate the field's research progress, enable a better understanding of DIET in complex microbial communities, and allow its utilization to alleviate various inhibitions in complex AD processes., Competing Interests: Declaration of Competing Interest The authors certify that they have no affiliations with or involvement in any organization or entity with any financial interest (such as honoraria; educational grants; participation in speakers' bureaus; membership, employment, consultancies, stock ownership, or other equity interest; and expert testimony or patent-licensing arrangements), or non-financial interest (such as personal or professional relationships, affiliations, knowledge or beliefs) in the subject matter or materials discussed in this manuscript., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Immune checkpoint blockade (ICB) is one of the leading immunotherapies, although a variable extent of resistance has been observed among patients and across cancer types. Among the efforts underway to overcome this challenge, the microbiome has emerged as a factor affecting the responsiveness and efficacy of ICB. Active research, facilitated by advances in sequencing techniques, is assessing the predominant influence of the intestinal microbiome, as well as the effects of the presence of an intratumoral microbiome. In this review, we describe recent findings from clinical trials, observational studies of human patients, and animal studies on the impact of the microbiome on the efficacy of ICB, highlighting the role of the intestinal and tumor microbiomes and the contribution of methodological advances in their study., Competing Interests: Declaration of interests The authors declare that they have no conflicts of interest., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Artificial regulation of plant rhizosphere microbial communities through the synthesis of microbial communities is one of the effective ways to improve plant stress resistance. However, the process of synthesizing stress resistant microbial communities with excellent performance is complex, time-consuming, and costly. To address this issue, we proposed a novel strategy for preparing functional microbial communities. We isolated a cultivable cold tolerant bacterial community (PRCBC) from the rhizosphere of peas, and studied its effectiveness in assisting rice to resist stress. The results indicate that PRCBC can not only improve the ability of rice to resist cold stress, but also promote the increase of rice yield after cold stress relieved. This is partly because PRCBC increases the nitrogen content in the rhizosphere soil, and promotes rice's absorption of nitrogen elements, thereby promoting rice growth and enhancing its ability to resist osmotic stress. More importantly, the application of PRCBC drives the succession of rice rhizosphere microbial communities, and promotes the succession of rice rhizosphere microbial communities towards stress resistance. Surprisingly, PRCBC drives the succession of rice rhizosphere microbial communities towards a composition similar to PRCBC. This provides a feasible novel method for artificially and directionally driving microbial succession. In summary, we not only proposed a novel and efficient strategy for preparing stress resistant microbial communities to promote plant stress resistance, but also unexpectedly discovered a possible directionally driving method for soil microbial community succession., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant-rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Microbiota affects carcinogenesis by altering energy equilibrium, increasing fat mass, synthesizing small signaling molecules, and formulating and regulating immune response and indigestible food ingredient, xenobiotic, and pharmaceutical compound metabolism. The intestinal microbiome can moderate oestrogen and other steroid hormone metabolisms, and secrete bioactive metabolites that are important for tumour microenvironment. Specifically, the breast tissue microbiome could become altered and lead to breast cancer development. The study of oestrobolome, the microbiomic component that metabolizes oestrogens, can contribute to better breast cancer understanding and subsequent treatment. Investigating oestrobolome-related oestrogen metabolism mechanisms in immune system regulation can shed light on how intestinal microorganisms regulate tumour microenvironment. Intestinal and regional breast microbiomes can determine treatment lines and serve as possible biomarkers for breast cancer. The aim of this study is to summarise current evidence on the role of microbiome in breast cancer progression with particular interest in therapeutic and diagnostic implementation., Competing Interests: Declaration of competing interestI The authors declare no conflicts of interest with regard to this manuscript., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Crop diversification practices offer numerous synergistic benefits. So far, research has traditionally been confined to exploring isolated, unidirectional single-process interactions among plants, soil, and microorganisms. Here, we present a novel and systematic perspective, unveiling the intricate web of plant-soil-microbiome interactions that trigger cascading effects. Applying the principles of cascading interactions can be an alternative way to overcome soil obstacles such as soil compaction and soil pathogen pressure. Finally, we introduce a research framework comprising the design of diversified cropping systems by including commercial varieties and crops with resource-efficient traits, the exploration of cascading effects, and the innovation of field management. We propose that this provides theoretical and methodological insights that can reveal new mechanisms by which crop diversity increases productivity., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Ignoring the dynamic nature of microbial communities risks underestimating the power of microbes to impact the health of their hosts. Microbiomes are thought to be important for host fitness, yet the coarse temporal scale and population-level focus of many studies precludes the ability to investigate the importance of among-individual variation in stability and identify the ecological contexts in which this variation matters. Here we briefly summarise current knowledge of temporal dynamics in wild host-associated microbial communities. We then discuss the implications of among-individual variation in microbiota stability and suggest analytical approaches for understanding these patterns. One major requirement is for future studies to conduct individual-level longitudinal analyses, with some systems already well set up for answering these questions., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The regulation of legume-rhizobia symbiosis by microorganisms has obtained considerable interest in recent research, particularly in the common rhizobacteria Bacillus. However, few studies have provided detailed explanations regarding the regulatory mechanisms involved. Here, we investigated the effects of Bacillus (Bac.B) on Bradyrhizobium-soybean (Glycine max) symbiosis and elucidated the underlying ecological mechanisms. We found that two Bradyrhizobium strains (i.e. Bra.Q2 and Bra.D) isolated from nodules significantly promoted nitrogen (N) efficiency of soybean via facilitating nodule formation, thereby enhanced plant growth and yield. However, the intrusion of Bac.B caused a reverse shift in the synergistic efficiency of N 2 fixation in the soybean-Bradyrhizobium symbiosis. Biofilm formation and naringenin may be importantin suppression of Bra.Q2 growth regulated by Bac.B. In addition, transcriptome and microbiome analyses revealed that Bra.Q2 and Bac.B might interact to regulateN transport and assimilation, thus influence the bacterial composition related to plant N nutrition in nodules. Also, the metabolisms of secondary metabolites and hormones associated with plant-microbe interaction and growth regulation were modulated by Bra.Q2 and Bac.B coinoculation. Collectively, we demonstrate that Bacillus negatively affects Bradyrhizobium-soybean symbiosis and modulate microbial interactions in the nodule. Our findings highlight a novel Bacillus-based regulation to improve N efficiency and sustainable agricultural development., (© 2024 John Wiley & Sons Ltd.)

Specialized host-microbe symbioses are ecological communities, whose composition is shaped by various processes. Microbial community assembly in these symbioses is determined in part by interactions between taxa that colonize ecological niches available within habitat patches. The outcomes of these interactions, and by extension the trajectory of community assembly, can display priority effects-dependency on the order in which taxa first occupy these niches. The underlying mechanisms of these phenomena vary from system to system and are often not well resolved. Here, we characterize priority effects in colonization of the squash bug ( Anasa tristis ) by bacterial symbionts from the genus Caballeronia , using pairs of strains that are known to strongly compete during host colonization, as well as strains that are isogenic and thus functionally identical. By introducing symbiont strains into individual bugs in a sequential manner, we show that within-host populations established by the first colonist are extremely resistant to invasion, regardless of strain identity and competitive interactions. By knocking down the population of an initial colonist with antibiotics, we further show that colonization success by the second symbiont is still diminished even when space in the symbiotic organ is available and ostensibly accessible for colonization. We speculate that resident symbionts exclude subsequent infections by manipulating the host environment, partially but not exclusively by eliciting tissue remodeling of the symbiont organ., Importance: Host-associated microbial communities underpin critical ecosystem processes and human health, and their ability to do so is determined in turn by the various processes that shape their composition. While selection deterministically acts on competing genotypes and species during community assembly, the manner by which selection determines the trajectory of community assembly can differ depending on the sequence by which taxa are established within that community. We document this phenomenon, known as a priority effect, during experimental colonization of a North American insect pest, the squash bug Anasa tristis , by its betaproteobacterial symbionts in the genus Caballeronia. Our study demonstrates how stark, strain-level variation can emerge in specialized host-microbe symbioses simply through differences in the order by which strains colonize the host. Understanding the mechanistic drivers of community structure in host-associated microbiomes can highlight both pitfalls and opportunities for the engineering of these communities and their constituent taxa for societal benefit., Competing Interests: The authors declare no conflict of interest.

The efficiency of microbial fuel cells (MFCs) in industrial wastewater treatment is profoundly influenced by the microbial community, which can be disrupted by variable industrial operations. Although microbial guilds linked to MFC performance under specific conditions have been identified, comprehensive knowledge of the convergent community structure and pathways of adaptation is lacking. Here, we developed a microbe-microbe interaction genome-scale metabolic model (mmGEM) based on metabolic cross-feeding to study the adaptation of microbial communities in MFCs treating sulfide-containing wastewater from a canned-pineapple factory. The metabolic model encompassed three major microbial guilds: sulfate-reducing bacteria (SRB), methanogens (MET), and sulfide-oxidizing bacteria (SOB). Our findings revealed a shift from an SOB-dominant to MET-dominant community as organic loading rates (OLRs) increased, along with a decline in MFC performance. The mmGEM accurately predicted microbial relative abundance at low OLRs (L-OLRs) and adaptation to high OLRs (H-OLRs). The simulations revealed constraints on SOB growth under H-OLRs due to reduced sulfate-sulfide (S) cycling and acetate cross-feeding with SRB. More cross-fed metabolites from SRB were diverted to MET, facilitating their competitive dominance. Assessing cross-feeding dynamics under varying OLRs enabled the execution of practical scenario-based simulations to explore the potential impact of elevated acidity levels on SOB growth and MFC performance. This work highlights the role of metabolic cross-feeding in shaping microbial community structure in response to high OLRs. The insights gained will inform the development of effective strategies for implementing MFC technology in real-world industrial environments., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Srinak et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Modic changes (MCs), vertebral end plate and bone marrow damage observed by magnetic resonance imaging, are an independent risk factor for low back pain. The compositions of and interaction between microbiota and metabolites in the lumbar cartilaginous end plates (LCEPs) of patients with MCs have not been identified., Methods: Patients with lumbar disc degeneration who were undergoing lumbar spinal fusion surgery were recruited between April 2020 and April 2021. LCEPs were collected for 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC/MS)-based targeted metabolomic profiling. Of the 54 patients recruited, 24 had no MCs and 30 had changes classified as Modic type 2 or 3. The primary goal was to identify specific genera of microbiota associated with MCs, and secondary goals included investigating differences in metabolites between patients with and without MCs and exploring the correlation between these metabolites and microorganisms., Results: Investigation of the microbiota community structure revealed that both alpha diversity and beta diversity were significantly different between patients with and without MCs, and the abundances of 26 genera were significantly different between these 2 groups. Metabolomic analysis revealed that 26 metabolites were significantly different between the 2 groups. The unsaturated fatty acid pathway was found to be the main pathway related to MCs. Multiomic correlation analysis suggested that Caulobacteraceae (unclassified) and Mycobacterium, Clostridium, Blautia, and Bifidobacterium at the genus level were linked to dysregulation of fatty acid metabolism, contributing to the pathogenesis of MCs., Conclusions: Our study represents a foundational effort to examine the landscape of the microbiota and metabolites in patients with MCs, informing future studies on the pathogenesis of and targeted therapy for MCs., Level of Evidence: Prognostic Level II . See Instructions for Authors for a complete description of levels of evidence., Competing Interests: Disclosure: Funding for this study was provided by the following grants: The Yunnan Province Ten Thousand People Plan Young Talent Program (YNWR-QNBJ-2019-184), The Yunnan Provincial Science and Technology Department/Kunming Medical University Joint Project of Basic Research (202301AY070001-080), The Reserve Talents for Academic and Technical Leaders of Middle-aged and Young People in Yunnan Province (202305AC160069), The Kunming University of Science and Technology School of Medicine Postgraduate Innovation Fund, and The Kunming University of Science and Technology Postgraduate Talent Program (CA22369M099A). Additional support was provided by the Yunnan Provincial Key Laboratory of Digital Orthopedics (202005AG070004), Yunnan Provincial Digital Orthopedics Innovation Team (202105AE160015), and Yunnan Provincial Spinal Cord Disease Clinical Medical Centre (ZX2022000101). The Disclosure of Potential Conflicts of Interest forms are provided with the online version of the article ( http://links.lww.com/JBJS/I102 )., (Copyright © 2024 The Authors. Published by The Journal of Bone and Joint Surgery, Incorporated.)

Background: The planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem., Methods: High-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora , mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray-Curtis metrics) was used to identify key soil factors driving bacterial community structure., Results: S. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO 3 - -N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata , were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors., Conclusions: Ecological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community., Competing Interests: The authors declare that they have no competing interests., (© 2024 Wang et al.)

Sea cucumbers are predominant deposit feeders in benthic ecosystems, providing protective benefits to coral reefs by reducing disease prevalence. However, how they receive sufficient nutrition from seabed sediments remains poorly understood. Here, we investigate Holothuria leucospilota, an ecologically significant tropical sea cucumber, to elucidate digestive mechanisms underlying marine deposit-feeding. Genomic analysis reveals intriguing evolutionary adaptation characterized by an expansion of digestive carbohydrase genes and a contraction of digestive protease genes, suggesting specialization in digesting microalgae. Developmentally, two pivotal dietary shifts, namely, from endogenous nutrition to planktonic feeding, and from planktonic feeding to deposit feeding, induce changes in digestive tract enzyme profiles, with adults mainly expressing carbohydrases and lipases. A nuanced symbiotic relationship exists between gut microbiota and the host, namely, specific resident bacteria supply crucial enzymes for food digestion, while other bacteria are digested and provide assimilable nutrients. Our study further identifies Holothuroidea lineage-specific lysozymes that are restrictedly expressed in the intestines to support bacterial digestion. Overall, this work advances our knowledge of the evolutionary innovations in the sea cucumber digestive system which enable them to efficiently utilize nutrients from seabed sediments and promote food recycling within marine ecosystems., (© 2024. The Author(s).)

Background: Nematodes are the most abundant metazoans in marine sediments, many of which are bacterivores; however, how habitat bacteria affect physiological outcomes in marine nematodes remains largely unknown.  RESULTS: Here, we used a Litoditis marina inbred line to assess how native bacteria modulate host nematode physiology. We characterized seasonal dynamic bacterial compositions in L. marina habitats and examined the impacts of 448 habitat bacteria isolates on L. marina development, then focused on HQbiome with 73 native bacteria, of which we generated 72 whole genomes sequences. Unexpectedly, we found that the effects of marine native bacteria on the development of L. marina and its terrestrial relative Caenorhabditis elegans were significantly positively correlated. Next, we reconstructed bacterial metabolic networks and identified several bacterial metabolic pathways positively correlated with L. marina development (e.g., ubiquinol and heme b biosynthesis), while pyridoxal 5'-phosphate biosynthesis pathway was negatively associated. Through single metabolite supplementation, we verified CoQ 10 , heme b, acetyl-CoA, and acetaldehyde promoted L. marina development, while vitamin B6 attenuated growth. Notably, we found that only four development correlated metabolic pathways were shared between L. marina and C. elegans. Furthermore, we identified two bacterial metabolic pathways correlated with L. marina lifespan, while a distinct one in C. elegans. Strikingly, we found that glycerol supplementation significantly extended L. marina but not C. elegans longevity. Moreover, we comparatively demonstrated the distinct gut microbiota characteristics and their effects on L. marina and C. elegans physiology., Conclusions: Given that both bacteria and marine nematodes are dominant taxa in sedimentary ecosystems, the resource presented here will provide novel insights to identify mechanisms underpinning how habitat bacteria affect nematode biology in a more natural context. Our integrative approach will provide a microbe-nematodes framework for microbiome mediated effects on host animal fitness., (© 2024. The Author(s).)

The global burden of mosquito-transmitted diseases, including malaria, dengue, West Nile, Zika, Usutu, and yellow fever, continues to increase, posing a significant public health threat. With the rise of insecticide resistance and the absence of effective vaccines, new strategies are emerging that focus on the mosquito's microbiota. Nevertheless, the majority of symbionts remain resistant to cultivation. Characterizing the diversity and function of bacterial genomes in mosquito specimens, therefore, relies on metagenomics and subsequent assembly and binning strategies. The obtention and analysis of Metagenome-Assembled Genomes (MAGs) from separated organs can notably provide key information about the specific role of mosquito-associated microbes in the ovaries (the reproductive organs), the midgut (key for food digestion and immunity), or the salivary glands (essential for the transmission of vector-borne diseases as pathogens must colonize them to enter the saliva and reach the bloodstream during a blood meal). These newly reconstructed genomes can then pave the way for the development of novel vector biocontrol strategies. To this aim, it is required to isolate mosquito organs while avoiding cross-contamination between them or with microorganisms present in other mosquito organs. Here, we describe an optimized and contamination-free dissection protocol for studying mosquito microbiome at the organ level.

In macroscale ecosystems, such as rainforests or coral reefs, the spatial localization of organisms is the basis of our understanding of community ecology. In the microbial world, likewise, microscale ecosystems are far from a random and homogeneous mixture of organisms and habitats. Accessing the spatial distribution of microbes is fundamental for understanding the functioning and ecology of the microbiota, as cohabiting species are more likely to interact and influence each other's physiology. An interkingdom microbial ecosystem is at the core of fungus-growing ant colonies, which cultivate basidiomycete fungi as a nutritional resource. Attine ants forage for diverse substrates (mostly plant-based), metabolized by the cultivated fungus while forming a spongy structure, a "microbial garden" that acts as an external gut. The garden is an intertwined mesh of fungal hyphae growing by metabolizing the substrate, opening niches for a characteristic and adapted microbiota to establish. The microbiota is thought to be a contributor to substrate degradation and fungal growth, though its spatial organization is yet to be determined. Here, we describe how we employ Scanning Electron Microscopy (SEM) to investigate, with unprecedented detail, the microbiota and biofilm spatial organization across different fungiculture systems of fungus-growing ants. SEM imaging has provided a description of the microbiota spatial structure and organization. SEM revealed that microbiota commonly assemble in biofilms, a widespread structure of the microbial landscapes in fungiculture. We present the protocols employed to fix, dehydrate, dry, sputter coating, and image such a complex community. These protocols were optimized to deal with delicate and heterogeneous samples, comprising plant and fungal biomass, as well as the microbiota and the biofilm.

Psoriasis is a common chronic inflammatory skin disease, associated with significant morbidity and a considerable negative impact on the patients' quality of life. The complex pathogenesis of psoriasis is still incompletely understood. Genetic predisposition, environmental factors like smoking, alcohol consumption, psychological stress, consumption of certain drugs, and mechanical trauma, as well as specific immune dysfunctions, contribute to the onset of the disease. Mounting evidence indicate that skin dysbiosis plays a significant role in the development and exacerbation of psoriasis through loss of immune tolerance to commensal skin flora, an altered balance between Tregs and effector cells, and an excessive Th1 and Th17 polarization. While the implications of skin dysbiosis in psoriasis pathogenesis are only starting to be revealed, the progress in the characterization of the skin microbiome changes in psoriasis patients has opened a whole new avenue of research focusing on the modulation of the skin microbiome as an adjuvant treatment for psoriasis and as part of a long-term plan to prevent disease flares. The skin microbiome may also represent a valuable predictive marker of treatment response and may aid in the selection of the optimal personalized treatment. We present the current knowledge on the skin microbiome changes in psoriasis and the results of the studies that investigated the efficacy of the different skin microbiome modulation strategies in the management of psoriasis, and discuss the complex interaction between the host and skin commensal flora.

Understanding the molecular mechanisms governing microbial interactions is crucial for unraveling the complexities of microbial communities and their ecological impacts. Here, we employed a two-species model system comprising the oral bacteria Aggregatibacter actinomycetemcomitans and Streptococcus gordonii to investigate how synergistic and antagonistic interactions between microbes impact their resilience to environmental change and invasion by other microbes. We used an in vitro colony biofilm model and focused on two S . gordonii -produced extracellular molecules, L-lactate and H 2 O 2 , which are known to impact fitness of this dual-species community. While the ability of A. actinomycetemcomitans to cross-feed on S. gordonii -produced L-lactate enhanced its fitness during co-culture, this function showed little impact on the ability of co-cultures to resist environmental change. In fact, the ability of A. actinomycetemcomitans to catabolize L-lactate may be detrimental in the presence of tetracycline, highlighting the complexity of interactions under antimicrobial stress. Furthermore, H 2 O 2 , known for its antimicrobial properties, had negative impacts on both species in our model system. However, H 2 O 2 production by S. gordonii enhanced A. actinomycetemcomitans tolerance to tetracycline, suggesting a protective role under antibiotic pressure. Finally, S. gordonii significantly inhibited the bacterium Serratia marcescens from invading in vitro biofilms, but this inhibition was lost during co-culture with A. actinomycetemcomitans and in a murine abscess model, where S. gordonii actually promoted S. marcescens invasion. These data indicate that microbial interactions can impact fitness of a bacterial community upon exposure to stresses, but these impacts are highly environment dependent., Importance: Microbial interactions are critical modulators of the emergence of microbial communities and their functions. However, how these interactions impact the fitness of microbes in established communities upon exposure to environmental stresses is poorly understood. Here, we utilized a two-species community consisting of Aggregatibacter actinomycetemcomitans and Streptococcus gordonii to examine the impact of synergistic and antagonistic interactions on microbial resilience to environmental fluctuations and susceptibility to microbial invasion. We focused on the S. gordonii -produced extracellular molecules, L-lactate and H 2 O 2 , which have been shown to mediate interactions between these two microbes. We discovered that seemingly beneficial functions, such as A. actinomycetemcomitans cross-feeding on S. gordonii -produced L-Lactate, can paradoxically exacerbate vulnerabilities, such as susceptibility to antibiotics. Moreover, our data highlight the context-dependent nature of microbial interactions, emphasizing that a seemingly potent antimicrobial, such as H 2 O 2 , can have both synergistic and antagonistic effects on a microbial community dependent on the environment., Competing Interests: The authors declare no conflict of interest.

Microorganisms are vital for the health of marine invertebrates, and their assembly is driven by both deterministic and stochastic factors that regulate residents (innate to the host) and transients (from ambient water). However, the role of water microbiota and the significance of deterministic and stochastic processes in aquatic hosts facing mortality threats are largely unknown. This study examines the shifts in water microbiota during an oyster mortality event using amplicon sequencing and compared with those of resident oysters to disentangle the balance of the deterministic and stochastic factors involved. Water temperature and dissolved oxygen significantly shape the microbial community with a distinct monthly pattern, and Cyanobacteria blooms might exacerbate oyster mortality. The comparative analysis of microbial communities in oysters and water revealed that ≤ 21% of the genera were shared between oysters and water, implying that water microbiota cannot easily transfer into oysters. Furthermore, these shared genera had different functions, with oysters more involved in promoting host digestion and nutrient acquisition and water bacteria enriched more in functions promoting their own growth and survival. These findings illustrate that oysters may possess specific selection or barrier mechanisms that permit a small percentage of transients, controlled by stochastic factors and having a minimal effect on oyster mortality, to enter, whereas the majority of oyster microbiota are residents governed by deterministic factors. Consequently, oysters exhibit some plasticity in their symbiotic microbiota, enabling them to maintain microbial homeostasis and adapt to complex microbial surroundings. This may be a shared mechanism among marine invertebrates for survival in complex marine environments.IMPORTANCEPacific oysters are widely cultured and play vital ecological roles. However, the summer mortality hinders sustainable oyster farming. Untangling causative mechanisms of oyster mortality is a complex task due to the intricate "interactome" involving environmental factors, hosts, and pathogens. Interactions between hosts and microorganisms offer an ideal avenue for investigating the truth. We systematically investigated the microbial community in water and resident oysters during a summer mortality event and proposed that the assembly of oyster microbiota is primarily governed by deterministic processes independent of mortality. Pathogens mainly originate from resident members of the oyster microbiota, with a limited influence from the microbial community in the water. Additionally, environmental degraders, such as Cyanobacteria blooms, cannot be overlooked as a contributing factor of oyster mortality. This study evaluated the weight of deterministic and stochastic factors in microbial assembly during an oyster mortality event and greatly broadened our understanding of the "interactome" through the interaction between oysters and water in microbiota., Competing Interests: The authors declare no conflict of interest.

The widespread prevalence of saline environments poses a significant global environmental challenge. Salt stress, induced by saline soils, disrupts soil microecology and affects the plant-microbe-soil cycling process. Utilizing microbial fungicides stands as a primary strategy to mitigate salt stress-induced damage to plants and soils. This study investigated the influence of Bacillus subtilis (Bs) inoculation on the microbial community, assembly processes, and functional changes in bacteria and fungi in Glycyrrhiza uralensis Fisch. (licorice) seedlings under varying salt stress levels, primarily employing microbiomics techniques. Soil enzyme activities displayed a declining trend with increasing salt stress, which was mitigated by Bs inoculation. Microbiome analysis revealed a significant increase in bacterial and fungal operational taxonomic units, particularly in Ascomycetes and Nitrogen-fixing Bacteria, thereby enhancing soil denitrification. The abundance of Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes in bacteria, as well as Ascomycota in fungi, increased with higher salt stress levels, a process facilitated by Bs inoculation. However, functional predictions indicated a reduction in the relative abundance of Dung Saprotrophs with Bs inoculation. Salt stress disrupted soil assembly processes, showcasing a continuous decline in diffusion limitation with increased salt concentration, where Bs inoculation reached a peak under moderate stress. In summary, this research elucidates the communication mechanism of Bs in enhancing salt tolerance in licorice from a microbiome perspective, contributing to a comprehensive understanding of abiotic and biotic factors.IMPORTANCELicorice is a herb that grows in deserts or saline soils. Enhancing the salt tolerance of licorice is necessary to maintain the quality of cultivated licorice and to ensure the supply of medicinal herbs. In the past, we have demonstrated the effectiveness of inoculation with Bacillus subtilis (Bs) to enhance the salt tolerance of licorice and revealed the key metabolic pathways for the development of salt tolerance through multi-omics. In this study, we used the microbiomics approach to reveal the plant-microbe-soil interactions at the level of inoculation of Bs affecting the dynamics of soil microbial communities from bacterial and fungal perspectives, thus bridging the interactions between biotic and abiotic factors., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Parkinson's disease (PD) is a common neurodegenerative disease with complex pathogenesis and no effective treatment. Recent studies have shown that dysbiosis of the oral microflora is closely related to the development of PD. The abnormally distributed oral microflora of PD patients cause degenerative damage and necrosis of dopamine neurons by releasing their own components and metabolites, intervening in the oral-gut-brain axis, crossing the biofilm, inducing iron dysregulation, activating inter-microflora interactions, and through the mediation of saliva,ultimately influencing the development of the disease. This article reviews the structure of oral microflora in patients with PD, the mechanism of development of PD caused by oral microflora, and the potential value of targeting oral microflora in developing a new strategy for PD prevention, diagnosis and treatment., Competing Interests: Declaration of Competing Interest The authors declare that they have no competing interests., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The deleterious effects of human activities on biodiversity in the vegetal and animal world, and on climate changes are now well-established facts. However, little is yet known on the impact of human activities on microbial diversity on the planet and more specifically on the human microbiota Large implementation of metagenomics allows exaustive microbial cataloguing with broad spatio-temporal resolution of human microbiota. A reduction in bacterial richness and diversity in the human microbiota, particularly in the intestinal tract, is now established and particularly obvious in the most industrialized regions of the planet. Massive, uncontrolled use of antibiotics, drastic changes in traditional food habits and some elements of the "global exposome" that remain to identify are usually considered as stressors accounting for this situation of "missing microbes". As a consequence, a dysbiotic situation develops, a "dysbiosis" being characterized by the erosion of the central core of shared bacterial species across individuals and the development of opportunistic "pathobionts" in response to a weaker barrier capacity of these impoverished microbiota. The current challenge is to establish a causality link between the extension of these dysbiotic situations and the steady emergence of epidemic, non-communicable diseases such as asthma, allergy, obesity, diabetes, autoimmune diseases and some cancers. Experimental animal models combined with controlled, prospective clinical interventions are in demand to consolidate causality links, with the understanding that in the deciphering of the mechanisms of alteration of the human-microbiome symbiosis resides a novel exciting chapter of medicine: "microbial medicine"., (© 2024 médecine/sciences – Inserm.)

The lung microbiome plays a crucial role in the development of chronic lung diseases, which may ultimately lead to the need for lung transplantation. Also, perioperative results seem to be connected with altered lung microbiomes and its dynamic changes providing a possible target for optimizing short-term outcome after transplantation. A literature review using MEDLINE, PubMed Central and Bookshelf was performed. Chronic lung allograft dysfunction (CLAD) seems to be influenced and partly triggered by changes in the pulmonary microbiome and dysbiosis, e.g. through increased bacterial load or abundance of specific species such as Pseudomonas aeruginosa. Additionally, the specific indications for transplantation, with their very heterogeneous changes and influences on the pulmonary microbiome, influence long-term outcome. Next to composition and measurable bacterial load, dynamic changes in the allografts microbiome also possess the ability to alter long-term outcomes negatively. This review discusses the "new" microbiome after transplantation and the associations with direct postoperative outcome. With the knowledge of these principles the impact of alterations in the pulmonary microbiome in hindsight to CLAD and possible therapeutic implications are described and discussed. The aim of this review is to summarize the current literature regarding pre- and postoperative lung microbiomes and how they influence different lung diseases on their progression to failure of conservative treatment. This review provides a summary of current literature for centres looking for further options in optimizing lung transplant outcomes and highlights possible areas for further research activities investigating the pulmonary microbiome in connection to transplantation., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery.)

This review highlights the significance of interactions between the microbiota, immune system, nervous and hormonal systems, and the brain on periodontal health and disease. Microorganisms in the microbiota, immune cells, and neurons communicate via homeostatic nervous and hormonal systems, regulating vital body functions. By modulating pro-inflammatory and anti-inflammatory adaptive immune responses, these systems control the composition and number of microorganisms in the microbiota. The strength of these brain-controlled responses is genetically determined but is sensitive to early childhood stressors, which can permanently alter their responsiveness via epigenetic mechanisms, and to adult stressors, causing temporary changes. Clinical evidence and research with humans and animal models indicate that factors linked to severe periodontitis enhance the responsiveness of these homeostatic systems, leading to persistent hyperactivation. This weakens the immune defense against invasive symbiotic microorganisms (pathobionts) while strengthening the defense against non-invasive symbionts at the gingival margin. The result is an increased gingival tissue load of pathobionts, including Gram-negative bacteria, followed by an excessive innate immune response, which prevents infection but simultaneously destroys gingival and periodontal tissues. Thus, the balance between pro-inflammatory and anti-inflammatory adaptive immunity is crucial in controlling the microbiota, and the responsiveness of brain-controlled homeostatic systems determines periodontal health., (© 2024 The Author(s). Periodontology 2000 published by John Wiley & Sons Ltd.)

Amyotrophic lateral sclerosis is a neurodegenerative disorder. Despite extensive studies, it remains challenging to treat ALS. Recent ALS studies have shown dysbiosis (e.g., loss of microbial diversity and beneficial function in the gut microbiota) is correlated with intestinal inflammation and change of intestinal integrity in ALS. The novel concepts and the roles of microbiome and microbial metabolites through the gut-microbiome-neuron axis in ALS pathogenesis have been slowly recognized by the neurology research field. Here, we will discuss the recent progress of microbiome, including bacteria, fungi, and viruses, in the ALS research. We will discuss our understanding of microbial metabolites in ALS. Micronutrition refers to the intake of essential vitamins, minerals, and other micronutrients. We will summarize the literation related to micronutrition and ALS. Furthermore, we will consider the mutual interactions of microbiome and micronutrition in the ALS progression and treatment. We further propose that the mechanistic and translational studies that shift from suspension of disbelief to cogent ingenuity, and from bench study to bed-side application, should allow new strategies of diagnosis and treatment for ALS., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Jun Sun reports financial support was provided by National Institutes of Health. Jun Sun reports financial support was provided by US Department of Veterans Affairs. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Inc.)

The prevailing consensus in scientific literature underscores the mutualistic bond between the microbiota and the human host, suggesting a finely tuned coevolutionary partnership that enhances the fitness of both parties. This symbiotic relationship has been extensively studied, with certain bacterial attributes being construed as hallmarks of natural selection favoring the benefit of the human host. Some scholars go as far as equating the intricate interplay between humans and their intestinal microbiota to that of endosymbiotic relationships, even conceptualizing microbiota as an integral human organ. However, amidst the prevailing narrative of bacterial species being categorized as beneficial or detrimental to human health, a critical oversight often emerges - the inherent functional diversity within bacterial strains. Such reductionist perspectives risk oversimplifying the complex dynamics at play within the microbiome. Recent genomic analysis at the strain level is highly limited, which is surprising given that strain information provides critical data about selective pressures in the intestine. These pressures appear to focus more on the well-being of bacteria rather than human health. Connected to this is the extent to which animals depend on metabolic activity from intestinal bacteria, which varies widely across species. While omnivores like humans exhibit lower dependency, certain herbivores rely entirely on bacterial activity and have developed specialized compartments to house these bacteria., Competing Interests: Declaration of competing interest The authors declared not to have any financial or personal relationships that could inappropriately influence this work., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Drought significantly affects crop productivity and poses a considerable threat to agricultural ecosystems. Plant growth-promoting bacteria (PGPB) and plant microbiome play important roles in improving drought resistance and plant performance. However, the response of the rhizosphere microbiota to PGPB during the development of plants and the interaction between inoculum, microbiota, and plants under drought stress remain to be explored. In the present study, we used culturomic, microbiomic, and metabonomic analyses to uncover the mechanisms by which Sphingomonas sp. Hbc-6, a PGPB, promotes Arabidopsis growth and enhances drought resistance. We found that the rhizosphere microbiome assembly was interactively influenced by developmental stage, Hbc-6, and drought; the bacterial composition exhibited three patterns of shifts with developmental stage: resilience, increase, and decrease. Drought diminished microbial diversity and richness, whereas Hbc-6 increased microbial diversity and helped plants recruit specific beneficial bacterial taxa at each developmental stage, particularly during the bolting stage. Some microorganisms enriched by Hbc-6 had the potential to promote carbon and nitrogen cycling processes, and 86.79 % of the isolated strains exhibited PGP characteristics (for example Pseudomonas sp. TA9). They jointly regulated plant physiological metabolism (i.e., upregulated drought resistant-facilitating substances and reduced harmful substances), thereby stimulating the growth of Arabidopsis and increasing plant biomass under drought stress conditions. Collectively, these results indicate that Hbc-6 mediates plant growth and drought resistance by affecting the microbiome. The study thus provides novel insights and strain resources for drought-resistant, high-yielding crop cultivation and breeding., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Background: Recently, associations between recurrent urinary tract infections (UTI) and the urinary microbiome (urobiome) composition have been identified in adults. However, little is known about the urobiome in children. We aimed to characterize the urobiome of children with species-level resolution and to identify associations based on UTI history., Study Design: Fifty-four children (31 females and 21 males) from 3 months to 11 years of age participated in the study. Catheterized urine specimens were obtained from children undergoing a clinically indicated voiding cystourethrogram. To improve the analysis of the pediatric urobiome, we used a novel protocol using filters to collect biomass from the urine coupled with synthetic long-read 16S rRNA gene sequencing to obtain culture-independent species-level resolution data. We tested for differences in microbial composition between sex and history of UTIs using non-parametric tests on individual bacteria and alpha diversity measures., Results: We detected bacteria in 61% of samples from 54 children (mean age 40.7 months, 57% females). Similar to adults, urobiomes were distinct across individuals and varied by sex. The urobiome of females showed higher diversity as measured by the inverse Simpson and Shannon indices but not the Pielou evenness index or number of observed species (p = 0.05, p = 0.04, p = 0.35, and p = 0.11, respectively). Additionally, several species were significantly overrepresented in females compared to males, including those from the genera Anaerococcus, Prevotella, and Schaalia (p = 0.03, 0.04, and 0.02, respectively). Urobiome diversity increased with age, driven mainly by males. Comparison of children with a history of 1, 2, or 3+ UTIs revealed that urobiome diversity significantly decreases in the group that experienced 3+ UTIs as measured by the Simpson, Shannon, and Pielou indices (p = 0.03, p = 0.05, p = 0.01). Several bacteria were also found to be reduced in abundance., Discussion: In this study, we confirm that urobiome can be identified from catheter-collected urine specimens in infants as young as 3 months, providing further evidence that the pediatric bladder is not sterile. In addition to confirming variations in the urobiome related to sex, we identify age-related changes in children under 5 years of age, which conflicts with some prior research. We additionally identify associations with a history of UTIs., Conclusions: Our study provides additional evidence that the pediatric urobiome exists. The bacteria in the bladder of children appear to be affected by early urologic events and warrants future research., (Copyright © 2024 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.)

The host-associated microbiota can promote colonization resistance against pathogens via a mechanism termed 'nutrient blocking', as highlighted in a recent article by Spragge et al. This implies that greater metabolic overlap between commensal taxa and pathogens leads to disease suppression. Here, we discuss future avenues for how this principle can be exploited in the rhizosphere microbiota to promote plant health., Competing Interests: Declaration of interests There are no interests to declare., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Comparative physiologists often compare physiological traits across organisms to understand the selective pressures influencing their evolution in different environments. Traditionally focused on the organisms themselves, comparative physiology has more recently incorporated studies of the microbiome-the communities of microbes living in and on animals that influence host physiology. In this commentary, we describe the utility of applying a comparative framework to study the microbiome, particularly in understanding how hosts vary in their dependence on microbial communities for physiological function, a concept we term the "microbial dependence continuum". This hypothesis suggests that hosts exist on a spectrum ranging from high to low reliance on their microbiota. Certain physiological traits may be highly dependent on microbes for proper function in some species but microbially independent in others. Comparative physiology can elucidate the selective pressures driving species along this continuum. Here, we discuss the microbial dependence continuum in detail and how comparative physiology can be useful to study it. Then, we discuss two example traits, herbivory and flight, where comparative physiology has helped reveal the selective pressures influencing host dependence on microbial communities. Lastly, we discuss useful experimental approaches for studying the microbial dependence continuum in a comparative physiology context., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

Background: Laryngeal injury associated with traumatic or prolonged intubation may lead to voice, swallow, and airway complications. The interplay between inflammation and microbial population shifts induced by intubation may relate to clinical outcomes. The objective of this study was to investigate laryngeal mechanics, tissue inflammatory response, and local microbiome changes with laryngotracheal injury and localized delivery of therapeutics via drug-eluting endotracheal tube., Methods: A simulated traumatic intubation injury was created in Yorkshire crossbreed swine under direct laryngoscopy. Endotracheal tubes electrospun with roxadustat or valacyclovir- loaded polycaprolactone (PCL) fibers were placed in the injured airway for 3, 7, or 14 days (n = 3 per group/time and ETT type). Vocal fold stiffness was then evaluated with normal indentation and laryngeal tissue sections were histologically examined. Immunohistochemistry and inflammatory marker profiling were conducted to evaluate the inflammatory response associated with injury and ETT placement. Additionally, ETT biofilm formation was visualized using scanning electron microscopy and micro-computed tomography, while changes in the airway microbiome were profiled through 16S rRNA sequencing., Results: Laryngeal tissue with roxadustat ETT placement had increasing localized stiffness outcomes over time and histological assessment indicated minimal epithelial ulceration and fibrosis, while inflammation remained severe across all timepoints. In contrast, vocal fold tissue with valacyclovir ETT placement showed no significant changes in stiffness over time; histological analysis presented a reduction in epithelial ulceration and inflammation scores along with increased fibrosis observed at 14 days. Immunohistochemistry revealed a decline in M1 and M2 macrophage markers over time for both ETT types. Among the cytokines, IL-8 levels differed significantly between the roxadustat and valacyclovir ETT groups, while no other cytokines showed statistically significant differences. Additionally, increased biofilm formation was observed in the coated ETTs with notable alterations in microbiota distinctive to each ETT type and across time., Conclusion: The injured and intubated airway resulted in increased laryngeal stiffness. Local inflammation and the type of therapeutic administered impacted the bacterial composition within the upper respiratory microbiome, which in turn mediated local tissue healing and recovery., (© 2024. The Author(s).)

Background: Soil nutrient status and soil-borne diseases are pivotal factors impacting modern intensive agricultural production. The interplay among plants, soil microbiome, and nutrient regimes in agroecosystems is essential for developing effective disease management. However, the influence of nutrient availability on soil-borne disease suppression and associated plant-microbe interactions remains to be fully explored. T his study aims to elucidate the mechanistic understanding of nutrient impacts on disease suppression, using phosphorous as a target nutrient., Results: A 6-year field trial involving monocropping of tomatoes with varied fertilizer manipulations demonstrated that phosphorus availability is a key factor driving the control of bacterial wilt disease caused by Ralstonia solanacearum. Subsequent greenhouse experiments were then conducted to delve into the underlying mechanisms of this phenomenon by varying phosphorus availability for tomatoes challenged with the pathogen. Results showed that the alleviation of phosphorus stress promoted the disease-suppressive capacity of the rhizosphere microbiome, but not that of the bulk soil microbiome. This appears to be an extension of the plant trade-off between investment in disease defense mechanisms versus phosphorus acquisition. Adequate phosphorus levels were associated with elevated secretion of root metabolites such as L-tryptophan, methoxyindoleacetic acid, O-phosphorylethanolamine, or mangiferin, increasing the relative density of microbial biocontrol populations such as Chryseobacterium in the rhizosphere. On the other hand, phosphorus deficiency triggered an alternate defense strategy, via root metabolites like blumenol A or quercetin to form symbiosis with arbuscular mycorrhizal fungi, which facilitated phosphorus acquisition as well., Conclusion: Overall, our study shows how phosphorus availability can influence the disease suppression capability of the soil microbiome through plant-microbial interactions. These findings highlight the importance of optimizing nutrient regimes to enhance disease suppression, facilitating targeted crop management and boosting agricultural productivity. Video Abstract., (© 2024. The Author(s).)

Nitrogen (N) is a vital nutrient and an essential component of biological macromolecules such as nucleic acids and proteins. Microorganisms are major drivers of N-cycling processes in all ecosystems, including the soil and plant environment. The availability of N is a major growth-limiting factor for plants and it is significantly affected by the plant microbiome. Plants and microorganisms form complex interaction networks resulting in molecular signaling, nutrient exchange, and other distinct metabolic responses. In these networks, microbial partners influence growth and N use efficiency of plants either positively or negatively. Harnessing the beneficial effects of specific players within crop microbiomes is a promising strategy to counteract the emerging threats to human and planetary health due to the overuse of industrial N fertilizers. However, in addition to N-providing activities (e.g. the well-known symbiosis of legumes and Rhizobium spp.), other plant-microorganism interactions must be considered to obtain a complete picture of how microbial-driven N transformations might affect plant nutrition. For this, we review recent insights into the tight interplay between plants and N-cycling microorganisms, focusing on microbial N-transformation processes representing N sources and sinks that ultimately shape plant N acquisition., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

The metabolic network of an organism can be analyzed as a constraint-based model. This analysis can be biased, optimizing an objective such as growth rate, or unbiased, aiming to describe the full feasible space of metabolic fluxes through pathway analysis or random flux sampling. In particular, pathway analysis can decompose the flux space into fundamental and formally defined metabolic pathways. Unbiased methods scale poorly with network size due to combinatorial explosion, but a promising approach to improve scalability is to focus on metabolic subnetworks, e.g., cells' metabolite exchanges with each other and the environment, rather than the full metabolic networks. Here, we applied pathway enumeration and flux sampling to metabolite exchanges in microbial species and a microbial community, using models ranging from central carbon metabolism to genome-scale and focusing on pathway definitions that allow direct targeting of subnetworks such as metabolite exchanges (elementary conversion modes, elementary flux patterns, and minimal pathways). Enumerating growth-supporting metabolite exchanges, we found that metabolite exchanges from different pathway definitions were related through a hierarchy, and we show that this hierarchical relationship between pathways holds for metabolic networks and subnetworks more generally. Metabolite exchange frequencies, defined as the fraction of pathways in which each metabolite was exchanged, were similar across pathway definitions, with a few specific exchanges explaining large differences in pathway counts. This indicates that biological interpretation of predicted metabolite exchanges is robust to the choice of pathway definition, and it suggests strategies for more scalable pathway analysis. Our results also signal wider biological implications, facilitating detailed and interpretable analysis of metabolite exchanges and other subnetworks in fields such as metabolic engineering and synthetic biology., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Wedmark et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Multispecies microbial communities drive most ecosystems on Earth. Chemical and biological interactions within these communities can affect the survival of individual members and the entire community. However, the prohibitively high number of possible interactions within a microbial community has made the characterization of factors that influence community development challenging. Here, we report a Microbial Community Interaction (µCI) device to advance the systematic study of chemical and biological interactions within a microbial community. The µCI creates a combinatorial landscape made up of an array of triangular wells interconnected with circular wells, which each contains either a different chemical or microbial strain, generating chemical gradients and revealing biological interactions. Bacillus cereus UW85 containing green fluorescent protein provided the "target" readout in the triangular wells, and antibiotics or microorganisms in adjacent circular wells are designated the "variables." The µCI device revealed that gentamicin and vancomycin are antagonistic to each other in inhibiting the target B. cereus UW85, displaying weaker inhibitory activity when used in combination than alone. We identified three-member communities constructed with isolates from the plant rhizosphere that increased or decreased the growth of B. cereus . The µCI device enables both strain-level and community-level insight. The scalable geometric design of the µCI device enables experiments with high combinatorial efficiency, thereby providing a simple, scalable platform for systematic interrogation of three-factor interactions that influence microorganisms in solitary or community life., Competing Interests: Competing interests statement:D.J.B. holds equity in Bellbrook Labs LLC, Tasso Inc., Salus Discovery LLC, Lynx Biosciences Inc., Stacks to the Future LLC, Onexio Biosystems LLC, Navitro Biosciences LLC, and Flambeau Diagnostics LLC. J.H. holds equity in Wacasa Pharmaceuticals, Inc. A patent application (US011185860B2) was filed through the Wisconsin Alumni Research Foundation for the device described in this work.