Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient's succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.

Rhizosphere bacterial community studies offer valuable insights into the environmental implications of genetically modified (GM) crops. This study compared the effects of a non-GM maize cultivar, namely Hi-IIA, with those of a herbicide-resistant maize cultivar containing the phosphinothricin N-acetyltransferase gene on the rhizosphere bacterial community across growth stages. 16s rRNA amplicon sequencing and data analysis tools revealed no significant differences in bacterial community composition or diversity between the cultivars. Principal component analysis revealed that differences in community structure were driven by plant growth stages rather than plant type. Polymerase chain reaction analysis was conducted to examine the potential horizontal transfer of the introduced gene from the GM maize to rhizosphere microorganisms; however, the introduced gene was not detected in the soil genomic DNA. Overall, the environmental impact of GM maize, particularly on soil microorganisms, is negligible, and the cultivation of GM maize does not alter significantly the rhizosphere bacterial community.

IgA-coated fractions of the intestinal microbiota of Crohn's disease (CD) patients have been shown to contain taxa that hallmark the compositional dysbiosis in CD microbiomes. However, the correlation between other cellular properties of intestinal bacteria and disease has not been explored further, especially for features that are not directly driven by the host immune-system, e.g. the expression of surface sugars by bacteria. By sorting and sequencing IgA-coated and lectin-stained fractions from CD patients microbiota and healthy controls, we found that lectin-stained bacteria were distinct from IgA-coated bacteria, but still displayed specific differences between CD and healthy controls. To exploit the discriminatory potential of both, immunoglobulin coated bacteria and the altered surface sugar expression of bacteria in CD, we developed a multiplexed single cell-based analysis approach for intestinal microbiota. By multi-parameter microbiota flow cytometry (mMFC) we characterized the intestinal microbiota of 55 CD patients and 44 healthy controls for 11-parameters in total, comprising host-immunoglobulin coating and the presence of distinct surface sugar moieties. The data were analyzed by machine-learning to assess disease-specific marker patterns in the microbiota phenotype. mMFC captured detailed characteristics of CD microbiota and identified patterns to classify CD patients. In addition, we identified phenotypic signatures in the CD microbiota which not only reflected remission after 6 weeks of anti-TNF treatment, but were also able to predict remission before the start of an adalimumab treatment course in a pilot study. We here present the proof-of-concept demonstrating that multi-parameter single-cell bacterial phenotyping by mMFC could be a novel tool with high translational potential to expand current microbiome investigations by phenotyping of bacteria to identify disease- and therapy-associated cellular alterations and to reveal novel target properties of bacteria for functional assays and therapeutic approaches.

Despite advancements in immunotherapy, particularly regarding programmed cell death protein 1 (PD-1)/programmed death-ligand 1 blockades, the clinical outcomes in non-small cell lung cancer (NSCLC) remain variable with limited predictive biomarkers currently available. The present study investigated respiratory microbiota diversity as a potential biomarker to predict the efficacy of PD-1 blockades in patients with advanced NSCLC. A retrospective analysis was conducted on 60 patients treated with PD-1 blockades from May 2019 to May 2023. Clinical data were collected and respiratory microbiota from deep induced sputum specimens were analyzed using 16S rRNA gene sequencing. An index of respiratory microbiota α diversity was applied and exploratory analysis was performed accordingly. The objective response rate (ORR) and disease control rate among the 60 patients receiving PD-1 blockades was 23.3% (95% CI, 13.4-36.0%) and 58.3% (95% CI, 44.9-70.9%), respectively. Analysis of prognostic data of patients with advanced NSCLC receiving PD-1 blockades monotherapy demonstrated a median progression-free survival of 3.4 months (95% CI, 2.54-4.26) and a median overall survival (OS) of 12.3 months (95% CI, 6.29-18.31). Patients were stratified into high and low α diversity groups based on the Shannon diversity index of respiratory microbiota. The ORR was increased in the high diversity group (26.7%) compared with that of the low diversity group (20.0%), although the difference was not statistically significant (P=0.542). Notably, the high diversity group demonstrated a longer median PFS (3.9 vs. 2.8 months; P=0.017) and median OS (16.8 vs. 6.8 months; P=0.016) compared with that of the low diversity group. These findings suggested that PD-1 blockades demonstrate promising therapeutic activity for patients with previously treated advanced NSCLC in clinical practice. Respiratory microbiota α diversity might serve as a potential biomarker to predict the efficacy of PD-1 blockades monotherapy in patients with advanced NSCLC in the future. Therefore, further prospective studies are warranted to validate these findings and to explore the underlying mechanisms by which respiratory microbiota might modulate the immune response to cancer therapy.

Chronic actinic dermatitis (CAD) is a refractory photoallergic skin disease characterized by inflammatory infiltration and UV sensitivity. While the role of microbiome dysbiosis has been established in various inflammatory skin conditions, its contribution to CAD pathogenesis remains unexplored.

To characterize the skin microbiome alterations in CAD patients and investigate their potential associations with disease severity and UV sensitivity.

Skin microbiome samples were collected from 15 CAD patients and 14 matched family controls, covering both photoexposed (PE) and photoprotected (PNE) areas. The microbial community composition was analyzed using 16S rRNA sequencing. Alpha and beta diversity analyses were performed, and correlations between microbial profiles, disease severity, and UV sensitivity were evaluated.

CAD patients exhibited significantly reduced microbial diversity compared to controls, particularly in photoexposed areas (p < 0.001). This reduction in diversity showed a negative correlation with disease severity. Notably, Staphylococcus abundance was significantly increased in CAD lesions and positively correlated with disease severity. Linear Discriminant Analysis identified Staphylococcus as a potential biomarker for CAD. Interestingly, no significant correlations were found between microbial profiles and UV sensitivity, suggesting independent pathogenic mechanisms.

Our findings reveal significant alterations in the skin microbiome of CAD patients, characterized by reduced diversity and increased Staphylococcus colonization, which correlates with disease severity but not UV sensitivity. These results provide new insights into CAD pathophysiology and suggest potential therapeutic strategies targeting the skin microbiome.

Soil and bromeliads are important habitats contributing to the biodiversity of the Atlantic Forest in Brazil. However, knowledge of unicellular eukaryotes and bacteria in these environments remains limited. This study compared the diversity and community structure of unicellular eukaryotes, fungi, metazoan, and bacteria in bromeliad water tanks (BWT) and adjacent soil using 16S and 18S rRNA gene metabarcoding. Communities differed significantly between habitats but shared some taxa, suggesting habitat connectivity. Ciliates dominated unicellular eukaryotes in BWT, while Cercozoa prevailed in soil. Bacterial communities were dominated by Pseudomonadota, while fungal composition was more uniform, with Ascomycota as the dominant phylum across samples. Metazoan communities varied among abundant phyla, and their presence in BWT suggests the use of this water resource within the forest. This study provides essential baseline data on eukaryotic and bacterial diversity in this unique ecosystem, highlighting how distinct habitats within the Atlantic Forest support different communities.

Free-living amoebae (FLA) are ubiquitous protists found in water, feeding mainly on bacteria. While most FLA are harmless, Acanthamoeba spp. and Naegleria fowleri can cause keratitis and/or meningitis. FLA can host amoeba-resistant bacteria (ARB), but their natural bacterial microbiota is largely unknown. This study aimed to identify the natural bacterial microbiota of Naegleria fowleri, Acanthamoeba castellanii, Acanthamoeba lenticulata, and Acanthamoeba sp. T17, isolated from untreated (rivers) and treated (tap) waters in Guadeloupe. The whole bacterial microbiota of the water source and the FLA grown with E. coli and under axenic culture conditions, during successive passages, were characterized using 16S rRNA gene metabarcoding. The culturable subset of ARB was identified by mass spectrometry (MALDI-TOF MS) followed by conventional 16S PCR, and bacterial antibiotic resistance was analyzed using the disk diffusion method. Transmission electron microscopy was used to locate ARB within the amoebae. The metabarcoding analyses identified Salmonella, Enterobacter and Klebsiella genera as the most abundant bacteria in untreated and treated waters. However, the most frequently detected amoeba-resistant bacteria (ARB) were from the Bosea, Escherichia-Shigella, Microbacterium, and Pseudomonas genera. Our findings revealed, for the first time, the natural occurrence of several bacteria within N. fowleri, including Pseudomonas spp. and Escherichia coli. Additionally, we detected Legionella in A. castellanii and Bordetella in A. lenticulata. The four pathogenic FLA showed both temporary and permanent associations with various bacterial genera, depending on the number of passages and culture conditions. Pseudomonas species isolated from distinct FLA exhibited resistance to different antibiotics. ARB were detected within the cytoplasm of trophozoites. The presence of pathogenic FLA and ARB in untreated and treated water in Guadeloupe's drinking systems pose health risks. Our results highlight the need for regular monitoring to ensure water safety and understanding amoebae-bacteria interactions for better management. The natural presence of ARB in pathogenic FLA also questions the host immune response during amoeba infection.

This study analyzed raw milk's microbial community and chemical profile during the natural creaming process of Parmigiano Reggiano production by comparing milk from farms following two different organic certifications. Specifically, the natural creaming process underlined the positive accumulation of potentially pro-dairy bacteria, particularly those of the genera Lactococcus and Streptococcus, and a significant reduction of negative bacterial genera, such as Acinetobacter and Rothia, in the final mix milk. Meanwhile, untargeted metabolomic analysis confirmed the representativeness of lipids and lipid-derivatives as chemical markers involved in the overnight creaming process, with fatty acid esters and long fatty acids enriched in the evening samples. Finally, by using a multi-omics approach, we integrated microbial and metabolomic datasets and identified correlations between specific microbial populations and metabolite changes. This integrative analysis revealed microbial-metabolite interactions that may be a starting point to better understand the pivotal role exerted by milk creaming on the final cheese quality.

Selection, dispersal and drift jointly contribute to generating variation in microbial composition within and between hosts, habitats and ecosystems. However, we have limited examples of how these processes interact as hosts and their microbes turn over across latitudinal gradients of biodiversity and climate. To bridge this gap, we assembled an extensive dataset of 580 skin bacteriomes from 22 amphibian species distributed across a 10° latitudinal range in Chile. Amphibians are susceptible to the fungal pathogen Batrachochytrium dendrobatidis (Bd), which infects their skin, potentially leading to changes in the normal skin microbiome (i.e., dysbiosis). Using comparative methods, accounting for pathogen infection and implementing resampling schemes, we found evidence of phylosymbiosis, characterised by more similar bacterial communities in closely related amphibian species. We also compared how neutral processes affected the assembly of skin bacteria by focusing on two widespread species from our dataset: the Chilean four-eyed frog (Pleurodema thaul) and Darwin's frog (Rhinoderma darwinii). Neutral models revealed that dispersal and chance largely facilitated the occurrence of ~90% of skin bacteria in both species. Deterministic processes (e.g., phylosymbiosis, active recruitment of microbes, microbe-microbe interactions) explained the remaining fraction of the bacteriomes. Amphibian species accounted for 21%-32% of the variance found in non-neutral bacterial taxa, whereas the interaction with Bd carried a weaker but still significant effect. Our findings provide evidence from ectotherms that most of their skin bacteria are subject to dispersal and chance, yet contemporary and historical contingencies leave strong signatures in their microbiomes even at large geographical scales.

Prahoc is a traditional fermented fish widely consumed in Cambodia. Nevertheless, the processing and nutritional values of this daily-consumed product were poorly described. This study offers a detailed analysis of the biochemistry, nutritional composition, and microbiota during the six-month Prahoc incubation. Macronutrients (e.g. lipids, proteins) are rather well preserved during the preparation of the fish paste but the fatty acid and amino acid profiles are slightly modified at the end of the unit operation. Free amino acids increased, which facilitates the in vitro digestibility of the final paste, while beneficial fatty acids, such as eicosapentaenoic and docosahexaenoic acids, decreased. At the end of the process, the peroxide value was nearly five times greater than the limit set by the Codex Alimentarius (10 meq O2/kg). Biogenic amines, particularly cadaverine, were present but remained within acceptable limits. Metabarcoding analysis revealed that salt-tolerant bacteria dominated the fermentation process, while fungal activity was minimal. Lactic acid bacteria, such as Vagococcus and Streptococcus, were predominant before salt addition, while the fish pathogen Aeromonas established itself immediately after. Clostridium remained steady throughout, and Lentibacillus became dominant after six months. Food safety concerns related to biogenic amines, peroxides, and Clostridium highlight the need for establishing standard operational practices among national processors to mitigate food risks.

The continuous use of Di(2-ethylhexyl) phthalate (DEHP) in plastic products turns it into a ubiquitous contaminant in the environment. However, DEHP can cause harm to human beings, wildlife, and ecosystems due to its estrogenicity and toxicity. Thus, finding an efficient approach to removing this contaminant from the environment is crucial. The present study aimed to prospect and characterize a bacterial consortium (MP001) isolated from a neotropical mangrove for DEHP bioremediation. A laboratory experiment was performed with environmentally relevant DEHP concentrations (0.05, 0.09, 0.19, 0.38, 0.75, 1.50, 3.00, and 6.00 mg L-1) to determine the consortium resistance to this contaminant and high-throughput sequencing was accomplished to assess the bacterial composition, diversity, and potential ecological function of consortium MP001. The consortium MP001 presented a significant biomass increase throughout short-term incubations with increasing concentrations of DEHP (GLMs, p< 0.001). MP001 was constituted by Paraclostridium sp. (78.99%) and Bacillus sp. (10.73%). After 48 h of consortia exposure to DEHP, the bacterial population changed to Paraclostridium (50.00%), Staphylococcus sp. (12.72%), Staphylococcus epidermidis (10.40%) and Bacillus sp. (17.63%). In the negative control, the bacteria community was composed of Paraclostridium sp. (54.02%), Pseudomonas stutzeri (19.44%), and Staphylococcus sp. (11.97%). The alpha diversity of the MP001 consortium was not significant (Kruskall-Wallis; p > 0.05), and no significant difference was found between the DEHP treatment and the negative control. Furthermore, the potential ecological function found in the consortium MP001 with higher potential for application in bioremediation purposes was fermentation. The results found in this study highlight the potential of a bacterial consortium to be used in the bioremediation of DEHP-contaminated aquatic environments.

This study is aimed at exploring the relationship between maternal weight categories, including pre-pregnancy body mass index (P-BMI) and gestational weight gain (GWG), and the composition of the infant gut microbiome in the early days of life. We recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples from the infants within the first 5 days postpartum. Using 16S ribosomal RNA gene sequencing (V3-V4 region), this study assessed microbial diversity and the relative abundance of specific bacterial taxa in these initial stool samples. Participants were categorized into groups based on maternal P-BMI and GWG, enabling a comprehensive comparison of the microbiota composition in the infants' meconium across different maternal weight metrics. Our analysis identified significant variations in the infant gut microbiome correlated with maternal weight categories. Key findings include a differential abundance of genera such as Sphingobacteriaceae, Bacillaceae, Cytophagaceae, and Alteromonadaceae across maternal P-BMI groups, whereas Moraxellaceae and Rhodospirillaceae varied across GWG groups. In the P-BMI category, infants born to overweight mothers demonstrated a higher abundance of Pseudopedobacter, and a lower abundance of Citrobacter and Lachnospira, while infants in the underweight group showed a higher abundance of Lachnospira and Weissella. In the normal weight group, Citrobacter and Pseudopedobacter were more abundant. Within the GWG category, infants in the inadequate group showed a higher abundance of Klebsiella, whereas the normal group showed a higher abundance of Holdemania. The composition of the infant gut microbiome in the early postnatal period is significantly influenced by maternal weight categories. Understanding the role of maternal weight in shaping early microbial colonization may provide insights into developing strategies to optimize infant health outcomes through targeted interventions before and during pregnancy.

Over the last decades, an insect meal has received great attention for finfish diets, due to its nutritional composition and low ecological footprint. In the present study, we assessed the response of gut microbiota composition and liver histology of gilthead seabream (Sparus aurata) fed four experimental diets including the black soldier fly (Hermetia illucens) meal (HI) used to replace 0 (HI0), 25 (HI25), 35 (HI35) and 50 (HI50) percent of fish meal in a 131-day feeding trial. At the end of the experiment, a remarkable change in gut microbiota composition related to HI inclusion was observed, with a preponderance of Cyanobacteriain the control and low HI groups (HI0, HI25) while Chloroflexi became prevalent in the higher HI inclusion groups (HI35, HI50). Predictive analysis on bacterial metabolic pathways showed a clear separation between HI0-HI25 and HI35-HI50 groups. The microbiota shifts observed suggest a pivotal role of HI in inducing a bacterial-mediated physiological response in this fish species, probably due to chitin content and the fatty acid profile of this ingredient. Liver histology showed a higher hepatocyte size in fish from the HI50 group, suggesting lipid dysmetabolism due to the HI meal fatty acid profile, while a marginal adaptive response was observed in the HI25 group. In conclusion, while up to 25% inclusion of black soldier fly meal showed limited adverse effects, 50% HI dietary inclusion is not recommended in gilthead seabream diet, since possible alteration in lipid deposition, particularly at hepatic level, were highlighted in this fish species.

Microbial community responses to environmental stressors are often characterised by assessing changes in taxonomic structure, but such changes, or lack thereof, may not reflect functional changes that are critical to ecosystem processes. We investigated the individual and combined effects of nutrient enrichment ( + 10 mg/L N, + 1 mg/L P) and salinisation ( + 15 g/L NaCl)-key stressors in freshwater systems-on the taxonomic structure and metabolic function of benthic microbial communities using 1000 L open freshwater ponds established >10 years ago in the field. Combined stressors drove strong decreases in maximum and mean total carbon metabolic rates and shifted carbon metabolic profiles compared to either stressor individually and compared to ambient conditions. These metabolic functional changes did not recover through time and occurred without significant alterations in bacterial community taxonomic structure. These results imply that critical functions, including organic carbon release, are likely to be impaired under multiple stressors, even when taxonomic structure remains stable.

In this study, we investigated the effect of Shenling Baizhu San(SLBZS), Quzhi Ruangan Fang(QZRGF) and Gexia Zhuyu Tang(GXZYT) on the intestinal flora of NAFLD rats through network pharmacology and experimental validation.

Protein-protein interaction, Gene Ontology (GO), and molecular docking were performed. Male Sprague-Dawley (SD) rats were divided into 6 groups: Normal, Model, SLBZS (7.2g/kg), QZRGF (27.72g/kg), GXZYT (28.8 g/kg) and positive control (Fenofibrate, 18mg/kg); the NAFLD model was established by High-fat diet. After one week of acclimatisation feeding consecutively, continuous gavage was given for 8 W and 12 W. Serum, liver and faeces were collected and biochemical and pathological indices were determined. The diversity and abundance of intestinal flora were also analyzed using 16S rDNA amplified sequencing.

A total of 132 active ingredients were obtained from the screening results of SLBZS. A total of 202 active ingredients were obtained from the screening results of GXZYT. The screening results of QZRGF obtained 34 active ingredients. Nine common hub genes were screened from the PPI network. GO functional analysis reported that these targets were mainly closely related to the response to bacterial molecules. The molecular docking results indicated that the 11 core constituents in three compound prescriptions has good binding ability with MAPK1, AKT1, CASP3, FOS, TP53, STAT3, MAPK3.

The Chinese herbal compounds SLBZS, QZRGF and GXZYT may exert lipid-lowering effects through multi-components, multi-targets and multi-methods for the treatment of NAFLD while improving the diversity and abundance of the intestinal flora of the rats, and the best effect was achieved with SLBZS.

Canopy-forming brown macroalgae (Fucales) offer numerous key ecosystem services in Mediterranean coastal areas. However, anthropogenic pressures and climate change have significantly impacted their habitats, leading to an extensive population decline. Interactions between algae and microbiota are a major ecological aspect, yet they represent a significant knowledge gap. In our baseline study, we describe the diversity and host specificity of the microbiome of two genetically identical but morphologically distinct populations of Gongolaria barbata from anthropogenically impacted northern Adriatic Sea. Our preliminary results showed that the microbiomes of G. barbata exhibited low host specificity, with 75% of the algae-associated amplicon sequence variants (ASVs) being part of the core coastal ecosystem microbiome. However, microbiomes of specific algal parts, ambient seawater, and sediment differed significantly in terms of alpha diversity and composition. In contrast, the holdfast and axis show higher similarity with sediment microbiomes, indicating potential horizontal transmission pathways. Microbiomes associated with deciduous parts of morphologically distinct G. barbata populations showed no difference in alpha diversity and composition. In contrast, higher variation in alpha diversity and lower sequence proportion of shared ASVs were observed in the holdfast and axis of the two distinct populations. Our observational study provides valuable new insights and baseline for future hypothesis-driven research on the interactions between algae and associated microbiota-a knowledge gap that needs to be addressed in the future for better understanding of the ecological and evolutionary dynamics of coastal ecosystems.IMPORTANCEOur study focuses on the microbiomes of canopy-forming brown macroalgae from the Fucales order, essential habitat builders in Mediterranean coastal areas. These habitats, offering key ecosystem services, face significant declines due to anthropogenic pressures and climate change. We used next-generation 16S rRNA amplicon sequencing to reveal novel insights into the diversity and host specificity of Gongolaria barbata populations in impacted ecosystems. Our findings suggest environmental factors influence the structure of the algae microbiome, with potential recruitment from adjacent sediment communities. This research enhances the understanding of marine ecosystems' ecological and evolutionary dynamics, providing valuable insights for conservation and management efforts.

Passive remediation systems (PRSs) treating either acidic or neutral abandoned coal mine drainage (AMD) are colonized by bacteria that can bioremediate iron (Fe) through chemical cycling. Due to the low pH in acidic AMD, iron oxidation from soluble Fe(II) to precipitated Fe(III) is mainly directed by microbial oxidation. Less well described are biotic reactions that lead to iron remediation through abiotic secondary reactions. We describe here iron oxidation in acidic AMD that is mediated by the bacterial reduction of nitrate to nitrite followed by the geochemical oxidation of Fe(II). Within an acidic PRS, 4,560 bacteria cultured from the microbial community were screened for their ability to oxidize iron and to perform nitrate-dependent iron oxidation (NDFO). Iron oxidation in the culturable community was observed in every pond of the system, ranging from 2.1% to 11.4%, and NDFO was observed in every pond, ranging from 1.4% to 6.0% of the culturable bacteria. Five NDFO isolates were purified and identified as Paraburkholderia spp. One of our isolates, Paraburkholderia sp. AV18 was shown to drive NDFO through the bacterial production of nitrite that in turn chemically oxidizes Fe(II) (nitrate reduction-iron oxidation; NRIO). AV18 expressed nitrate reductase, napA, concurrent to nitrite production. Burkholderiales are found by 16S rRNA gene sequencing in every pond of the PRS. The frequency of NDFO metabolism in the culturable microbial community and abundance of Burkholderiales in the PRS suggest nitrite producers contribute to the bioremediation of iron in acidic AMD and may be an unharnessed opportunity to increase iron bioremediation in acidic conditions.

Our study sheds light on a poorly defined biogeochemical interaction, nitrate-dependent iron oxidation (NDFO), that has been described in several environments. We show that bacterial nitrate reduction produces nitrite, which can chemically oxidize ferrous iron, leading to insoluble ferric iron. We show that bacteria capable of the nitrate reduction-iron oxidation (NRIO) reactions are prevalent throughout multiple passive remediation systems that treat acidic coal mine drainage, indicating this may be a widespread mechanism for iron removal under acidic conditions. In acidic coal mine remediation, iron precipitation has been shown to be solely bacterially mediated, and NRIO provides a simple mechanism for aerobic oxidation of iron in these conditions.

In the marine environment, uncontained crude oil is dispersed and degraded by abiotic or biotic processes; native bacterial populations gradually adapt to integrate interspecific and intraspecific metabolic networks for efficient and dynamic utilization of xenobiotic substrates as carbon source. Aromatic compounds accumulate in marine sediments and bacterial populations at these sites play a crucial role in the mobilization of those complex molecules into the global geochemical cycles. The aim of this work was to use native bacteria from a marine sediment sample in the Gulf of Mexico to enhance the biodegradation of the aromatic fraction from a heavy crude oil, as the sole carbon source, during a 200-day microcosm experiment. This process involved the gradual increase of the aromatic fraction into the culture to promote bacterial enrichment; the increase in viable cells correlated well with a biodegradation pattern of the aromatic fraction at some points. Bacterial biodiversity, as revealed by metagenomic and microbiological approaches, indicates that bacterial groups are present at all fraction concentrations, but with changes in abundance, richness and dominance. Population dynamics revealed the presence of bacteria that modify emulsification and surface tension reduction values, which could promote the incorporation of the highly hydrophobic polyaromatic compounds into the culture aqueous phase for their biodegradation by hydrocarbonoclastic bacteria present. On the other hand, the presence of non-hydrocarbonoclastic bacteria probably is sustained by cross-feeding events involving sugars, amino acids, short carbon compounds, lipids produced by the former bacteria by co-metabolism of complex aromatic substrates, which are transformed into diverse biomolecules for biofilm development to promote a bacterial population dynamics adapted to this environment.

Ultraviolet (UV) disinfection and solar pasteurization are commonly used methods for rainwater treatment, but the changes in water quality and pathogenic species during long-term storage require further investigation. This study conducts a 60-day static rainwater storage experiment to evaluate changes in microbial community structure and pathogen characteristics under different disinfection methods, providing guidance for the resource utilization of rainwater. The results show that both UV disinfection and solar pasteurization effectively reduce microbial diversity and the abundance of pathogenic species. During storage, UV disinfection is particularly effective in controlling pathogenic species, while solar pasteurization has a more pronounced effect on improving water quality. Pathogens species in UV-disinfected rainwater begin to increase around the 20th day of storage, whereas their growth in solar-pasteurized rainwater persists throughout the storage period. UV-disinfected rainwater is suitable for domestic non-potable uses and livestock in the early stages, but as storage time increases, it becomes more appropriate for agricultural use. The lowest health risk occurs on the 20th day, with secondary disinfection recommended on the 60th day. Similarly, during the first 20 days, solar pasteurized rainwater is comparable to UV-disinfected rainwater in terms of usability. However, by the 60th day, due to an increase in animal-associated pathogenic species, solar pasteurized rainwater becomes more suitable for agricultural use. Multiple disinfections on the 20th and 60th days are advised to reduce microbial risks. Additionally, UV disinfection reduces pathogenic diversity, forming stable microbial clusters, while solar pasteurization increases diversity and promotes complex interactions. These findings provide new insights into microbial community structure and pathogenic species changes during long-term rainwater storage and offer important guidance for rainwater reuse.

The human skin microbiome is crucial for health and immunity, especially under the extreme conditions military personnel face. Soldiers often encounter unique stressors and hygienic challenges that can alter their skin's microbial composition, particularly in field environments. In this study, we aimed to investigate the impact of military field exercises on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study of Norwegian soldiers (n = 19) participating in outdoor training operations during the NATO winter exercise Cold Response 2022. Skin swabs were taken from soldiers' hands and forearms before and after the 10-day military exercise, and following a 3-week post-exercise leave. Our results reveal hand- and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers' microbiomes converged during the exercise, then diverged in the post-exercise leave period, and neither skin site returned to baseline composition at follow-up. Our findings highlight the impact of collaborative outdoor activities on microbial communities and suggest that resilience and stability differ between skin sites.IMPORTANCEOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the body's first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome but can also inform hygiene management and disease prevention in comparable situations.

Gut microbiota play a crucial role in metabolic diseases, including type 2 diabetes (T2DM) and hyperuricemia (HUA). One-third of uric acid is excreted into the intestinal tract and further metabolized by gut microbiota. Thus, the gut microbiota might be a new therapeutic target for HUA. Empagliflozin significantly lowers serum uric acid levels and contributes to cardiovascular benefits which are partly attributed to altered gut microbiota. We hypothesize that gut dysbiosis in patients with diabetes and HUA, and the reduction of uric acid by empagliflozin, may be mediated by gut microbiota.

To investigate dysbiosis in patients with T2DM and HUA, and the effect of empagliflozin on gut microbiota associated with purine metabolism.

In this age and sex-matched, case-control study, we recruited 30 patients with T2DM and HUA; 30 with T2DM; and 30 healthy controls at the Henan Provincial People's Hospital between February 2019 and August 2023. Nine patients with T2DM and HUA were treated with empagliflozin for three months. Gut microbiota profiles were assessed using the 16S rRNA gene.

Patients with T2DM and HUA had the highest total triglycerides (1.09 mmol/L in heathy control vs 1.56 mmol/L in T2DM vs 2.82 mmol/L in T2DM + HUA) and uric acid levels (302.50 μmol/L in heathy control vs 288.50 μmol/L in T2DM vs 466.50 μmol/L in T2DM + HUA) among the three groups. The composition of the gut microbiota differed significantly between patients with T2DM and HUA, and those with T2DM/healthy controls (P < 0.05). Notably, patients with T2DM and HUA demonstrated a deficiency of uric acid-degrading bacteria such as Romboutsia, Blautia, Clostridium sensu stricto 1 (P < 0.05). Empagliflozin treatment was associated with significantly reduced serum uric acid levels and purine metabolism-related pathways and genes in patients with T2DM and HUA (P < 0.05).

Gut dysbiosis may contribute to the pathogenesis of HUA in T2DM, and empagliflozin may partly restore the gut microbiota related to uric acid metabolism.

Treated effluent of wastewater treatment plants (WWTPs) are major sources of extracellular antimicrobial resistance genes (eARGs) into aquatic environments. This study aimed to clarify the fate and origins of eARGs from influent to treated effluent at a full-scale WWTP. The compositions of eARG and intracellular ARG (iARG) were acquired via shotgun metagenomic sequencing in influent wastewater, activated sludge, and treated effluent of the target WWTP, where identical wastewater was treated by conventional activated sludge (CAS) and membrane bioreactor (MBR) processes. The proportion of eARGs to iARGs increased from influent to effluent in both processes, reaching almost half of the total ARG. Most eARGs in influent were associated with clinically important antimicrobials, whereas eARGs in sludge and effluent were dominated by aminoglycoside resistance genes of aadA and APH variants. Although the eARGs composition in influent wastewater mirrored that of iARGs, a substantial shift occurred in activated sludge and effluent, highlighting the presence of distinct dissemination and reduction mechanisms between eARGs and iARGs. Notably, the origin of eARGs in treated effluent was mainly iARGs in the effluent rather than the carryover of eARG from activated sludge, which were substantially reduced in MBR, compared to CAS. Consequently, these differences in selective mechanisms led to different fates between eARG and iARG during wastewater treatment.

Early life gut microbiota is being increasingly recognized as a major contributor to short and/or long-term human health and diseases. However, little is known about these early-life events in the human microbiome of the lower respiratory tract. This study aims to investigate fungal and bacterial colonization in the lower airways over the first year of life by analyzing lung tissue from autopsied infants. The fungal and bacterial communities of lung tissue samples from 53 autopsied infants were characterized by Next-Generation Sequencing (NGS), based on universal PCR amplification of the ITS region and the 16S rRNA gene, respectively. Our study highlights a high degree of inter-individual variability in both fungal and bacterial communities inhabiting the infant lung. The lower respiratory tract microbiota is mainly composed of transient microorganisms that likely travel from the upper respiratory tract and do not establish permanent residence. However, it could also contain some genera identified as long-term inhabitants of the lung, which could potentially play a role in lung physiology or disease. At 3-4 months of age, important dynamic changes to the microbial community were observed, which might correspond to a transitional time period in the maturation of the lung microbiome. This timeframe represents a susceptibility period for the colonization of pathogens such as Pneumocystis. The asymptomatic colonization of Pneumocystis was associated with changes in the fungal and bacterial communities. These findings suggest that the period of 2-4 months of age is a "critical window" early in life. Pneumocystis jirovecii could be a potential pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly, and to the future health of children.

We sequenced the V3-V4 region of 16S rRNA genes and transcripts to assess entire (DNA) and active (RNA) soil bacterial communities in four different Indonesian land use systems (jungle rubber, rubber, oil palm, and rainforest). Acidobacteriota and Planctomycetes were dominant, with higher relative abundances at active community level.

Pyrite oxidation drives iron and sulfur availability across Earth's subsurface and is partly microbially mediated. Subsurface microbial communities accelerate this process at circumneutral pH directly by weathering pyritic surfaces and indirectly by causing changes to the surrounding microenvironment, thereby further accelerating pyrite weathering. However, our understanding of community structure dynamics and associated biogeochemistry in Fe- and S-rich lithologies, e.g. pyritic coal, is limited. Here, we present the first comprehensive regional and seasonal genus-level survey of bacterial groundwater communities in a pyritic coal-based aquifer in the South Wales Coalfield (SWC), using 16S rRNA gene amplicon sequencing. Seasonal changes in community structure were limited, suggesting limited influence of surface processes on subsurface communities. Instead, hydrogeologically distinct mine water blocks (MWB) and coal rank largely explained bacterial community structure variation across sites. Fe(II)-oxidizing Betaproteobacteriales genera Gallionella and Sideroxydans dominated the bacterial communities across nine sites and seven MWBs, while three sites within a single MWB, were dominated by S-oxidizing Epsilonbacteraeota genera Sulfuricurvum and Sulfurovum. The cooccurrence of pairs of Fe(II)- and S-oxidizing bacterial genera suggests functional redundancy, which coupled with genus-specific morphologies and life strategies, indicates the importance of distinct environmental and ecological niches within the SWC groundwater at seasonal and regional scales.

The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.

Glucoamylases are enzymes that release free glucose by hydrolyzing consecutive α-1,4 bonds at the non-reducing ends of starch molecules. This enzyme was purified using ammonium sulfate precipitation, and its molecular mass was determined to be approximately 65.2 kDa via SDS-PAGE. Using zymogram analysis, the purified sample's active glucoamylase content was verified. Nano-Liquid Chromatography Mass Spectrometry (nLC-MS/MS) characterization identified peptides covering 46 % of the glucoamylase protein sequence, indicating partial characterization of the enzyme. It was found that the ideal pH and temperature for glucoamylase activity were 6.0 and 37 °C, respectively. Using soluble starch as a substrate, the kinetic parameters were calculated: the Km (substrate concentration at half-maximal velocity) was 30.21 μM, and the Vmax (maximum reaction velocity) was 35.59 μmol mg protein-1 min-1. The enzyme demonstrated optimal activity with soluble starch, highlighting its specificity for starch hydrolysis. Additionally, the enzymatic activity was enhanced in the presence of CaCl2, indicating a positive effect of calcium ions. Its optimal conditions and kinetic parameters provide valuable insights for its industrial and biomedical use.

This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).

A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.

Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.

Not applicable.

Modern agriculture faces the challenge of optimizing fertilization practices while maintaining soil resilience and microbial diversity, both critical for sustainable crop production. We evaluated the effects of multiple fertilization strategies on soil microbial communities and plant performance, comparing conventional methods (urea-based and phosphorus fertilizers applied manually or via drone-assisted precision delivery) with biofertilization using a synthetic microbial consortium (SynCom) derived from teosinte-associated microbes. This SynCom consisted of seven bacterial strains: Serratia nematodiphila EDR2, Klebsiella variicola EChLG19, Bacillus thuringiensis EML22, Pantoea agglomerans EMH25, Bacillus thuringiensis EBG39, Serratia marcescens EPLG52, and Bacillus tropicus EPP72. High-throughput sequencing revealed significant shifts in bacterial and fungal communities across treatments. Untreated soils showed limited diversity, dominated by Enterobacteriaceae (>70%). Conventional fertilization gradually reduced Enterobacteriaceae while increasing Pseudomonas and Lysinibacillus populations. Drone-assisted conventional fertilization notably enhanced Acinetobacter and Rhizobiales growth. Biofertilization treatments produced the most pronounced shifts, reducing Enterobacteriaceae below 50% while significantly increasing beneficial taxa like Bacillus, Pantoea, and Serratia. Network analysis demonstrated that microbial interaction complexity increased across treatments, with Bacillus emerging as a keystone species. Drone-assisted biofertilization fostered particularly intricate microbial networks, enhancing synergistic relationships involved in nutrient cycling and biocontrol, though maintaining the stability of these complex interactions requires careful monitoring. Our findings provide key insights into how precision biofertilization with teosinte-derived microbial consortia can sustainably reshape the maize microbiome, improving crop performance and soil resilience.

Ambrosia beetles (Curculionidae: Scolytinae and Platypodinae) are wood-boring insects studied as examples of fungus-insect symbiosis and for their success as invasive species. While most research on their microbiota has focused on fungal associates, their bacterial communities remain largely understudied. In this review, we synthesize current knowledge on the bacterial microbiota of ambrosia beetles, identify critical gaps in the field, and provide recommendations for future research. To date, eight metabarcoding studies have explored bacterial communities in ambrosia beetles, analyzing a total of 13 species, mostly within the tribe Xyleborini (Scolytinae). These studies have examined the presence of bacteria in ambrosia beetle mycetangia, organs specialized for transporting fungal symbionts, as well as bacterial diversity in fungal gardens and whole beetles, across different life stages, and under varying environmental conditions. In general, bacterial communities appear to be highly specific to the beetle species, and differ between the beetles and their fungal gardens. Most studies employed 16S rRNA gene metabarcoding, and the optimal primer combination for characterizing bacterial communities in environmental samples is 515F/806RB (V4). Various methods for collecting beetles have been used, such as ethanol-baited traps, direct collection from galleries, logs kept in emergence cages, and rearing, but which of them to select when planning a study depends on the specific aim. A significant knowledge gap remains regarding the functional roles of dominant bacterial taxa, as metabarcoding studies often assume that these roles are similar to those played in other beetle species, such as bark beetles. More studies should be conducted to test hypotheses regarding the various factors influencing microbial composition and function, and advanced molecular techniques, including (meta-) genome and transcriptome sequencing, which have been employed in only a limited number of studies, could offer great potential to help bridging this knowledge gap.

The colonization and evolution of gut microbiota early in life play a vital role in shaping a healthy, robust immune system for infant health, whether in combating short-term illness or improving long-term health outcomes. Early-life clinical practices may interrupt or disrupt the normal colonization process of the infant gut microbiota, thereby increasing disease susceptibility. In this prospective cohort study, we analyzed the gut microbiota of 46 term and 23 preterm infants using 16S rRNA gene metagenomic sequencing. Fecal samples were collected at six timepoints during the first three months of life. Notably, gestational age was the main factor contributing to differences in the meconium microbial composition. Intriguingly, our study unveiled a more homogeneous microbial composition in preterm infants with more abundant Bifidobacterium from the postnatal age (PNA) of one month. Concurrently, the beneficial bacteria Bifidobacterium and Lactobacillus gradually increased, and the potentially pathogenic bacteria Clostridium, Enterobacter, Enterococcus, Klebsiella, and Pseudomonas gradually decreased. Furthermore, our study underscored a link between decreased microbial diversity of preterm infants and exclusive breastfeeding and antibiotic exposure. Moreover, preterm infants with patent ductus arteriosus (PDA) exhibited reduced microbial diversity but higher abundances of Streptococcus oralis and Streptococcus mitis.

This study aimed to evaluate the intestinal microbiota development in the first week of life of preterm newborns (PTNB) treated at a public hospital in a municipality in the Brazilian Northeast.

This is an observational, longitudinal, and descriptive study with 23 PTNBs. Two stool samples were collected from each neonate (fasting/meconium and seventh day of life) for stool microbiota analysis by 16S rRNA gene sequencing. The authors analyzed alpha diversity (Chao1, Shannon, and Simpson indices) and principal coordinates of beta diversity.

Forty-six stool samples from 23 PTNBs were analyzed at the taxonomic level. Microbiota's development was dynamic with low diversity. The authors observed a statistical association with the genera Enterobacterales, Streptococcus, Bacteroides, Clostridium_sensu_stricto_1, Enterococcus, and Bifidobacterium in the fasting samples when compared to the day-7 samples. The genus Staphylococcus also dominated at both times.

Dynamics were observed in the intestinal microbiota development, with an alpha diversity decrease in the stool samples collected at fasting/meconium and on the seventh day of life.

Mycotoxins perturb the gut microbiota performance. Bioactive compounds have been recently used as a new food strategy to diminish mycotoxins bioaccessibility and prevent their toxic effects on human and animal health. Male and female Wistar rats were exposed orally to twelve different diets containing aflatoxin B1 (AFB1) and/or ochratoxin A (OTA) with or without fermented whey (FW) and pumpkin (P) for 28 days. Fecal microbiota using 16S rRNA gene sequencing and subsequent metagenomics analysis were analyzed to study the effect of 28-day exposure through diet of contaminated and enriched feed. QIIME 2 microbiome analysis package (version 2024.5) was used to analyze the demultiplexed data. Mycotoxins-functional ingredients combination contributed more to microbial phylogenetic faith α-diversity rather than the functional ingredients alone, while the same combination reported a microbial α-diversity enhancement in comparison to the mycotoxins alone. Proteobacteria phylum was reduced in rat samples fed with contaminated diets (AFB1, OTA, and AFB1+OTA), while there was an increase-although not in all groups-when adding the functional ingredients. The main difference between the sexes was found in FW+AFB1+OTA group, with males (25%) showing higher % of Proteobacteria than females (1.86%). Phylogenetic diversity faith only focuses on microbial genetic (dis)similarity, not considering the biological function. Morganella morganii, a Proteobacteria found in some groups presents anticancer activity, but it is also related to inflammatory bowel disease and colorectal cancer. To sum up, both mycotoxins and functional ingredients trigger changes in the microbiota profile of Wistar rats in a sex-specific manner.

Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L-1) and a eutrophic (105.35 μg C L-1) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.

This work studied wine lees as a novel source of microorganisms for biohydrogen production from vegetable residue (VR). Green tomatoes (WLGT), bell peppers (WLBP), green beans (WLGB), zucchini (WLZ), peas (WLP), and (WLE) eggplants were used as a substrate for dark fermentation, which was conducted in batch assays at 37 °C for 60 d. The cumulative hydrogen yield was approximately 350, 344, 319, 314, 302, 170, and 149 mL H2/g VS in WLZ, WLE, WLRT, WLGT, WLP, WLGB, and WLBP, respectively. A total volatile fatty acid (VFA) accumulation of about 2059 - 4995 mg HAc/L accompanied the bio-H2 production. From day 61 to day 147, dark-fermentative digestate was subjected to an anaerobic digestion batch process under mesophilic conditions to allow the bioconversion of VFAs into renewable methane, as confirmed by a Pearson correlation value of 0.778, final VFA concentrations ≤ 131 mg HAc/L and key functional genes (e.g., K00925). Clostridium_sensu_stricto_12 and Caproiciproducens genera accounted for 44 - 78 % of relative abundance after the dark fermentation stage. The taxonomic classification also revealed a presence of Methanosaeta archaea comprised between 45 and 98 % after the two-stage anaerobic fermentation. Finally, a rough energy comparison was performed to evaluate the feasibility of the bioprocess by including practical implications and limitations.

Polyhydroxybutyrate (PHB) has attracted attention as a representative polymer for biodegradable plastics produced by microorganisms. Since information regarding the fate of PHB released into the environment is limited, it is necessary to identify them based on metagenomic information. We estimated the PHB biodegradability in coastal water samples collected from 15 near shore sites around Japan using oxygen consumption as an indicator in laboratory-scale incubation experiments and conducted 16S rRNA gene-based microbial community profiling. The PHB-biodegradation-rate was significantly positively correlated with the diversity indices of the microbial community in seawater prior to incubation, indicating that seawater with higher diversity is more advantageous for biodegradation. We identified 41 operational taxonomic units exhibiting a significant positive correlation between their abundance and PHB-degradation-rates; these included several microorganisms with hitherto unreported PHB-degrading ability. Next, we analyzed gene expression patterns over incubation time using seawater samples employing metagenomic and metatranscriptomic approaches. Fifty-seven putative extracellular PHB/PHA depolymerase genes were found in 38 metagenomic bins and their expression changed with increasing biodegradation rates, indicating that PHB released into the marine environment is subject to degradation by phylogenetically diverse PHB-depolymerase-producing bacteria. These findings should contribute to expanding the knowledge on degradation of biodegradable plastics by complex marine microbial ecosystems.

Fire is a common ecological disturbance that structures terrestrial ecosystems and biological communities. The ability of fires to contribute to ecosystem heterogeneity has been termed pyrodiversity and has been directly linked to biodiversity (i.e., the pyrodiversity-biodiversity hypothesis). Since climate change models predict increases in fire frequency, understanding how fire pyrodiversity influences soil microbes is important for predicting how ecosystems will respond to fire regime changes. Here we tested how fire frequency-driven changes in burn patterns (i.e., pyrodiversity) influenced soil microbial communities and diversity. We assessed pyrodiversity effects on soil microbes by manipulating fire frequency (annual vs. biennial fires) in a tallgrass prairie restoration and evaluating how changes in burn patterns influenced microbial communities (bacteria and fungi). Annual burns produced more heterogeneous burn patterns (higher pyrodiversity) that were linked to shifts in fungal and bacterial community composition. While fire frequency did not influence microbial (bacteria and fungi) alpha diversity, beta diversity did increase with pyrodiversity. Changes in fungal community composition were not linked to burn patterns, suggesting that pyrodiversity effects on other ecosystem components (e.g., plants and soil characteristics) influenced fungal community dynamics and the greater beta diversity observed in the annually burned plots. Shifts in bacterial community composition were linked to variation in higher severity burn pattern components (grey and white ash), suggesting that thermotolerance contributed to the observed changes in bacterial community composition and lower beta diversity in the biennially burned plots. This demonstrates that fire frequency-driven increases in pyrodiversity augment biodiversity and may influence productivity in fire-prone ecosystems.

Antibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mortality and morbidity in swine production. Furthermore, PWD is a recurrent disease for certain farms, suggesting a link between gut microbial composition and animal health. The aim of this study was to identify the intestinal microbiota of pigs on farms with high health status (HHS) and low health status (LHS) to determine the relationships between sanitary status and gut health. Therefore, three pig farms with LHS presenting recurrent problems of PWD and three farms with HHS were selected to characterise the intestinal microbiome of sows and their piglets. 16 S rRNA gene sequencing technology was used to determine the associations of the gut microbiome with health. With the aim of bringing the MinION Nanopore device to the field for its portability and taxonomic resolution, the results obtained with Illumina were compared to those obtained with Nanopore.

Overall, the results indicated remarkable differences in intestinal microbial communities between animals from LHS farms and those from HHS farms, suggesting that the microbiomes of LHS animals were enriched with potential pathogenic microorganisms, mainly from the Pseudomonadota phylum, such as the genus Escherichia-Shigella, and their associated related species. Moreover, animals from HHS were enriched with beneficial microorganisms, such as Lactobacillus spp., Christensenellaceae R7 group, Treponema, Acetitomaculum and Oscillospiraceae UCG-005.

This study identifies potential microorganisms that may contribute to health and disease in pig farms with HHS and LHS, suggesting that tracking their occurrence might provide insight into sanitary conditions. Moreover, this research highlights the compatibility between Illumina and Nanopore sequencing platforms, justifying the use of MinION Nanopore device in field applications for in situ studies of PWD. This application has the potential to enhance sustainable economic growth in swine farms by enabling more effective monitoring and management of animal health.