The perturbation of the symbiotic relationship between microbes and intestinal immune system contributes to gut inflammation and Inflammatory Bowel Disease (IBD) development. The host mucosa glycans (glycocalyx) creates a major biological interface between gut microorganisms and host immunity that remains ill-defined. Glycans are essential players in IBD immunopathogenesis, even years before disease onset. However, how changes in mucosa glycosylation shape microbiome and how this impact gut immune response and inflammation remains to be clarified. Here, we revealed that alterations in the expression of complex branched N-glycans at gut mucosa surface, modeled in glycoengineered mice, resulted in dysbiosis, with a deficiency in Firmicutes bacteria. Concomitantly, this mucosa N-glycan switch was associated with a downregulation of type 3 innate lymphoid cells (ILC3)-mediated immune response, leading to the transition of ILC3 toward an ILC1 proinflammatory phenotype and increased TNFα production. In addition, we demonstrated that the mucosa glycosylation remodeling through prophylactic supplementation with glycans at steady state was able to restore microbial-derived short-chain fatty acids and microbial sensing (by NOD2 expression) alongside the rescue of the expression of ILC3 module, suppressing intestinal inflammation and controlling disease onset. In a complementary approach, we further showed that IBD patients, often displaying dysbiosis, exhibited a tendency of decreased MGAT5 expression at epithelial cells that was accompanied by reduced ILC3 expression in gut mucosa. Altogether, these results unlock the effects of alterations in mucosa glycome composition in the regulation of the bidirectional crosstalk between microbiota and gut immune response, revealing host branched N-glycans/microbiota/ILC3 axis as an essential pathway in gut homeostasis and in preventing health to intestinal inflammation transition.

The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for drug dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance, which could be influenced by differences in microbiota, and yet no study design has capitalized upon this natural variation. We leveraged natural behavioral variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained sustained antinociception. Mice that did not develop tolerance maintained a higher capacity for production of the short-chain fatty acid (SCFA) butyrate known to bolster intestinal barriers and promote neuronal homeostasis. Both fecal microbial transplantation (FMT) from donor mice that did not develop tolerance and dietary butyrate supplementation significantly reduced the development of tolerance independently of suppression of systemic inflammation. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.

Despite extensive investigations into the microbiome and metabolome changes associated with colon polyps and colorectal cancer (CRC), the microbiome and metabolome profiles of individuals with colonic polyposis, including those with (Gene-pos) and without (Gene-neg) a known genetic driver, remain comparatively unexplored. Using colon biopsies, polyps, and stool from patients with Gene-pos adenomatous polyposis (N = 9), Gene-neg adenomatous polyposis (N = 18), and serrated polyposis syndrome (SPS, N = 11), we demonstrated through 16S rRNA sequencing that the mucosa-associated microbiota in individuals with colonic polyposis is representative of the microbiota associated with small polyps, and that both Gene-pos and SPS cohorts exhibit differential microbiota populations relative to Gene-neg polyposis cohorts. Furthermore, we used these differential microbiota taxa to perform linear discriminant analysis to differentiate Gene-neg subjects from Gene-pos and from SPS subjects with an accuracy of 89% and 93% respectively. Stool metabolites were quantified via 1H NMR, revealing an increase in alanine in SPS subjects relative to non-polyposis subjects, and Partial Least Squares Discriminant Analysis (PLS-DA) analysis indicated that the proportion of leucine to tyrosine in fecal samples may be predictive of SPS. Use of these microbial and metabolomic signatures may allow for better diagnostric and risk-stratification tools for colonic polyposis patients and their families as well as promote development of microbiome-targeted approaches for polyp prevention.

The gut microbiome is known to have a bidirectional relationship with sex hormone homeostasis; however, its role in mediating interactions between the primary regulatory axes of sex hormones and their productions is yet to be fully understood. We utilized both conventionally raised and gnotobiotic mouse models to investigate the regulatory role of the gut microbiome on the hypothalamic-pituitary-gonadal (HPG) axis. Male and female conventionally raised mice underwent surgical modifications as follows: (1) hormonally intact controls; (2) gonadectomized males and females; (3) gonadectomized males and females supplemented with testosterone and estrogen, respectively. Fecal samples from these mice were used to colonize sex-matched, intact, germ-free recipient mice through fecal microbiota transplant (FMT). Serum gonadotropins, gonadal sex hormones, cecal microbiota, and the serum global metabolome were assessed. FMT recipients of gonadectomized-associated microbiota showed lower circulating gonadotropin levels than recipients of intact-associated microbiota, opposite to that of FMT donors. FMT recipients of gonadectomized-associated microbiota also had greater testicular weights compared to recipients of intact-associated microbiota. The gut microbiota composition of recipient mice differed significantly based on the FMT received, with the male microbiota having a more concerted impact in response to changes in the HPG axis. Network analyses showed that multiple metabolically unrelated pathways may be involved in driving differences in serum metabolites due to sex and microbiome received in the recipient mice. In sum, our findings indicate that the gut microbiome responds to the HPG axis and subsequently modulates its feedback mechanisms. A deeper understanding of interactions between the gut microbiota and the neuroendocrine-gonadal system may contribute to the development of therapies for sexually dimorphic diseases.

Raising farm animals imparts various exposures that may shape the human microbiome. The oral microbiome has been increasingly implicated in disease development. Animal farming has also been associated with certain chronic diseases such as cancer; however, underlying biological mechanisms are unclear. We investigated associations between raising farm animals and the oral microbiome in the Agricultural Health Study.

This analysis included 1,245 participants (865 farmers and 380 spouses) who provided oral wash specimens and information on types and numbers of specific animals raised on their farms within 2 years before sample collection. The oral microbiome was measured by sequencing the V4 region of the 16S ribosomal RNA gene. We evaluated associations of farm animal exposures with alpha and beta diversity metrics (within- and between-sample diversity, respectively), as well as presence and relative abundance of specific bacterial genera. All analyses adjusted for potential confounders (e.g., age, sex, smoking, alcohol consumption).

Overall, 63 % of participants raised farm animals, most commonly cattle (46 %) and hogs (20 %). Those who raised a large number of hogs (≥2,000 vs. no hogs) had higher alpha diversity. Conversely, raising sheep/goats and raising larger numbers of poultry were associated with lower alpha diversity. Beta diversity was not significantly different between participants with and without any farm animals. Participants raising any farm animals had higher relative abundance of Porphyromonas and lower relative abundances of Prevotella and Ruminococcaceae UCG-014. Several genera were more likely to be absent with specific animal exposures (e.g., Capnocytophaga for cattle and sheep/goats; Corynebacterium, Dialister, Stomatobaculum, and Solobacterium for sheep/goats and poultry).

This was the largest study of farm animal exposures and the human microbiome to date. Findings suggest that raising specific farm animals may influence the oral microbiome, supporting the need to further investigate the potential role of animal farming in disease etiology.

Coral growth anomalies (GA) affect many coral genera across the world, yet the etiology of GAs remains unknown, with limited knowledge of associated bacteria. In this study, we investigated bacterial associations between the growth anomalies (GAs) and healthy (H) portions of coral colonies in Acropora faraonis for two seasons to understand microbial dynamics. Additionally, we examined bacteria in water (W), which could be affecting coral bacterial communities. We found that alpha diversity remained consistent between healthy and GA coral tissues, but their relative abundances differed significantly. Notably, differential analysis revealed the abundance of Endozoicomonas spp., differed significantly between GA and H tissue, although it remains the dominant genus in both GA and H tissue. The high relative abundance of Endozoicomonas spp. in both GA and healthy tissue underscores its potential role in maintaining coral health. Structural modifications in GAs, such as changes in polyp sizes or densities, could be responsible for these differences in bacterial abundance. Similarly, microbial community composition remained consistent between seasons but differed in abundance again. We found differences between microbial communities of GAs and water, but no significant differences were observed between GAs and H, and no previously established bacterial pathogens were detected in GA tissue. These findings describe bacterial community patterns in GAs, but their potential role in its pathogenesis remains unknown. Further metagenomic and meta-transcriptomic analyses are needed to understand potential bacterial involvement in GAs. Additionally, investigating viruses and fungi in GA tissue is recommended to gain deeper insights into GA pathogenesis.

About 90 % of global lactate production is derived from bacterial fermentation of sugars via pure homofermentative cultures in batch mode. Acid whey, which is a lactose-rich wastewater from the yogurt industry, can be used as an alternative substrate for commercial lactate production. Operating reactor microbiomes reduces the lactate production costs by circumventing sterilization, while continuous operation with biomass retention achieves higher productivity at shorter production times. To find the best reactor configuration with biomass retention for lactate production from acid whey, we operated three different reactor configurations: (1) an upflow anaerobic sludge blanket (UASB) reactor; (2) an anaerobic filter reactor (AFR); and (3) an anaerobic continuously stirred tank reactor (CSTR) with a hollow-fiber membrane module. We operated at different hydraulic retention times (HRTs) to find the optimum production parameters at a temperature of 50 °C and a pH of 5.0. We did not use an inoculum but enriched the endogenous D-lactate-producing Lactobacillus spp. that later dominated the reactor microbiomes (> 90 % relative abundance). Undissociated lactic acid concentrations of more than 60 mmol C L-1 inhibited the microbiomes. We alleviated the inhibition effect by shortening the HRT to 0.6 days and using diluted acid-whey substrate (1.67-fold dilution) to achieve almost complete conversion of the acid-whey sugars to lactate. At the 0.6-day HRT, the AFR and CSTR performed better than the UASB reactor due to their better cell retention abilities. During the period between Day 365-384, we experienced an error in the pH control of the CSTR system during which the pH value dropped to 4.3. After this pH-error period, the lactose and galactose-into-lactate (LG-into-LA) conversion efficiency for the CSTR considerably improved and surpassed the AFR. We achieved the highest lactate conversion rate of 1256 ± 46.3 mmol C L-1 d-1 (1.57 ± 0.06 g L-1 h-1) at a LG-into-LA conversion efficiency of 82.2 ± 3.4 % (in mmol C), with a yield of 0.85 ± 0.02 mmol C mmol C-1 (product per consumed substrate) for the CSTR.

Evidence suggests that a significant interplay exists between the host gut microbiota and both the transmission and severity of malaria. Therefore, we explored the association between malaria and the gut microbiota across various geographic regions, considering host's nutritional habits, helminth coinfections and age. This observational study was conducted in 3 malaria-endemic provinces of Rwanda: West, South and East. Demographic data, blood and fecal samples were collected from 169 participants (85 females and 84 males) aged between 2-78 years. We used questionnaire-derived qualitative data based on geographic regions, age, and nutrition. Malaria and soil-transmitted helminth diagnosis was assessed by microscopy. The gut microbial composition was analyzed based on bacterial 16S rRNA gene amplicon sequencing. We observed that preschool children had a significantly lower microbiota diversity compared to both school children (q = 0.027, K-Wallis) and adults (q = 0.011, K-Wallis). Unlike age, infection status (uninfected, malaria alone, soil-transmitted helminth alone or coinfection) was not significantly associated with the gut microbiota. However, using Bray-Curtis distances, we found a significantly differential gut microbial beta-diversity with a convergent distribution in the Western province compared to the other provinces (q = 0.0045, pairwise PERMANOVA). This geographic difference was not explained by any change in energy intake, protein, lipids, or carbohydrates consumption but was likely due to lower dietary fibre intake in the West compared to the South (q < 0.0001, ANOVA) and the East (q = 0.07, ANOVA). In conclusion, we have not found significant links between infection and gut microbiota. However, we showed a significant difference in the gut microbiota composition of people living in different geographic locations in Rwanda, possibly due to their nutritional habits.

This study investigates Q fever in sheep and goats, key reservoirs for human infection, by metabarcoding and comparing it with q-PCR and serology. Samples from 26 small ruminants (aborted and normal-delivery) and six males across three Q fever-affected herds were analyzed. In sheep herds, seropositivity was 50 and 80 % respectively, with Coxiella (C.) burnetii shedding detected vaginally in the second herd. In goats, 100 % seropositivity and 90 % C. burnetii detection were observed, with nasal and vaginal samples showing the highest detection rates. Metabarcoding revealed significant differences in alpha diversity, with greater richness in blood and evenness in milk from normal-delivery sheep and higher evenness in faeces from aborted sheep. Beta diversity showed distinct vaginal microbiota in normal-delivery females compared to aborted ones. Firmicutes was the most abundant phylum observed. Dominant genera included: Moraxella (nasal), Mycoplasma (blood), Streptococcus (milk), Ureaplasma (vaginal and preputial), Rikenellaceae RC9 gut group (faeces). Significant differences in bacterial composition, including infertility-linked vaginal pathogens, were found across female groups in all herds in the anatomical locations studied, revealing new species and tropisms. Moreover, taxonomic analysis identified C. burnetii in vaginal, milk and environmental samples. This first report of C. burnetii in the caprine nasal cavity suggests an underestimated tropism that may improve Q fever diagnosis. These findings underscore the need for herd-wide Q fever control measures, including males and normal-delivery females. Our findings contribute to new insights into the pathogen's impact on small ruminant microbiota and a novel approach to studying infectious diseases in this sector.

The relationship between owner and companion animal represents an underestimated opportunity for the studying of One Health relationships between humans, animals, and the environment they share. Microbiome exchanges between owner and pet have been documented for the gut, skin, oral, and nasal microbiomes. These studies give a unique insight into bacterial flows between humans and animals, but come with their specific challenges. This review discusses the data and sample collection challenges, as well as laboratory, bioinformatic and data analysis challenges specific to One Health studies on companion animal and owner microbiomes. We provide an overview of possible data to be collected and pitfalls to avoid during sample collection and conservation, DNA extraction, and library preparation. We present the main bioinformatics pipelines in sequencing-data microbiome analysis, as well as data analysis specific to pet-owner microbiome comparison. We review and compare three beta-diversity measures (Bray-Curtis dissimilarity, unweighted, and weighted UniFrac distances) for pet-owner distances and the tests to compare them. Finally, we propose a framework with key considerations to bear in mind when designing and carrying out owner-companion animal studies, as well as best practices to implement them. Although these studies come with additional difficulties compared to species-specific microbiome studies, they offer the opportunity to identify biomarkers, environmental triggers, and impacts of pet-owner interactions across species.

The spatial distribution of soil bacterial communities in agrosilvopastoral systems remains understudied, despite its fundamental role in ecosystem functioning. This study investigates the spatial dynamics of dominant copiotrophic and oligotrophic bacterial phyla in grazing areas of Southwest Spain, focusing on their interactions with land management, soil properties, and environmental covariates. Five management systems; occasional grazing (OG), holistic management (HM), organic farming (OF), conventional rangeland (CR), and conventional grassland (CG) were analyzed across three topographic positions (hilltop, mid-slope, valley bottom), representing a gradient of grazing intensity. A total of 71 soil samples were collected and analyzed using 16S rRNA metabarcoding. Alpha and beta diversity metrics revealed significant shifts in community composition driven by both management and topography, with HM showing higher richness compared to CR and CG. Among dominant phyla, copiotrophic groups such as Proteobacteria and Actinobacteriota were more abundant in upper slope areas and under higher grazing intensity, whereas oligotrophic Verrucomicrobiota was enriched in valley bottoms and under lower grazing pressure. Spatial prediction models based on Random Forest and recursive feature elimination (RFE) identified key environmental drivers, with vegetation indices being more relevant for Proteobacteria and Verrucomicrobiota, and topographic features for Actinobacteriota. RDA and SEM confirmed that animal stocking rate and soil organic matter were major predictors of β-diversity. This study provides novel insights into microbial spatial heterogeneity in Mediterranean grazing systems, highlighting the interplay of management practices, soil characteristics, and topography. The findings underscore the ecological benefits of holistic management in enhancing bacterial diversity and inform strategies for sustainable land use in agrosilvopastoral ecosystems.

Preventing oral microbiome dysbiosis is crucial for averting the onset and progression of periodontal diseases. Phellodendron bark extract (PBE) and its active component berberine exhibit antibacterial properties against periodontal pathogenic bacteria. Although they inhibit Porphyromonas gingivalis (P. gingivalis)-induced dysbiosis in vitro in multiple species of saliva-derived planktonic cultures, their effects on microcosm biofilm models remain unclear. In this study, we aimed to elucidate the dysbiosis-suppressive effects of PBE and berberine chloride (BC) on biofilm formation.

PBE or BC was added during the formation of in vitro microcosm biofilms containing saliva and P. gingivalis, which were anaerobically cultured for one week. Next-generation sequencing was performed to assess microbiota composition, while quantitative real-time PCR was used to measure bacterial concentrations. Additionally, the butyrate concentration in the culture supernatant was assessed as biofilm pathogenicity.

PBE and BC treatments reduced the relative abundance of periodontal pathogenic bacteria, including P. gingivalis, and significantly increased the relative abundance of the genus Streptococcus and nitrate-reducing bacteria, including the genera of Neisseria and Haemophilus. Moreover, the treatment groups exhibited significantly decreased butyrate concentrations.

Our findings suggest that PBE and BC could suppress dysbiosis triggered by P. gingivalis in microcosm biofilms in vitro by decreasing the relative abundance and amount of periodontal pathogenic bacteria and enhancing those of nitrate-reducing bacteria that have a high relative abundance in orally healthy individuals. In summary, PBE and BC may contribute to the prevention of periodontal disease through their dysbiosis-suppressive and anti-inflammatory effects.

Antibiotic use in apiculture is often necessary to ensure the survival of honey bee colonies. However, beekeepers are faced with the dilemma of needing to combat bacterial brood infections while also knowing that antibiotics kill beneficial bacteria important for bee health. In recent years, bee probiotics have become increasingly purchased by beekeepers because of product claims like being able to "replenish the microbes lost due to agricultural modifications of honey bees' environment" or "promote optimal gut health." Unfortunately, these products have little scientific evidence to support their efficacy, and previous lab experiments have refuted some of their claims. Here, we performed hive-level field experiments to test the effectiveness of SuperDFM-HoneyBee™ - the most commonly purchased honey bee probiotic in the United States - on restoring the honey bee gut microbiota after antibiotic treatment. We found slight but significant changes in the microbiota composition of bees following oxytetracycline (TerraPro) treatment and no difference between the microbiota of antibiotic treated bees with or without subsequent probiotic supplementation. Moreover, the microorganisms in the probiotic supplement were never found in the guts of the worker bee samples. These results highlight that more research is needed to test the efficacy and outcomes of currently available commercial honey bee probiotic supplements.

The subgingival microbiome plays a key role in the gingivitis development, but the impact of toothbrushing with toothpaste on the subgingival microbial composition is not well understood. Therefore, this study aimed to evaluate the microbiological safety and subgingival impact of a toothpaste containing CPC and cymenol, compared to a fluoride-based toothpaste, and assessed overall subgingival microbiome changes after 6 weeks of routine toothbrushing in patients with gingival inflammation.

A 6-week randomized clinical trial was conducted in patients with gingival inflammation allocated to the use of either a toothpaste with cetylpyridinium chloride and cymenol or a toothpaste with sodium monofluorophosphate. Subgingival samples were collected at baseline and after 6 weeks and processed using high-throughput sequencing technology (Miseq®). Diversity metrics were calculated and the microbiome composition was analyzed using PERMANOVA, ANOSIM and PERMDISP.

A total of 116 samples from 60 patients were analyzed. No significant changes in diversity were observed in either group after 6 weeks. Among taxa with > 1% abundance, the toothpaste with cetylpyridinium chloride and cymenol exhibited a higher reduction in Aggregatibacter (p = 0.023) and a significant decrease in Fusobacterium nucleatum (p = 0.030), while the toothpaste with sodium monofluorophosphate showed a significant increase in the phylum Firmicutes (p = 0.033). The relative abundance of Porphyromonas gingivalis, Prevotella intermedia and Tannerella forsythia were not affected by either toothpaste (p > 0.05).

The daily use of a CPC/cymenol toothpaste was microbiologically safe, with no negative effects on the composition of the subgingival microbiome in patients with gingival inflammation, when compared to a fluoride-based toothpaste. The overall composition of the subgingival microbiome was not significantly affected by the daily use of either toothpaste after 6 weeks. In both groups, the observed changes affected mainly the low-abundance taxa.

Registration Number: ISRCTN17497809; Registration Date: 12/07/2023 (ISRCTN.org).

To combat the increasing levels of carbon dioxide (CO2) released from the combustion of fossil fuels, microalgae have emerged as a promising strategy for biological carbon capture, utilization, and storage. This study used a marine microalgal strain, Nannochloropsis oceanica IMET1, which thrives in high CO2 concentrations. A high-pH, high-alkalinity culture was designed for CO2 capture through algal biomass production as well as permanent sequestration through calcium carbonate (CaCO3) precipitation. This was accomplished by timed pH elevation and the addition of sodium bicarbonate to cultures of N. oceanica grown at lab scale (1 L) and pilot scale (500 L) with 10% and 5% CO2, respectively. Our data showed that 0.02 M NaHCO3 promoted algal growth and that sparging cultures with ambient air after 12 days raised pH and created favorable CaCO3 formation conditions. At the 1 L scale, we reached 1.52 g L-1 biomass after 12 days and an extra 9.3% CO2 was captured in the form of CaCO3 precipitates. At the 500 L pilot scale, an extra 60% CO2 was captured (Day 40) with a maximum CO2 capture rate of 63.2 g m-2 day-1 (Day 35). Bacterial communities associated with the microalgae were dominated by two novel Patescibacteria. Functional analysis revealed that genes for several plant growth-promotion traits (PGPTs) were enriched within this group. The microalgal-bacterial coculture system offers advantages for enhanced carbon mitigation through biomass production and simultaneous precipitation of recalcitrant CaCO3 for long-term CO2 storage.IMPORTANCECapturing carbon dioxide (CO2) released from fossil fuel combustion is of the utmost importance as the impacts of climate change continue to worsen. Microalgae can remove CO2 through their natural photosynthetic pathways and are additionally able to convert CO2 into a stable, recalcitrant form as calcium carbonate (CaCO3). We demonstrate that microalgae-based carbon capture systems can be greatly improved with high pH and high alkalinity by providing optimal conditions for carbonate precipitation. Our results with the microalga, Nannochloropsis oceanica strain IMET1, show an extra 9.3% CO2 captured as CaCO3 at the 1 L scale and an extra 60% CO2 captured at the 500 L (pilot) scale. Our optimized system provides a novel approach to capture CO2 through two mechanisms: (i) as organic carbon within microalgal biomass and (ii) as inorganic carbon stored permanently in the form of CaCO3.

Microplastics (MPs) transport bacteria from rivers to oceans, impacting aquatic ecosystems. In situ incubation, a common method for studying bacterial communities on MPs, cannot reproduce complex and realistic environmental dynamics. Herein, a natural incubation experiment was performed to reproduce the migration of nine different substrates from rivers to the sea and examine the succession of bacterial communities on their surfaces. Furthermore, an in situ sequential incubation experiment and the natural incubation experiment were compared. Substantial structural changes were observed in the bacterial communities on MPs along riverine courses to the ocean, with implications for biosecurity, elemental cycling, and degradation potential in aquatic ecosystems. Rapid fluctuations in salinity were the prevalent factor for the significant changes in the bacterial community on MPs. The type of substrate has a significant effect on the formation and structure of bacterial communities, which depend on substrate structure and composition. Unlike in situ incubation, natural incubation reproduces realistic environmental dynamics, providing more comprehensive information on bacterial species composition, diversity, functional metabolism, and structure on MPs. This study introduces a novel methodological approach for MP research and enhances our understanding of the ecological risks associated with MPs transported from rivers to the ocean.

Groundwater is one of the largest reservoirs of liquid fresh water on earth. Aquifers are complex environments where water quality can be affected by geological origins, geochemistry and biological activity. These environments are under pressure due to climate change and pollution. Strongly involved in the biogeochemistry of groundwater ecosystems, microorganisms can also contribute to reducing pollution and potentially be used as indicators of water quality. However, the diversity and role of microorganisms in groundwater remains largely unknown. The present work aimed to characterize bacterial diversity in 60 wells over 8000 km2 in the Beauce Aquifer, France, determine the baseline diversity expected in relation to the hydro geochemical signatures and identify variations that could be due to anthropogenic pressures. We analysed amplicon sequence variants (ASVs) of the 16S rRNA gene as well as the abundance of functional genes associated to arsenic and nitrate (aioA, arsB, narG), organic carbon contents and the geochemical composition. Bacterial diversity and bacterial co-occurrences were found to change according to the hydrogeochemical signatures identified in the aquifer. A lower diversity was measured in confined aquifers, where low oxygen and reducing conditions occurred with high levels of dissolved iron and manganese. This could indicate a higher vulnerability in the face of pressure. Finally, a baseline bacterial diversity composition was found to be linked to each hydrogeochemical signature and several wells that differed from the expected variations of this diversity were identified.

ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships with sepsis, organ failure, and mortality. In parallel, we quantified serum lipopolysaccharides as a marker of bacterial translocation. Fecal samples from 33 patients and 20 healthy controls (HCs) were obtained. The IMs were characterized by 16S-rRNA amplicon sequencing, the metagenomic functional predictive profiles were analyzed by PICRUSt2, and LPS quantification was performed by ELISA. Patients with ACLF showed significant alterations in alpha and beta diversity compared to the HCs. A strong dominance index accurately predicted 28-day and 90-day mortalities. The IMs showed a polarization toward Proteobacteria associated with increased LPS. The LPS correlated with clinical severity, organ dysfunction, and higher pathogenic taxa. The Klebsiella/Faecalibacterium ratio showed good performance in identifying sepsis (AUROC = 0.83). Furthermore, Morganella, Proteus, and Klebsiella were enriched in patients with multiorgan failure. Lactobacillus, Escherichia/Shigella, Veillonella, and Ruminococcus gnavus exhibited potential in predicting 28- and 90-day mortalities. The IM alterations in ACLF may be useful as clinical biomarkers of poor prognosis, primarily for mortality and sepsis. These findings are representative of western Mexico.

Impoundment shell disease (ISD) in the American lobster (Homarus americanus) is a distinct pathological condition from the more well-known epizootic shell disease. It is commonly observed at low prevalences in live American lobsters held overwinter in tidal pounds and significantly reduces their economic value. Impoundment shell disease was originally described in 1937; however, its etiology remains unclear. The main goal of this study was to characterize the bacterial community associated with ISD in Canadian lobsters. Lobsters were collected from a pound in southwest Nova Scotia, Canada, and the full 16S rRNA gene of bacterial communities from lesion and healthy shell areas of asymptomatic (As), moderately symptomatic (MS) and severely symptomatic (SS) animals was sequenced. Pielou evenness and Shannon diversity indexes of alpha-diversity were higher in healthy areas compared to lesion areas. Beta-diversity metrics indicate that the bacterial diversity differences are driven mainly by the relative abundance of a small number of bacteria, rather than the specific taxa present in the samples. Taxa were designated as being potentially involved with ISD based on their relative frequency, relative abundance or being core bacteriome in the lesion shell area. Among those found in this study, Tenacibaculum and Vibrio were previously described in ISD lesions; but others, such as Cellvibrionaceae, Polaribacter, Maribacter and Sulfitobacter were not. Altogether, the findings of this study indicate that ISD is driven by dysbiosis. Moreover, the inconsistency of taxa with previous studies may indicate that ISD consists of a combination of specific functional groups of bacteria, rather specific taxa.

The amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus, Batrachochytrium dendrobatidis (Bd). Bd is known to preferentially infect ventral skin surfaces and feet of host amphibians, often leaving dorsal surfaces like the back uninfected. Within-individual variation in infection distribution across the skin, therefore, may relate to differences in microbiomes among skin regions. However, microbiome heterogeneity within amphibian individuals remains poorly characterized.

We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of 10 body regions from nine captive Rana sierrae individuals and their tank environments. These individuals were naive to Bd, allowing us to assess whether microbiomes differed among body regions prior to any impacts that may be caused by infection.

We found that frog skin and tank environments harbored distinct microbial communities. On frog skin, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant, driven in large part by relative abundances of undescribed members of these families that were significantly higher on frogs than in their environment. Within individuals, we detected differences between microbiomes of body regions where Bd infection would be expected compared to regions that infrequently experience infection. Notably, putative Bd-inhibitory relative abundance was significantly higher on body regions where Bd infection is often localized.

These findings suggest that microbiomes in certain skin regions may be predisposed for interactions with Bd. Further, our results highlight the importance of considering intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.

The gut microbiota plays a crucial role in maintaining host health. While numerous studies have explored the impact of antibiotics on the gut microbiota in humans, limited research has examined how antibiotics affect the gut microbiome in dogs. This study investigated the effects of antibiotic treatment on the gut microbiota of dogs and assessed whether probiotic supplementation could prevent antibiotic-induced dysbiosis. Fourteen healthy young dogs undergoing castration were included in the study. All dogs received a single injection of cefovecin immediately after surgery. The probiotics group (7 dogs) was given a probiotic complex daily starting on the day of surgery and continuing for two weeks, while the non-probiotics group (7 dogs) received no supplementation. Fecal samples were collected on the day of surgery and two weeks later during the follow-up visit for suture removal for microbiome analysis. In microbial diversity analysis, α-diversity was significantly higher in the probiotic-supplemented group compared to the non-probiotics group (p < 0.05). β-diversity analysis revealed significant differences in microbial community composition in the non-probiotics group after antibiotic treatment (p < 0.05), while no significant differences were observed in the probiotics group. Relative abundance analysis indicated that Clostridioides, a marker of antibiotic-induced dysbiosis, significantly increased in dogs without probiotics after antibiotic treatment (p < 0.05). In contrast, Butyricicoccus, a butyrate-producing bacterium with gut health benefits, was significantly enriched in the probiotics group (p < 0.05). These findings suggest that probiotic supplementation supports healthier gut microbiome recovery following antibiotic treatment and highlights its potential to enhance gut microbiota restoration and mitigate gut dysbiosis caused by antibiotics.

Cervical carcinoma (CC) remains one of the significant cancers threatening women's health globally. Increasing evidence suggests that alterations in the microbiota are closely associated with cancer development. However, the understanding of reliable biomarkers and underlying mechanisms during the aggravation of cervical neoplasia such as cervical intraepithelial neoplasia (CIN) and CC is still relatively limited.

In this study, cervical swab samples from 53 healthy controls, 51 high-grade squamous intraepithelial lesion (HSIL), and 52 CC patients were subjected to 16S rDNA sequencing and metabolomics analysis.

We observed significant differences in the cervical microbiota between CC patients and healthy controls or HSIL groups. Compared to the healthy controls, CC patients exhibited increased microbial diversity, decreased abundance of Lactobacillus, and notable changes in microbial composition. Metabolomics analysis revealed significantly elevated levels of the inflammatory mediator Prostaglandin E2 (PGE2) in CC samples. Through random forest modeling and ROC curve analysis, we identified a combination of key microbiota (Porphyromonas, Pseudofulvibacter) and metabolites (Cellopentaose, PGE2) as diagnostic biomarkers with high diagnostic value for CC. Furthermore, we found a significant correlation between the cervical microbiota Porphyromonas and the metabolite PGE2, suggesting a potential role of key microbiota in inducing inflammation.

These findings indicate that alterations in cervical microbiota and metabolites may be closely associated with the occurrence and aggravation of cervical neoplasia, providing new insights for further understanding the mechanisms of cervical neoplasia progression and developing novel diagnostic markers and therapeutic approaches.

Consumers are increasingly interested in healthier, less processed food products, driving the meat industry to improve the quality and health benefits of its offerings. Growing concerns about additives and allergens have encouraged the replacement of these ingredients with natural alternatives, presenting both challenges and opportunities. However, consumer rejection of additives and the actual health effects of their replacement remain poorly understood. In previous work, two new meat products-cooked turkey breast and cooked ham-were developed, where additives and allergens were replaced with natural extracts. These products demonstrated potential health benefits in vitro, including improvements in protein quality and microbiota composition.

This study assessed consumer perceptions of additives through a survey and evaluated the two new meat products in a double-blind, randomized clinical trial conducted over a 5-week period. Biomarkers of interest were measured in blood, faeces, and urine samples at baseline and at the end of this study. Additionally, a separate study tested the satiating effect of these products using VAS score surveys.

The additive perception survey revealed that consumers associate additive-free products with being more natural and less harmful to health, with differences observed based on age, gender, and knowledge of additives. In the clinical trial, both the intervention and control groups showed significant decreases in serum levels of ox-LDL and GPx, with no differences between the groups. However, significant differences between the groups were found in inflammation markers TNF-α and IL-1β. Furthermore, the intervention group exhibited a significant reduction in nitrate excretion and a decrease in nitrification-related gut bacteria. Finally, the reformulated products demonstrated a satiating effect, reducing hunger.

These findings suggest that the new additive- and allergen-free reformulated meat products may offer potential oxidative and anti-inflammatory benefits to consumers.

Modern microbialites are sedimentary structures that offer a window into Earth's geologic history and the intricate interplay between geology and microorganisms. Microbialites are formed by the interaction between microbial communities and the environment leading to mineral precipitation. This study provides a comprehensive analysis of the bacterial and archaeal composition (using the V4 region of the 16S rRNA), along with mineralogy, geochemistry, and hydrogeochemical characterizations of microbialites of five aquatic systems (Bacalar, Muyil, Chichancanab, Azul and Cenote Azul) in southeastern Yucatan Peninsula, México. Dominant taxa were distributed within Pseudomonadota, Cyanobacteriota, Bacillota, Bacteroidota, Chloroflexota, and Planctomycetota, while NB1-j, Myxoscoccota, Verrucomicrobiota, Acidobacteriota, and Crenarchaeota (Archaea) were less abundant. Microbialites from Cenote Azul, a deep sinkhole, were the most different and biodiverse. Notably, potential new families of Cyanobacteriota were observed in all microbialite sites. The primary mineral constituents in microbialites were calcite, magnesian calcite, and gypsum. Hydrogeochemical conditions differed among sites despite their hydrological connectivity. Overall, the karstic ecosystem, hydrogeochemical conditions, tropical climate, and shallow coastal landscapes have favored the occurrence of microbialites in the Yucatan Peninsula, a hotspot region for the formation of these communities. However, their safeguarding becomes crucial, emphasizing the urgency of our role in environmental conservation, in the face of challenging conditions associated with climate change and increased anthropogenic activities detrimental to the environment.

One of the main global issues in animal production is the antimicrobial use (AMU) as prophylactic additives in diet. Despite the availability of a variety of antibiotic alternative additives, their use is not widespread. In this study, we analyzed samples from a trial conducted on a commercial farm, evaluating cecal and litter microbiota with the inclusion of antibiotics or tannins (as AMU-free alternative) in the diet. We observed differential modulation depending on the additive used. Specifically, tannins treatment led to an increased Firmicutes/Bacteroidetes ratio, due to a rise in Clostridiales order, which is associated with improved gut health and better energy efficiency in birds. Poultry litter microbiota contained typical gastrointestinal tract bacteria, along with pathogenic and environmental species. This information becomes relevant for litter reuse in poultry sheds, acting as an inoculum for new birds in the next cycle, determining their microbiota; or when litter is used as organic fertilizer, and these bacteria potentially spread to the environment. This study highlights the potential of tannins as a promising AMU-free alternative in food-producing animals, contributing to new productive paradigms that consider human health, animal welfare, environmental impact, and production efficiency.

Oral microbiome composition has been linked to onset and progression of several localized and systemic diseases. Associations with allergy in adults have been less explored.

We sought to identify oral microbiota associated with allergy outcomes in adults using high-throughput sequencing data.

We characterized bacterial communities of gingival samples from 453 Norwegian adults (average age, 28 years) using 16S rRNA gene amplicon sequencing. We examined more than 2200 bacterial taxa in relation to self-reported current asthma, eczema, or rhinitis, and seroatopy (IgE > 0.70 kU/L). We used linear regression to determine whether overall bacterial diversity differed by each allergic outcome and analysis of composition of microbiomes with bias correction (ANCOM-BC2) to identify differentially abundant taxa.

Less diverse oral bacterial communities were observed (P < .05) in individuals with atopy or rhinitis compared with those without. Bacterial diversity did not differ by asthma and eczema status. While no bacterial taxa were differentially abundant by asthma, many were differentially abundant (P < .05 after multiple-testing correction) in relation to atopy, eczema, and rhinitis. These taxa include several from the genera Leptotrichia and Fusobacterium. Some, including Streptococcus, were previously implicated in respiratory health, whereas others were novel. We also found taxa related to nasal medication use in individuals with rhinitis. Notably, microbial network interconnections differed by allergy status.

Bacterial community compositions of oral gingival samples may play a role in allergic outcomes in adults. These findings could contribute to the development of novel treatment strategies.

The composition of animal gut microbiota is significantly affected by a variety of factors. Seasonal variation in environmental factors is believed to have a significant impact on the composition of mammalian gut microbiota. Therefore, studying the seasonal differences in gut microbiota diversity in wildlife is of great importance to explore their ecological adaptability. This study compared the diversity of gut microbiota of the short-faced moles (Scaptochirus moschatus) in spring, summer, and autumn by using 16S rRNA amplification sequencing. Our results reveal significant seasonal differences in the diversity and function of the short-faced moles gut microbiota. Compared to spring, the diversity and function of the gut microbiota in summer and autumn of short-faced moles are more similar to each other. The relative abundance of Firmicutes is higher in spring than in summer and autumn, while the relative abundance of Proteobacteria in summer and autumn is higher than that of spring. There are significant differences in carbohydrate metabolism between spring and summer, and between spring and autumn. The correlation analysis results suggest that climatic factors are strongly associated with seasonal variation in gut microbiota of the short-faced moles, especially temperature and relative humidity. The present study discusses the seasonal variations in the gut microbiota diversity of short-faced moles and the significant impact of climatic factors on gut microbiota diversity. These results will highlight the potential impact of climatic factors on the seasonal changes of the gut microbiota of subterranean mammals and provide a new view for comprehensively understanding the ecological adaptation of subterranean mammals.

A vast amount of plastic waste enters the ocean every year and the Mediterranean Sea is particularly affected by this issue. Biodegradable polymers like poly(lactic acid) (PLA) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), may help mitigate this problem. We investigated bacterial biofilm development and succession on these polymers over one year in the Western Mediterranean Sea. Scanning electron microscopy (SEM) and confocal laser scanning were used to examine microbial colonization and surface erosion, while bacterial community abundance and composition were assessed through culture plate counting and 16S rRNA gene amplicon sequencing. SEM revealed significant surface erosion on PHBV, indicative of microbial degradation, while PLA exhibited minor and irregular erosion. Culture-based quantification showed higher bacterial colonization on PHBV compared to PLA, suggesting that PHBV provides a more favourable surface for bacterial attachment Amplicon sequencing of the 16S rRNA gene revealed high bacterial diversity, with 17,781 operational taxonomic units across all samples. Proteobacteria, Bacteroidota, and Planctomycetota were the dominant phyla, with the Shannon index consistently exceeding 8, corroborating the bacterial diversity across all materials. Temporal shifts in bacterial community composition were significant, with exposure time explaining 29.8 % of the variation, suggesting biofilm succession as a key factor shaping microbial assemblages. While polymer type had a limited impact on bacterial composition, PHBV biofilms exhibited greater bacterial abundance and diversity compared to PLA. This study highlights PHBV's role in shaping biofilms and its relevance in assessing biodegradable plastics in marine environments. Understanding microbial interactions with bioplastics is crucial for evaluating their environmental impact and degradation dynamics.

Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.

Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.

We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.

Coccidiosis is a gastrointestinal disease caused by Eimeria parasites which leads to major economic losses in the poultry industry worldwide. Eimeria infection may alter the gut microbiota, which has been associated with chicken health and performance. This study aimed to determine the effects of Eimeria maxima infection on the luminal and mucosal microbiota of the cecum (CeL and CeM) at multiple time points post-infection (days 3, 5, 7, 10, and 14). Infection decreased Shannon diversity at d 3 (P = 0.03), increased observed features (ASVs) at d 5 (P < 0.01), and increased Shannon diversity at d 10 (P = 0.04) in the CeL microbiota compared to the control. In CeM microbiota, infection increased observed features at d 5 (P = 0.03), but later decreased observed features at d 14 (P = 0.01). Relative abundance of potential butyrate-producing bacteria such as [Ruminococcus] torques group in CeL and Butyricicoccus in CeM were decreased in infected birds, and some metabolic pathways related to butyrate production were predicted to be decreased. These findings show E. maxima may affect cecal microbiota alpha diversity in a time-dependent manner and reduce abundance of bacteria potentially important to gut health.

Dietary alternatives help effectively in obesity management. The present study examines the gut microbiota diversity in obesity-induced rats treated with intermittent fasting, fermented camel milk (FCM), and FCM-incorporated Sukkari date or their combinations. The metagenomic analysis of the gut microbiome through 16 S rRNA revealed 226 families, 499 genera, and 879 bacterial species. In the taxonomy distributions and heatmap analysis, Bacteroidota (i.e., Prevotella) had the uppermost relative abundance in groups before treatments (Before_Groups, most samples clustered in one sub-cluster) reached 80.50% in sample S11 (Before_G2), whereas Firmicutes (i.e., Lactobacillus) presented the dominant in groups after treatments (After_Groups, generality samples grouped in another sub-cluster) and counted 70.86% in sample S88 (After_G6), reflecting potential short-chain fatty acids production. The alpha and beta diversity explored by Shannon and PCoA indices presented high diversity in most groups after treatment. Deferribacterota and Fusobacteriota, in addition to Stenotrophomonas and Listeria, were the key phylotypes in the treated groups at the Phylum and genus levels, respectively. The proposed functional pathways involving mannan, rhamnose I, glucose, and xylose degradation were the most supported pathways in After_Groups with potential carbohydrate degradation. Eventually, intermittent fasting and probiotic fermented camel milk increased microbiome diversity and accelerated weight loss, preventing health issues.

Clostridioides difficile causes debilitating colitis via secreted toxins that disrupt the intestinal barrier, and toxemia is associated with severe disease. Thus, therapies that fortify the intestinal barrier will reduce the severity of infection. Innate lymphoid cells (ILCs) are critical in the defense against acute C. difficile infection and represent a promising therapeutic target to limit disease. Here, we report that oral administration of the Toll-like receptor (TLR) 7 agonist R848 limits intestinal damage and protects mice from lethal C. difficile infection without impacting pathogen burden or altering the intestinal microbiome. R848 induced interleukin (IL)-22 secretion by ILCs, leading to STAT3 phosphorylation in the intestinal epithelium and increased stem cell proliferation. Genetic ablation of ILCs, IL-22, or epithelial-specific STAT3 abrogated R848-mediated protection. R848 reduced intestinal permeability following infection and limited systemic toxin dissemination. Combined, these data identify an immunostimulatory molecule that activates IL-22 production in ILCs to enhance host tissue defenses following C. difficile infection.

Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities cultured in vitro from human stool to develop a predictive model of community composition upon addition of single nutrients from central carbon metabolism to a complex medium. Among these communities, membership was largely determined by the donor stool, whereas relative abundances were determined by the supplemental carbon source. The absolute abundance of most taxa was independent of the supplementing nutrient due to the ability of a few organisms to quickly exhaust their niche in the complex medium and then exploit and monopolize the supplemental carbon source. Relative abundances of dominant taxa could be predicted from the nutritional preferences and growth dynamics of species in isolation, and exceptions were consistent with strain-level variation in growth capabilities. Our study reveals that assembly of this community of gut commensals can be explained by nutrient utilization dynamics that provide a predictive framework for manipulating community composition through nutritional perturbations.

This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.

Sorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a stratified soil microbiome that plays a crucial role in plant health, growth, and carbon storage. Microbiome studies on agricultural soils, particularly fields growing S. bicolor, have been mostly limited to surface soils (<30 cm). Here we investigated the abiotic factors of soil properties, field location, depth, and the biotic factors of sorghum type across 38 genotypes of the soil microbiome. Utilizing 16S rRNA gene amplicon sequencing, our analysis reveals significant changes in microbial composition and decreasing diversity at increasing soil depths within S. bicolor fields, regardless of genotype or field, with microbial richness and diversity declining to a minimum at the 60-90 cm layer and increasing beyond the 90 cm depth. Notably, specific microbial families, such as Thermogemmatisporaceae and an unclassified family within the ABS-6 order, were enriched in deeper soil layers beyond 30 cm. These findings highlight the importance of soil depth in agricultural soil microbiome studies.IMPORTANCESorghum bicolor is a valuable model for studying the microbiome in deep soils, which is crucial for enhancing carbon sequestration in agricultural systems. As we look to crops with deeper roots for improved carbon storage, it is essential to move beyond the traditional focus on surface soils in agricultural settings. This study shifts that focus by investigating microbial dynamics at greater soil depths, revealing significant changes in microbial composition and diversity with increasing depth, revealing the critical role of deep-soil microbiomes in nutrient cycling and carbon sequestration in agricultural fields with the deep-rooted crop S. bicolor. By exploring these processes beyond surface soils, this research supports the development of sustainable agricultural practices that can better harness the potential of deep-rooted crops for long-term carbon storage.