Microbial Ecosystem Research Articles

Urine microbiota and bladder cancer

Urine analysis data obtained using modern microbiological methods and 16S rRNA gene sequencing technology indicate that the urinary system has its own microbial ecosystem. Individual microbiota members can play a key role in the development of cancer. Certain bacterial taxa have been revealed in bladder urothelial carcinoma cells that can affect carcinogenesis, treatment response, and the development of relapses through various mechanisms. The studies are conducted to use not only vaccine strains, but also probiotic strains and oncolytic bacteria for the treatment and prevention of relapses.

Effective Microbial Strategies to Remediate Contaminated Agricultural Soils and Conserve Functions

The growing global emphasis on sustainable agriculture has brought increased attention to the health and productivity of soils, especially through the lens of soil microbiology. Microbial communities in soil are essential for nutrient cycling, organic matter decomposition, and maintaining overall soil health. However, agricultural practices, including synthetic fertilizers and intensive farming, have led to short time impacts in these microbial ecosystems, potentially threatening soil fertility and environmental quality. Agricultural expansion and food production generate waste and chemical inputs, such as heavy metals, pesticides, and herbicides, leading to significant environmental contamination. This scenario requires the implementation of remediation strategies that are both sustainable and energy efficient. In this context, microbiological processes present a much promising approach to mitigating the environmental impacts of soil pollution. Techniques such as bioremediation, which harness the natural metabolic capabilities of soil microorganisms, and bioaugmentation, which involves the introduction of specific microbial strains to increase degradation processes, are being explored. These approaches are vital for restoring soil health, contributing to environmental conservation and soil biodiversity, improving nutrient cycling, and promoting long-term agricultural productivity.

New fermented plant-based ingredients in sourdough breads enhanced nutritional value and impacted on gut microbiota

Two new recipes of baker's yeast bread fortified with fermented apple by-products and avocado or walnut were designed resulting in enhanced profiles of total free amino acids, in vitro protein digestibility (IVPD) and predicted glycemic index (pGI). Concurrently, pools of lactic acid bacteria and yeast were screened to select the most promising starters for sourdough preparation. The type II sourdough with Lactiplantibacillus plantarum CR1, Furfurilactobacillus rossiae CR5 and Saccharomyces cerevisiae E10 had the highest acidification and total free amino acids value, while resulting in bread with the highest IVPD and the lowest pGI.Sourdough breads were manufactured with the new recipes. They had improved protein digestibility and starch hydrolysis, and enhanced content of dietary fiber, phenolics and unsaturated free fatty acids. The impact of new fortified sourdough breads on colon microbial ecosystems was investigated by the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). The intake promoted the short-chain fatty acids synthesis and expanded several bacterial taxa with potential to exert beneficial activities. The synergic combination of sourdough fermentation and fortification with fermented plant-based matrices (including by-products) was a suitable strategy to promote better nutritional and digestibility properties in breads, and to promisingly address the modulation of gut microbiota.

Biotics and bacterial function: impact on gut and host health.

The human gut microbiota, the vast community of microbes inhabiting the gastrointestinal tract, plays a pivotal role in maintaining health. Bacteria are the most abundant organism, and the composition of bacterial communities is strongly influenced by diet. Gut bacteria can degrade complex dietary carbohydrates to produce bioactive compounds such as short-chain fatty acids. Such products influence health, by acting on systemic metabolism, or by virtue of anti-inflammatory or anti-carcinogenic properties. The composition of gut bacteria can be altered through overgrowth of enteropathogens (e.g., Campylobacter, Salmonella spp.), leading to dysbiosis of the gut ecosystem, with some species thriving under the altered conditions whereas others decline. Various "biotics" strategies, including prebiotics, probiotics, synbiotics, and postbiotics, contribute to re-establishing balance within the gut microbial ecosystem conferring health benefits. Prebiotics enhance growth of beneficial members of the resident microbial community and can thus prevent pathogen growth by competitive exclusion. Specific probiotics can actively inhibit the growth of pathogens, either through the production of bacteriocins or simply by reducing the gastrointestinal pH making conditions less favorable for pathogen growth. This review discusses the importance of a balanced gut ecosystem, and strategies to maintain it that contribute to human health.

Assembly of functional microbial ecosystems: from molecular circuits to communities.

Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. Firstly, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn (cDBTL) procedure including function specification, chassis selection, interaction design, system build, performance test, modelling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.

Enhanced remediation of acetochlor-contaminated soils using phosphate-modified biochar: Impacts on environmental fate, microbial communities, and plant health

Given that acetochlor (ACT) persists in soil for extended periods, disrupting microbial community structure and causing phytotoxicity to sensitive crops, this study investigated the potential of phosphate-modified biochar (PBC-800) to remediate ACT-contaminated soil. Incorporating 0.5 % PBC-800 into fluvo-aquic, red, and black soils increased their adsorption capacities by 80.4 mg g−1, 76.6 mg g−1, and 76.0 mg g−1, respectively. Even after six months of aging, the Kf values remained 1.6 to 5.1 times higher than in untreated soils. PBC-800 also accelerated ACT degradation across all three soil types, reducing residual ACT levels by 34.3 % to 76.4 % after 60 days, and shortening the degradation half-life by 5 to 7 days. High-throughput sequencing revealed that ACT reduced soil microbial diversity and disrupted community structure, while 0.5 % PBC-800 amendments promoted the growth of degradation-capable genera such as Rhodococcus, Lysobacter, and Gemmatimonas, enhancing microbial ecosystem stability. Furthermore, the amendment of soil with 0.5 % PBC-800 reduced ACT residue concentrations in maize and soybeans by 76.5 % to 82.9 %, and restored plant biomass, leaf chlorophyll content, and mesophyll cell ultrastructure to levels comparable to the control. Therefore, amending ACT-contaminated soil with PBC-800 mitigates ecological and environmental risks, boosts microbial activity, and safeguards plant health.

Microplastics alter the functioning of marine microbial ecosystems

AbstractMicroplastics pervade ocean ecosystems. Despite their effects on individuals or populations are well documented, the consequences of microplastics on ecosystem functioning are still largely unknown. Here, we show how microplastics alter the structure and functioning of pelagic microbial ecosystems. Using experimental pelagic mesocosms, we found that microplastics indirectly affect marine productivity by changing the bacterial and phytoplankton assemblages. Specifically, the addition of microplastics increased phytoplankton biomass and shifted bacterial assemblages' composition. Such changes altered the interactions between heterotrophic and autotrophic microbes and the cycling of ammonia in the water column, which ultimately benefited photosynthetic efficiency. The effects of microplastics on marine productivity were consistent for different microplastic types. This study demonstrates that microplastics affect bacteria and phytoplankton communities and influence marine productivity, which ultimately alters the functioning of the whole ocean ecosystem.

The Rumen Microbiome Composition of Raramuri Criollo and European Cattle in an Extensive System

Understanding the relationship between Raramuri Criollo cattle (RC) and their microbial ruminal ecosystem will help identify advantageous characteristics of adapted cattle as alternatives to achieve sustainable beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to Angus and Hereford breeds (European, E) and the cross between them (E × RC). Ruminal fluid was collected from 63 cows in their second productive cycle after grazing in the same paddock for 45 d, in the dry (n = 28) and rain (n = 35) seasons. DNA from ruminal fluid was isolated for 16s rRNA gene next-generation sequencing. The data were analyzed with QIIME2 and compared against the SILVA 16s rRNA database. Beta diversity was different (p < 0.05) between RC and E in both seasons. A microbial core was represented by the most abundant phyla. Planctomycetes and Spirochaetes represented above 1% in the rain season and below 1% in the dry one, whereas Euryarchaeota was below 1% and around 3%, respectively. LEfSe analysis identified differentiated (p < 0.05) key microbial groups that explain the differences between lineages at different taxonomic levels, reflecting the ability of the rumen ecosystem of RC cattle to adapt to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous content.

Microbial Dynamics in Periodontal Regeneration: Understanding Microbiome Shifts and the Role of Antifouling and Bactericidal Materials: A Narrative Review

Periodontal regeneration is a multifaceted therapeutic approach to restore the tooth-supporting structures lost due to periodontal diseases. This manuscript explores the intricate interactions between regenerative therapies and the oral microbiome, emphasizing the critical role of microbial balance in achieving long-term success. While guided tissue regeneration (GTR), bone grafting, and soft tissue grafting offer promising outcomes in terms of tissue regeneration, these procedures can inadvertently alter the oral microbial ecosystem, potentially leading to dysbiosis or pathogenic recolonization. Different grafting materials, including autografts, allografts, xenografts, and alloplasts, influence microbial shifts, with variations in the healing timeline and microbial stabilization. Biologics and antimicrobials, such as enamel matrix derivatives (EMD) and sub-antimicrobial dose doxycycline (SDD), play a key role in promoting microbial homeostasis by supporting tissue repair and reducing pathogenic bacteria. Emerging strategies, such as enzyme-based therapies and antifouling materials, aim to disrupt biofilm formation and enhance the effectiveness of periodontal treatments. Understanding these microbial dynamics is essential for optimizing regenerative therapies and improving patient outcomes. The future of periodontal therapy lies in the development of advanced materials and strategies that not only restore lost tissues but also stabilize the oral microbiome, ultimately leading to long-term periodontal health.

Predicting the Microbiome and Metabolome Dynamics of Natural Apple Fermentation Towards the Development of Enhanced Functional Vinegar

Natural vinegar fermentation is a complex process influenced by the interplay between microbial communities and metabolites. This study examined the interplay between the microbiome and the metabolome over a three-month period, with samples collected every ten days. Using Illumina sequencing and chromatographic techniques (HPLC and GC-MS), we mapped microbial shifts and metabolite profiles. Early fermentation showed a diverse microbial presence, including genera such as Cronobacter, Luteibacter, and Saccharomyces. A stable microbial ecosystem established between days 15 and 70, characterized by the dominance of Leuconostoc, Gluconobacter, and Saccharomyces, which facilitated consistent substrate consumption and metabolite production, including various organic acids and ethanol. By day 70, Acetobacter prevalence increased significantly, correlating with a peak acetic acid production of 12.4 g/L. Correlation analyses revealed significant relationships between specific microbes and volatile organic compounds. This study highlights the crucial roles of these microbes in developing sensory profiles suited for industrial applications and proposes an optimal microbial consortium for enhancing vinegar quality. These data suggest that an optimal microbial consortium for vinegar fermentation should include Saccharomyces for efficient alcohol production, Leuconostoc for ester-mediated flavor complexity, and Acetobacter for robust acetic acid production. The presence of Komagataeibacter could further improve the sensory and functional qualities due to its role in producing bacterial cellulose.

LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data.

We describe LnCeCell 2.0 (http://bio-bigdata.hrbmu.edu.cn/LnCeCell), an updated resource for lncRNA-associated competing endogenous RNA (ceRNA) networks and web tools based on single-cell and spatial transcriptomics sequencing(stRNA-seq)data. We have updated the LnCeCell 2.0 database with significantly expanded data and improved features, including(i) 257 single-cell RNA sequencingandstRNA-seqdatasets across 86 diseases/phenotypes and 80 human normal tissues, (ii) 836581 cell-specific and spatial spot-specific ceRNA interactions and functional networks for 1002988 cells and 367971 spatial spots, (iii) 15489 experimentally supported lncRNA biomarkers related to disease pathology, diagnosis and treatment, (iv) detailed annotation of cell type, cell state, subcellular and extracellular locations of ceRNAs through manual curationand (v) ceRNA expression profiles and follow-up clinical information of 20326 cancer patients. Further, a panel of 24 flexible tools (including 8 comprehensive and 16 mini-analysis tools) was developed to investigate ceRNA-regulated mechanisms at single-cell/spot resolution. The CeCellTraject tool, for example, illustrates the detailed ceRNA distribution of different cell populations and explores the dynamic change of the ceRNA network along the developmental trajectory. LnCeCell 2.0 will facilitate the study of fine-tuned lncRNA-ceRNA networks with single-cell and spatial spot resolution, helping us to understand the regulatory mechanisms behind complex microbial ecosystems.

Effects of weed management on soil metagenomic composition in cultivated chickpea fields

Abstract Non-chemical methods, including mechanical and manual weed management are important for improving crop yields and preserving soil microbial diversity. In Tunisia, chickpea cultivation uses a combination of these methods to suppress weeds. This study aimed to evaluate the impact of weeding practices on chickpea (Cicer arietinum L. cultivar REBHA) yield and soil microbial diversity. Field experiments were conducted at the Technical Center for Biological Agriculture in Essaida, Tunisia, using six plots with manual and no weeding treatments. Chickpea yield was measured, and soil samples were collected for metagenomic analysis. Floristic surveys identified 13 weed species, with Chenopodium album L., Rumex acetosa L., and Urtica dioica L. being the most dominant. Seed yield ranged from 23.2 to 26.2 qls/ha in non-weeded plots and from 25.1 to 30.1 qls/ha in weeded plots, showing an increase in yield (11.75%) with manual weeding.
Soil metagenomics revealed changes in bacterial community composition between the two treatments. The dominant phylum was Pseudomonadota, whose relative abundance increased from 24.88% in non-weeded plots to 34.76% in weeded plots. Alpha diversity indices showed lower species richness and diversity in weeded soils, with 62000 OTUs in weeded plots compared to 43202 OTUs in non-weeded plots. Betaproteobacteria and Alphaproteobacteria exhibited higher OTU counts in weeded soils. The Simpson diversity index was lower in non-weeded soils (0.025) than in weeded soils (0.075), indicating a more irregular microbial distribution in non-weeded plots. Thus, manual weeding improved chickpea yield and altered the soil bacterial community, increasing diversity in key microbial taxa. This study highlights the complex interaction between weed management practices and soil microbial ecosystems, which may influence crop productivity.

Microbial Dynamics and Pathogen Control During Fermentation of Distiller Grains: Effects of Fermentation Time on Feed Safety.

Determining the effects of fermentation duration on the microbial ecosystem, potential pathogenic risks, and metabolite generation during the fermentation of distilled grains is essential for safeguarding the safety and enhancing the nutritional profile of animal feed. This study investigates the effect of varying fermentation times (9, 30, and 60 days) on microbial diversity, pathogenic risk, and metabolite profiles in distiller grains using 16S rDNA sequencing and LC-MS-based metabolomics. The results showed that early fermentation (9-30 days) enhanced the abundance of beneficial bacteria, such as Lactobacillus reuteri and Lactobacillus pontis (p < 0.05), while pathogenic bacteria, like Serratia marcescens and Citrobacter freundii, were significantly reduced (p < 0.05). Metabolomic analysis revealed an increase in unsaturated fatty acids and the degradation of biogenic amines during early fermentation. However, prolonged fermentation (60 days) led to a resurgence of pathogenic bacteria and reduced the synthesis of essential metabolites. These findings suggest that fermentation duration must be optimized to balance microbial safety and nutrient quality, with 30 days being the optimal period to reduce pathogenic risks and enhance feed quality.

Does Encapsulation Improve the Bioavailability of Polyphenols in Humans? A Concise Review Based on In Vivo Human Studies.

Polyphenols offer an array of health benefits that can contribute to well-being. Nevertheless, their bioactivity can be compromised due to their low bioavailability. Encapsulation has been explored as a strategy to enhance the stability and bioavailability of polyphenols. During encapsulation, polyphenols are protected from degradation by a wall material that acts as a protective coating. This coating shields the polyphenols from the harsh physiological conditions of digestion, ensuring their delivery to the intestine. However, the majority of evidence, particularly regarding bioavailability after digestion, is derived from in vitro studies. While these studies provide valuable preliminary insights, they cannot definitively confirm the effects in vivo due to their inability to accurately replicate physiological conditions and the complex gut microbial ecosystem. Consequently, this review seeks to evaluate the current evidence from in vivo human studies to elucidate the efficacy of encapsulation in improving polyphenols' bioavailability. Current clinical evidence on the impact of encapsulation on polyphenol bioavailability is primarily focused on polyphenols derived from grape pomace, cocoa, and bilberries, as well as individual polyphenols such as fisetin, hesperidin, and curcumin. Encapsulation has been an effective technique in improving the bioavailability of individual polyphenols like hesperidin, fisetin, and curcumin. However, this approach has not yielded consistent results when applied to groups of polyphenols, such as bilberry anthocyanins or cocoa phenolic acids. Encapsulation by micellization has shown promising results in improving the bioavailability of curcumin in a nutraceutical context. Further studies are needed to explore the bioavailability of encapsulated polyphenols, especially in the functional food context.

Microbial solutions must be deployed against climate catastrophe.

Injecting H2 in deep underground to store this energy carrier will produce artificial subsurface lithoautotrophic microbial ecosystems that modify the taxonomic diversity of indigenous microbial communities and their metabolic activities.

Artificial subsurface lithoautotrophic microbial ecosystems and gas storage in deep subsurface.

Over the next few years, it is planned to convert all or part of the underground gas storage (UGS) facilities used for natural gas (salt caverns, depleted hydrocarbon reservoirs, and deep aquifers) into underground dihydrogen (H2) storage reservoirs. These deep environments host microbial communities, some of which are hydrogenotrophic (sulfate reducers, acetogens, and methanogens). The current state of microbiological knowledge is thus presented for the three types of UGS facilities. In the mid-1990s, the concept of anaerobic subsurface lithoautotrophic microbial ecosystems, or SLiMEs, emerged. It is expected that the large-scale injection of H2 into subsurface environments will generate new microbial ecosystems called artificial SLiMEs, which could persist over time. These artificial SLiMEs could lead to H2 loss, an intense methanogenic activity, a degradation of gas quality and a risk to installations through sulfide production. However, recent studies on salt caverns and deep aquifers suggest that hydrogenotrophic microbial activity also leads to alkalinization (up to pH 10), which can constrain hydrogenotrophy. Therefore, studying and understanding these artificial SLiMEs is both a necessity for the development of the H2 industry and presents an opportunity for ecologists to monitor the evolution of deep environments in real time.

Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape

The Southern Ocean microbial ecosystem, with its pronounced seasonal shifts, is vulnerable to the impacts of climate change. Since viruses are key modulators of microbial abundance, diversity, and evolution, we need a better understanding of the effects of seasonality on the viruses in this region. Our comprehensive exploration of DNA viral diversity in the Southern Ocean reveals a unique and largely uncharted viral landscape, of which 75% was previously unidentified in other oceanic areas. We uncover novel viral taxa at high taxonomic ranks, expanding our understanding of crassphage, polinton-like virus, and virophage diversity. Nucleocytoviricota viruses represent an abundant and diverse group of Antarctic viruses, highlighting their potential as important regulators of phytoplankton population dynamics. Our temporal analysis reveals complex seasonal patterns in marine viral communities (bacteriophages, eukaryotic viruses) which underscores the apparent interactions with their microbial hosts, whilst deepening our understanding of their roles in the world’s most sensitive and rapidly changing ecosystem.

Changes in Microbial Ecosystems and Serum Metabolomics by Diet Supplementation With Enramycin in Weaning Piglets.

Antibiotics are used in swine production for growth promotion and disease prevention, raising concerns about environmental contamination and antibiotic resistance. In this study, we investigated the effects of enramycin supplementation on piglet growth, gut microbiota and blood metabolites. Enramycin promotes piglet growth and temporarily reduces diarrhoea. Gut microbiota analysis revealed changes in microbial composition, including an increase in the abundance of Limosilactobacillus reuteri. Metabolomic analysis has identified elevated levels of dimethylglycine, a known growth-promoting factor, in the enramycin group. Liver gene expression analysis revealed increased mRNA levels of ALDH and dimethylglycine dehydrogenase, which are enzymes involved in dimethylglycine metabolism. The enramycin-treated group had a higher concentration of acetic acid in caecal contents, and their caecal acetic acid concentrations were positively correlated with the abundance of L. reuteri and the content of serum dimethylglycine, respectively. These findings suggest that the promotion effect of enramycin on piglet growth is related to the gut microbiota, blood metabolites and liver gene expression, which provide insights into antibiotic alternatives for swine production.

Microbes as medicine.

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.

Microbial Ecosystems as Guardians of Food Security and Water Resources in the Era of Climate Change

Microbial Ecosystems as Guardians of Food Security and Water Resources in the Era of Climate Change