Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies

Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults

Antibiotics are deployed against bacterial pathogens, but their targeting of conserved microbial processes means they also collaterally perturb the commensal microbiome. To understand acute and persistent effects of antibiotics on the gut microbiota of healthy adult volunteers, we quantify microbiome dynamics before, during, and 6 months after exposure to 4 commonly used antibiotic regimens. We observe an acute decrease in species richness and culturable bacteria after antibiotics, with most healthy adult microbiomes returning to pre-treatment species richness after 2 months, but with an altered taxonomy, resistome, and metabolic output, as well as an increased antibiotic resistance burden. Azithromycin delays the recovery of species richness, resulting in greater compositional distance. A subset of volunteers experience a persistent reduction in microbiome diversity after antibiotics and share compositional similarities with patients hospitalized in intensive care units. These results improve our quantitative understanding of the impact of antibiotics on commensal microbiome dynamics, resilience, and recovery.

Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system

Sucrose is an effective carbon source for creating more reliable and environmentally friendly conditions for shrimp growth by regulating bacteria in biofloc-based culture systems. However, the influence of sucrose addition on the interaction, co-occurrence networks, and assembly mechanisms of bacterial communities in biofloc-based culture systems remains largely unknown. Here, we comprehensively investigated the effects of sucrose addition on bacterial communities in three habitats (water, bioflocs, and gut). The bacterial community structures and compositions of these three habitats became more similar in groups with sucrose addition, compared with those in controls. More than 50% gut bacterial communities were mainly derived from water and biofloc communities in the sucrose addition groups, but only about 33% bacterial communities migrated from water and biofloc to the gut in the control culture system. Sucrose addition accordantly enriched core taxa belonging to the phylum Actinobacteria and the families Rhodobacteraceae and Flavobacteriaceae in water, biofloc, and gut habitats. These core taxa were important for maintaining bacterial network stability in the sucrose addition culture systems and some were identified as keystone taxa for improving shrimp growth. Furthermore, after sucrose addition, gut bacterial community assembly from water and biofloc was dominated by the heterogeneous select with the ratios of 55–91% and 67–83%, respectively, indicating that sucrose addition can directionally shape the bacterial assembly of the shrimp culture system. These results provide a basis for selectively regulating certain beneficial taxa to improve shrimp growth in culture systems.

Rumen and lower gut microbiomes relationship with feed efficiency and production traits throughout the lactation of Holstein dairy cows

Fermentation of dietary nutrients in ruminants' gastrointestinal (GI) tract is an essential mechanism utilized to meet daily energy requirements. Especially in lactating dairy cows, the GI microbiome plays a pivotal role in the breakdown of indigestible plant polysaccharides and supply most AAs, fatty acids, and gluconeogenic precursors for milk synthesis. Although the contribution of the rumen microbiome to production efficiency in dairy cows has been widely researched over the years, variations throughout the lactation and the lower gut microbiome contribution to these traits remain poorly characterized. Therefore, we investigated throughout lactation the relationship between the rumen and lower gut microbiomes with production efficiency traits in Holstein cows. We found that the microbiome from both locations has temporal stability throughout lactation, yet factors such as feed intake levels played a significant role in shaping microbiome diversity. The composition of the rumen microbiome was dependent on feed intake. In contrast, the lower gut microbiome was less dependent on feed intake and associated with a potentially enhanced ability to digest dietary nutrients. Therefore, milk production traits may be more correlated with microorganisms present in the lower gut than previously expected. The current study's findings advance our understanding of the temporal relationship of the rumen and lower gut microbiomes by enabling a broader overview of the gut microbiome and production efficiency towards more sustainable livestock production.

Microbial keystone taxa drive crop productivity through shifting aboveground-belowground mineral element flows

Unbalanced fertilization of nutritional elements is a potential threat to environmental quality and agricultural productivity in acid soil. Harnessing keystone taxa in soil microbiome represents a promising strategy to enhance crop productivity as well as reducing the adverse environmental effects of fertilizers, with the goal of agricultural sustainability. However, there is a lack of information on which and how soil microbial keystone taxa contribute to sustainable crop productivity in acid soil. Here, we examined soil microbial communities (including bacteria, fungi, and archaea) and soil nutrients, and the mineral nutrition and yield of maize subjected to different inorganic and organic fertilization treatments over 35 years in acid soil. The application of organic fertilizer alone or in combination with inorganic fertilizers sustained high maize yield when compared with the other fertilization treatments. Microbial abundances and community structures rather than their alpha diversities explained the main variation in maize yield among different treatments. Sixteen soil keystone taxa (a fungal operational taxonomic unit and 15 bacterial operational taxonomic units) were identified from the microbial co-occurrence network. Among them, five keystone taxa (in Hypocreales, Bryobacter, Solirubrobacterales, Thermomicrobiales, and Roseiflexaceae) contributed to high maize yield through increasing phosphorus flow and inhibiting toxic aluminum and manganese flow from soils to plants. However, the remaining eleven keystone taxa (in Conexibacter, Acidothermus, Ktedonobacteraceae, Deltaproteobacteria, Actinobacteria, Elsterales, Ktedonobacterales, and WPS-2) exerted the opposite effects. As a result, maize productivity varied among different fertilization treatments because of the altered maize mineral element flows by microbial keystone taxa. We conclude that microbial keystone taxa drive crop productivity through shifting aboveground-belowground mineral element flows in acid soil. This study highlights the importance of microbial keystone taxa for sustainable crop productivity in acid soil and provides deep insights into the relationships between soil microbial keystone taxa, crop mineral nutrition, and productivity.

Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities

The composition of microbial communities found in association with plants is influenced by host phenotype and genotype. However, the ways in which specific genetic architectures of host plants shape microbiomes are unknown. Genome duplication events are common in the evolutionary history of plants and influence many important plant traits, and thus, they may affect associated microbial communities. Using experimentally induced whole-genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis thaliana. We performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genetic backgrounds (Columbia versus Landsberg) and ploidy levels (diploid versus tetraploid). We modeled relative abundances of bacterial taxa using a hierarchical Bayesian approach. We found that host genetic background and ploidy level affected rhizosphere community composition. We then tested to what extent microbiomes derived from a specific genetic background or ploidy level affected plant performance by inoculating sterile seedlings with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genetic backgrounds. These findings suggest an interplay between host genetic background and ploidy level and bacterial community assembly with potential ramifications for host fitness. Given the prevalence of ploidy-level variation in both wild and managed plant populations, the effects on microbiomes of this aspect of host genetic architecture could be a widespread driver of differences in plant microbiomes. IMPORTANCE Plants influence the composition of their associated microbial communities, yet the underlying host-associated genetic determinants are typically unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits. Using Arabidopsis thaliana, we characterized how whole-genome duplication affected the composition of rhizosphere bacterial communities and how bacterial communities associated with two host plant genetic backgrounds and ploidy levels affected subsequent plant growth. We observed an interaction between ploidy level and genetic background that affected both bacterial community composition and function. This research reveals how genome duplication, a widespread genetic feature of both wild and crop plant species, influences bacterial assemblages and affects plant growth.

Associations and recovery dynamics of the nasopharyngeal microbiota during influenza-like illness in the aging population

Influenza-like illness (ILI), a disease caused by respiratory pathogens including influenza virus, is a major health concern in older adults. There is little information on changes and recovery dynamics of the nasopharyngeal (NP) microbiota of older adults associated with an ILI. Here, we compared the NP microbiota in older adults reporting (n = 240) or not (n = 157) ILI during the 2014-2015 influenza season at different times of the ILI event. A small but significant effect of the ILI was observed on the microbiota community composition and structure when compared to controls and samples collected at recovery. Corynebacterium was negatively associated with ILI and its abundance increased after recovery. Potential pathobionts such as Haemophilus, Porphyromonas and Gemella had higher abundances during acute-ILI. Stability and changes in the NP microbial community showed individual dynamics. Key core genera, Corynebacterium, Moraxella and Dolosigranulum exhibited higher inter-individual variability in acute-ILI, but showed comparable variability to controls after recovery. Participants in the ILI group with higher core microbiota abundances at the acute phase showed higher microbiota stability after recovery. Our findings demonstrate that acute-ILI is associated with alterations in the phylogenetic structure of the NP microbiota in older adults. The variation in the core microbiota suggests imbalances in the ecosystem, which could potentially play a role in the susceptibility and recovery of the NP microbiota after an ILI event.

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP-taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host-microbiota interactions and their association with disease.

The intestinal microbiota and metabolites in patients with anorexia nervosa

Brain-gut microbiota interactions are intensively studied in connection with various neurological and psychiatric diseases. While anorexia nervosa (AN) pathophysiology is not entirely clear, it is presumably linked to microbiome dysbiosis. We aimed to elucidate the gut microbiota contribution in AN disease pathophysiology. We analyzed the composition and diversity of the gut microbiome of patients with AN (bacteriome and mycobiome) from stool samples before and after renourishment, and compared them to healthy controls. Further, levels of assorted neurotransmitters and short-chain fatty acids (SCFA) were analyzed in stool samples by MS and NMR, respectively. Biochemical, anthropometric, and psychometric profiles were assessed. The bacterial alpha-diversity parameter analyses revealed only increased Chao 1 index in patients with AN before the realimentation, reflecting their interindividual variation. Subsequently, core microbiota depletion signs were observed in patients with AN. Overrepresented OTUs (operation taxonomic units) in patients with AN taxonomically belonged to Alistipes, Clostridiales, Christensenellaceae, and Ruminococcaceae. Underrepresented OTUs in patients with AN were Faecalibacterium, Agathobacter, Bacteroides, Blautia, and Lachnospira. Patients exhibited greater interindividual variation in the gut bacteriome, as well as in metagenome content compared to controls, suggesting altered bacteriome functions. Patients had decreased levels of serotonin, GABA, dopamine, butyrate, and acetate in their stool samples compared to controls. Mycobiome analysis did not reveal significant differences in alpha diversity and fungal profile composition between patients with AN and healthy controls, nor any correlation of the fungal composition with the bacterial profile. Our results show the changed profile of the gut microbiome and its metabolites in patients with severe AN. Although therapeutic partial renourishment led to increased body mass index and improved psychometric parameters, SCFA, and neurotransmitter profiles, as well as microbial community compositions, did not change substantially during the hospitalization period, which can be potentially caused by only partial weight recovery.

Exploring the universal healthy human gut microbiota around the World

The human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, available information is biased towards western microbiomes in both genome databases and most core taxa studies. To tackle these limitations, we tested a database enrichment strategy and analyzed public datasets of whole-genome shotgun data, generated from 545 fecal samples, comprising three gradients of westernization. The NT database was selected as a baseline of biological diversity, subsequently being combined with various studies of interest related to the human microbiota. This enrichment strategy made it possible to improve classification capacity, compared to the original unenriched database, regarding the various lifestyles and populations studied. The effects of incomplete-taxonomy metagenome-assembled genomes on genome database enrichment were also examined, revealing that, while they are helpful, they should be used with caution depending on the taxonomic level of interest. Moreover, in terms of high prevalence, the core analysis revealed a conserved set of bacterial taxa in the healthy human gut microbiota worldwide, despite apparent lifestyle differences. Such taxa show a set of traits, metabolic roles, and ancestral status, making them suitable candidates for a hypothetical phylogenetic core of mutualistic microorganisms co-evolving with the human species.

Microbiome and Cardiovascular Disease

Atherosclerotic cardiovascular disease (ASCVD) is a prime example of a systems disease. In the initial phase, apolipoprotein B-containing cholesterol-rich lipoproteins deposit excess cholesterol in macrophage-like cells that subsequently develop into foam cells. A multitude of systemic as well as environmental factors are involved in further progression of atherosclerotic plaque formation. In recent years, both oral and gut microbiota have been proposed to play an important role in the process at different stages. Particularly bacteria from the oral cavity may easily reach the circulation and cause low-grade inflammation, a recognized risk factor for ASCVD. Gut-derived microbiota on the other hand can influence host metabolism on various levels. Next to translocation across the intestinal wall, these prokaryotes produce a great number of specific metabolites such as trimethylamine and short-chain fatty acids but can also metabolize endogenously formed bile acids and convert these into metabolites that may influence signal transduction pathways. In this overview, we critically discuss the novel developments in this rapidly emerging research field.

Localized reshaping of the fungal community in response to a forest fungal pathogen reveals resilience of Mediterranean mycobiota

Mediterranean forests are facing the impact of pests such as the soilborne Phytophthora cambivora, the causal agent of Ink disease, and this impact is made more severe by global changes. The status and resilience of the soil microbial ecosystem in areas with such a disturbance are little known; however, the assessment of the microbial community is fundamental to preserve the ecosystem functioning under emerging challenges. We profile soil fungal communities in a chestnut stand affected by ink disease in Italy using metabarcoding, and couple high-throughput sequencing with physico-chemical parameters and dendrometric measurements. Since the site also includes an area where the disease symptoms seem to be suppressed, we performed several analyses to search for determinants that may contribute to such difference. We demonstrate that neither pathogen presence nor trees decline associate with the reduction of the residing community diversity and functions, but rather with microbial network reshaping through substitutions and new interactions, despite a conservation of core taxa. We predict interactions between taxa and parameters such as soil pH and C/N ratio, and suggest that disease incidence may also relate with disappearance of pathogen antagonists, including ericoid- and ectomycorrhizal (ECM) fungi. By combining metabarcoding and field studies, we infer the resilient status of the fungal community towards a biotic stressor, and provide a benchmark for the study of other threatened ecosystems.

Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM

BACKGROUND

Men who have sex with men (MSM) have been disproportionately affected by HIV-1 since the beginning of the AIDS pandemic, particularly in the USA and Europe. Compared to men who have sex with women (MSW), MSM have a distinct fecal microbiome regardless of HIV-1 infection. However, it is unclear whether the MSM-associated gut microbiome affects the susceptibility and progression of HIV-1 infection. We studied fecal microbiome profiles, short-chain fatty acids, and blood plasma inflammatory cytokines of 109 HIV-1 seroconverters (SC) from the early, 1984-1985 phase of the HIV-1 pandemic in the Multicenter AIDS Cohort Study (MACS) before and after HIV-1 infection compared to 156 HIV-1-negative MACS MSM (negative controls [NC]).

RESULTS

We found that family Succinivibrionaceae, S24-7, Mogibacteriaceae, Coriobacteriaceae, and Erysipelotrichaceae were significantly higher (p<0.05), whereas Odoribacteraceae, Verucomicrobiaceae, Bacteroidaceae, Barnesiellaceae, and Rikenellaceae were significantly lower (p<0.05), in SC before HIV-1 infection compared to NC. At the species level, Prevotella stercorea, Eubacterium biforme, and Collinsella aerofaciens were significantly higher (p<0.05), and Eubacterium dolichum, Desulfovibrio D168, Alistipes onderdonkii, Ruminococcus torques, Bacteroides fragilis, Bacteroides caccae, Alistipes putredinis, Akkermansia muciniphila, Bacteroides uniformis, and Bacteroides ovatus were significantly lower (p<0.05) in SC before HIV-1 infection compared to NC. After HIV-1 infection, family Prevotellaceae and Victivallaceae and species Bacteroides fragilis and Eubacterium cylindroides were significantly higher (p<0.05) in SC who developed AIDS within 5 years compared to the SC who were AIDS free for more than 10 years without antiretroviral therapy (ART). In addition, family Victivallaceae and species Prevotella stercorea, Coprococcus eutactus, and Butyrivibrio crossotus were significantly higher (p<0.05) and Gemmiger formicilis and Blautia obeum were significantly lower (p<0.05) after HIV-1 infection in SC who developed AIDS within 5-10 years compared to the SC who were AIDS-free for more than 10 years without ART. Furthermore, plasma inflammatory cytokine levels of sCD14, sCD163, interleukin 6, and lipopolysaccharide binding protein were significantly higher in SC with p<0.05 before HIV-1 infection compared to NC.

CONCLUSIONS

Our results suggest that pathogenic changes in the gut microbiome were present in MSM several months prior to infection with HIV-1 in the early phase of the AIDS pandemic in the USA. This was associated with increased inflammatory biomarkers in the blood and risk for development of AIDS. Video abstract.

Modeling approaches for probing cross-feeding interactions in the human gut microbiome

Microbial communities perform emergent activities that are essentially different from those carried by their individual members. The gut microbiome and its metabolites have a significant impact on the host, contributing to homeostasis or disease. Food molecules shape this community, being fermented through cross-feeding interactions of metabolites such as lactate, acetate, and amino acids, or products derived from macromolecule degradation. Mathematical and experimental approaches have been applied to understand and predict the interactions between microorganisms in complex communities such as the gut microbiota. Rational and mechanistic understanding of microbial interactions is essential to exploit their metabolic activities and identify keystone taxa and metabolites. The latter could be used in turn to modulate or replicate the metabolic behavior of the community in different contexts. This review aims to highlight recent experimental and modeling approaches for studying cross-feeding interactions within the gut microbiome. We focus on short-chain fatty acid production and fiber fermentation, which are fundamental processes in human health and disease. Special attention is paid to modeling approaches, particularly kinetic and genome-scale stoichiometric models of metabolism, to integrate experimental data under different diet and health conditions. Finally, we discuss limitations and challenges for the broad application of these modeling approaches and their experimental verification for improving our understanding of the mechanisms of microbial interactions.

Balanced fertilization over four decades has sustained soil microbial communities and improved soil fertility and rice productivity in red paddy soil

The influence of long-term fertilization on soil microbial communities is critical for revealing the association between belowground microbial flora and aboveground crop productivity-a relationship of great importance to food security, environmental protection, and ecosystem functions. Here, we examined shifts in soil chemical properties, microbial communities, and the nutrient uptake and yield of rice subjected to different chemical and organic fertilization treatments over a 40-year period in red paddy soil. Ten different treatments were used: a control without fertilizer, and applications of nitrogen (N), phosphorus (P), potassium (K), NP, NK, PK, NPK, double NPK, or NPK plus manure. Compared with the effects of withholding one or two nutrients (N, P, or K), the balanced application of chemical NPK and organic fertilizers markedly improved soil nutrient status and rice yield. This improvement of soil fertility and rice yield was not associated with bacterial, archaeal, or fungal alpha diversities. The bacterial abundance and community structure and archaeal abundance effectively explained the variation in rice yield, whereas those of fungi did not. The community structure of bacteria and archaea, but not that of fungi, was correlated with soil properties. Among various soil properties, P was the key factor influencing rice yield and soil microbial communities because of the extremely low content of soil available P. Seven keystones at the operational taxonomic unit level were identified: four archaea (belonging to Thermoplasmata, Methanosaeta, Bathyarchaeia, and Nitrososphaeraceae) and three bacteria (in Desulfobacteraceae and Acidobacteriales). These keystones, which were mainly related to soil C and N transformation and pH, may work cooperatively to influence rice yield by regulating soil fertility. Our results collectively suggest that four decades of balanced fertilization has sustained the bacterial and archaeal abundances, bacterial community structure, and keystones, which potentially contribute to soil fertility and rice yield in red paddy soil.

Colon-Targeted Adhesive Hydrogel Microsphere for Regulation of Gut Immunity and Flora

Intestinal immune homeostasis and microbiome structure play a critical role in the pathogenesis and progress of inflammatory bowel disease (IBD), whereas IBD treatment remains a challenge as the first-line drugs show limited therapeutic efficiency and great side effect. In this study, a colon-targeted adhesive core-shell hydrogel microsphere is designed and fabricated by the ingenious combination of advanced gas-shearing technology and ionic diffusion method, which can congregate on colon tissue regulating the gut immune-microbiota microenvironment in IBD treatment. The degradation experiment indicates the anti-acid and colon-targeted property of the alginate hydrogel shell, and the in vivo imaging shows the mucoadhesive ability of the thiolated-hyaluronic acid hydrogel core of the microsphere, which reduces the systematic exposure and prolongs the local drug dwell time. In addition, both in vitro and in vivo study demonstrate that the microsphere significantly reduces the secretion of pro-inflammatory cytokines, induces specific type 2 macrophage differentiation, and remarkably alleviates colitis in the mice model. Moreover, 16S ribosomal RNA sequencing reveals an optimized gut flora composition, probiotics including Bifidobacterium and Lactobacillus significantly augment, while the detrimental communities are inhibited, which benefits the intestinal homeostasis. This finding provides an ideal clinical candidate for IBD treatment.

Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test

This study demonstrated that a microbial community dominated by fungi can be selected and maintained in the long-term under non-sterile conditions, in a pilot-scale packed-bed reactor fed with tannery wastewater. During the start-up phase, the reactor, filled with 0.6 m³ of polyurethane foam cubes, was inoculated with a pure culture of Aspergillus tubingensis and Quebracho tannin, a recalcitrant compound widely used by tannery industry, was used as sole carbon source in the feeding. During the start-up, fungi grew attached as biofilm in carriers that filled the packed-bed reactor. Subsequently, the reactor was tested for the removal of chemical oxygen demand (COD) from an exhaust tanning bath collected from tanneries. The entire experiment lasted 121 days and average removals of 29% and 23% of COD and dissolved organic carbon (DOC) from the tannins bath were achieved, respectively. The evolution of the microbial consortium (bacteria and fungi) was described through biomolecular analyses along the experiment and also developed as a function of the size of the support media.

Model Selection Reveals the Butyrate-Producing Gut Bacterium Coprococcus eutactus as Predictor for Language Development in 3-Year-Old Rural Ugandan Children

Introduction

The metabolic activity of the gut microbiota plays a pivotal role in the gut-brain axis through the effects of bacterial metabolites on brain function and development. In this study we investigated the association of gut microbiota composition with language development of 3-year-old rural Ugandan children.

Methods

We studied the language ability in 139 children of 36 months in our controlled maternal education intervention trial to stimulate children’s growth and development. The dataset includes 1170 potential predictors, including anthropometric and cognitive parameters at 24 months, 542 composition parameters of the children’s gut microbiota at 24 months and 621 of these parameters at 36 months. We applied a novel computationally efficient version of the all-subsets regression methodology and identified predictors of language ability of 36-months-old children scored according to the Bayley Scales of Infant and Toddler Development (BSID-III).

Results

The best three-term model, selected from more than 266 million models, includes the predictors Coprococcus eutactus at 24 months of age, Bifidobacterium at 36 months of age, and language development at 24 months. The top 20 four-term models, selected from more than 77 billion models, consistently include C. eutactus abundance at 24 months, while 14 of these models include the other two predictors as well. Mann–Whitney U tests suggest that the abundance of gut bacteria in language non-impaired children (n = 78) differs from that in language impaired children (n = 61). While anaerobic butyrate-producers, including C. eutactus, Faecalibacterium prausnitzii, Holdemanella biformis, Roseburia hominis are less abundant, facultative anaerobic bacteria, including Granulicatella elegans, Escherichia/Shigella and Campylobacter coli, are more abundant in language impaired children. The overall predominance of oxygen tolerant species in the gut microbiota was slightly higher in the language impaired group than in the non-impaired group (P = 0.09).

Conclusion

Application of the all-subsets regression methodology to microbiota data established a correlation between the relative abundance of the anaerobic butyrate-producing gut bacterium C. eutactus and language development in Ugandan children. We propose that the gut redox potential and the overall bacterial butyrate-producing capacity in the gut are important factors for language development.

Weaning Induced Gut Dysfunction and Nutritional Interventions in Nursery Pigs: A Partial Review

Weaning is one of the most stressful events in the life of a pig. Unsuccessful weaning often leads to intestinal and immune system dysfunctions, resulting in poor growth performance as well as increased morbidity and mortality. The gut microbiota community is a complex ecosystem and is considered an "organ," producing various metabolites with many beneficial functions. In this review, we briefly introduce weaning-associated gut microbiota dysbiosis. Then, we explain the importance of maintaining a balanced gut microbiota. Finally, we discuss dietary supplements and their abilities to restore intestinal balance and improve the growth performance of weaning pigs.

Effect of arabinogalactan on the gut microbiome: A randomized, double-blind, placebo-controlled, crossover trial in healthy adults

OBJECTIVE

Promising evidence suggests beneficial health effects of arabinogalactan, but little is known about the effect of this non-digestible carbohydrate on the gut microbiota, a crucial mediator of human health. The objective of this study was to investigate the effect of an arabinogalactan product (ResistAid) on the fecal microbiome and short-chain fatty acids and gastrointestinal tolerance in healthy adults in a randomized, double-blind, crossover trial.

METHODS

Thirty adults were randomly assigned to consume 15 g/d maltodextrin (control) or ResistAid for 6 wk.

RESULTS

At week 6, compared to placebo, ResistAid supplementation led to a significant decrease in the ratio of fecal Firmicutes to Bacteroidetes, driven by an increase in Bacteroidetes and a decrease in Firmicutes. Moreover, the relative abundance of Bifidobacterium tended to increase with ResistAid supplementation. Additionally, ResistAid significantly decreased the α-diversity of the fecal microbiome. Predicted functional abundances based on 16S rRNA sequences showed that ResistAid supplementation increased the gene abundance of the gut microbiome for α-l-rhamnosidase, β-fructosidase, and levanase, as well as tricarboxylic acid and vitamin B₆ biosynthesis pathways. Fecal isovaleric, valeric, and hexanoic acids were significantly lower after ResistAid consumption. There were no statistically significant changes in bowel habit, stool consistency, gastrointestinal tolerance symptoms, chemistry profile, metabolic panel, or vitals, suggesting that consumption of 15 g daily ResistAid over 6 wk is safe.

CONCLUSION

These results demonstrate that the gut microbiome composition and predicted functions can be modulated by ResistAid consumption, perhaps suggesting a mechanistic explanation on its reported benefits in metabolic parameters and the immune system.

Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health

The human gut microbiome is a complex ecosystem, densely colonised by thousands of microbial species. It varies among individuals and depends on host genotype and environmental factors, such as diet and antibiotics. In this review, we focus on stability and resilience as essential ecological characteristics of the gut microbiome and its relevance for human health. Microbial diversity, metabolic flexibility, functional redundancy, microbe-microbe and host-microbe interactions seem to be critical for maintaining resilience. The equilibrium of the gut ecosystem can be disrupted by perturbations, such as antibiotic therapy, causing significant decreases in functional richness and microbial diversity as well as impacting metabolic health. As a consequence, unbalanced states or even unhealthy stable states can develop, potentially leading to or supporting diseases. Accordingly, strategies have been developed to manipulate the gut microbiome in order to prevent or revert unhealthy states caused by perturbations, including faecal microbiota transplantation, supplementation with probiotics or non-digestible carbohydrates, and more extensive dietary modifications. Nevertheless, an increasing number of studies has evidenced interindividual variability in extent and direction of response to diet and perturbations, which has been attributed to the unique characteristics of each individual's microbiome. From a clinical, translational perspective, the ability to improve resilience of the gut microbial ecosystem prior to perturbations, or to restore its equilibrium afterwards, would offer significant benefits. To be effective, this therapeutic approach will likely need a personalised or subgroup-based understanding of individual genetics, diet, gut microbiome and other environmental factors that might be involved.

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

The human gut microbiota performs functions that are essential for the maintenance of the host physiology. However, characterizing the functioning of microbial communities in relation to the host remains challenging in reference-based metagenomic analyses. Indeed, as taxonomic and functional analyses are performed independently, the link between genes and species remains unclear. Although a first set of species-level bins was built by clustering co-abundant genes, no reference bin set is established on the most used gut microbiota catalog, the Integrated Gene Catalog (IGC). With the aim to identify the best suitable method to group the IGC genes, we benchmarked nine taxonomy-independent binners implementing abundance-based, hybrid and integrative approaches. To this purpose, we designed a simulated non-redundant gene catalog (SGC) and computed adapted assessment metrics. Overall, the best trade-off between the main metrics is reached by an integrative binner. For each approach, we then compared the results of the best-performing binner with our expected community structures and applied the method to the IGC. The three approaches are distinguished by specific advantages, and by inherent or scalability limitations. Hybrid and integrative binners show promising and potentially complementary results but require improvements to be used on the IGC to recover human gut microbial species.

Conducting research on diet-microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design

Diet is one of the strongest modulators of the gut microbiome. However, the complexity of the interactions between diet and the microbial community emphasises the need for a robust study design and continued methodological development. This review aims to summarise considerations for conducting high-quality diet-microbiome research, outline key challenges unique to the field, and provide advice for addressing these in a practical manner useful to dietitians, microbiologists, gastroenterologists and other diet-microbiome researchers. Searches of databases and references from relevant articles were conducted using the primary search terms 'diet', 'diet intervention', 'dietary analysis', 'microbiome' and 'microbiota', alone or in combination. Publications were considered relevant if they addressed methods for diet and/or microbiome research, or were a human study relevant to diet-microbiome interactions. Best-practice design in diet-microbiome research requires appropriate consideration of the study population and careful choice of trial design and data collection methodology. Ongoing challenges include the collection of dietary data that accurately reflects intake at a timescale relevant to microbial community structure and metabolism, measurement of nutrients in foods pertinent to microbes, improving ability to measure and understand microbial metabolic and functional properties, adequately powering studies, and the considered analysis of multivariate compositional datasets. Collaboration across the disciplines of nutrition science and microbiology is crucial for high-quality diet-microbiome research. Improvements in our understanding of the interaction between nutrient intake and microbial metabolism, as well as continued methodological innovation, will facilitate development of effective evidence-based personalised dietary treatments.

When a Neonate Is Born, So Is a Microbiota

In recent years, the role of human microbiota as a short- and long-term health promoter and modulator has been affirmed and progressively strengthened. In the course of one’s life, each subject is colonized by a great number of bacteria, which constitute its specific and individual microbiota. Human bacterial colonization starts during fetal life, in opposition to the previous paradigm of the “sterile womb”. Placenta, amniotic fluid, cord blood and fetal tissues each have their own specific microbiota, influenced by maternal health and habits and having a decisive influence on pregnancy outcome and offspring outcome. The maternal microbiota, especially that colonizing the genital system, starts to influence the outcome of pregnancy already before conception, modulating fertility and the success rate of fertilization, even in the case of assisted reproduction techniques. During the perinatal period, neonatal microbiota seems influenced by delivery mode, drug administration and many other conditions. Special attention must be reserved for early neonatal nutrition, because breastfeeding allows the transmission of a specific and unique lactobiome able to modulate and positively affect the neonatal gut microbiota. Our narrative review aims to investigate the currently identified pre- and peri-natal factors influencing neonatal microbiota, before conception, during pregnancy, pre- and post-delivery, since the early microbiota influences the whole life of each subject.

Bacterial associations in the healthy human gut microbiome across populations

In a microbial community, associations between constituent members play an important role in determining the overall structure and function of the community. The human gut microbiome is believed to play an integral role in host health and disease. To understand the nature of bacterial associations at the species level in healthy human gut microbiomes, we analyzed previously published collections of whole-genome shotgun sequence data, totaling over 1.6 Tbp, generated from 606 fecal samples obtained from four different healthy human populations. Using a Random Forest Classifier, we identified 202 signature bacterial species that were prevalent in these populations and whose relative abundances could be used to accurately distinguish between the populations. Bacterial association networks were constructed with these signature species using an approach based on the graphical lasso. Network analysis revealed conserved bacterial associations across populations and a dominance of positive associations over negative associations, with this dominance being driven by associations between species that are closely related either taxonomically or functionally. Bacterial species that form network modules, and species that constitute hubs and bottlenecks, were also identified. Functional analysis using protein families suggests that much of the taxonomic variation across human populations does not foment substantial functional or structural differences.

Dynamic characteristics and co-occurrence patterns of microbial community in tobacco leaves during the 24-month aging process

Purpose

Microorganisms are important in tobacco aging. These are used to improve the quality of tobacco leaves after threshing and redrying. However, the response of microbial community to the storage environment and time during the tobacco aging process has been less explored. This study aimed to characterize the dynamic changes in microbial community composition and diversity in tobacco leaf samples.

Methods

In this study, 16S and ITS rRNA gene amplicon sequencing techniques were used to characterize the composition, diversity, and co-occurrence of the microbial community in tobacco leaves stored in two different cities during the 24-month aging. Furthermore, the activities of several enzymes were measured spectrophotometrically, and the correlation between the microbiota and enzyme activity was analyzed by network analysis.

Results

Shannon diversity and Chao richness of bacterial communities gradually increased during the first 18 months, whereas those of the fungal community decreased. The relative abundance of Proteobacteria decreased, whereas that of Actinobacteria and Bacteroidetes increased. The proportion of Ascomycota gradually increased during the first 18 months and then rapidly decreased, whereas the proportion of Basidiomycota exhibited a completely opposite pattern. The change in the composition of bacterial community and dominant genera in leaves was not significant between Guiyang city and Maotai city storerooms, but that in the fungal community was significant. The network analysis revealed that fungal networks were more complex and compact than bacterial networks, and a strong negative correlation existed between bacteria and fungi. Moreover, the bacterial microbiome showed a strong positive association with amylase activity, while the fungal microbiome positively correlated with cellulase activity.

Conclusions

This study demonstrated a significant spatiotemporal heterogeneity in the composition of the microbial community during tobacco aging and highlighted the possible influence of the interactions and enzyme activity on microbial diversity and composition. The findings provided a scientific basis for using microorganisms to regulate and control tobacco aging.

A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson's correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.

Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models

The present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota’s abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

BACKGROUND

Aquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod (Gadus morhua) is just 2.5% of total market production. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial.

RESULTS

The results demonstrated there was no significant difference in fish condition, gut morphology or hindgut microbiota between the U. rigida supplemented fish group and the control group at any time-point. This trend was not observed with the A. nodosum treatment. Fish within this group were further categorised as either 'Normal' or 'Lower Growth'. 'Lower Growth' individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota was largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales (Lachnoclostridium).

CONCLUSIONS

Our study indicates that U. rigida macroalgae can be supplemented at 10% inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. nodosum is not a suitable feed supplement in a farmed cod diet.

Dietary Organic Acids Modulate Gut Microbiota and Improve Growth Performance of Nursery Pigs

Feed additives have been suggested to improve animal growth performance through modulating the gut microbiota. The hypothesis of this study was that the combination of two organic acids would exert synergistic effects on the growth performance and gut microbiota of weaning pigs. To test this hypothesis, we followed 398 weaning pigs from two university experiment stations (University of Illinois at Urbana-Champaign (UIUC) and University of Arkansas (UA)) to determine the effects of increasing levels (0%, 0.035%, 0.070%, and 0.105%) of sodium butyrate combined with 0.5% benzoic acid on the growth performance of nursery pigs. At the UA, an additional negative control diet was included and the gut microbiota analysis was carried out. At both universities, increasing levels of sodium butyrate in a diet containing 0.5% benzoic acid improved growth performance, which reached a plateau in the pigs fed 0.035% (SBA0.035) or 0.070% (SBA0.070) butyrate. Gut microbiota analysis revealed that pigs fed the SBA0.035 diet had more diverse microbiota and contained more potentially beneficial bacteria such as Oscillospira, Blautia, and Turicibacter and reduced levels of Veillonella and Sarcina. Results of the present study indicated that the inclusion of sodium butyrate at moderate levels in a diet containing 0.5% benzoic acid improved growth performance of weaning pigs and established potential health benefits on gut microbiota.

Emerging computational tools and models for studying gut microbiota composition and function

The gut microbiota and its metabolites play critical roles in human health and disease. Advances in high-throughput sequencing, mass spectrometry, and other omics assay platforms have improved our ability to generate large volumes of data exploring the temporal variations in the compositions and functions of microbial communities. To elucidate mechanisms, methods and tools are needed that can rigorously model the dependencies within time-series data. Longitudinal data are often sparse and unevenly sampled, and nontrivial challenges remain in determining statistical significance, normalization across different data types, and model validation. In this review, we highlight recent developments in models and software tools for the analysis of time series microbiome and metabolome data, as well as integration of these data.

Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes

Background

Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems.

Objective

The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis.

Methods

Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer’s instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform.

Results

Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane.

Conclusion

The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.

Recovery and resiliency of skin microbial communities on the southern leopard frog (Lithobates sphenocephalus) following two biotic disturbances

BACKGROUND

Microorganisms have intimate functional relationships with invertebrate and vertebrate taxa, with the potential to drastically impact health outcomes. Perturbations that affect microbial communities residing on animals can lead to dysbiosis, a change in the functional relationship, often associated with disease. Batrachochytrium dendrobatidis (Bd), a fungal pathogen of amphibians, has been responsible for catastrophic amphibian population declines around the globe. Amphibians harbor a diverse cutaneous microbiome, including some members which are known to be antagonistic to Bd (anti-Bd). Anti-Bd microorganisms facilitate the ability of some frog populations to persist in the presence of Bd, where other populations that lack anti-Bd microorganisms have declined. Research suggests disease-antagonistic properties of the microbiome may be a function of microbial community interactions, rather than individual bacterial species. Conservation efforts have identified amphibian-associated bacteria that exhibit anti-fungal properties for use as 'probiotics' on susceptible amphibian populations. Probiotic application, usually with a single bacterial species, may benefit from a greater understanding of amphibian species-specific microbiome responses to disturbances (e.g. dysbiosis vs. recovery). We assessed microbiome responses to two microbial disturbance events over multiple time points.

RESULTS

Exposing Lithobates sphenocephalus (southern leopard frog) adults to the biopesticidal bacteria Bacillus thuringiensis, followed by exposure to the fungal pathogen Bd, did not have long term impacts on the microbiome. After initial shifts, microbial communities recovered and returned to a state that resembled pre-disturbance.

CONCLUSIONS

Our results indicate microbial communities on L. sphenocephalus are robust and resistant to permanent shifts from some disturbances. This resiliency of microbial communities may explain why L. sphenocephalus is not experiencing the population declines from Bd that impacts many other species. Conservation efforts may benefit from studies outlining amphibian species-specific microbiome responses to disturbances (e.g. dysbiosis vs. recovery). If microbial communities on a threatened amphibian species are unlikely to recover following a disturbance, additional measures may be implemented to ameliorate the impacts of physical and chemical stressors on host-associated microbial communities.

The Oral Microbiome of Healthy Japanese People at the Age of 90

For a healthy oral cavity, maintaining a healthy microbiome is essential. However, data on healthy microbiomes are not sufficient. To determine the nature of the core microbiome, the oral-microbiome structure was analyzed using pyrosequencing data. Saliva samples were obtained from healthy 90-year-old participants who attended the 20-year follow-up Niigata cohort study. A total of 85 people participated in the health checkups. The study population consisted of 40 male and 45 female participants. Stimulated saliva samples were obtained by chewing paraffin wax for 5 min. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene were amplified by PCR. Pyrosequencing was performed using MiSeq. Operational taxonomic units (OTUs) were assigned on the basis of a 97% identity search in the EzTaxon-e database. Using the threshold of 100% detection on the species level, 13 species were detected: Streptococcus sinensis, Streptococcus pneumoniae, Streptococcus salivarius, KV831974_s, Streptococcus parasanguinis, Veillonella dispar, Granulicatella adiacens, Streptococcus_uc, Streptococcus peroris, KE952139_s, Veillonella parvula, Atopobium parvulum, and AFQU_vs. These species represent potential candidates for the core make-up of the human microbiome.

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study

Animal-associated microbiota is expected to impose crucial effects on the host's fitness-related performance, including reproduction. Most research to date has focused on interactions between the host with its gut microbiota; however, there remain considerable gaps in knowledge regarding microbial consortia in other organs, including interspecific divergence, temporal stability, variation drivers, and their effects on the host. To fill these gaps, we examined oral and vaginal microbiota composition in four free-living mouse species of the genus Apodemus, each varying in the degree of female promiscuity. To assess temporal stability and microbiota resistance to environmental change, we exposed one of the species, Apodemus uralensis, to standardized captive conditions and analyzed longitudinal changes in its microbiota structure. Our results revealed the existence of a "core" oral microbiota that was not only shared among all four species but also persisted almost unchanged in captivity. On the other hand, vaginal microbiota appears to be more plastic in captive conditions and less species-specific in comparison with oral microbiota. This study is amongst the first to describe oral microbiota dynamics. Furthermore, the vaginal microbiota results are especially surprising in light of the well-known role of stable vaginal microbiota as a defense against pathogens. The results indicate the existence of diverse mechanisms that shape each microbiota. On the other hand, our data provides somewhat ambiguous support for the systematic effect of phylogeny and social system on both oral and vaginal microbiota structures.

Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community

Major changes in the microbiome are associated with health and disease. Some microbiome states persist despite seemingly unfavorable conditions, such as the proliferation of aerobe-anaerobe communities in oxygen-exposed environments in wound infections or small intestinal bacterial overgrowth. Mechanisms underlying transitions into and persistence of these states remain unclear. Using two microbial taxa relevant to the human microbiome, we combine genome-scale mathematical modeling, bioreactor experiments, transcriptomics, and dynamical systems theory to show that multistability and hysteresis (MSH) is a mechanism describing the shift from an aerobe-dominated state to a resilient, paradoxically persistent aerobe-anaerobe state. We examine the impact of changing oxygen and nutrient regimes and identify changes in metabolism and gene expression that lead to MSH and associated multi-stable states. In such systems, conceptual causation-correlation connections break and MSH must be used for analysis. Using MSH to analyze microbiome dynamics will improve our conceptual understanding of stability of microbiome states and transitions between states.

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments

BACKGROUND

Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood.

RESULTS

Here, we used a combined metagenomic and metatranscriptomic approach to investigate the metabolic activity of methanogens in mangrove sediments in Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing one class (Methanofastidiosa) and five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, and Methanosarcinales) of methanogens, including the two novel methanogens. Comprehensive annotation indicated the presence of an H₂-dependent methylotrophic methanogenesis pathway in Methanofastidiosa and Methanomassiliicoccales. Based on the functional gene analysis, hydrogenotrophic and methylotrophic methanogenesis are the dominant pathways in mangrove sediments. MAG mapping revealed that hydrogenotrophic Methanomicrobiales were the most abundant methanogens and that methylotrophic Methanomassiliicoccales were the most active methanogens in the analyzed sediment profile, suggesting their important roles in methane production.

CONCLUSIONS

Partial or near-complete genomes of two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales, in natural environments were recovered and analyzed here for the first time. The presented findings highlight the ecological importance of the two novel methanogens and complement knowledge of how methane is produced in mangrove ecosystem. This study implies that two novel methanogens play a vital role in carbon cycle. Video Abstract.

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate. With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in the metabolism of these methanogens towards co-utilization of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.

[Gut Microbiota and Pancreatobiliary System]

The gut microbiota is part of the human body that is involved in body metabolism and the occurrence of various diseases. Detecting and analyzing their genetic information (microbiome) is as important as analyzing human genes. The core microbiome, the key functional genes shared by all humans, helps better understand the physiology of the human body. Information on the gut microbiome of a diseased person can help diagnose and treat disease. The pancreatobiliary system releases functional antimicrobial substances, such as bile acids and antimicrobial peptides, which affect the gut microbiota directly. In response, the gut microbiota influences pancreatobiliary secretion by controlling the generation and emission of substances through indirect signaling. This crosstalk maintains homeostasis of the pancreatobiliary system secretion and microbiota. Dysbiosis and disease can occur if this fails to work properly. Bile acid therapy has been used widely and may affect the microbial environment in the intestine. An association of the gut microbiota has been reported in many cases of pancreatobiliary diseases, including malignant tumors. Traditionally, most pancreatobiliary diseases are accompanied by infections from the gut microbiota, which is an important target for treatment. The pancreatobiliary system can control its function through physical and drug therapy. This may be a new pioneering field in the study or treatment of the gut microbiota.

Alterations of the bile microbiome in primary sclerosing cholangitis

BACKGROUND

Patients with primary sclerosing cholangitis (PSC) display an altered colonic microbiome compared with healthy controls. However, little is known on the bile duct microbiome and its interplay with bile acid metabolism in PSC.

METHODS

Patients with PSC (n=43) and controls without sclerosing cholangitis (n=22) requiring endoscopic retrograde cholangiography were included prospectively. Leading indications in controls were sporadic choledocholithiasis and papillary adenoma. A total of 260 biospecimens were collected from the oral cavity, duodenal fluid and mucosa and ductal bile. Microbiomes of the upper alimentary tract and ductal bile were profiled by sequencing the 16S-rRNA-encoding gene (V1-V2). Bile fluid bile acid composition was measured by high-performance liquid chromatography mass spectrometry and validated in an external cohort (n=20).

RESULTS

The bile fluid harboured a diverse microbiome that was distinct from the oral cavity, the duodenal fluid and duodenal mucosa communities. The upper alimentary tract microbiome differed between PSC patients and controls. However, the strongest differences between PSC patients and controls were observed in the ductal bile fluid, including reduced biodiversity (Shannon entropy, p=0.0127) and increase of pathogen Enterococcus faecalis (FDR=4.18×10^-5) in PSC. Enterococcus abundance in ductal bile was strongly correlated with concentration of the noxious secondary bile acid taurolithocholic acid (r=0.60, p=0.0021).

CONCLUSION

PSC is characterised by an altered microbiome of the upper alimentary tract and bile ducts. Biliary dysbiosis is linked with increased concentrations of the proinflammatory and potentially cancerogenic agent taurolithocholic acid.

Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration

The human gastrointestinal (GI) tract contains communities of microbes (bacteria, fungi, viruses) that vary by anatomic location and impact human health. Microbial communities differ in composition based on age, diet, and location in the gastrointestinal tract. Differences in microbial composition have been associated with chronic disease states. In terms of function, microbial metabolites provide key signals that help maintain healthy human physiology. Alterations of the healthy gastrointestinal microbiome have been linked to the development of various disease states including inflammatory bowel disease, diabetes, and colorectal cancer. While the definition of a healthy GI microbiome cannot be precisely identified, features of a healthy gut microbiome include relatively greater biodiversity and relative abundances of specific phyla and genera. Microbes with desirable functional profiles for the human host have been identified, in addition to specific metabolic features of the microbiome. This article reviews the composition and function of the healthy human GI microbiome, including the relative abundances of different bacterial taxa and the specific metabolic pathways and classes of microbial metabolites contributing to human health and disease prevention.

Systematic review: gastric microbiota in health and disease

BACKGROUND

Helicobacter pylori is the most infamous constituent of the gastric microbiota and its presence is the strongest risk factor for gastric cancer and other gastroduodenal diseases. Although historically the healthy stomach was considered a sterile organ, we now know it is colonised with a complex microbiota. However, its role in health and disease is not well understood.

AIM

To systematically explore the literature on the gastric microbiota in health and disease as well as the gut microbiota after bariatric surgery.

METHODS

A systematic search of online bibliographic databases MEDLINE/EMBASE was performed between 1966 and February 2019 with screening in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Randomised controlled trials, cohort studies and observational studies were included if they reported next-generation sequencing derived microbiota analysis on gastric aspirate/tissue or stool samples (bariatric surgical outcomes).

RESULTS

Sixty-five papers were eligible for inclusion. With the exception of H pylori-induced conditions, overarching gastric microbiota signatures of health or disease could not be determined. Gastric carcinogenesis induces a progressively altered microbiota with an enrichment of oral and intestinal taxa as well as significant changes in host gastric mucin expression. Proton pump inhibitors usage increases gastric microbiota richness. Bariatric surgery is associated with an increase in potentially pathogenic proteobacterial species in patient stool samples.

CONCLUSION

While H pylori remains the single most important risk factor for gastric disease, its capacity to shape the collective gastric microbiota remains to be fully elucidated. Further studies are needed to explore the intricate host/microbial and microbial/microbial interplay.

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species

BACKGROUND

Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world's domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra).

RESULTS

Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant.

CONCLUSIONS

Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.

Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants

BACKGROUND

Stress-induced hormones are essential for plants to modulate their microbiota and dynamically adjust to the environment. Despite the emphasis of the role of the phytohormone ethylene in the plant physiological response to heterospecific neighbour detection, less is known about how this activated signal mediates focal plant rhizosphere microbiota to enhance plant fitness. Here, using 3 years of peanut (Arachis hypogaea L.), a legume, and cyanide-containing cassava (Manihot esculenta Crantz) intercropping and peanut monocropping field, pot and hydroponic experiments in addition to exogenous ethylene application and soil incubation experiments, we found that ethylene, a cyanide-derived signal, is associated with the chemical identification of neighbouring cassava and the microbial re-assemblage in the peanut rhizosphere.

RESULTS

Ethylene production in peanut roots can be triggered by cyanide production of neighbouring cassava plants. This gaseous signal alters the microbial composition and re-assembles the microbial co-occurrence network of peanut by shifting the abundance of an actinobacterial species, Catenulispora sp., which becomes a keystone in the intercropped peanut rhizosphere. The re-assembled rhizosphere microbiota provide more available nutrients to peanut roots and support seed production.

CONCLUSIONS

Our findings suggest that root ethylene acts as a signal with a dual role. It plays a role in perceiving biochemical cues from interspecific neighbours, and also has a regulatory function in mediating the rhizosphere microbial assembly, thereby enhancing focal plant fitness by improving seed production. This discovery provides a promising direction to develop novel intercropping strategies for targeted manipulations of the rhizosphere microbiome through phytohormone signals. Video abstract.

Interactions between Intestinal Microflora/Probiotics and the Immune System

The digestive tract is home to millions of microorganisms and is the main and most important part of bacterial colonization. On one hand, the abundant bacterial community in intestinal tissues may pose potential health challenges such as inflammation and sepsis in cases of opportunistic invasion. Thus, the immune system has evolved and adapted to maintain the symbiotic relationship between host and microbiota. On the other hand, the intestinal microflora also exerts an immunoregulatory function to maintain host immune homeostasis, which cannot be neglected. In addition, the interaction of either microbiota or probiotics with immune system in regard to therapeutic applications is an area of great interest, and novel therapeutic strategies remain to be investigated. The review will elucidate interactions between intestinal microflora/probiotics and the immune system as well as novel therapeutic strategies.

Skin Exposure to Narrow Band Ultraviolet (UVB) Light Modulates the Human Intestinal Microbiome

The recent worldwide rise in idiopathic immune and inflammatory diseases such as multiple sclerosis (MS) and inflammatory bowel diseases (IBD) has been linked to Western society-based changes in lifestyle and environment. These include decreased exposure to sunlight/UVB light and subsequent impairment in the production of vitamin D, as well as dysbiotic changes in the makeup of the gut microbiome. Despite their association, it is unclear if there are any direct links between UVB light and the gut microbiome. In this study we investigated whether exposing the skin to Narrow Band Ultraviolet B (NB-UVB) light to increase serum vitamin D levels would also modulate the makeup of the human intestinal microbiota. The effects of NB-UVB light were studied in a clinical pilot study using a healthy human female cohort (n = 21). Participants were divided into those that took vitamin D supplements throughout the winter prior to the start of the study (VDS+) and those who did not (VDS−). After three NB-UVB light exposures within the same week, the serum 25(OH)D levels of participants increased on average 7.3 nmol/L. The serum response was negatively correlated to the starting 25-hydroxy vitamin D [25(OH)D] serum concentration. Fecal microbiota composition analysis using 16S rRNA sequencing showed that exposure to NB-UVB significantly increased alpha and beta diversity in the VDS− group whereas there were no changes in the VDS+ group. Bacteria from several families were enriched in the VDS− group after the UVB exposures according to a Linear Discriminant Analysis (LDA) prediction, including Lachnospiracheae, Rikenellaceae, Desulfobacteraceae, Clostridiales vadinBB60 group, Clostridia Family XIII, Coriobacteriaceae, Marinifilaceae, and Ruminococcus. The serum 25(OH)D concentrations showed a correlation with the relative abundance of the Lachnospiraceae, specifically members of the Lachnopsira and Fusicatenibacter genera. This is the first study to show that humans with low 25(OH)D serum levels display overt changes in their intestinal microbiome in response to NB-UVB skin exposure and increases in 25(OH)D levels, suggesting the existence of a novel skin-gut axis that could be used to promote intestinal homeostasis and health.

Clinical Trial Registration:clinicaltrials.gov, NCT03962673. Registered 23 May 2019 – Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT03962673?term=NCT03962673&rank=1.

Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes

Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.