Microbial Contribution Research Articles

The interplay between microbial communities and soil properties.

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

Multi-faceted attributes of salivary cell-free DNA as liquid biopsy biomarkers for gastric cancer detection

BackgroundRecent advances in circulating cell-free DNA (cfDNA) analysis from biofluids have opened new avenues for liquid biopsy (LB). However, current cfDNA LB assays are limited by the availability of existing information on established genotypes associated with tumor tissues. Certain cancers present with a limited list of established mutated cfDNA biomarkers, and thus, nonmutated cfDNA characteristics along with alternative biofluids are needed to broaden the available cfDNA targets for cancer detection. Saliva is an intriguing and accessible biofluid that has yet to be fully explored for its clinical utility for cancer detection.MethodsIn this report, we employed a low-coverage single stranded (ss) library NGS pipeline “Broad-Range cell-free DNA-Seq” (BRcfDNA-Seq) using saliva to comprehensively investigate the characteristics of salivary cfDNA (ScfDNA). The identification of cfDNA features has been made possible by applying novel cfDNA processing techniques that permit the incorporation of ultrashort, ss, and jagged DNA fragments. As a proof of concept using 10 gastric cancer (GC) and 10 noncancer samples, we examined whether ScfDNA characteristics, including fragmentomics, end motif profiles, microbial contribution, and human chromosomal mapping, could differentiate between these two groups.ResultsIndividual and integrative analysis of these ScfDNA features demonstrated significant differences between the two cohorts, suggesting that disease state may affect the ScfDNA population by altering nuclear cleavage or the profile of contributory organism cfDNA to total ScfDNA. We report that principal component analysis integration of several aspects of salivary cell-free DNA fragmentomic profiles, genomic element profiles, end-motif sequence patterns, and distinct oral microbiome populations can differentiate the two populations with a p value of < 0.0001 (PC1).ConclusionThese novel features of ScfDNA characteristics could be clinically useful for improving saliva-based LB detection and the eventual monitoring of local or systemic diseases.

Adaptations of soil microbes to stoichiometric imbalances in regulating their carbon use efficiency under a range of different grazing intensities

Grazing has a profound impact on the availability of soil resources like carbon (C), nitrogen (N), and phosphorus (P) in grasslands. These changes can potentially make it difficult to meet microbial elemental demands, thus affecting microbial C use efficiency (CUE) and soil C dynamics. Nevertheless, it remains unclear how soil microbes respond to stoichiometric imbalances and their consequent effect on microbial CUE. In this study, we investigated the stoichiometry of soil labile resources, microbial biomass, extracellular enzymes, as well as the microbial community composition and microbial CUE, microbial respiration, microbial quotient (qMB), and soil organic carbon (SOC) changes, at sites with four grazing intensities (no grazing, light, medium, and heavy grazing) in a temperate steppe of northern China. Grazing led to decreased stoichiometric imbalances between soil labile resources and microbial biomass, thereby exacerbating limitations of available C on soil microbes. To alleviate this limitation of C, microbes raised the microbial threshold elemental ratios and microbial biomass, and increased fungi dominance rather than increased activities of C-, N-, and P- acquiring enzymes due to increased microbial own growth. Microbes also improved microbial CUE, qMB, and microbial respiration while decreasing SOC under increasing grazing intensity. These integrated adaptations denote that grazing can reduce SOC which is closely affected by soil microbial C utilization induced by resource change conditions despite the increased microbial biomass contribution to SOC. These findings illustrate the regulation of stoichiometric imbalances in soil C dynamics driven by microbes under grazing and improve our understanding of how stoichiometric changes influences soil C flows in semi-arid grassland.

Seasonal dynamics and interaction of shallow groundwater geochemical properties and microbial community patterns

Characterizing the temporal variation of microbial community is essential to better understand the biogeochemical cycles in groundwater systems. So far, the roles of microbial metabolisms in affecting the seasonal variation of shallow groundwater biogeochemistry remains largely unknown. In this study, shallow groundwater was sampled during rainy season (RS) and dry season (DS) at Yuncheng Basin, a semi-arid region in northern China. Based on results of hydrogeochemical, environmental isotopic (δ18O, δ2H and δ13C) and high-throughput sequencing analysis, we found that 1) the seasonal variation of groundwater geochemistry is closely related to the stronger evaporation, mineral dissolution, and anthropogenic activities in DS and enhanced cation exchange and stronger recharge in RS; 2) the seasonal dynamics of microbial community were mostly driven by groundwater temperature (T) and total organic carbon (TOC); 3) potential functional consequences indicated stronger microbial carbon fixation and denitrification in RS; 4) the microbial contribution to SO42− in groundwater may increase when gypsum dissolution was weaker while sulfur oxidation was stronger during RS. Our findings suggest that the seasonal variation of microbial metabolisms play important roles in the dynamic characteristics of groundwater geochemistry.

Enhanced microbial contribution to mineral-associated organic carbon accrual in drained wetlands: Beyond direct lignin-iron interactions

Drainage poses a major threat to the tremendous soil organic carbon (SOC) reservoir in wetlands. However, drainage-induced carbon loss may be mitigated by the accumulation of mineral-associated organic carbon (MAOC) via both microbial processes and iron (Fe)-organic matter (especially lignin) interactions, which remains under-investigated in wetlands. Here using a novel analytical approach, we quantitatively examined the response of MAOC to drainage and the driving mechanisms in four distinct wetlands. Contrary to the prevailing assumption, MAOC consisted a significant fraction (7%∼91%) of wetland SOC, and increased with mineral-bound (microbial-dominated) sugars, but decreased with Fe-bound lignin phenols in SOC assessed after removal of reactive soil minerals. Furthermore, mineral-bound sugars increased with clay and reactive aluminum instead of Fe, and overrode Fe-bound lignin regarding contribution to MAOC after long-term drainage. These results indicate that microbial processes leading to microbial sugars accumulation played a prominent role in wetland MAOC accrual after long-term drainage, especially in soils rich in reactive Al and clay. Our study highlights the prevalent yet under-investigated microbial regulation on MAOC accrual in wetlands during long-term drainage. Given the large stock and persistence of MAOC in wetlands, its increase may partly compensate for particulate organic carbon loss during drainage, and may underpin wetland SOC stabilization in the long term.

Metagenome-wide association study of gut microbiome features for myositis

PurposeThe clinical relevance and pathogenic role of gut microbiome in both myositis and its associated interstitial lung disease (ILD) are still unclear. The purpose of this study was to investigate the role of gut microbiome in myositis through comprehensive metagenomic-wide association studies (MWAS). MethodsWe conducted MWAS of the myositis gut microbiome in a Chinese cohort by using whole-genome shotgun sequencing of high depth, including 30 myositis patients and 31 healthy controls (HC). Among the myositis patients, 11 developed rapidly progressive interstitial lung disease (RP-ILD) and 10 had chronic ILD (C-ILD). ResultsAnalysis for overall distribution level of the bacteria showed Alistipes onderdonkii, Parabacteroides distasonis and Escherichia coli were upregulated, Lachnospiraceae bacterium GAM79, Roseburia intestinalis, and Akkermansia muciniphila were downregulated in patients with myositis compared to HC. Bacteroides thetaiotaomicron, Parabacteroides distasonis and Escherichia coli were upregulated, Bacteroides A1C1 and Bacteroides xylanisolvens were downregulated in RP-ILD cases compared with C-ILD cases.A variety of biological pathways related to metabolism were enriched in the myositis and HC, RP-ILD and C-ILD comparison. And in the analyses for microbial contribution in metagenomic biological pathways, we have found that E. coli played an important role in the pathway expression in both myositis group and myositis-associated RP-ILD group. Anti-PL-12 antibody, anti-Ro-52 antibody, and anti-EJ antibody were found to have positive correlation with bacterial diversity (Shannon-wiener diversity index and Chao1, richness estimator) between myositis group and control groups. The combination of E. coli and R. intestinalis could distinguish myositis group from HC effectively. R. intestinalis can also be applied in the distinguishment of RP-ILD group vs. C-ILD group in myositis patients. ConclusionOur MWAS study first revealed the link between gut microbiome and pathgenesis of myositis, which may help us understand the role of gut microbiome in the etiology of myositis and myositis-associated RP-ILD.

Genetic and gut microbiome determinants of SCFA circulating and fecal levels, postprandial responses and links to chronic and acute inflammation

ABSTRACT Short-chain fatty acids (SCFA) are involved in immune system and inflammatory responses. We comprehensively assessed the host genetic and gut microbial contribution to a panel of eight serum and stool SCFAs in two cohorts (TwinsUK, n = 2507; ZOE PREDICT-1, n = 328), examined their postprandial changes and explored their links with chronic and acute inflammatory responses in healthy individuals and trauma patients. We report low concordance between circulating and fecal SCFAs, significant postprandial changes in most circulating SCFAs, and a heritable genetic component (average h2 : serum = 14%(SD = 14%); stool = 12%(SD = 6%)). Furthermore, we find that gut microbiome can accurately predict their fecal levels (AUC>0.71) while presenting weaker associations with serum. Finally, we report different correlation patterns with inflammatory markers depending on the type of inflammatory response (chronic or acute trauma). Our results illustrate the breadth of the physiological relevance of SCFAs on human inflammatory and metabolic responses highlighting the need for a deeper understanding of this important class of molecules.

Yeasts are essential for mucilage degradation of coffee beans during wet fermentation.

During wet fermentation, mucilage layers in coffee cherries must be removed completely. To explain mucilage degradation, several controversial hypotheses have been proposed. The aim of this work was to improve our understanding of the kinetics of mucilage breakdown. Pulped coffee beans were wet fermented with seven different treatments for 36 h. Endogenous bacteria and yeasts are selectively suppressed, and pectinases or lactic acid are added. They also involve maintaining the beans at pH 7 throughout fermentation and using spontaneous fermentation without additives as a control. During spontaneous fermentation, yeast and lactic acid bacteria were detected and significantly increased to 5.5 log colony-forming units(CFU)/mL and 5.2 log CFU/mL, respectively. In the first 12 h of fermentation, there was a significant degree of endogenous pectinolytic activity, which resulted in partly destroyed beans in the absence of microorganisms. By adding pectinase and lactic acid to the fermentation mass, the breakdown process was accelerated in less than 8 h. When yeast was present throughout the fermentation, complete degradation was achieved. Bacteria played no critical role in the degradation. Klebsiella pneumoniae and Erwinia soli were found in a lower population and showed weaker pectinolytic activities compared to Hanseniaspora uvarum and Pichia kudriavzevii. During wet fermentation, mucilage degradation appears to be mediated by endogenous enzymes at the early stage, whereas microbial contributions, mainly yeasts, occur subsequently. H. uvarum and P. kudriavzevii may be promising candidates to be tested in future studies as coffee starter cultures to better control the mucilage degradation process.

Influence of tree species on soil microbial residue accumulation and distribution among soil aggregates in subtropical plantations of China

BackgroundMicrobial residues are significant contributors to stable soil organic carbon (SOC). Soil aggregates effectively protect microbial residues against decomposition; thus, microbial residue accumulation and distribution among soil aggregates determine long-term SOC stability. However, how tree species influence accumulation and distribution of soil microbial residues remains largely unknown, hindering the chances to develop policies for SOC management. Here, we investigated microbial residue accumulation and distribution in soil aggregates under four subtropical tree species (Cunninghamia lanceolata, Pinus massoniana, Michelia macclurei, and Schima superba) after 29 years of afforestation.ResultsAccumulation of microbial residues in the 0–10 cm soil layer was 13.8–26.7% higher under S. superba than that under the other tree species. A structural equation model revealed that tree species affected the accumulation of microbial residues directly by altering fungal biomass. Additionally, tree species significantly affected microbial residue distribution and contribution to SOC in the top 20 cm soil. In particular, microbial residue distribution was 17.2–33.4% lower in large macro-aggregates (LMA) but 60.1–140.7% higher in micro-aggregates (MA) under S. superba than that under the other species in the 0–10 cm soil layer, and 14.3–19.0% lower in LMA but 43–52.1% higher in MA under S. superba than that under C. lanceolata and M. macclurei in the 10–20 cm soil layer. Moreover, the contribution of microbial residues to SOC was 44.4–47.5% higher under S. superba than under the other tree species. These findings suggest a higher stability of microbial residues under S. superba than that under the other studied tree species.ConclusionsOur results demonstrate that tree species influence long-term microbial persistence in forest soils by affecting accumulation and stabilization of microbial residues.

Grazing and reclamation-induced microbiome alterations drive organic carbon stability within soil aggregates in alpine steppes

Grazing and reclamation are the major modulators of soil organic carbon (SOC) stability in alpine steppes. However, our understanding of changes in SOC caused by grazing and reclamation at the aggregate scale is limited, and the mediating role of microorganisms remains unclear. Here, based on a long-term observation transect, we selected three land-use types: a long-term enclosed natural steppe (NS), a grazed steppe (GS), and a steppe reclaimed as cropland (CL). We investigated the impacts of grazing and reclamation on soil aggregate distributions, SOC fractions and the microbial community, and microbial contributions to SOC stability. Overall, GS and CL significantly decreased the proportion of >2 mm aggregates (by 32.25–33.72%), and enhanced SOC stability within different aggregate sizes, with the highest SOC stability observed in 0.25–2 mm and <0.25 mm sizes. GS significantly decreased bacterial diversity and increased the relative abundance of Gammaproteobacteria, while CL significantly increased microbial diversity and the relative abundance of Alphaproteobacteria. Importantly, GS enhanced the complexity of the bacterial OTUs networks in >2 mm and <0.25 mm aggregates. GS and CL caused changes in the assembly processes of bacterial communities, shifting from being mainly controlled by variable selection to being mainly controlled by homogenizing dispersal. However, there were only minor differences observed in the microbial community assembly within different aggregate sizes under the same treatment. Random forest models and correlation analysis revealed that the bacterial community, especially the network patterns and community assembly, was a key determinant of SOC stability in soil aggregates. In conclusion, we emphasize the important contribution of soil bacterial network patterns and community assembly to SOC stability in the context of human activities, providing information that may be useful for developing alpine steppe management strategies to enhance soil carbon sequestration.

Microbially mediated climate feedbacks from wetland ecosystems.

Wetlands are crucial nodes in the carbon cycle, emitting approximately 20% of global CH4 while also sequestering 20%-30% of all soil carbon. Both greenhouse gas fluxes and carbon storage are driven by microbial communities in wetland soils. However, these key players are often overlooked or overly simplified in current global climate models. Here, we first integrate microbial metabolisms with biological, chemical, and physical processes occurring at scales from individual microbial cells to ecosystems. This conceptual scale-bridging framework guides the development of feedback loops describing how wetland-specific climate impacts (i.e., sea level rise in estuarine wetlands, droughts and floods in inland wetlands) will affect future climate trajectories. These feedback loops highlight knowledge gaps that need to be addressed to develop predictive models of future climates capturing microbial contributions. We propose a roadmap connecting environmental scientific disciplines to address these knowledge gaps and improve the representation of microbial processes in climate models. Together, this paves the way to understand how microbially mediated climate feedbacks from wetlands will impact future climate change.

A rapid assay for assessing bacterial effects on Arabidopsis thermotolerance

BackgroundThe role of beneficial microbes in mitigating plant abiotic stress has received considerable attention. However, the lack of a reproducible and relatively high-throughput screen for microbial contributions to plant thermotolerance has greatly limited progress in this area, this slows the discovery of novel beneficial isolates and the processes by which they operate.ResultsWe designed a rapid phenotyping method to assess the effects of bacteria on plant host thermotolerance. After testing multiple growth conditions, a hydroponic system was selected and used to optimize an Arabidopsis heat shock regime and phenotypic evaluation. Arabidopsis seedlings germinated on a PTFE mesh disc were floated onto a 6-well plate containing liquid MS media, then subjected to heat shock at 45 °C for various duration. To characterize phenotype, plants were harvested after four days of recovery to measure chlorophyll content. The method was extended to include bacterial isolates and to quantify bacterial contributions to host plant thermotolerance. As an exemplar, the method was used to screen 25 strains of the plant growth promoting Variovorax spp. for enhanced plant thermotolerance. A follow-up study demonstrated the reproducibility of this assay and led to the discovery of a novel beneficial interaction.ConclusionsThis method enables rapid screening of individual bacterial strains for beneficial effects on host plant thermotolerance. The throughput and reproducibility of the system is ideal for testing many genetic variants of Arabidopsis and bacterial strains.

Soil microbe-mediated carbon and nitrogen cycling during primary succession of biological soil crusts in tailings ponds

Tailings ponds resulting from mining operations have led to serious environmental hazards, and their bioremediation is an area of ongoing exploration. Primary succession represents the starting point of biotic community establishment and development, with soil carbon and nitrogen cycling being critical to this process. To investigate the soil microbial-mediated carbon and nitrogen cycling patterns accompanying primary succession, we selected three types of tailings ponds as study areas and set up sampling sites for different stages of primary succession. The results showed that primary succession promoted microbe-mediated carbon and nitrogen cycling. It also led to improvements in soil nutrient availability and enzyme activity. In primary succession, the main pathways of carbon cycling are 3HP and rTCA, and nitrogen cycling is nitrate assimilation. In the early stages, microbes mediated more anaerobic and microaerobic processes. As succession proceeded, the pattern of microbial contributions to the carbon and nitrogen cycles changed. As succession proceeds, the functional metabolic potential of the carbon cycle gradually rises, while the nitrogen cycle shows a dramatic increase after the accumulation of autotrophic biomass. In addition, we found a positive coupling pattern between the carbon and nitrogen cycles. These findings support the optimization of bioremediation strategies for tailings ponds.

Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial

The gut microbiome is emerging as a key modulator of human energy balance. Prior studies in humans lacked the environmental and dietary controls and precision required to quantitatively evaluate the contributions of the gut microbiome. Using a Microbiome Enhancer Diet (MBD) designed to deliver more dietary substrates to the colon and therefore modulate the gut microbiome, we quantified microbial and host contributions to human energy balance in a controlled feeding study with a randomized crossover design in young, healthy, weight stable males and females (NCT02939703). In a metabolic ward where the environment was strictly controlled, we measured energy intake, energy expenditure, and energy output (fecal and urinary). The primary endpoint was the within-participant difference in host metabolizable energy between experimental conditions [Control, Western Diet (WD) vs. MBD]. The secondary endpoints were enteroendocrine hormones, hunger/satiety, and food intake. Here we show that, compared to the WD, the MBD leads to an additional 116 ± 56 kcals (P < 0.0001) lost in feces daily and thus, lower metabolizable energy for the host (89.5 ± 0.73%; range 84.2-96.1% on the MBD vs. 95.4 ± 0.21%; range 94.1-97.0% on the WD; P < 0.0001) without changes in energy expenditure, hunger/satiety or food intake (P > 0.05). Microbial 16S rRNA gene copy number (a surrogate of biomass) increases (P < 0.0001), beta-diversity changes (whole genome shotgun sequencing; P = 0.02), and fermentation products increase (P < 0.01) on an MBD as compared to a WD along with significant changes in the host enteroendocrine system (P < 0.0001). The substantial interindividual variability in metabolizable energy on the MBD is explained in part by fecal SCFAs and biomass. Our results reveal the complex host-diet-microbiome interplay that modulates energy balance.

Organic-rich bimineralic ooids record biological processes in Shark Bay, Western Australia.

Marine ooids have formed in microbially colonized environments for billions of years, but the microbial contributions to mineral formation in ooids continue to be debated. Here we provide evidence of these contributions in ooids from Carbla Beach, Shark Bay, Western Australia. Dark 100-240 μm diameter ooids from Carbla Beach contain two different carbonate minerals. These ooids have 50-100 μm-diameter dark nuclei that contain aragonite, amorphous iron sulfide, detrital aluminosilicate grains and organic matter, and 10-20 μm-thick layers of high-Mg calcite that separate nuclei from aragonitic outer cortices. Raman spectroscopy indicates organic enrichments in the nuclei and high-Mg calcite layers. Synchrotron-based microfocused X-ray fluorescence mapping reveals high-Mg calcite layers and the presence of iron sulfides and detrital grains in the peloidal nuclei. Iron sulfide grains within the nuclei indicate past sulfate reduction in the presence of iron. The preservation of organic signals in and around high-Mg calcite layers and the absence of iron sulfide suggest that organics stabilized high-Mg calcite under less sulfidic conditions. Aragonitic cortices that surround the nuclei and Mg-calcite layers do not preserve microporosity, iron sulfide minerals nor organic enrichments, indicating growth under more oxidizing conditions. These morphological, compositional, and mineralogical signals of microbial processes in dark ooids from Shark Bay, Western Australia, record the formation of ooid nuclei and the accretion of magnesium-rich cortical layers in benthic, reducing, microbially colonized areas.

New insights into the relationships between livestock grazing behaviors and soil organic carbon stock in an alpine grassland

Grazing affects soil carbon (C) storage in grassland ecosystems through livestock trampling, defoliation, and excretion of urine and dung. However, independent effects of those grazing behaviors on soil organic C (SOC) remains unclear, particularly in alpine grassland ecosystems. To address this knowledge gap, a one-year field experiment was conducted on the eastern edge of the Qinghai-Tibetan Plateau to study the effect of grazing behaviors, including light vs. heavy trampling, light vs. heavy defoliation, and excretion of urine and dung, of yak (Bos grunniens) on SOC stock. Our results showed that trampling, particularly light trampling, significantly increased SOC stock in the 0–10 cm soil layer. The increase of soil bulk density and SOC concentration were the main reasons for the increase of surface SOC stock under trampling. Heavy defoliation significantly increased SOC stock in the 20–30 cm depth in comparison to light defoliation (4.4 vs. 2.9 kg C m-2), but neither affected SOC stock in the 0–30 cm soil profile. In contrast, excretion significantly lowered SOC stock by 9.3 kg C m-2 (0–30 cm), linked to the decreased soil bulk density and SOC concentration, and the decreased microbial biomass C, which might have lowered the microbial contribution to SOC storage. Our study of independent grazing effects showed that short-term livestock excretion caused the loss of SOC stock while intensive trampling or defoliation did not. Our findings have implications for managing livestock grazing behavior to maintain SOC stock in alpine grassland ecosystems.

Molecular insights into the impacts of acid mine drainage on dissolved organic matter dynamics in pit lakes

Pit lakes are artificial hydrological features created by mining operations that typically suffer from acid mine drainage (AMD), which not only endangers water quality but also exacerbates carbon loss. However, the impacts of AMD on the fate and role of dissolved organic matter (DOM) in pit lakes remain unclear. This study employed negative electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) combined with biogeochemical analysis to examine DOM molecular variations and environmental controls across the AMD-induced acidic and metalliferous gradients in five pit lakes. The results demonstrated distinct DOM pools in pit lakes characterized by the prevalence of smaller aliphatic compounds compared to other waterbodies. AMD-induced geochemical gradients promoted DOM heterogeneity among pit lakes, with acidic pit lakes containing more lipid-like compounds. Acidity and metals enhanced DOM photodegradation, reducing the content, chemo-diversity and aromaticity. Organic sulfur was detected in high abundance, potentially from sulfate photo-esterification and mineral flotation agent. Furthermore, microbial involvements in carbon cycling were revealed by DOM-microbe correlation network, but microbial contributions to the DOM pools decreased under acidic and metal stresses. These findings highlight abnormal carbon dynamics caused by AMD pollution and integrate DOM fate into pit lake biogeochemistry, thereby contributing to management and remediation.

Microbial β-glucuronidases drive human periodontal disease etiology.

Periodontitis is a chronic inflammatory disease associated with persistent oral microbial dysbiosis. The human β-glucuronidase (GUS) degrades constituents of the periodontium and is used as a biomarker for periodontitis severity. However, the human microbiome also encodes GUS enzymes, and the role of these factors in periodontal disease is poorly understood. Here, we define the 53 unique GUSs in the human oral microbiome and examine diverse GUS orthologs from periodontitis-associated pathogens. Oral bacterial GUS enzymes are more efficient polysaccharide degraders and processers of biomarker substrates than the human enzyme, particularly at pHs associated with disease progression. Using a microbial GUS-selective inhibitor, we show that GUS activity is reduced in clinical samples obtained from individuals with untreated periodontitis and that the degree of inhibition correlates with disease severity. Together, these results establish oral GUS activity as a biomarker that captures both host and microbial contributions to periodontitis, facilitating more efficient clinical monitoring and treatment paradigms for this common inflammatory disease.

Roles of the gut microbiome in weight management.

Overweight, obesity, undernutrition and their respective sequelae have devastating tolls on personal and public health worldwide. Traditional approaches for treating these conditions with diet, exercise, drugs and/or surgery have shown varying degrees of success, creating an urgent need for new solutions with long-term efficacy. Owing to transformative advances in sequencing, bioinformatics and gnotobiotic experimentation, we now understand that the gut microbiome profoundly impacts energy balance through diverse mechanisms affecting both sides of the energy balance equation. Our growing knowledge of microbial contributions to energy metabolism highlights new opportunities for weight management, including the microbiome-aware improvement of existing tools and novel microbiome-targeted therapies. In this Review, we synthesize current knowledge concerning the bidirectional influences between the gut microbiome and existing weight management strategies, including behaviour-based and clinical approaches, and incorporate a subject-level meta-analysis contrasting the effects of weight management strategies on microbiota composition. We consider how emerging understanding of the gut microbiome alters our prospects for weight management and the challenges that must be overcome for microbiome-focused solutions to achieve success.

Environmental and microbial factors influence affective and cognitive behavior in C57BL/6 sub-strains.

C57BL/6 mice are one of the most widely used inbred strains in biomedical research. Early separation of the breeding colony has led to the development of several sub-strains. Colony separation led to genetic variation development driving numerous phenotypic discrepancies. The reported phenotypic behavior differences between the sub-strains were, however; not consistent in the literature, suggesting the involvement of factors other than host genes. Here, we characterized the cognitive and affective behavior of C57BL/6J and C57BL/6N mice in correlation with the immune cell profile in the brain. Furthermore, faecal microbiota transfer and mice co-housing techniques were used to dissect microbial and environmental factors' contribution, respectively, to cognitive and affective behavior patterns. We first noted a unique profile of locomotor activity, immobility pattern, and spatial and non-spatial learning and memory abilities between the two sub-strains. The phenotypic behavior profile was associated with a distinct difference in the dynamics of type 2 cytokines in the meninges and brain parenchyma. Analysing the contribution of microbiome and environmental factors to the noted behavioral profile, our data indicated that while immobility pattern was genetically driven, locomotor activity and cognitive abilities were highly sensitive to alterations in the gut microbiome and environmental factors. Changes in the phenotypic behavior in response to these factors were associated with changes in immune cell profile. While microglia were highly sensitive to alteration in gut microbiome, immune cells in meninges were more resilient. Collectively, our findings demonstrated a direct impact of environmental conditions on gut microbiota which subsequently impacts the brain immune cell profile that could modulate cognitive and affective behavior. Our data further highlight the importance of characterizing the laboratory available strain/sub-strain to select the most appropriate one that fits best the study purpose.