Beneficial Microbiome Research Articles

Study on the hepatoprotective effect of Sporidiobolus pararoseus polysaccharides under the “gut microbiome-amino acids metabolism” network

The “gut–liver” axis plays an important role in the mechanism of alcoholic liver disease (ALD). Sporidiobolus pararoseus polysaccharides (SPP) have been shown to improve the gut barrier and liver damage in mice with ALD. However, the process is modulated via the gut microbiome and amino acids in the gut–liver axis has not been elucidated. In this study, the gut microbiome and metabolic function were explored for the mechanism by which SPP improve ALD. The results showed that after the SPP were metabolized by ALD mice, microbial diversity was altered, and the relative abundances of Lachnospiraceae, Alistipes, Eubacterium siraeum, and Bacteroides increased. The predicted results of microbiome functions promoted the biosynthesis of amino acids, tyrosine, tryptophan, valine, leucine, and isoleucine were enhanced. Metabolomics results also confirmed that butanoate metabolism and biosynthesis of phenylalanine, tyrosine, and tryptophan are the main regulatory pathways of SPP. The gut microbiome metabolizes the hallmark metabolites of SPP were l-tyrosine, l-histidine, and l-serine. Correlation analysis and interaction network deeply mine gut microbiome (Lachnospiraceae, Eubacterium siraeum, Erysipelotrichaceae), metabolites (L−serine, L−tyrosine), and metabolism (biosynthesis of amino acids, valine, leucine, and isoleucine biosynthesis) may be key factors in the SPP-gut microbiome–metabolites–metabolism in ALD mice. Therefore, SPP have the effect of proliferating beneficial gut microbiome that metabolize polysaccharides, promoting the production of amino acids, and regulating liver metabolic disorders.

Pseudomonas spp. Enriched in Endophytic Community of Healthy Cotton Plants Inhibit Cotton Verticillium Wilt.

The plant microbiome plays a fundamental role in plant growth and health. However, detailed information regarding the plant endophytic microbiome during the infection period of a pathogen is largely unknown. Here, we investigated the microbial community of healthy and diseased cotton plants and the root exudate profiles of susceptible and resistant cultivars utilizing high-throughput sequencing and metabolomics. The results showed that the pathogen infection reduced bacterial diversity and significantly affected the bacterial community composition. The microbiome assembly is shaped predominantly by cultivars. The endophytic microbiome of the infected plants showed greater complexity than the healthy plants in network analysis. The results displayed that a total of 76 compounds were significantly different in the two groups, with 18 compounds showing a higher relative abundance in the resistant cultivars and 58 compounds in the susceptible cultivars. Pathway enrichment analysis showed that pathways related to plant hormone signal transduction, biosynthesis of various secondary metabolites, and biosynthesis and metabolism of amino acids were prominently altered. We also demonstrate that plants inoculated with Pseudomonas sp. strains showed increased resistance to the cotton Verticillium wilt compared with the control plants in pot experiments. Overall, it showed that the pathogen infection affected the community composition, and healthy plants displayed an enriched beneficial microbiome to combat the plant disease. These findings significantly advance our understanding of the endophytic microbiome assembly under the pathogen infection and develop microbiome-based solutions for sustainable crop production systems.

Flooding-induced rhizosphere Clostridium assemblage prevents root-to-shoot cadmium translocation in rice by promoting the formation of root apoplastic barriers

Water managements are the most effective agricultural practices for restraining cadmium (Cd) uptake and translocation in rice, which closely correlated with rhizosphere assembly of beneficial microbiome. However, the role of the assemblage of specific microbiota in controlling root-to-shoot Cd translocation in rice remains scarcely clear. The aim of this study was to ascertain how water managements shaped rhizosphere microbiome and mediated root-to-shoot Cd translocation. To disentangle the acting mechanisms of water managements, we performed an experiment monitoring Cd uptake and transport in rice and changes in soil microbial communities in response to continuously flooding and moistening irrigation. Continuously flooding changed rhizosphere microbial communities, leading to the increased abundance of anaerobic bacteria such as Clostridium populations. Weighted gene co-expression network analysis (WGCNA) showed that a dominant OTU163, corresponding to Clostridium sp. CSP1, exhibited a strong negative correlation with root-to-shoot Cd translocation. An integrated analysis of transcriptome and metabolome further indicated that the Clostridium-secreted butyric acid was involved in the regulation of phenylpropanoid pathway in rice roots. The formation of endodermal suberized barriers and lignified xylems was remarkably enhanced in the Clostridium-treated roots, which led to more Cd retained in root cell wall and less Cd in the xylem sap. Collectively, our results indicate that the development of root apoplastic barriers can be orchestrated by beneficial Clostridium strains that are assembled by host plants grown under flooding regime, thereby inhibiting root-to-shoot Cd translocation.

The effects of polyunsaturated fatty acid (PUFA) administration on the microbiome-gut-brain axis in adolescents with anorexia nervosa (the MiGBAN study): study protocol for a longitudinal, double-blind, randomized, placebo-controlled trial

BackgroundAnorexia nervosa (AN) is a severe psychiatric disease that often takes a chronic course due to insufficient treatment options. Emerging evidence on the gut-brain axis offers the opportunity to find innovative treatments for patients with psychiatric disorders. The gut microbiome of patients with AN shows profound alterations that do not completely disappear after weight rehabilitation. In previous studies, the administration of polyunsaturated fatty acids (PUFA) resulted in effects that might be beneficial in the treatment of AN, affecting the microbiome, body weight and executive functions. Therefore, the MiGBAN study aims to examine the effects of a nutritional supplementation with PUFA on the gut microbiome and body mass index (BMI) in patients with AN.MethodsThis is a longitudinal, double-blind, randomized, placebo-controlled trial. Within 2 years, 60 adolescent patients aged 12 to 19 years with AN will receive either PUFA or placebo for 6 months additional to treatment as usual. After 1 year, the long-term effect of PUFA on the gut microbiome and consecutively on BMI will be determined. Secondary outcomes include improvement of gastrointestinal symptoms, eating disorder psychopathology, and comorbidities. Additionally, the interaction of the gut microbiome with the brain (microbiome-gut-brain axis) will be studied by conducting MRI measurements to assess functional and morphological changes and neuropsychological assessments to describe cognitive functioning. Anti-inflammatory effects of PUFA in AN will be examined via serum inflammation and gut permeability markers. Our hypothesis is that PUFA administration will have positive effects on the gut microbiota and thus the treatment of AN by leading to a faster weight gain and a reduction of gastrointestinal problems and eating disorder psychopathology.DiscussionDue to previously heterogeneous results, a systematic and longitudinal investigation of the microbiome-gut-brain axis in AN is essential. The current trial aims to further analyse this promising research field to identify new, effective therapeutic tools that could help improve the treatment and quality of life of patients. If this trial is successful and PUFA supplementation contributes to beneficial microbiome changes and a better treatment outcome, their administration would be a readily applicable additional component of multimodal AN treatment.Trial registrationGerman Clinical Trials Register DRKS00017130. Registered on 12 November 2019.

Functional biomes beyond the bacteriome in the oral ecosystem.

Selective constraint and pressures upon the host tissues often signifies a beneficial microbiome in any species. In the context of oral microbiome this displays a healthy microbial cosmos resisting the colonization and helps in rendering protection. This review highlights the endeavors of the oral microbiome beyond the bacteriome encompassing virome, mycobiome, protozoa and archaeomes in maintaining the oral homeostasis in health and disease. Scientific data based on the peer-reviewed publications on the microbial communities of the oral microbiome were selected and collated from the scientific database collection sites of web of science (WOS), pubmed central, Inspec etc., from 2010 to 2021 using the search key words like oral microbiome, oral microbiota, oral virome, oral bacteriome, oral mycobiome and oral archaeome. Data excluded were from conference proceedings, abstracts and book chapters. The oral homeostasis in both the health and disease conditions, mostly is balanced by the unrevealed virome, mycobiome, oral protozoa and archaeome. The review documents the need to comprehend the diversity that prevails among the kingdoms in order to determine the specific role played by each domain. Oral microbiome is also a novel research arena to develop drug and targeted therapies to treat various oro-dental infections.

Bioturbation Intensity Modifies the Sediment Microbiome and Biochemistry and Supports Plant Growth in an Arid Mangrove System.

ABSTRACTIn intertidal systems, the type and role of interactions among sediment microorganisms, animals, plants and abiotic factors are complex and not well understood. Such interactions are known to promote nutrient provision and cycling, and their dynamics and relationships may be of particular importance in arid microtidal systems characterized by minimal nutrient input. Focusing on an arid mangrove ecosystem on the central Red Sea coast, we investigated the effect of crab bioturbation intensity (comparing natural and manipulated high levels of bioturbation intensity) on biogeochemistry and bacterial communities of mangrove sediments, and on growth performance of Avicennia marina, over a period of 16 months. Along with pronounced seasonal patterns with harsh summer conditions, in which high sediment salinity, sulfate and temperature, and absence of tidal flooding occur, sediment bacterial diversity and composition, sediment physicochemical conditions, and plant performance were significantly affected by crab bioturbation intensity. For instance, bioturbation intensity influenced components of nitrogen, carbon, and phosphate cycling, bacterial relative abundance (i.e., Bacteroidia, Proteobacteria and Rhodothermi) and their predicted functionality (i.e., chemoheterotrophy), likely resulting from enhanced metabolic activity of aerobic bacteria. The complex interactions among bacteria, animals, and sediment chemistry in this arid mangrove positively impact plant growth. We show that a comprehensive approach targeting multiple biological levels provides useful information on the ecological status of mangrove forests.IMPORTANCE Bioturbation is one of the most important processes that governs sediment biocenosis in intertidal systems. By facilitating oxygen penetration into anoxic layers, bioturbation alters the overall sediment biogeochemistry. Here, we investigate how high crab bioturbation intensity modifies the mangrove sediment bacterial community, which is the second largest component of mangrove sediment biomass and plays a significant role in major biogeochemical processes. We show that the increase in crab bioturbation intensity, by ameliorating the anoxic condition of mangrove sediment and promoting sediment bacterial diversity in favor of a beneficial bacterial microbiome, improves mangrove tree growth in arid environments. These findings have significant implications because they show how crabs, by farming the mangrove sediment, can enhance the overall capacity of the system to sustain mangrove growth, fighting climate change.

Mating Leads to a Decline in the Diversity of Symbiotic Microbiomes and Promiscuity Increased Pathogen Abundance in a Moth.

Mating may promote microbial diversity through sexual transmission, while mating-induced immune responses may decrease it. Therefore, the study of mating-induced microbiomes changes under different mating systems is informative to unravel its biological relevance and evolutionary significance. Here, we studied the microbiomes in a community context within the abdomen of Spodoptera frugiperda females using 16S rDNA sequences by setting virgin females, and females mated once, twice, or thrice with the same or different males. Alpha and beta diversities revealed that mating significantly affected the composition of microbiomes in S. frugiperda females, wherein virgin females have the highest diversity, followed by one-time mated females and females mated with multiple males, while females mated repeatedly with the same male showed the lowest diversity. The low diversity in females mated repeatedly with the same male may be due to lower sexual transmission as only mated with one mate and higher immune response from repeated matings. Functional prediction by FAPROTAX and literature searching found 17 possible pathogens and 12 beneficial microbiomes. Multiple mating turned over the abundance of pathogens and beneficial microbes, for example, Enterococcus and Lactobacillus spp. (beneficial) showed higher abundance in virgin females while Morganella and Serratia spp. (pathogens) showed higher abundance in females mated with multiple males. These results suggest that mating causes a decline in the diversity of symbiotic microbiomes and promiscuity incurs a higher pathogen abundance in S. frugiperda females, which may be the result of sexual transmission of bacterial strains and immune responses targeting members of the microbiomes. To our knowledge, we demonstrate microbiomes changes in female insects under virgin and different mating regimes for the first time.

Triclosan targeting of gut microbiome ameliorates hepatic steatosis in high fat diet-fed mice.

Antibiotic use provides a promising strategy for the treatment of non-alcoholic fatty liver disease (NAFLD) by regulating the gut microbiota composition. Triclosan, a widely used antibiotic, may improve gut microbiome dysbiosis associated with NAFLD through the suppression of pathogenic gram-negative bacteria. However, the effects of triclosan on gut microbiota and hepatic steatosis and have not been explored in NAFLD mouse model. In this study, C57BL/6J mice were fed with high fat diet (HFD) for continuous 20 weeks and treated with triclosan at 400 mg/kg/d for 8 weeks from week 13. We explored the effects of triclosan on hepatic lipid accumulation and gut microbiome in HFD-fed mice by histological examination and 16 S ribosomal RNA sequencing, respectively. Analysis on the composition of gut microbiota indicated that triclosan suppressed pathogenic gram-negative bacteria, including Helicobacter, Erysipelatoclostridium and Citrobacter, and increased the ratio of Bacteroidetes/Firmicutes in HFD-fed mice. Meanwhile, triclosan increased the relative abundance of beneficial gut microbiomes including Lactobacillus, Bifidobacterium and Lachnospiraceae, which protected against metabolic abnormality. The results of alpha-diversity and beta-diversity also showed the improvement of triclosan on bacterial diversity and richness in HFD-fed mice. Pathway analysis further confirmed that triclosan can regulate nutrient and energy metabolism through the elimination of deleterious bacteria. As a result, triclosan intervention significantly reduced lipid accumulation and alleviated hepatic steatosis in HFD-fed mice. In conclusion, our results suggest that triclosan can alleviate liver steatosis in HFD-fed mice by targeting the gut microbiome.

Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review

While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.

Microbial Community and Function-Based Synthetic Bioinoculants: A Perspective for Sustainable Agriculture.

Interactions among the plant microbiome and its host are dynamic, both spatially and temporally, leading to beneficial or pathogenic relationships in the rhizosphere, phyllosphere, and endosphere. These interactions range from cellular to molecular and genomic levels, exemplified by many complementing and coevolutionary relationships. The host plants acquire many metabolic and developmental traits such as alteration in their exudation pattern, acquisition of systemic tolerance, and coordination of signaling metabolites to interact with the microbial partners including bacteria, fungi, archaea, protists, and viruses. The microbiome responds by gaining or losing its traits to various molecular signals from the host plants and the environment. Such adaptive traits in the host and microbial partners make way for their coexistence, living together on, around, or inside the plants. The beneficial plant microbiome interactions have been exploited using traditional culturable approaches by isolating microbes with target functions, clearly contributing toward the host plants’ growth, fitness, and stress resilience. The new knowledge gained on the unculturable members of the plant microbiome using metagenome research has clearly indicated the predominance of particular phyla/genera with presumptive functions. Practically, the culturable approach gives beneficial microbes in hand for direct use, whereas the unculturable approach gives the perfect theoretical information about the taxonomy and metabolic potential of well-colonized major microbial groups associated with the plants. To capitalize on such beneficial, endemic, and functionally diverse microbiome, the strategic approach of concomitant use of culture-dependent and culture-independent techniques would help in designing novel “biologicals” for various crops. The designed biologicals (or bioinoculants) should ensure the community’s persistence due to their genomic and functional abilities. Here, we discuss the current paradigm on plant-microbiome-induced adaptive functions for the host and the strategies for synthesizing novel bioinoculants based on functions or phylum predominance of microbial communities using culturable and unculturable approaches. The effective crop-specific inclusive microbial community bioinoculants may lead to reduction in the cost of cultivation and improvement in soil and plant health for sustainable agriculture.

Long-term sod-based rotation promotes beneficial root microbiomes and increases crop productivity

Long-term sod-based rotation promotes beneficial root microbiomes and increases crop productivity

Flavonoid mediated selective cross-talk between plants and beneficial soil microbiome.

Plants generate a wide variety of organic components during their different growth phases. The majority of those compounds have been classified as primary and secondary metabolites. Secondary metabolites are essential in plants’ adaptation to new changing environments and in managing several biotic and abiotic stress. It also invests some of its photosynthesized carbon as secondary metabolites to establish a mutual relationship with soil microorganisms in that specific niche. As soil harbors both pathogenic and beneficial microorganisms, it is essential to identify some specific metabolites that can discriminate beneficial and pathogenic ones. Thus, a detailed understanding of metabolite’s architectures that interact with beneficial microorganisms could open a new horizon of ecology and agricultural research. Flavonoids are used as classic examples of secondary metabolites in this study to demonstrate recent developments in understanding and realizing how these valuable metabolites can be controlled at different levels. Most of the research was focused on plant flavonoids, which shield the host plant against competitors or predators, as well as having other ecological implications. Thus, in the present review, our goal is to cover a wide range of functional and signalling activities of secondary metabolites especially, flavonoids mediated selective cross-talk between plant and its beneficial soil microbiome. Here, we have summarized recent advances in understanding the interactions between plant species and their rhizosphere microbiomes through root exudates (flavonoids), with a focus on how these exudates facilitate rhizospheric associations.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11101-022-09806-3.

Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation

The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.

Exotoxin-Targeted Drug Modalities as Antibiotic Alternatives.

The paradigm of antivirulence therapy dictates that bacterial pathogens are specifically disarmed but not killed by neutralizing their virulence factors. Clearance of the invading pathogen by the immune system is promoted. As compared to antibiotics, the pathogen-selective antivirulence drugs hold promise to minimize collateral damage to the beneficial microbiome. Also, selective pressure for resistance is expected to be lower because bacterial viability is not directly affected. Antivirulence drugs are being developed for stand-alone prophylactic and therapeutic treatments but also for combinatorial use with antibiotics. This Review focuses on drug modalities that target bacterial exotoxins after the secretion or release-upon-lysis. Exotoxins have a significant and sometimes the primary role as the disease-causing virulence factor, and thereby they are attractive targets for drug development. We describe the key pre-clinical and clinical trial data that have led to the approval of currently used exotoxin-targeted drugs, namely the monoclonal antibodies bezlotoxumab (toxin B/TcdB, Clostridioides difficile), raxibacumab (anthrax toxin, Bacillus anthracis), and obiltoxaximab (anthrax toxin, Bacillus anthracis), but also to challenges with some of the promising leads. We also highlight the recent developments in pre-clinical research sector to develop exotoxin-targeted drug modalities, i.e., monoclonal antibodies, antibody fragments, antibody mimetics, receptor analogs, neutralizing scaffolds, dominant-negative mutants, and small molecules. We describe how these exotoxin-targeted drug modalities work with high-resolution structural knowledge and highlight their advantages and disadvantages as antibiotic alternatives.

Seaweed Fertilizer Prepared by EM-Fermentation Increases Abundance of Beneficial Soil Microbiome in Paddy (Oryzasativa L.) during Vegetative Stage

Excessive use of chemical fertilizer could potentially decrease soil productivity by decreasing soil microbiome diversity. In this study, we evaluated the effects of fermented seaweed fertilizer in the soil microbial community of paddy plants (Oryza sativa L.). The paddy seedlings were divided into five groups, control (C0), chemical fertilizer (CF), seaweed fertilizer (SF), chemical and seaweed fertilizer combination 50:50 (CFSF1), and chemical and fertilizer combination 75:25 (CFSF2). The CFSF1 combination showed to be the most effective in inducing plant height (83.99 ± 3.70 cm) and number of tillers (24.20 ± 4.08). After 8 weeks after transplantation, the isolated DNA from each soil treatment were subjected to 16S rRNA (v3–v4 region) next-generation sequencing. The beneficial Acidobacteriota was most abundant in CFSF1. At genus level, the nitrifying bacteria MND1 was seen to be abundant in CFSF1 and also present in other SF treatments. The genus Chujaibacter is highly abundant in CF, which potentially plays a role in denitrification resulting in soil degradation. In addition, the CFSF1-treated soils show significantly higher diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The current results could potentially contribute to the utilization of SF as a bioremediator and promoting green agriculture practice by reducing the amount of CF usage.

Adrenomedullin: Not Just Another Gastrointestinal Peptide.

Adrenomedullin (AM) and proadrenomedullin N-terminal 20 peptide (PAMP) are two bioactive peptides derived from the same precursor with several biological functions including vasodilation, angiogenesis, or anti-inflammation, among others. AM and PAMP are widely expressed throughout the gastrointestinal (GI) tract where they behave as GI hormones, regulating numerous physiological processes such as gastric emptying, gastric acid release, insulin secretion, bowel movements, or intestinal barrier function. Furthermore, it has been recently demonstrated that AM/PAMP have an impact on gut microbiome composition, inhibiting the growth of bacteria related with disease and increasing the number of beneficial bacteria such as Lactobacillus or Bifidobacterium. Due to their wide functions in the GI tract, AM and PAMP are involved in several digestive pathologies such as peptic ulcer, diabetes, colon cancer, or inflammatory bowel disease (IBD). AM is a key protective factor in IBD onset and development, as it regulates cytokine production in the intestinal mucosa, improves vascular and lymphatic regeneration and function and mucosal epithelial repair, and promotes a beneficial gut microbiome composition. AM and PAMP are relevant GI hormones that can be targeted to develop novel therapeutic agents for IBD, other GI disorders, or microbiome-related pathologies.

N-Cycling Microbiome Recruitment Differences Between Modern and Wild Zea mays

Rewilding modern agricultural cultivars by reintroducing beneficial ancestral traits is a proposed approach to improve sustainability of modern agricultural systems. In this study, we compared recruitment of the rhizosphere microbiome among modern inbred maize and wild teosinte to assess whether potentially beneficial plant microbiome traits have been lost through maize domestication and modern breeding. To do this, we surveyed the bacterial and fungal communities along with nitrogen (N)-cycling functional groups in the rhizosphere of six modern domesticated maize genotypes and ancestral wild teosinte genotypes, while controlling for environmental conditions and starting soil inoculum. Using a combination of high-throughput sequencing and quantitative PCR, we found that the rhizosphere microbiomes of modern inbred and wild teosinte differed substantially in taxonomic composition, species richness, and abundance of N-cycling functional genes. Furthermore, the modern versus wild designation explained 27% of the variation in the prokaryotic microbiome, 62% of the variation in N-cycling gene richness, and 66% of N-cycling gene abundance. Surprisingly, we found that modern inbred genotypes hosted microbial communities with higher taxonomic and functional gene diversity within their microbiomes compared with ancestral genotypes. These results imply that modern maize and wild maize differ in their interaction with N-cycling microorganisms in the rhizosphere and that genetic variation exists within genus Zea to potentially “rewild” microbiome-associated traits (i.e., exudation, root phenotypes, and so on).

Probiotic effect of Lactococcus lactis subsp. cremoris RPG-HL-0136 on intestinal mucosal immunity in mice

Lactococcus lactis subsp. cremoris is a lactic acid bacterium commonly used in the cheese manufacturing industry. It is known to produce antibacterial peptides and has recently received attention for its role as a probiotic strain. Here, we report the isolation of a new strain, Lactococcus lactis subsp. cremoris RPG-HL-0136 (RPG0136) from dried compost, which exhibits strong antibacterial activity. When RPG0136 was fed to mice, it increased the intestinal population of two beneficial bacteria, Lactobacillus and Bifidobacterium, whereas it decreased the intestinal population of two harmful bacteria, Bacteroides and Enterobacter. In addition, it increased the concentration of short-chain fatty acids, including acetic acid, propionic acid, and butyric acid, with a simultaneous decrease in pH, and accelerated the catabolic degradation of proteins, lipids, and starch. Lastly, RPG0136 increased the plasma IgG and intestinal mucosal SIgA concentrations and upregulated Reg3r, MUC1, and MUC2 expression to improve the intestinal mucosal immune function. The results of this study suggest that RPG0136 is a potential probiotic strain that supports the growth of a beneficial microbiome by promoting the synthesis of organic acids and enhancing intestinal immune function.

Modulation of the Tomato Rhizosphere Microbiome via Changes in Root Exudation Mediated by the Ethylene Receptor NR.

Plant hormones have been recently shown to exert an indirect influence on the recruitment of plant-associated microbiomes. However, it remains unclear the extent to which the disruption of the ethylene (ET) signaling pathway affects the assembly and functioning of plant-root microbiomes. In this study, the Never-ripe tomato mutant (Nr) was profiled for differences compared to the wild type (control). Tomato plants were subjected to root exudate profiling and the characterization of bacterial and fungal communities. Compared to the control, Nr revealed differences in the composition of root exudates, including lower amounts of esculetin, gallic acid, L-fucose, eicosapentaenoic acid, and higher amounts of β-aldehyde. Interestingly, Nr significantly differed in the composition and functioning of the rhizosphere bacterial community. We also identified the taxa that occurred at relatively higher abundances in Nr, including the genus Lysobacter, which displayed a significant negative correlation with changes in eicosapentaenoic acid and esculetin, and a significant positive correlation with changes in β-aldehyde. Taken together, our study provides evidence that a mutation in the ET receptor exerts predictable changes in the root-associated microbial taxa of tomato plants. These indirect effects can potentially be explored towards new strategies to engineer beneficial plant microbiomes via targeted changes in plant genetics and physiology.

The end of hunger: fertilizers, microbes and plant productivity.

SummaryIt is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and biodiversity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil biodiversity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant‐associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome‐based innovations to promote plant productivity and contribute to the end of hunger.