Microbial Function Research Articles

Dysregulation of saliva and fecal microbiota as novel biomarkers of colorectal cancer

The aim of this study was to investigate the biomarkers of salivary and fecal microbiota in Colorectal cancer (CRC). Initially, the study scrutinized the microbial community composition disparities among groups. Utilizing Lasso analysis, it sifted through operational taxonomic units (OTUs) to pinpoint distinctive features. Subsequently, by intersecting feature OTUs across groups, it curated a set of core-shared OTUs and devised a corresponding network. Concluding with functional enrichment analysis, the research delved into the divergent biological functions of these microbial communities within the studied groups. Analysis revealed higher bacterial diversity in saliva compared to feces, with distinct differences at both phylum and genus levels. Feces primarily contained Firmicutes, while saliva was dominated by Bacteroidetes and Proteobacteria. Notably, Escherichia-Shigella and Fusobacterium in feces and Streptococcus in saliva showed increasing abundance from average to adenoma to colorectal cancer. Specific dominant flora was identified within and between groups, including CRC and adenomas across different stages. Seventeen core shared OTUs were identified, and networks of shared OTUs were constructed for each group. Functional enrichment analysis highlighted distinct microbial community functions among the groups. This study’s findings on characteristic OTUs in saliva and fecal samples offer valuable insights for distinguishing between healthy individuals, adenoma patients, and those with colorectal cancer. This study identified distinctive OTUs in saliva and feces to distinguish between healthy individuals, adenoma patients, and those with CRC, offering a valuable diagnostic reference.

Impact of Different Land-Use Types on Soil Microbial Carbon Metabolism Function in Arid Region of Alpine Grassland

There are discrepancies that exist in the effects of different land uses on soil organic carbon (SOC) and soil microbial carbon metabolism functions. However, the impact of land-use type changes on soil microbial carbon metabolism in alpine grassland arid areas is not well understood, hindering our understanding of the carbon cycling processes in these ecosystems. Therefore, we chose three types of land use (continuous reclamation of grassland (RG), abandoned grassland (AG), and natural grazing grassland (GG)) to study the microbial carbon metabolism and its driving factors by the Biolog-ECO method. The results showed that the soil organic carbon content decreased by 16.02% in the RG and by 32.1% in the AG compared to the GG in the 0–20 cm soil layer (p < 0.05). Additionally, microorganisms have the highest utilization efficiency of carbohydrate carbon sources, the average values of average well color development (AWCD) were RG (0.26), AG (0.35), and GG (0.26). In the 0–20 cm soil layer, the Shannon–Wiener and the Simpson indices were 3% and 1% higher in the AG compared to the GG, respectively. The soil TOC/TN and soil available phosphorus (AP) were key factors that affected the diversity of soil microbial and carbon metabolism. They were closely related to land-use types. This study holds that abandoning grasslands accelerates the carbon metabolism of microorganisms, leading to the loss of SOC content.

Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing

The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.

Microbial functional diversity and redundancy: moving forward.

Microbial functional ecology is expanding as we can now measure the traits of wild microbes that affect ecosystem functioning. Here, we review techniques and advances that could be the bedrock for a unified framework to study microbial functions. These include our newfound access to environmental microbial genomes, collections of microbial traits, but also our ability to study microbes' distribution and expression. We then explore the technical, ecological, and evolutionary processes that could explain environmental patterns of microbial functional diversity and redundancy. Next, we suggest reconciling microbiology with biodiversity-ecosystem-functioning studies by experimentally testing the significance of microbial functional diversity and redundancy for the efficiency, resistance, and resilience of ecosystem processes. Such advances will aid in identifying state shifts and tipping points in microbiomes, enhancing our understanding of how and where will microbiomes guide Earth's biomes in the context of a changing planet.

The effect of complementary foods on the colonic microbiota of weaning infants: a systematic review.

The transition from breastmilk to solid foods (weaning) is a decisive stage for the development of the colonic microbiota. However, little is known about how complementary foods influence the composition and function of the colonic microbiota in infants. This systematic review collected evidence of the effect of individual foods on the fecal microbiota of weaning infants (4-12 months old) using five databases: PubMed, CENTRAL, Scopus, Web of Science, and ScienceDirect. A total of 3625 records were examined, and seven randomized clinical trials met the review's eligibility criteria. Altogether, 983 participants were enrolled, and plant-based foods, meats, and dairy products were used as interventions. Wholegrain cereal increased the fecal abundance of the order Bacteroidales in the two included studies. Pureed beef increased the fecal abundances of the genus Bacteroides and the Clostridium XIVa group, as well as microbial richness in two of the three included studies. However, the conclusions of this review are limited by the small number of studies included. No conclusions could be drawn about the impact of complementary foods on fecal metabolites. Further clinical trials assessing the effect of dietary interventions on both fecal microbial composition and function are needed to fill this knowledge gap in infant nutrition.

Integrative analysis of gut microbiota and fecal metabolites in cynomolgus monkeys with spontaneous type 2 diabetes mellitus.

Accumulating evidence suggests that gut microbiota (GM) is clearly associated with the pathogenesis of type 2 diabetes mellitus (T2DM). However, the underlying mechanism of GM dysbiosis participates the onset of T2DM is not fully understood. The spontaneous T2DM cynomolgus monkeys are a powerful model for understanding the pathological mechanism of T2DM. Fecal samples were collected from 7 spontaneous T2DM cynomolgus monkeys and 7 healthy controls matched with similar age for multi-omics analysis, including shotgun metagenomic sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chain fatty acids (SCFAs). Lastly, the correlation network between differential gut microbial species and fecal metabolites was performed to explore the potential biomarkers of T2DM. We found that 17 low-abundance species showed significant differences between the two groups. Analysis of gut microbial functions revealed that 16 KEGG pathways and 51 KEGG modules were significantly different in the two groups. Meanwhile, 276 fecal DEMs were identified, and these DEMs were enriched in the KEGG pathways, including Nucleotide metabolism, ABC transporters, Purine metabolism and so on. Lastly, Spearman correlation network analysis showed that the species of Anaerostipes_hadrus and Lachnoanaerobaculum_umeaense, and the metabolites including Glycerophospho-N-palmitoyl ethanolamine and 2-Hydroxycinnamic acid might serve as potential biomarkers of T2DM. Our study provides novel insights into specific alterations in the GM composition, gene functions, and fecal metabolic profiles in spontaneous T2DM cynomolgus monkeys.

Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments.

The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.

Transforming Agricultural and Sulfur Waste into Fertilizer: Assessing the Short-Term Effects on Microbial Biodiversity via a Metagenomic Approach

Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a solution, enabling the direct extraction of DNA from soil to uncover microbial diversity and functions. This study utilized metagenomics to analyze the rhizosphere of two-year-old Tonda di Giffoni hazelnut saplings treated with synthetic NPK, composted olive pomace, and an innovative fertilizer derived from sulfur-based agro-industrial waste stabilized with bentonite clay. Using 16S rDNA for bacteria and ITS2 for fungi, Illumina sequencing provided insights into microbial responses to different fertilizer treatments. The results highlighted a significant increase in the abundance of beneficial microorganisms such as Thiobacillus, Pseudoxanthomonas, and Thermomyces, especially when organic materials were included. Additionally, microbial biodiversity improved with organic inputs, as shown by increased species richness (Chao1) and diversity (Bray-Curtis) greater than 20% compared with NPK and unfertilized soils (CTR). These findings emphasize the importance of organic fertilization in enhancing soil microbial health, offering a sustainable approach to improving soil quality and hazelnut productivity.

Fishmeal intervention after short-term novel proteins stimulates compensatory growth and affects intestinal health in largemouth bass (Micropterus salmoides).

This research utilized a compensatory growth phenomenon aimed at reducing the use of fishmeal in aquatic animal feed. However, the compensatory growth triggered by fishmeal restriction with novel protein replacement has yet to be understood. Five isonitrogenous and isolipidic diets containing different proteins were manufactured, with fishmeal serving as the control and diets containing novel proteins, i.e., Chlorella (Chlorella vulgaris), cottonseed protein concentrate, Clostridium autoethanogenum, and yellow mealworm (Tenebrio molitor), serving as the experimental diets. Largemouth bass (Micropterus salmoides) with a starting body weight of 4.73 ± 0.04g were respectively fed these five diets for the first 29days (first stage), followed by a fishmeal diet for the remaining 29days (second stage). The diet of fishmeal, Chlorella vulgaris, cottonseed protein concentrate, Clostridium autoethanogenum, and Tenebrio molitor was referred to as FM, ChM, CSM, CAP, and TM, respectively. All novel protein groups showed a 60-73% higher weight gain compared to the fishmeal group during the second phase; however, they did not reach the weight level seen in the control group. In addition, the second stage of fishmeal intervention resulted in a reduction of approximately 35% in the area of positive Alcian blue (AB) staining of intestinal tissues in the CSM group, and about 40% in the CAP group, compared to the first stage. Furthermore, the area of intestinal apoptosis in TM was enlarged after fishmeal intervention while it was decreased in other experimental groups. At day 58, gene expression analysis of the CAP group fish at the end of the trial revealed increased levels of the anti-apoptotic gene bcl-2, as well as higher expression of intestinal inflammatory cytokines il-1β, tnf-α, nf-κb p65, and il-10, compared to the FM group. In terms of the biochemical indices, the levels of catalase (CAT) and glutathione peroxidase (GSH-Px) were reduced in CSM on day 58. An assessment of potential microbial function at end of trial demonstrated that CAP could reduce the lipid metabolism and amino acid metabolism, and increased carbohydrate metabolism pathways in the largemouth bass intestine. In conclusion, both CAP and ChM groups showed promise to reduce fishmeal with respect to intestinal health rather than growth. This study should be of value to practitioners wishing to use novel proteins to reduce fishmeal via the utilization of the compensatory growth phenomenon.

Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures

Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area （LH） and the reclamation fertilization area （MM）. The results suggested that： ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen （TN）, total phosphorus （TP）, available phosphorus （AP）, and available potassium （AK） contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively （P<0.05）. ② The dominant bacterial and fungal communities did not change under the LH and MM treatments； however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% （P<0.05）. Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.） The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.

Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface

Abstract Aims Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere. Methods The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing. Results We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla (Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific. Conclusions The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

Exploring the Microbial Ecology of Nitrification Denitrification in Wastewater Treatment: Innovations and Future Directions

The nitrification-denitrification process serves as a critical mechanism in the biological removal of nitrogen from wastewater, a necessity for mitigating the environmental impact of nitrogen compounds on aquatic ecosystems. This complex process is orchestrated by diverse microbial communities, whose ecological interactions and functional capabilities are central to the efficiency and stability of nitrogen removal. In recent years, advances in molecular biology and microbial ecology have shed new light on the intricate dynamics within these microbial communities, revealing the roles of lesser known microbial taxa and the importance of microbial community structure and function in optimizing nitrification denitrification processes. This review provides a comprehensive examination of the microbial ecology involved in nitrification and denitrification, exploring the roles of key microbial players, including ammonia oxidizing bacteria (AOB), Nitrite oxidizing Bacteria (NOB), ammonia oxidizing archaea (AOA), and denitrifying bacteria. The review also delves into the environmental factors that influence microbial community dynamics, such as pH, temperature, oxygen availability, and the presence of inhibitory substances. By understanding these factors, the review highlights the challenges of maintaining stable and efficient nitrogen removal processes, particularly in the face of environmental fluctuations and operational disturbances, the review discusses recent innovations in wastewater treatment technologies that leverage microbial ecology to enhance process efficiency. These include bio-augmentation strategies, where specific microbial strains are introduced to bolster nitrification and denitrification, and advanced bioreactor designs, such as moving bed biofilm reactors (MBBRs) and membrane bioreactors (MBRs), which provide optimized environments for microbial growth and activity. The integration of anaerobic ammonium oxidation (anammox) processes, which offer significant energy savings and reduce greenhouse gas emissions, is also explored as a promising alternative to traditional nitrification pathways.

Broad Microbial Community Functions in a Conventional Activated Sludge System Exhibit Temporal Stability.

Wastewater microbial communities within conventional activated sludge (CAS) systems can perform hundreds of biotransformations whose relative importance, frequency, and temporal stability remain largely unexplored. To improve our understanding of biotransformations in CAS systems, we collected 24 h composite samples from the influent and effluent of a CAS system over 14 days, analyzed samples using high-resolution mass spectrometry (HRMS), and conducted a nontarget analysis of our HRMS acquisitions. We found that over 50% of the chemical features in the influent were completely removed, and the daily number of detected features exhibited low variability with a coefficient of variation of 0.07. Additionally, we found 352 Core chemical features present in every sample at both locations. We used chemical features to search for evidence of 19 potential biotransformations and detected 9 of these biotransformations at a frequency of over 80 times per day, where evidence for dehydrogenations, hydroxylations, and acetylations was most frequently detected. The daily number of detections for the 9 biotransformations exhibited coefficients of variation ranging from 0.13-0.20, revealing the broad temporal stability for these wastewater microbial community functions. This stability contrasts with the previously observed temporal variability for micropollutant biotransformations, suggesting that micropollutant biotransformations are linked to specialized microbial community functions.

Stable Diversity but Distinct Metabolic Activity of Microbiome of Roots from Adult and Young Chinese Fir Trees

The tree-associated microbiome is vital for both individual trees and the forest ecosystem. The microbiome is dynamic; however, it is influenced by the developmental stages and environmental stresses experienced by host trees. Chinese fir (Cunninghamia lanceolata) is an economically important tree species in the subtropical regions of China. This study investigated the diversity of microbial communities, including bacteria and fungi, in the roots and bulk soil of young (2 years old) and old (46 years old) Chinese fir. It specifically examined the functional characteristics of these microbial communities. Through a non-metric multidimensional scaling (NMDS) analysis, we examined differences in microbial community structures among root and soil samples of Chinese fir. Evaluations using α-diversity metrics (Chao1, Shannon, Pielou, etc.) confirmed significant differences in diversity and structure between soil and root samples but high similarity between young and old tree samples. A network analysis identified key bacterial and fungal genera, such as Burkholderia and Russula, which play pivotal roles in the microbiome structure. We also demonstrated significant variations in microbial metabolic functions, such as dioxin and benzoic acid degradation metabolic pathways, which might relate to stress alleviation for tree fitness. Additionally, for the detection of endophytic microorganisms in Chinese fir seeds, only small amounts (less than 10%) of fungal endophytes and bare bacterial endophytes were identified. In summary, this study revealed that the stable structure of the rhizosphere microbiome was established in the early stage of tree life in Chinese fir, which mostly originated from surrounding soil rather than seed endophytes. The associated microbial metabolic activity naturally decreased with tree aging, implicating the tree microbial dynamics and the need for the addition of an actively functional synthetic community for tree fitness.

The effect of Torreya grandis inter-cropping with Polygonatum sibiricum on soil microbial community.

Inter-cropping is a reasonable planting pattern between different plants. Inter-cropping of Torreya grandis with Polygonatum sibiricum is a relatively mature planting pattern in China, which has been applied to improve soil ecological environment and reduce the occurrence of pests and diseases in China. However, there is currently limited knowledge on the response of soil microbial communities to this practice. In this study, we employed Illumina MiSeq sequencing coupled with Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Fungi Functional Guild (FUNGuild) analyses to investigate the dynamic changes in soil microbial communities across seven treated groups [the bulk soil of the T. grandis inter-cropping with P. sibiricum (IB), the bulk soil for mono-cropping of P. sibiricum (PB), the bulk soil for mono-cropping of T. grandis (TB), the P. grandis rhizosphere soil of the T. grandis inter-cropping with P. sibiricum (IPR), the rhizosphere soil for mono-cropping of P. sibiricum (PR), the T. grandis rhizosphere soil of the T. grandis inter-cropping with P. sibiricum (ITR), and the rhizosphere soil for mono-cropping of T. grandis (TR)]. The results showed that the rhizosphere soil of Torreya-Polygonatum inter-cropping exhibited higher microbial community richness, diversity and evenness than mono-cropping (ITR > TR, IPR > PR). Inter-cropping increased the abundance of Micrococcaceae, Xanthobacteraceae, Saitozyma, while decreased Bacillus, Burkholderia, Streptomyces, Cladosporium, and Gibberella significantly of the rhizosphere soil of T. grandis. Further, the abundance of pathogens, such as Fusarium and Neocosmospora, was higher in mono-cropping samples compared to inter-cropping. There existed distinct variations in bacterial and fungal communities among all groups except for IB and TB. The FAPROTAX and FUNGuild analyses results indicated that inter-cropping significantly enhanced soil microbial function associated with nutrient cycling and exhibited a consistent increase in the relative abundance of nitrogen-cycling and carbon-cycling bacteria, and decreased the abundance of plant pathogen guild in the inter-cropping sample ITR compared to the mono-cropping TR. Our findings suggest that T. grandis inter-cropping with P. sibiricum not only enhance the diversity of soil microbial communities, but also improve the nitrogen and carbon cycling functions. In addition, the inter-cropping can effectively reduce the relative abundance of some soil-borne pathogens for T. grandis and P. sibiricum, indicating that this intercropping method may alleviate the impact of pathogens on crops, thus providing assistance for plant disease prevention and sustainable management.

Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes

BackgroundDeadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing specialized functions in breaking down organic matter, but the specific roles of individual microorganisms in this process are still not fully understood.ResultsHere, we characterized the deadwood microbiome in a natural mixed temperate forest in Central Europe using PacBio HiFi long-read sequencing and a genome-resolved transcriptomics approach in order to uncover key microbial contributors to wood decomposition. We obtained high quality assemblies, which allowed attribution of complex microbial functions such as nitrogen fixation to individual microbial taxa and enabled the recovery of metagenome-assembled genomes (MAGs) from both abundant and rare deadwood bacteria. We successfully assembled 69 MAGs (including 14 high-quality and 7 single-contig genomes) from 4 samples, representing most of the abundant bacterial phyla in deadwood. The MAGs exhibited a rich diversity of carbohydrate-active enzymes (CAZymes), with Myxococcota encoding the highest number of CAZymes and the full complement of enzymes required for cellulose decomposition. For the first time we observed active nitrogen fixation by Steroidobacteraceae, as well as hemicellulose degradation and chitin recycling by Patescibacteria. Furthermore, PacBio HiFi sequencing identified over 1000 biosynthetic gene clusters, highlighting a vast potential for secondary metabolite production in deadwood, particularly in Pseudomonadota and Myxococcota.ConclusionsPacBio HiFi long-read sequencing offers comprehensive insights into deadwood decomposition processes by advancing the identification of functional features involving multiple genes. It represents a robust tool for unraveling novel microbial genomes in complex ecosystems and allows the identification of key microorganisms contributing to deadwood decomposition.

Neuroprotective effect of Bacillus subtilis in haloperidol induced rat model, targeting the microbiota-gut-brain axis.

Functional microbes regulate Parkinson's disease (PD), according to contemporary research. The mechanism by which probiotics (PBT) improve PD was not fully explored yet. We examined the antioxidant impact and mechanism of PBT (Bacillus subtilis) on PD using gut-brain axis regulation. To establish a model of PD, rats were given haloperidol (HAL) intraperitoneally (i.p.) in this study. The standard group received L-DOPA for 21days. After that, the motor function was assessed using different neurobehavioral tests. Further estimation comprehends the build up of alpha-synuclein, the manifestation of monoamine oxidase-B (MAO-B) activity, the deterioration of dopaminergic neurons and the induction of an oxidative stress reaction. In addition, the concentration of intestinal microbes was measured. These findings demonstrated that the administration of PBT in combination with L-dopa could alleviate motor impairments caused by HAL, the deterioration of dopaminergic neurons, and the build up of α-synuclein. Furthermore, the levels of superoxide dismutase (SOD) and dopamine were considerably raised by co-administration of L-dopa and PBT in the case of HAL-treated rats, whereas the levels of alpha-synuclein, MAO-B, and malondialdehyde (MDA) were reduced. Particularly, PBT administration reduced the gut microbial dysbiosis, which in turn raised the concentration of good bacteria i.e., Bifidobacterium and reduced the concentration of E. coli in experimental animals. These findings indicated that PBT might represent a promising candidate to inhibit the progression of Parkinson's disease by targeting the gut-brain axis.

Rethreading the needle: A novel molecular index of soil health (MISH) using microbial functional genes to predict soil health management

Soil health relies on the actions and interactions of an abundant and diverse biological community. Current soil health assessments rely heavily on a suite of soil biological, chemical, and physical indicators, often excluding molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can help guide management practices. To explore the role of microbial function in soil health, 536 soil samples were collected from 26 U.S. states, representing 52 different crops and grazing lands, and analyzed for various soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 to predict metagenome functions. Functional data were used as predictors in eXtreme Gradient Boosting (XGBoost), a powerful machine learning algorithm, and enzymes important to soil health indicators were compiled into a Molecular Index of Soil Health (MISH). The overall MISH score significantly correlated with non-molecular measures of soil health and management practice adoption. Additionally, several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This low-cost, DNA-based approach to measuring soil health is robust and generalizable across climates.

The role of the proteosurfaceome and exoproteome in bacterial coaggregation.

Bacterial coaggregation is a critical process in multispecies biofilm formation, driven by specific molecular interactions that facilitate the adhesion and aggregation of bacterial cells. These interactions are essential for the development and persistence of complex microbial communities. This review provides a comprehensive analysis of the roles of the proteosurfaceome and exoproteome in bacterial coaggregation. The proteosurfaceome, comprising surface-bound molecules such as adhesins, drives species-specific interactions crucial for partner recognition and adhesion. In parallel, the exoproteome, particularly extracellular polymeric substances (EPS), enhances aggregate stability by reinforcing structural integrity and facilitating intercellular communication, although its direct role in coaggregation remains to be fully clarified. By integrating these perspectives, this review aims to elucidate how the proteosurfaceome and exoproteome influence bacterial coaggregation, offering insights into their combined impact on microbial community structure and function. Furthermore, we highlight existing knowledge gaps and propose directions for future research.

Organic Matter Composition and Water Stoichiometry Are Main Drivers of Heterotrophic Nitrate Uptake in Mediterranean Headwater Streams

AbstractHeterotrophic bacteria can contribute to improve stream water quality by taking up nitrate (NO3−) from the water column, although microbial demand for this nutrient is usually lower than for other inorganic nitrogen (N) forms, such as ammonium. Heterotrophic NO3− uptake has been related to the availability of dissolved organic carbon (DOC) relative to nutrients (i.e., DOC: nutrients ratios). Yet, how dissolved organic matter (DOM) composition and specific microbial assemblages influence NO3− uptake remains poorly understood. We conducted laboratory incubations to investigate heterotrophic NO3− uptake kinetics in 9 Mediterranean freshwater ecosystems, primarily headwater streams, exhibiting wide variation in DOC:NO3 ratios (from 1.5 to 750). Moreover, we characterized DOM composition using spectroscopic indexes and its degradation via a reactivity continuum model approach. Microbial community composition and functioning were assessed by analyzing extracellular enzymatic activities and the potential abundance of N‐cycling genes. Our results revealed that NO3− uptake rates (kNO3) were positively related with DOC:NO3 ratios (r2 = 0.4) and to NO3:SRP ratios as well (r2 = 0.6). Furthermore, kNO3 was negatively correlated to the humification index (r2 = 0.7), suggesting that a higher proportion of humic‐like compounds slow down heterotrophic NO3− uptake. A partial least squares regression model (PLS) pinpointed that DOC and nutrient stoichiometry, DOM composition and reactivity, and microbial composition and activity collectively contributed to explain the variability in kNO3 observed across treatments. Our findings suggest that heterotrophic NO3− uptake may show significant responsiveness to shifts toward more labile DOM sources and nutrient imbalances induced by global change.