Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis

Obstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have implicated gut microbiota and metabolites in atherogenesis, we dissected their contributions to OSA-induced atherosclerosis. Atherosclerotic lesions were compared between conventionally-reared specific pathogen free (SPF) and germ-free (GF) Apoe-/- mice following a high fat high cholesterol diet (HFHC), with and without IHC conditions. The fecal microbiota and metabolome were profiled using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry (LC-MS/MS) respectively. Phenotypic data showed that HFHC significantly increased atherosclerosis as compared to regular chow (RC) in both aorta and pulmonary artery (PA) of SPF mice. IHC exacerbated lesions in addition to HFHC. Differential abundance analysis of gut microbiota identified an enrichment of Akkermansiaceae and a depletion of Muribaculaceae (formerly S24-7) family members in the HFHC-IHC group. LC-MS/MS showed a dysregulation of bile acid profiles with taurocholic acid, taurodeoxycholic acid, and 12-ketodeoxycholic acid enriched in the HFHC-IHC group, long-chain N-acyl amides, and phosphatidylcholines. Interestingly, GF Apoe-/- mice markedly reduced atherosclerotic formation relative to SPF Apoe-/- mice in the aorta under HFHC/IHC conditions. In contrast, microbial colonization did not show a significant impact on the atherosclerotic progression in PA. In summary, this research demonstrated that (1) IHC acts cooperatively with HFHC to induce atherosclerosis; (2) gut microbiota modulate atherogenesis, induced by HFHC/IHC, in the aorta not in PA; (3) different analytical methods suggest that a specific imbalance between Akkermansiaceae and Muribaculaceae bacterial families mediate OSA-induced atherosclerosis; and (4) derived bile acids, such as deoxycholic acid and lithocholic acid, regulate atherosclerosis in OSA. The knowledge obtained provides novel insights into the potential therapeutic approaches to prevent and treat OSA-induced atherosclerosis.

2'-FL and cross-feeding bifidobacteria reshaped the gut microbiota of infants with atopic dermatitis ex vivo and prevented dermatitis in mice post-microbiota transplantation through retinol metabolism activation

2'-Fucosyllactose (2'-FL), a predominant human milk oligosaccharide, plays a crucial role in the development of the infant gut microbiota and immune system. However, the microbiota of infants with atopic dermatitis (AD) often has difficulty utilizing 2'-FL. Here, we found that strains from human milk, Bifidobacterium bifidum FN120 and Bifidobacterium longum subsp. longum FN103, utilized 2'-FL for growth by cross-feeding. Through an ex vivo continuous fermentation system, we found that 2'-FL and cross-feeding bifidobacteria synergistically enhanced the production of short-chain fatty acids (SCFAs), particularly acetate and propionate, while reshaping the gut microbiota in infants with AD. The reshaped microbiota was then transplanted into oxazolone-induced mice. We observed that AD symptoms in mice were effectively prevented, with significant changes in the ileum microbiota and increased intestinal SCFA levels. RNA sequencing analysis of Peyer's patches in the small intestine revealed activation of the retinol metabolic pathway. Nontargeted metabolomics analysis revealed a significant increase in plasma retinoate levels, which correlated markedly with AD-related markers. Collectively, our study demonstrated that supplementation with cross-feeding bifidobacteria and 2'-FL reshaped the gut microbiota, activated retinol metabolic pathways, promoted immune tolerance, and thereby prevented AD. Our findings provide novel insights into the therapeutic potential of combining prebiotics and probiotics to modulate the gut - skin axis and support immune tolerance in early life, offering a promising strategy for infantile AD management and prevention.

Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers

Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL-1) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.

Mucus-penetrating microbiota drive chronic low-grade intestinal inflammation and metabolic dysregulation

Metabolic syndrome is, in humans, associated with alterations in the composition and localization of the intestinal microbiota, including encroachment of bacteria within the colon's inner mucus layer. Possible promoters of these events include dietary emulsifiers, such as carboxymethylcellulose (CMC) and polysorbate-80 (P80), which, in mice, result in altered microbiota composition, encroachment, low-grade inflammation and metabolic syndrome. While assessments of gut microbiota composition have largely focused on fecal/luminal samples, we hypothesize an outsized role for changes in mucus microbiota in driving low-grade inflammation and its consequences. In support of this notion, we herein report that both CMC and P80 led to stark changes in the mucus microbiome, markedly distinct from those observed in feces. Moreover, transfer of mucus microbiota from CMC- and P80-fed mice to germfree mice resulted in microbiota encroachment, low-grade inflammation, and various features of metabolic syndrome. Thus, we conclude that mucus-associated bacteria are pivotal determinants of intestinal inflammatory tone and host metabolism.

Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver

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.

In-situ intermittent micro-aeration in food waste and sewage sludge anaerobic co-digestion: Performance, stability, and microbial dynamics

Anaerobic co-digestion (AcoD) of sewage sludge (SS) with food waste (FW) is a practical approach in urban areas due to spatio-temporal availability of these co-substrates. While micro-aeration could enhance hydrolysis and control acidification during mono-digestion, the effects of micro-aeration on AcoD remains unclear. This study explored the influence of oxidation-reduction potential (ORP)-based in-situ micro-aeration on AcoD performance of SS and FW. Although mono-digestion of FW failed due to acidification and micro-aeration of SS was unstable due to high solids content and viscosity, micro-aeration improved specific biogas and methane yields by 21.1 % and 13.1 %, respectively, at the FW:SS ratio of 60:40 ((volatile solids (VS) basis). This improvement was observed at an organic loading rate of 2.25 g VS/L·d and alkalinity below 5000 mg CaCO3/L. The observed positive effect of micro-aeration was accompanied by changes in relative abundance of Aminicenantes. Functional analysis suggested that AcoD was driven by homoacetogenesis and acetoclastic methanogenesis.

Association between oral microbiome and depression: A population-based study

OBJECTIVE

Depression is a global mental health issue, particularly affecting adolescents and young adults. While the role of gut microbiota in depression has been extensively studied, the influence of the oral microbiome remains underexplored. Recent studies suggest that the oral microbiome may affect systemic and brain health through the oral-brain axis. This study aimed to investigate the relationship between oral microbiome diversity and depression using data from 6212 participants in the National Health and Nutrition Examination Survey (NHANES) 2009-2012.

METHODS

Oral microbiome diversity was assessed through oral rinse samples using 16S rRNA sequencing, focusing on α-diversity metrics (observed ASVs and Faith's phylogenetic diversity) and β-diversity measures. Depressive symptoms were evaluated with the Patient Health Questionnaire (PHQ-9). Weighted logistic regression models were employed to assess associations between α-diversity and depression, while linear regression was used to examine the relationship between α-diversity and PHQ-9 scores. β-diversity differences were analyzed via permutational analysis of variance (PERMANOVA).

RESULTS

10.03% of the participants were diagnosed with depression. Higher α-diversity in the oral microbiome was negatively correlated with depression: observed ASVs (OR: 0.713 [CI: 0.508-0.999], P = 0.050) and Faith's phylogenetic diversity (OR: 0.584 [CI: 0.367-0.931], P = 0.025). Linear regression indicated that greater α-diversity was associated with lower PHQ-9 scores, reflecting fewer depressive symptoms. Furthermore, β-diversity analysis revealed significant differences in the microbiome composition between depressed and non-depressed individuals.

CONCLUSION

Reduced oral microbiome diversity is associated with an increased risk and severity of depression. The study underscores the importance of exploring the oral-brain axis and highlights the need for further research into the mechanisms and therapeutic strategies targeting this relationship.

The temperate seagrass species Cymodocea nodosa and the associated bacteria co-response to sunscreen pollution

Sunscreens are included among the contaminants of emerging concern (CECs) as their production and use have spread over years while damaging aquatic biota. Sunscreens can damage the photosynthetic systems and change the microbiome of seagrasses, triggering alterations in carbon metabolism -including primary production and dissolved organic carbon (DOC) fluxes- and ecological functions. Here, we conducted a 31-day mesocosm experiment exposing Cymodocea nodosa plants to a mixture of commercial sunscreens. Sunscreens produced a significant reduction on net production rates, switching the system from autotrophic to heterotrophic, which was ascribable to an increase in heterotrophic bacteria families (some known to degrade complex substrates) and, more importantly, to a significant reduction of photosynthetic pigments in plants. Moreover, a significant release of DOC at night attributed to exudation from disrupted roots was recorded, which accounted for the observed increase in bacteria abundance and family richness recorded in the phyllosphere. A higher accumulation of starch in rhizomes suggests a certain degree of resistance of this species. However, we observed a trend to reduce some protective bacteria taxa, whereas promoted the growth of other pathogenic ones for seagrasses, along with other taxa related with the consumption of plant-derived polysaccharides and lignin compounds. Therefore, our results indicated that this CEC may reduce the contribution of seagrasses to the blue carbon pool, among others ecosystem services, and suggest a possible prompt of seagrass diseases if stressing conditions are maintained over time.

Metataxonomic, chemical, and sensory aspects of cocoa fermentation using single hybrids and combinations of hybrids and their effects on chocolate quality

Extensive research has been conducted on cocoa fermentation in single hybrids. However, comparisons between hybrid combinations and single hybrids are limited. This study investigated cacao fermentation using a hybrid combination (PS 1319, PH 16, BN 34, CEPEC 2002, SJ02, CCN 10, and Ipiranga) and SJ02 hybrid alone. Microbial diversity was determined by next-generation sequencing (NGS), organic acids, carbohydrates, and alcohols by HPLC, volatile compounds by GC/MS, and the sensory analysis by acceptance test and Check-All-That-Apply (CATA). The NGS analysis identified 64 fungal species and 60 bacterial species with Hanseniaspora uvarum, Hanseniaspora opuntiae, Pichia manshurica, Pichia kluyveri, and Saccharomyces sp. as the dominant yeasts. Carbohydrates were metabolized entirely in the hybrid combination by the end of fermentation. Higher ethanol concentrations were found in SJ02 at 72 h. As the fermentation progressed, citric acid concentrations decreased, while lactic and acetic acid concentrations increased by 72 h on SJ02 fermentation. Acetobacter sp. was strongly correlated with acetic acid production in hybrid combination fermentation. SJ02 showed higher concentrations of volatile compounds, with fatty acids being the most abundant class, followed by esters. The alcohol 2-nonanol was detected only in the hybrid combination fermentation. SJ02 chocolate was attributed to higher taste, texture, and overall score. The descriptors bitter and citric acidity were more perceived in chocolates from the hybrid combination, while the earthy descriptor was more evident in the SJ02 hybrid. Thus, fermentations using a hybrid combination and the SJ02 hybrid allow the production of fine chocolates with varied sensory profiles.

Urban soils immobilize harmful microbes and antibiotic resistance genes

Exposure to harmful microbiomes and antibiotic resistance genes (ARGs) can negatively affect human health. However, the contribution of vegetation and soils to the airborne microbiota transferred indoors (AMTI) remains unclear. We used our newly-developed airborne microbial sampler (VenTube) to collect AMTI samples from 72 neighborhoods in Shanghai. The AMTI sampling coincided with simultaneous adjacent phyllosphere and soil microbes. We characterized the microbial communities using next-generation sequencing and quantitative PCR, and employed traceability analysis to identify the sources of AMTI. Our findings revealed that both bacterial and fungal communities in AMTI predominantly originated from phyllosphere, which was estimated to contribute up to 52.3 % and 67.2 % of the bacterial and fungal communities, respectively. Notably, there was extensive co-transfer of potential human pathogens (PHP) between phyllosphere microbes and AMTI. Surprisingly, although the soil harbored higher levels of PHP and respiratory diseases (RDs)-associated ARGs than AMTI, it contained fewer RDs-associated microbes overall. Furthermore, soil sulfur enrichment due to an increase in Ligustrum trees influenced the release of RDs-associated microorganisms from the soil. Collectively, our study emphasizes that the elevated levels of RDs-associated microbes in AMTI primarily derived from phyllosphere microbes. We also highlight that soils may limit the spread of RDs-associated microbes and ARGs.

Safety Evaluation of Human-Derived Uric Acid Degrading Lacticaseibacillus paracasei M2a and Its Impact on Gut Microbiota

We report the identification of a human-derived uric acid (UA)-degrading bacterial strain, analyzed its degradation efficiency, and assessed its safety to provide a scientific basis for future clinical applications in the treatment of hyperuricemia (HUA) and gout. Here, we isolated the M2a strain from feces of healthy young men. The strain was identified as Lacticaseibacillus paracasei (formerly Lactobacillus paracasei) via 16S rRNA and biochemical analyses. The in vitro and in vivo efficiencies of M2a uric acid degradation were found to be 45.53% and up to 47.88%, respectively. Strain M2a exhibited no detectable pathogenicity, demonstrated robust tolerance to simulated gastrointestinal conditions, and displayed a favorable safety profile. The strain ameliorated hyperuricemia-associated liver and kidney dysfunction, as evidenced by improved biochemical markers (ALT, AST, BUN, and CRE; P < 0.05) and histopathological findings showing reduced inflammatory cell infiltration and preserved tissue architecture in HE-stained liver and kidney sections. Furthermore, it regulated intestinal microbiota in HUA mice, increased the relative content of beneficial bacteria (e.g., Lacticaseibacillus) in the mouse intestine, and reduced the intestinal presence of Klebsiella and Blautia in mice. Further study of M2a is warranted to elucidate pathways for lowering blood levels of uric acid via clinical utilization of probiotic and associated biologic interventions.

Chia Oil (Salvia hispanica L.) Improves the Intestinal Health of Wistar Rats Fed a Hypercaloric Diet

BACKGROUND

A diet rich in fat and sugar is present in society everyday life, leading to the development of metabolic changes, especially in intestinal microbiota. Chia oil is a source of alpha-linolenic acid, which has antioxidant and anti-glycemic effects. Based on this, we hypothesized that chia oil may promote intestinal health.

OBJECTIVE

The study aims to investigate the effects of chia oil on gut microbiota and intestinal health in Wistar rats fed a high-fat and high-fructose diet (HFHF).

METHODS

The animals were separated into two groups and received the following diets: standard murine diet (AIN-93M) (n = 10) and HFHF (n = 20) to induce metabolic changes (phase I) during eight weeks. After that, the AIN-93M group remained unchanged, while the HFHF group was divided into two groups: HFHF (n = 10) and HFHF with chia oil (HFHF+CO) (n = 10) for ten weeks (phase II, chia oil treatment). We analyzed immunoglobulin A (IgA) levels, cecal pH, short-chain fatty acids (SCFAs), intestinal permeability, intestinal microbiome composition, histomorphometry, and murinometric parameters.

RESULTS

Chia oil consumption increased alpha-linolenic acid intake, IgA levels, propionic acid production, cecum weight, goblet cell number, thickness and depth of intestinal crypts, and the thickness of both circular and longitudinal muscle layers of the colon, and decreased cecal pH. No change was observed in the alpha and beta diversity between the HFHF and HFHF+CO groups. The HFHF+CO diet increased the relative abundance of genera Lactobacillus sp., Faecalibacterium sp., and Erysipelatoclostridium sp., compared to the AIN-93M group. No difference was observed in the intestinal permeability among the groups.

CONCLUSION

Chia oil consumption is an alternative for improving the intestinal health of rats fed a HFHF diet.

Distinctive microbial communities linked with pH and heavy metals in mine drainages across all regions of Japan

Passive treatment using microorganisms is a promising method for removing toxic metals from acid mine drainage (AMD). To provide a better understanding of the compositions of mine microbial communities and their relationship with pH and metal concentrations in mine water, we analyzed both physicochemical data and 16S rRNA gene amplicon sequences from 40 untreated drainages from 30 abandoned mines across all regions of Japan. In the 40 mine drainages, higher concentrations of metals (iron, lead, cadmium, copper, and manganese) were detected in mine drainages with acidic pH (< 4.5; 24 samples) than in those with circumneutral pH (> 6.0; 16 samples), except for arsenic. Comparison of principal coordinate analysis scatter plots between mine drainages of acidic and circumneutral pH revealed a relatively clear separation of microbial compositions except for one mine drainage sample. In the 24 AMDs, the dominant operational taxonomic units (OTUs) found at relative abundance levels >3 % were generally one of three related to Caballeronia arationis, Ferrovum myxofaciens, or Gallionella capsiferriformans, except for two mine drainage samples. Although the microbial communities of the 40 mine drainages were obtained from a single sampling time (triplicate analysis), they may reflect the typical microbial communities of each mine drainage, because analysis of drainage samples taken from the same sampling point over three different seasons (summer, autumn, and winter) revealed similar communities regardless of the season. Among mine drainages analyzed in this study, the OTU showing 96.8 % identity to C. arationis was the most prevalent bacterial OTU, which was found in 23 drainages (the top OTU in 15 mine drainages) with >3 % relative abundance.

Nitrous oxide emissions treating hypersaline wastewater in suspended and attached partial nitritation - anammox reactors

Nitrous oxide (N2O) emissions from partial nitritation- anammox (PN/A) processes for deammonification has become an important issue as the technology has become more widespread, however, N2O emissions from PN/A treating hypersaline wastewater has been little reported. Here, N2O emissions from completely mixed suspended and attached single-stage PN/A reactors treating hypersaline (4 % salinity; 40 g/kg) wastewater for ammonium removal were first investigated without the addition of organics. Results show that N2O emissions in fixed bed and suspended PN/A reactors without organic addition ranged from 0.08 % to 1.0 % and 0.09 % to 1.5 % of ammonium removed, respectively. Bulk ammonium and nitrite concentrations were shown to be the main controlling factors for N2O emissions. The presence of influent organics was subsequently studied to see its effect on nitrogen removal and N2O emissions. The addition of acetate to both fixed bed and suspended reactors reduced N2O emissions by 52.5 % and 72.4 %, respectively. Quantitative PCR results showed an increase in the functional genes related to denitrification with the addition of acetate, however, deammoniafication was not significantly affected.

Variable phylosymbiosis and cophylogeny patterns in wild fish gut microbiota of a large subtropical river

The persistence and specificity of fish host-microbial interaction during evolution is an important part of exploring the host-microbial symbiosis mechanism. However, it remains unclear how the environmental and host factors shape fish host-microbe symbiotic relationships in subtropical rivers with complex natural environments. Freshwater fish are important consumers in rivers and lakes and are considered keystone species in maintaining the stability of food webs there. In this study, patterns and mechanisms shaping gut microbiota community in 42 fish species from the Pearl River, in the subtropical zone of China, were investigated. The results showed that fish host specificity is a key driver of gut microbiota evolution and diversification. Different taxonomic levels of the host showed different degrees of contribution to gut microbiota variation. Geographical location and habitat type were the next most important factors in shaping gut microbiota across the 42 fishes, followed by diet and gut trait. Our results emphasized the contribution of stochastic processes (drift and homogenizing dispersal) in the gut microbial community assembly of freshwater fishes in the middle and lower reaches of the Pearl River. Phylosymbiosis is evident at both global and local levels, which are jointly shaped by complex factors including ecological or host physiological filtration and evolutionary processes. The core microbiota showed co-evolutionary relationships of varying degrees with different taxonomic groups. We speculate that host genetic isolation or habitat variation facilitates the heterogeneous selection (deterministic process), which occurs and results in different host-core bacterium specificity.

IMPORTANCE

Freshwater fish are regarded as the dominant consumers in rivers and lakes. Due to their diverse feeding modes, fish significantly enhance the trophic link and nutrient recycling/retention in aquatic habitats. For this, they are often considered keystone species in maintaining the stability of food webs in rivers and lakes. A significant part of fish nutrition is essentially mediated by their gut microbiota, which can enhance fish tolerance to fluctuations in external resources and improve the efficiency of nutrients extracted from various food sources. As gut bacterial symbionts have a profound impact on the nutrition and development of their hosts, as well as their overall fitness, it is critical to answer the question of how hosts maintain these benefits by procuring or inheriting these vital symbionts, which is still largely unanswered, especially for freshwater fish. Our study provides new insights into the co-evolutionary relationship between wild fish and their symbiotic microbiome, the hidden diversity of gut microbiome, and the ecological adaptation potential of wild freshwater fish.

Conventional and organic farms with more intensive management have lower soil functionality

Organic farming is often considered to be more sustainable than conventional farming. However, both farming systems comprise highly variable management practices. In this study, we show that in organic and conventional arable fields, the multifunctionality of soils decreases with increasing agricultural management intensity. Soil organic carbon content and bacterial biomass, respectively, were the strongest abiotic and biotic predictors of soil multifunctionality. Greater soil multifunctionality was associated with less-frequent inversion tillage and higher frequency of grass-legume cover cropping, and organic farming did not outperform conventional farming. Our results suggest that reducing management intensity will enhance soil multifunctionality in both conventional and organic farming. This implies that, in contexts where high-yielding, high-intensity agriculture prevails, the paradigm of sustainable intensification should be replaced by "productive deintensification."

Effects of soluble electron shuttles on microbial iron reduction and methanogenesis

In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.

The "Fe-S wheel": A new perspective on methylmercury production dynamics in subalpine peatlands

The cycling of iron (Fe) and sulfur (S) in peatland ecosystems plays a pivotal role in modulating methylmercury (MeHg) formation. This study integrates data on Fe and S fractions, geochemical factors, microbial communities, and statistical modeling to propose the novel "Fe-S wheel" conceptual framework. This framework explores the coupled cycling of Fe, S, and Hg in the Dajiuhu peatland (DJH), an exemplary natural laboratory in central China. Through this framework, we demonstrate that the "Fe-S wheel" exerts a strong direct inhibitory effect on MeHg formation. However, when the S/Fe molar ratio is less than 0.25, the "Fe-S wheel", influenced by microbial communities, can indirectly enhance MeHg generation by promoting humic acid-bound Hg. Conversely, when the S/Fe molar ratio exceeds 0.25, the "Fe-S wheel", under the influence of dissolved oxygen, suppresses MeHg formation by inhibiting strong-complexed Hg and sulfide-bound Hg. Global peatland data corroborate these findings, showing a significant negative correlation between the S/Fe ratio and MeHg concentrations. Given the uncertainties in the interaction and transformation mechanisms between Fe and S, the S/Fe molar ratio is likely to serve as a key parameter reflecting their coupled effects on MeHg. This study highlights the critical role of Fe and S interactions in regulating MeHg generation within peatland ecosystems.

Nutrient enrichment alters the microbiome and increases chytrid load in the American bullfrog Lithobates catesbeianus

Agricultural practices have a profound impact on watershed dynamics, water quality, and the well-being of aquatic life. One major concern is agricultural pollution, particularly the excess of nutrients, which can elevate disease risks in various host-pathogen relationships. However, the exact mechanisms driving this effect remain uncertain. Elevated nutrient levels are believed to significantly influence populations of aquatic environmental bacteria, potentially reshaping the microbiomes of aquatic organisms and affecting their vulnerability to disease. Despite this, the impact of nutrient enrichment on host microbiomes as a link to diseases in aquatic organisms has been largely overlooked. In this study, we investigated the impact of nutrient enrichment on the skin-associated microbial communities of the American bullfrog Lithobates catesbeianus. We observed a significant shift in bacterial richness and community composition in nutrient-enriched ponds compared with reference ponds. Although the proportion of the community inhibitory towards Batrachochytrium dendrobatidis (Bd) did not change significantly, Bd loads were markedly higher in nutrient-enriched ponds. Nutrient enrichment significantly altered carbon utilization patterns as measured by Biolog EcoPlates, and antibiotic resistance was prevalent across all ponds and samples, with resistance to trimethoprim, sulfamethazine, and chloramphenicol significantly higher in nutrient-enriched ponds. Our findings indicate that nutrient enrichment affects the structure and function of skin-associated microbial communities in American bullfrogs, influencing both Bd load and antibiotic resistance.

Probiotic treatment induces sex-dependent neuroprotection and gut microbiome shifts after traumatic brain injury

BACKGROUND

Recent studies have highlighted the potential influence of gut dysbiosis on traumatic brain injury (TBI) outcomes. Alterations in the abundance and diversity of Lactobacillus species may affect immune dysregulation, neuroinflammatory responses, anxiety- and depressive-like behaviors, and neuroprotective mechanisms activated in response to TBI.

OBJECTIVE

This study aims to evaluate the protective and preventive effects of Pan-probiotic (PP) treatment on the inflammatory response during both the acute and chronic phases of TBI.

METHODS

Males and female mice underwent controlled cortical impact (CCI) injury or sham. They received a PP mixture in drinking water containing strains of Lactobacillus plantarum, L. reuteri, L. helveticas, L. fermentum, L. rhamnosus, L. gasseri, and L. casei. In the acute group, mice received PP or vehicle (VH) treatment for 7 weeks before TBI, continuing until 3 days post-injury (dpi). In the chronic group, treatment began 2 weeks before TBI and was extended through 35 dpi. The taxonomic microbiome profiles of fecal samples were evaluated using 16S rRNA V1-V3 sequencing analysis, and Short-chain fatty acids (SCFAs) were measured. Immunohistochemical, in situ hybridization, and histological analyses were performed to assess neuroinflammation post-TBI, while behavioral assessments were conducted to evaluate sensorimotor and cognitive functions.

RESULTS

Our findings suggest that a 7-week PP administration induces specific microbial changes, including increased abundance of beneficial bacteria such as Lactobacillaceae, Limosilactobacillus, and Lactiplantibacillus. PP treatment reduces lesion volume and cell death at 3 dpi, elevates SCFA levels at 35 dpi, and decreases microglial activation at both time points, particularly in males. Additionally, PP treatment improved motor recovery in males and alleviated depressive-like behaviors in females.

CONCLUSION

Our findings indicate that PP administration modulates microbiome composition, reduces neuroinflammation, and improves motor deficits following TBI, with these effects being particularly pronounced in male mice.

Community stability of free-living and particle-attached prokaryotes in coastal waters across four seasons: insights from 9.5 years of weekly sampling

Free-living (FL) and particle-attached (PA) prokaryotes, having distinct ecological niches, play significant roles in marine ecosystems. These communities respond rapidly to environmental changes and exhibit seasonal patterns. However, their temporal stability, crucial for maintaining microbial community structure and function, remains poorly understood. This study assessed community stability, particularly in terms of resistance to environmental perturbations, and inferred regulatory mechanisms using weekly collected samples over 9.5 years from FL and PA communities in coastal water. Short-read amplicon sequencing revealed habitat-specific microbial compositions, with Actinobacteria and Euryarchaeota dominating FL community, while Planctomycetes and Verrucomicrobia prevailed in PA community. Network analysis, constructed based on relative abundance, uncovered seasonal co-occurrence patterns and highlighted keystone taxa, such as Nitrosopumilus in FL and Synechococcus in PA community, as critical for maintaining stability within specific seasons and niches. Seasonal variations in community stability indices suggest that higher network complexity can enhance resistance; however, excessive interactions with greater complexity may also undermine it. Furthermore, it was found that FL community stability was primarily affected by abiotic factors, likely due to direct exposure to environmental changes, whereas PA community stability was more influenced by biotic factors, as their association with particles fosters localized interactions and biological processes. These findings reveal the intricate balance between network complexity and stability and the importance of niche-specific approaches in ecological research. Our results contribute to a deeper understanding of marine microbial niche partitioning and provide insights into ecosystem management and conservation strategies, particularly regarding keystone taxa.

Effect of Elaeagnus angustifolia Linn. on the Physicochemical Properties and Microbial Community Structure of Inter-Rhizosphere Soils

AIMS

The aim of this study was to elucidate the effect of Elaeagnus angustifolia Linn. (E. angustifolia L.) on the structure and abundance of the soil microbial community. This paper provides a theoretical foundation for guiding the establishment of E. angustifolia L. forests to enhance the physicochemical properties of soil.

METHODS

This study employed high-throughput sequencing technology to analyse the composition, diversity, and structural changes of various soil fungal and bacterial communities and correlated the results with soil physicochemical properties.

RESULTS

The results indicated a significant increase in the total nitrogen (0.66 g/kg-0.87 g/kg), ammonium nitrogen (3.60 mg/kg-6.56 mg/kg), and organic matter (1.06-1.38%) contents of the inter-rhizosphere soil of E. angustifolia L. after 3, 4, and 5 months of planting. Additionally, the total phosphorus, potassium, and nitrate nitrogen contents increased, whereas soil pH and salinity decreased. The abundance of soil microbial communities also increased. The fungal phyla with relative abundances greater than 1% were Ascomycota, Fungi_unclassified, Basidiomycota, Zygomycota, and Glomeromycota. Chytridiomycota, Rozellomycota, Mortierellomycota, and Olpidiomycota were not found in the bare soil control but were observed in the rhizosphere soil of the date palm. The relative abundance of bacteria from the phyla Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Chloroflexi in the inter-root soil of jujube dates showed an increase in comparison with the control group. At the same time, correlation analysis found that soil total phosphorus, nitrogen content, and soil enzyme activity were positively correlated with the bacterial level, with TN (p < 0.01) and NO3--N (p < 0.05) showing significant positive correlations. Conversely, soil pH and salinity were mostly negatively correlated with the fungi, and soil enzyme activity was significantly correlated with the fungal and bacterial at different RAD levels.

CONCLUSIONS

The introduction of E. angustifolia L. markedly affected the physicochemical properties and microbial community composition of the soil.

Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions

Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.

IMPORTANCE

Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.

Differential effects of environmentally relevant concentrations of ibuprofen on denitrification and nitrous oxide emissions in river sediments

The increasing presence of ibuprofen in aquatic ecosystems poses significant challenges to their biogeochemical functions, including nitrogen transformations. In this study, we employed 15N-labeling techniques to investigate the effects of environmentally relevant concentrations of ibuprofen (0-10,000 ng L-1) on denitrification and the associated nitrous oxide (N2O) emissions in river sediments over a 60-day period. The results revealed a hump-shaped response in denitrification rates to ibuprofen addition across a range of nitrate concentrations (1-60 mg N L-1), with rates peaking near 200 ng L-1 ibuprofen, followed by inhibition at certain higher concentrations, leading to a reduction of up to 25.8 % compared to the treatment without ibuprofen. Kinetic analysis showed that the maximum denitrification rate followed the same hump-shaped trend, despite a decrease in nitrate affinity with increasing ibuprofen concentrations. The abundance of denitrifying bacteria mirrored the pattern observed in denitrification rates across different ibuprofen concentrations. However, increasing ibuprofen concentrations consistently accelerated N2O production rates. Microbial analysis suggests that the increase in N2O production genes was faster than for reduction genes, while the decrease was slower with increasing ibuprofen concentrations. This study highlights the hump-shaped response of denitrification rates and the consistent increase in N2O emissions induced by ibuprofen, offering insights for developing environmental management strategies to mitigate ibuprofen and nitrogen pollution, as well as reducing N2O emissions.

Endozoicomonas dominance and Vibrionaceae stability underpin resilience in urban coral Madracis auretenra

Coral resilience varies across species, with some exhibiting remarkable stability and adaptability, often mediated by their associated microbiomes. Given the species-specific nature of coral-microbiome interactions, investigating the microbiomes of urban-adapted corals provides critical insights into the health, dynamics, and functioning of coral holobionts. In this study, we examined the microbiome of Madracis auretenra, a Caribbean coral from Santa Marta, Colombia, across contrasting environmental conditions. Over two years, we compared the microbiomes of healthy and stressed coral colonies from two distinct reef habitats-urban and protected-using 16S rRNA gene sequencing (V4 region) to assess microbial diversity. Our findings revealed microbial richness and diversity were primarily influenced by seasonal and local factors rather than host-specific traits such as interaction with algae, health status, or microhabitat. These variations were not substantial enough to disrupt the overall microbial community structure, which remained stable across temporal and spatial scales. Dominant taxa included Endozoicomonas, along with Vibrionaceae and Rhodobacteraceae, which form dense ecological interaction networks. Notably, nutrient and oxygen levels emerged as key drivers of microbiome fluctuations, yet Vibrionaceae populations exhibited exceptional temporal stability. These findings highlight the presence of a well-structured and resilient coral microbiome with minimal seasonal variability, even in urban-influenced environments. We propose that the dominance of Endozoicomonas and the stability of Vibrionaceae populations play a pivotal role in maintaining microbiome balance, ultimately contributing to the ecological resilience of M. auretenra in dynamic reef habitats.

Rhizosphere Bacterial Communities Alter in Process to Mycorrhizal Developments of a Mixotrophic Pyrola japonica

Rhizosphere bacteria work in synergy with mycorrhizal fungi to promote plant growth. The community structure of rhizosphere bacteria may be influenced by continuous changes in fungal associations with host plants. Asiatic herbaceous plant Pyrola japonica (Ericaceae) forms arbutoid mycorrhizas without fungal mantles, with its mycorrhizal development being visually distinguishable at the cellular level. This study aimed to investigate roles of rhizosphere bacteria and their community shifts along with mycorrhizal developments. We examined bacterial communities at three different developmental stages of mycorrhizal roots-limited, full, and digested-via a partial 16S rRNA amplicon sequencing. Both α- and β-diversities in the full condition were significantly lower than those in the limited and digested conditions. Significant clusters of bacterial compositions were found among all treatments. In terms of ecological processes of community assembly, communities in limited conditions and bulk soil were influenced by both deterministic and stochastic processes, whereas those in full and digested conditions were regulated only by stochastic ways. Furthermore, the order Rhizobiales and Actinomycetales known as mycorrhizal helper bacteria were characterized in the full and digested conditions through phylogenetic analysis and detection of indicator taxa. These results suggest that mycorrhizal fungi may play ecologically important roles not only as temporal drivers initiating the formation rhizosphere bacterial communities but also as key founders exerting continuous influences to establish priority effects. Moreover, the rhizosphere bacterial community remains after mycorrhizal degeneration and their historical continuity may contribute to maintaining plant-mycorrhizal fungi-bacterial associations.

Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus)

Monotreme and marsupial development is characterized by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programmes in the future.

Integrating traditional omics and machine learning approaches to identify microbial biomarkers and therapeutic targets in pediatric inflammatory bowel disease

Background

Pediatric inflammatory bowel disease (IBD), especially Crohn's disease, significantly affects gut health and quality of life. Although gut microbiome research has advanced, identifying reliable biomarkers remains difficult due to microbial complexity.

Methods

We used RNA-seq-based microbial profiling and machine learning (ML) to find robust biomarkers in pediatric IBD. Microbial taxa were profiled at phylum, genus, and species levels using kraken2 on Crohn's disease and non-IBD ileal biopsies. We performed abundance-based analyses and applied four ML models (Logistic Regression, Random Forest, Support Vector Machine, XGBoost) to detect discriminative taxa. An independent cohort of 36 pediatric stool samples assessed by 16S rRNA sequencing validated top ML results.

Results

Traditional abundance-based methods showed compositional shifts but identified few consistently significant taxa. ML models had better discriminatory performance, with XGBoost outperforming others and pinpointing Orthotospovirus and Vescimonas as key genera. These findings were confirmed in the validation cohort, where only one traditionally noted genus, Actinomyces, maintained significance.

Discussion

Integrating conventional omics with AI-driven analytics boosts reproducibility and clinical relevance of microbial biomarker discovery, opening new possibilities for targeted therapies and precision medicine in pediatric IBD.

Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation

Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2 × MIC (low concentration) and 4 × MIC RSQ01 (high concentration). Integrated 16S rDNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, while probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and amino acids) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors- and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.

Microbial communities on dry natural rocks are richer and less stressed than those on man-made playgrounds

In modern urbanized societies, the incidence of major immune-mediated diseases is several times higher than before World War II. A potential explanation is that these diseases are triggered by limited possibilities to be exposed to rich environmental microbiota. This requires that the urban environment hosts less and poorer microbiota than the natural environment. The current study was designed to test the assumption that urban man-made environments host less and poorer environmental microbiota, compared to natural habitats. We selected two types of dry environments, natural rocks and playground rubber mats, both of which were used daily and extensively by children. In quantitative PCR and next-generation sequencing, bacterial abundance and richness were higher on the natural rocks than the rubber mats. Altogether, 67 amplicon sequence variants (ASVs) belonging mostly to Actinobacteria and Proteobacteria were indicative of rock microbiota, while three ASVs were indicative of rubber mats. Interestingly, bacteria formed more complex networks on rubber mats than natural rocks. Based on the literature, this indicates that the studied artificial dry environment is more challenging and stressful for bacterial communities than dry natural rocks. The results support the hypothesis that urban man-made environments host poor microbial communities, which is in accordance with the biodiversity hypothesis of immune-mediated diseases.IMPORTANCEThe current study provides new evidence that artificial urban play environments host poor microbial communities and provide a stressful environment for microbes, as compared to dry natural rocks. Through this, the current study underlines the need to enhance microbial diversity in urban areas, especially in outdoor play environments, which have a crucial role in providing essential microbial exposure for the development of children's immune system. This research can potentially offer guidance for urban planning and public health strategies that support planetary health.

Assessment of Soil Health Through Metagenomic Analysis of Bacterial Diversity in Russian Black Soil

Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity, in general, and higher representation of certain bacterial species-Bradyrhizobium spp. The results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field.

Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant

Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.

Blanking on blanks: few insect microbiota studies control for contaminants

Research on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial biomass. Such low-biomass samples are common across insect taxa, developmental stages, and tissue types. Identifying putative contaminants is essential to distinguish between true microbiota and introduced contaminant DNA. It is therefore important that studies control for contamination, but how often this is done is unknown. To investigate the status quo of contamination control, we undertook a systematic literature review to quantify the prevalence of negative control usage and contamination control across the literature on insect microbiota (specifically bacterial communities) over a 10 year period. Two-thirds of the 243 insect microbiota studies evaluated had not included blanks (negative controls), and only 13.6% of the studies sequenced these blanks and controlled for contamination in their samples. Our findings highlight a major lack of contamination control in the field of insect microbiota research. This result suggests that a number of microbes reported in the literature may be contaminants as opposed to insect-associated microbiota and that more rigorous contamination control is needed to improve research reliability, validity, and reproducibility. Based on our findings, we recommend the previously developed guidelines outlined in the RIDE checklist, with the addition of one more guideline. We refer to this as the RIDES checklist, which stands for Report methodology, Include negative controls, Determine the level of contamination, Explore contamination downstream, and State the amount of off-target amplification.IMPORTANCEOur systematic review reveals a major lack of methodological rigor within the field of research on insect-associated microbiota. The small percentage of studies that control for contamination suggests that an unknown but potentially considerable number of bacteria reported in the literature could be contaminants. The implication of this finding is that true microbiota may be masked or misrepresented, especially in insects with low microbial biomass.

Actively N2O-Reducing Oxygen-Tolerant Microbial Consortium Attained by Using a High-Dilution-Rate Chemostat Fed with Methanol

Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB consortium under intermittent oxygen and N2O supplies. 15N tracer analysis showed that the N2O consumption activity of the enriched consortium was higher than its N2O production activity in the presence of either a single or multiple electron acceptors (i.e., nitrogen oxides). The observed maximum N2O consumption was 80.7 μmol·g-biomass-1·h-1. Quantitative PCR results showed that clade I nosZ bacteria overwhelmed clade II nosZ bacteria at high (0.41 mmol·min-1) and low (0.08 mmol·min-1) N2O loading rates. The dilution rate and N2O loading rate affected the microbial community composition and activity. A higher N2O loading rate stimulated active and oxygen-tolerant N2ORB that boosted N2O consumption by approximately 50% in the presence of oxygen. Metagenomic analysis unraveled the predominance of a novel methylotrophic N2ORB, possessing entire denitrifying genes and high-affinity terminal oxidase genes, from the reactor with a high N2O loading rate. The unique physiological traits of the consortium enriched by methanol shed light on a novel function─aerobic N2O consumption by N2ORB─and pave the way for innovative N2O mitigation strategies applying powerful N2O sinks in engineered systems.

In vitro microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier

BACKGROUND

Non-absorbed dietary emulsifiers, including carboxymethylcellulose (CMC), directly disturb intestinal microbiota, thereby promoting chronic intestinal inflammation in mice. A randomised controlled-feeding study (Functional Research on Emulsifiers in Humans, FRESH) found that CMC also detrimentally impacts intestinal microbiota in some, but not all, healthy individuals.

OBJECTIVES

This study aimed to establish an approach for predicting an individual's sensitivity to dietary emulsifiers via their baseline microbiota.

DESIGN

We evaluated the ability of an in vitro microbiota model (MiniBioReactor Arrray, MBRA) to reproduce and predict an individual donor's sensitivity to emulsifiers. Metagenomes were analysed to identify signatures of emulsifier sensitivity.

RESULTS

Exposure of human microbiotas, maintained in the MBRA, to CMC recapitulated the differential CMC sensitivity previously observed in FRESH subjects. Furthermore, select FRESH control subjects (ie, not fed CMC) had microbiotas that were highly perturbed by CMC exposure in the MBRA model. CMC-induced microbiota perturbability was associated with a baseline metagenomic signature, suggesting the possibility of using one's metagenome to predict sensitivity to dietary emulsifiers. Transplant of human microbiotas that the MBRA model deemed CMC-sensitive, but not those deemed insensitive, into IL-10-/- germfree mice resulted in overt colitis following CMC feeding.

CONCLUSION

These results suggest that an individual's sensitivity to emulsifier is a consequence of, and can thus be predicted by, examining their baseline microbiota, paving the way to microbiota-based personalised nutrition.

Effects of Yeast Products on the Apparent Total Tract Macronutrient Digestibility, Oxidative Stress Markers, Skin Measures, and Fecal Characteristics and Microbiota Populations of Healthy Adult Dogs

Brewer's yeast has high nutritional value and contains bioactive compounds that may promote health. Functionalized canola meal (FCM) is a high-fiber ingredient that has been proposed as a carrier for brewer's yeast. The objective of this experiment was to determine the apparent total tract digestibility (ATTD) of diets containing yeast-enriched FCM and test their effects on the fecal characteristics and microbiota, skin measures, and serum oxidative stress markers of adult dogs. Twelve dogs were fed four extruded kibble diets (control (no FCM or yeast), FCM + low yeast dose, FCM + medium yeast dose, and FCM + high yeast dose) in a replicated 4x4 LSD. Dogs fed yeast-enriched FCM had greater wet fecal output (~15% greater than control). The ATTD of DM, OM, and fat was lower in the diets containing FCM, although the values remained >80% for all macronutrients. The yeast-enriched FCM altered the relative abundance of a few bacterial genera (Eubacterium brachy, Peptoclostridium, Ruminococcus gnavus) and fecal phenol and indole concentrations. Other fecal characteristics, metabolites, bacterial diversity indices, skin measures, or oxidative stress markers were not affected. These findings suggest that yeast-enriched FCM can be incorporated into canine diets without compromising stool quality or nutrient digestibility and may affect microbial metabolism.

Effect of the vaginal live biotherapeutic LACTIN-V (Lactobacillus crispatus CTV-05) on vaginal microbiota and genital tract inflammation among women at high risk of HIV acquisition in South Africa: a phase 2, randomised, placebo-controlled trial

BACKGROUND

Absence of vaginal lactobacilli and accompanying genital inflammation is associated with HIV acquisition. We aimed to assess how a vaginal live biotherapeutic containing Lactobacillus crispatus affects cervicovaginal microbiota and markers of HIV susceptibility in South African women.

METHODS

This randomised, placebo-controlled, phase 2 trial evaluated LACTIN-V (L crispatus CTV-05), a vaginal live biotherapeutic, compared with placebo in cisgender women in South Africa, aged 18-23 years, recruited at a community-based research clinic. Eligible participants with a Nugent score of 4-10 (indicating intermediate vaginal microbiota or bacterial vaginosis) completed 7 days of oral metronidazole and were randomly assigned (2:1) to LACTIN-V (2 × 109 colony forming units per dose) or placebo (the substrate alone) via an independently generated randomisation sequence. Pharmacists, participants, and investigators were masked to treatment assignment. The study product (or placebo) was dosed daily for 5 days in week 1, then twice per week for an additional 3 weeks. Adverse events were evaluated 4 weeks and 8 weeks after starting the study product. Vaginal swabs (for 16S rRNA sequencing of the vaginal microbiome) and cervicovaginal lavage (for Luminex analysis of immune markers) were collected before metronidazole treatment, before study product (or placebo) administration, and at the week 4 and week 8 follow-up visits. An endocervical cytobrush for flow cytometry analysis of immune cell populations (including CD3+CD4+ T cells, and presence of CCR5 and the activation markers CD38 or HLA-DR) was collected before study product use and at 4 weeks and 8 weeks after study product use. The coprimary outcomes for the trial were (1) safety and acceptability of LACTIN-V, as measured by number of adverse events and a validated questionnaire; (2) presence of a Lactobacillus-dominant vaginal microbial community by 16S rRNA gene sequencing at week 4 and week 8; and (3) comparison of change in genital tract inflammatory markers from before metronidazole treatment to week 4 and week 8 between groups. Safety analyses were done in the intention-to-treat population and efficacy analyses in a modified intent-to-treat population (ie, excluding one person assigned placebo who erroneously received LACTIN-V). This trial is completed and registered on ClinicalTrials.gov (NCT05022212).

FINDINGS

45 Black South African women were randomly assigned to receive LACTIN-V (n=32) or placebo (n=13). One woman in each group discontinued the trial during the intervention and two women discontinued during the follow-up. No severe or serious adverse events were observed. Solicited adverse events occurred in 35 (78%) of 45 participants with no significant difference by group (risk ratio 1·17, 95% CI 0·79-1·75; p=0·44). All local solicited adverse events were mild. 32 (71%) of 45 participants strongly agreed or agreed they would use the product again. L crispatus dominant microbiomes were identified in 13 (41%) of 32 participants in the LACTIN-V group at week 4 and eight (26%) of 31 at week 8, compared with none at week 4 and one (9%) of 11 in week 8 in the placebo group (week 4 p=0·0088; week 8 p=0·40). The proportion of activated endocervical HIV target cells out of total T cells increased from after metronidazole treatment to week 4 in the placebo group (median log2 fold change 1·891, IQR 1·731-4·018) but not in the LACTIN-V group (1·062, 0·449-1·424; p=0·016). Changes in the concentrations of 13 immune markers from before metronidazole treatment to week 4 or week 8 were not significantly different by group.

INTERPRETATION

The use of LACTIN-V after metronidazole significantly increased vaginal L crispatus colonisation during 4 weeks of use, although this increase was transient, and women in the placebo group had an increase in endocervical CD4+ HIV target cells during recovery compared with the LACTIN-V group. These results show that vaginal colonisation with an L crispatus live biotherapeutic is possible in an African context, and that optimisation of this strategy might be a way to decrease risk for HIV.

FUNDING

US National Institute of Child Health and Human Development and US National Institute of Allergy and Infectious Diseases.

Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice

BACKGROUND

Alterations in the composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in non-ruminant mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Motor coordination and strength were analyzed by rotarod and grip strength tests, intestinal barrier function by serum LAL assay, transcriptional responses by single-cell RNA sequencing, and fecal microbial community properties by 16S rRNA gene profiling and metagenomics.

RESULTS

Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB implying more stable microbiome communities. Single-cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways as well as a decrease of age-dependent mesenchymal hallmark transcripts in enterocytes and TA cells, but reduced inflammatory signaling in macrophages.

CONCLUSIONS

Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including coordinative ability (rotarod), intestinal permeability, and both metabolic and inflammatory profiles mainly of macrophages but also of other immune cells. Video Abstract.

Definition of the microbial rare biosphere through unsupervised machine learning

The microbial rare biosphere, composed of low-abundance microorganisms in a community, lacks a standardized delineation method for its definition. Currently, most studies rely on arbitrary thresholds to define the microbial rare biosphere (e.g., 0.1% relative abundance per sample), hampering comparisons across studies. To address this challenge, we present ulrb (Unsupervised Learning based Definition of the Rare Biosphere), available as an R package. ulrb uses unsupervised machine learning to optimally classify taxa into abundance categories (e.g., rare, intermediate, or abundant) within microbial communities. We show that ulrb is more consistent than threshold-based approaches and can be applied to data derived from common microbial ecology protocols and non-microbial studies. ulrb can be used to identify different types of rarity and is statistically valid for the analysis of various dataset sizes. In conclusion, ulrb discerns rare from abundant organisms in a user-independent manner, finding applicability in selected ecological datasets.

Metataxonomic identification of microorganisms and sensory attributes of Coffea canephora under conventional processing and Self-Induced Anaerobiosis Fermentation

This study evaluates for the first time the modifications in the microbial communities and sensory attributes caused by Self-Induced Anaerobiosis Fermentation (SIAF) compared to the Conventional processing of Coffea canephora var. Conilon. Microorganisms were identified through high-throughput sequencing of the 16S rRNA V3/V4 region for bacteria and the ITS region for fungi. Sensory attributes of roasted coffee were evaluated by Q-Graders. The relationship between microbial population, processing methods, and sensory attributes was investigated using principal component analysis. Before fermentation, 74 bacterial and 21 fungal species were identified in the natural coffee, whereas 44 bacterial and 15 fungal species were found in the pulped coffee. Torulaspora, Wickerhamomyces, and Meyerozyma exhibited more ITS region sequences, while Acetobacter, Enterobacter, and Lysinibacillus were predominant in the 16S region. In the natural coffee, Wickerhamomyces showed the highest relative abundance (45%) at 0 h. After 72 h, Meyerozyma (45%) and Torulaspora (75%) prevailed in Conventional processing and SIAF, respectively. In the pulped coffee, Torulaspora was the most abundant in the SIAF method, before (92%) and after (81%) fermentation, while Wickerhamomyces (39%) dominated after 72 h in the Conventional method. Enterobacteriaceae levels decreased, while Lactobacillaceae levels increased in SIAF natural coffee during the fermentation process. SIAF favored the presence of yeast and LAB while inhibiting mycotoxigenic fungi and Enterobacteriaceae. Torulaspora, Lactiplantibacillus, and Lactococcus showed the highest Pearson correlation coefficient with flavor (0.92), aftertaste (0.99), and bitterness/sweetness (0.89), respectively. Changes in coffee microbiota during SIAF improved sensory attributes, resulting in better-quality beverages.

Community organization and network stability of co-occurring microbiota under the influence of Kuroshio Current

The Kuroshio Current structures environmental characteristics and biodiversity in the northwestern Pacific Ocean (NWPO), a region renowned for its dynamic oceanographic processes and rich marine ecosystems. However, the assembly and associations responses of prokaryotes and microeukaryotes to the Kuroshio Current remain largely unknown. Here, co-occurrence properties and stability of prokaryotic and eukaryotic microbiomes from three regions influenced by the Kuroshio: Kuroshio South of Japan (KSJ), Kuroshio Extension (KE), and the Kuroshio-Oyashio interfrontal zone (KOIZ) are systematically investigated. Microbiomes in the KE showed reduced phylogenetic distance and broader niche breadth than those in the KSJ and KOIZ. Microeukaryotic robustness was highest in the KE and lowest in the KOIZ, while prokaryotes showed the opposite pattern. Prokaryotic and microeukaryotic robustness and compositional stability formed complementary stabilizing and phylogenetic distance along vertical gradients in the KOIZ region, helping to maintain community and ecosystem stability. Prokaryotes and microeukaryotes formed complementary stabilizing under the influence of the Kuroshio Current. Overall, the network of prokaryotes was more stable than that of microeukaryotes, and microeukaryotes were more sensitive to environmental variations than prokaryotes. These results show how the Kuroshio Current influences the community organization and co-occurrence stability of prokaryotic and eukaryotic microbiomes, respectively, as well as their contrasting adaptability and survival strategies to environmental variation.

Picky eaters: Selective microbial diet of avian ectosymbionts

Individual organisms can function as ecosystems inhabited by symbionts. Symbionts may interact with each other in ways that subsequently influence their hosts positively or negatively, although the details of how these interactions operate collectively are usually not well understood. Vane-dwelling feather mites are common ectosymbionts of birds and are proposed to confer benefits to hosts by consuming feather-degrading microbes. However, it is unknown whether these mites exhibit generalist or selective diets, or how their dietary selection could potentially impact their symbiotic functional nature. In this study, we conducted 16S rDNA and ITS1 amplicon sequencing to examine the microbial diet of feather mites. We characterized and compared the diversity and composition of bacteria and fungi in the bodies of mites living on feathers of the Prothonotary Warbler, Protonotaria citrea, to microbial assemblages present on the same feathers. We found less diverse, more compositionally similar microbial assemblages within mites than on feathers. We also found that mites were resource-selective. Based on the identity and known functions of microbes found within and presumably preferred by mites, our results suggest that these mites selectively consume feather-degrading microbes. Therefore, our results support the proposition that mites confer benefits to their hosts. This study provides insight into symbioses operating at multiple biological levels, highlights the ecological and evolutionary importance of the synergistic interactions between species, and greatly expands our understanding of feather mite biology.

Soil biome variation of Lupinus nipomensis in wet-cool vs. dry-warm microhabitats and greenhouse

PREMISE

Environmental DNA (eDNA) can be used to determine the composition of the soil biome community, revealing beneficial and antagonistic microbes and invertebrates associated with plants. eDNA analyses can complement traditional soil community studies, offering more comprehensive information for conservation practitioners. Studies are also needed to examine differences between field and greenhouse soil biomes because greenhouse-grown plants are often transplanted in the field during restoration efforts.

METHODS

We used eDNA multilocus metabarcoding to test how the soil biome of the federally and state-endangered species, Lupinus nipomensis, differed between wet-cool and dry-warm microhabitats. At Arroyo Grande, California, 20 experimental plots were sampled, representing a factorial combination of wet-cool vs. dry-warm soil and plots that did or did not contain L. nipomensis. In a simultaneous greenhouse study, L. nipomensis was grown in drought and well-watered conditions to compare soil communities between field and greenhouse.

RESULTS

A diversity of carbon-cycling microorganisms but not nitrogen-fixers were overrepresented in the field, and nitrogen-fixing bacteria were overrepresented in some greenhouse treatments. The microbial communities in the field soils were more species-rich and evenly distributed than in greenhouse communities. In field plots, microhabitats significantly influenced community beta diversity, while field plots with or without L. nipomensis had no significant differences in alpha or beta diversity.

CONCLUSIONS

Our study shows the utility of eDNA soil analysis in elucidating soil biome community differences for conservation and highlights the influence of plant microhabitats on soil microbe associations.

Fecal microbiome composition in neonates with or without urinary tract infection

BACKGROUND

Most infants with febrile urinary tract infection (UTI) do not have an underlying anatomical risk factor. Thus, other non-anatomical risk factors should be considered. Since the most common pathogens arise from the fecal microbiota, our aim was to investigate whether the gut microbiota composition differs between febrile infants younger than 2 months with or without UTI.

METHODS

In this prospective, case-control, pilot study, we performed 16S ribosomal ribonucleic acid amplicon sequencing to characterize gut microbiota of febrile neonates with and without UTI admitted to the pediatric ward at Shamir Medical Center between February 2019 and May 2021.

RESULTS

The study cohort included 42 febrile neonates: 17 with and 25 without febrile UTI. We found a significant difference in beta diversity (i.e. between-sample/study group similarity indices) between the UTI and non-UTI group (p = 0.016). There were also distinct differences in the relative abundance of the 20 most prevalent genera. Furthermore, several genera were significantly enriched in the UTI group, with others dominating the non-UTI group. Streptococci were underrepresented in the UTI group. There was no difference in alpha diversity (i.e. within-sample diversity/richness) between groups.

CONCLUSION

Febrile neonates with UTI have a different fecal microbiota composition (beta-diversity), but not alpha diversity, in comparison to febrile neonates without UTI. A larger study is warranted to confirm these findings and their potential applications.

Dietary Short-Chain Fatty Acids Supplementation Improves Reproductive Performance and Gut Microbiota in Gilts

BACKGROUND

Short-chain fatty acids (SCFAs) have emerged as critical modulators of female reproductive function and host gut microbiota.

OBJECTIVES

This study aimed to investigate the impact of dietary SCFAs supplementation on reproductive performance and gut microbiota in gilts, and to elucidate the underlying mechanisms.

METHODS

Eighty gilts (95 d old) were randomly assigned to either a control group (Ctrl, 40 gilts) receiving a basal diet, or a SCFAs treatment group (SCFAs, 40 gilts) receiving a basal diet supplemented with 0.13% sodium acetate, 0.11% sodium propionate, and 0.09% sodium butyrate. At third estrus, 13 gilts (6 from Ctrl and 7 from SCFAs) were killed for follicular development and gut microbiota analysis, whereas the remaining gilts completed gestation for reproductive performance assessment.

RESULTS

SCFAs group had higher total number born (11.97 compared with 9.44) and total number born alive (11.28 compared with 9.34) compared with Ctrl group (P < 0.05). SCFAs group had increased counts of secondary follicles (36.14 compared with 26.83), antral follicles (10.29 compared with 6.67), and corpus luteum (25.09 compared with 19.33), alongside had reduced atretic follicles (15.32 compared with 20.67) compared with Ctrl group (P < 0.05). Proteomic analysis revealed that SCFAs-induced differentially expressed proteins (DEPs) were significantly enriched in the follicular development-related pathways (P < 0.05). Apoptosis-related DEPs positively correlated with follicular development indices (P < 0.05), consistent with the reduced apoptosis observed in ovarian granulosa cells of the SCFAs group. Additionally, SCFAs supplementation improved both the composition and alpha-diversity (P < 0.05) of gilts' gut microbiota. Furthermore, both the SCFAs-enriched bacteria and plasma SCFAs concentrations showed positive associations with gilts' follicular development indices (P < 0.05).

CONCLUSIONS

Dietary SCFAs supplementation enhances reproductive performance in gilts by promoting ovarian follicular maturation and optimizing gut microbiota composition.

Cultivation of anammox bacteria from a tropical lake in Indonesia using a novel filter bioreactor to enhance nitrogen removal efficiency

This study presents a novel strategy for cultivating anammox bacteria from tropical environments using a filter bioreactor (FtBR). Two bioreactors were inoculated with sediment sludge from an Indonesian lake and operated at different temperatures: tropical ambient (22-28 °C) in Reactor 1 and 35 °C in Reactor 2. After 106 days, Reactor 1 developed a red carmine anammox biofilm, while Reactor 2 remained similar to its initial state. Reactor 1 achieved a higher and more stable nitrogen removal rate (0.27 kg-N/m3·d) compared with Reactor 2 (0.21 kg-N/m3·d), indicating a 28.6% greater efficiency. The operational temperature significantly influenced the diversity and abundance of anammox bacteria. Candidatus Brocadia caroliensis (6.20%) was detected in Reactor 1, whereas Candidatus Anammoxoglobus propionicus (7.64%) and Candidatus Brocadia sinica (1.77%) were found only in Reactor 2. Additionally, Candidatus Brocadia fulgida was more abundant in Reactor 1 (20.04%) than in Reactor 2 (6.84%). These findings demonstrate that temperature plays a crucial role in starting the anammox process in FtBRs with a resident inoculum from tropical environments, significantly affecting bacterial growth and nitrogen removal efficiency.

UV-aging reduces the effects of biodegradable microplastics on soil sulfamethoxazole degradation and sul genes development

In recent years, the biodegradable plastics has extensively used in industry, agriculture, and daily life. Herein, the effects of two biodegradable microplastics (BMPs), poly(butyleneadipate-co-terephthalate) (PBAT) and polyhydroxyalkanoate (PHA), on soil sulfamethoxazole (SMX) degradation and sul genes development were comparatively studied based on the type, dosage, and state. The addition of virgin BMPs significantly increased soil DOC following a sequential order PBAT > PHA and high dose > low dose. Meanwhile virgin PBAT significantly reduced soil pH. In general, the addition of BMPs not only promoted soil SMX degradation but also increased the abundance of sul genes, with an exception that pH reduction in virgin PBAT inhibited the proliferation of sul genes. The driving effects of BMPs on soil microbial diversity following the same order as that on DOC. Specific bacteria stimulated by BMPs, such as Arthrobacter and two genera affiliated with phylum TM7, accounted for the accelerated degradation of SMX. Intriguingly, UV-aging hindered the release of DOC from BMPs and the reduction in pH, mitigated the stimulation of microbial communities, and ultimately reduced the promotion effect of BMPs on SMX degradation and sul genes proliferation. Our results suggest that more attention should be paid to the proliferation risk of ARGs in the environment affected by BMPs and UV-aging can be employed sometimes to reduce this risk.

Bacterial and DNA contamination of a small freshwater waterway used for drinking water after a large precipitation event

Sewage contamination of freshwater occurs in the form of raw waste or as effluent from wastewater treatment plants (WWTP's). While raw waste (animal and human) and under-functioning WWTP's can introduce live enteric bacteria to freshwater systems, most WWTP's, even when operating correctly, do not remove bacterial genetic material from treated waste, resulting in the addition of bacterial DNA, including antibiotic resistance genes, into water columns and sediment of freshwater systems. In freshwater systems with both raw and treated waste inputs, then, there will be increased interaction between live sewage-associated bacteria (untreated sewage) and DNA contamination (from both untreated and treated wastewater effluent). To evaluate this understudied interaction between DNA and bacterial contamination in the freshwater environment, we conducted a three-month field-based study of sewage-associated bacteria and genetic material in water and sediment in a freshwater tributary of the Hudson River (NY, USA) that supplies drinking water and receives treated and untreated wastewater discharges from several municipalities. Using both DNA and culture-based bacterial analyses, we found that both treated and untreated sewage influences water and sediment bacterial communities in this tributary, and water-sediment exchanges of enteric bacteria and genetic material. Our results also indicated that the treated sewage effluent on this waterway serves as a concentrated source of intI1 (antibiotic resistance) genes, which appear to collect in the sediments below the outfall along with fecal indicator bacteria. Our work also captured the environmental impact of a large rain event that perturbed bacterial populations in sediment and water matrices, independently from the outflow. This study suggests that large precipitation events are an important cause of bacterial and DNA contamination for freshwater tributaries, with runoff from the surrounding environment being an important factor.

Identifying Potential Geochemical and Microbial Impacts of Hydrogen Storage in a Deep Saline Aquifer

Hydrogen is valuable commodity and a promising energy carrier for variable energy production. Storage of hydrogen may occur through injection of hydrogen or a hydrogen/methane gas blend in subsurface reservoirs. However, the geochemical and biological reactions that may impact the stored hydrogen are not yet understood. Therefore, we collected samples from a deep storage aquifer located in the St. Peter Formation in southern Illinois. The reservoir material was primarily quartz with sulphur and iron deposits, while the major constituents of the fluid were chloride and sulphate. 16S rRNA gene amplicon sequencing revealed a low biomass microbial community that contained no obvious hydrogen-consuming bacteria. Next, we enriched a field sample to increase the biomass and completed a metagenomic analysis, finding a low number of genes present that are associated with hydrogen consumption. Then, we completed a series of reactor experiments under reservoir conditions with 15% H2/85% CH4 gas simulating a short-term hydrogen storage, high withdrawal scenario. We found minimal changes in the geochemistry or microbiology for the reactor experiments. This work suggests that short-term storage may be highly successful, although significant additional work needs to be completed in order to accurately evaluate the risks associated with long-term hydrogen storage scenarios. It is essential we continue to expand our understanding of the dynamics present in saline aquifers and provide new insights into how hydrogen storage may impact underground geological storage environments.

Exploring the relationship between ultra-processed food consumption and gut microbiota at school age in a Brazilian birth cohort

Dietary patterns significantly impact health outcomes and gut microbiota composition. However, longitudinal studies associating ultra-processed food consumption with gut microbiota composition, especially among adolescents in low- and middle-income countries, are lacking. This study aimed to explore this association using data collected from 364 participants at ages 6, 11, and 12 years from the 2004 Pelotas (Brazil) Birth Cohort. Microbiota data was obtained at age 12 after 16S rRNA gene sequencing of self-collected fecal samples. Linear or logistic regression models evaluated the relationship between age groups and gut microbiota outcomes (alpha diversity, beta diversity and relative abundances at the phylum and genus levels), considering dietary covariates and demographic, socioeconomic, health-related, and behavioral factors. No significant associations between ultra-processed food consumption and alpha diversity were observed after multiple testing corrections, and there was no strong evidence linking ultra-processed food consumption and beta diversity, with unweighted metrics explaining little variance at ages 11 and 12. Nominal associations were found between ultra-processed food and relative abundances of Actinobacteria (p = 0.032) and Proteobacteria (p = 0.045) (phyla), Bacteroides (p = 0.037 at age 6; p = 0.015 at age 11) and Peptostreptococcus (p = 0.025 at age 6; p = 0.010 at age 11) (genera). However, these associations lost statistical significance after adjustments for multiple comparisons. These findings highlight the need for more longitudinal studies to better understand the complex interaction between ultra-processed food intake and gut microbiota composition in adolescent populations in low- and middle-income countries.