Abundant Genera Research Articles

Insights into the lemon (Citrus limon) epiphytic microbiome: impact of the biocontrol yeast Clavispora lusitaniae 146

BackgroundPostharvest lemons are affected by several fungal infections, and as alternatives to chemical fungicides for combating these infections, different microbial biocontrol agents have been studied, with the Clavispora lusitaniae 146 strain standing out. Although strain 146 has proven to be an effective agent, the influence of a microbial biological control agent on the postharvest lemon microbiome has not been studied until now. Thus, this study aimed to evaluate how the epiphytic microbiome of postharvest lemons is affected by the application of the biocontrol yeast C. lusitaniae 146.ResultsIn terms of bacterial composition, the most abundant genera were Sphingomonas, Pelomonas, and Bacillus and no significant differences in the composition were detected between the treated and control samples. Among fungi, Clavispora was predominant not only in the treated samples but also in the control, and statistics indicated differences, suggesting its significant role in modulating the epiphytic community composition of lemon. Understanding fruit microbiomes is vital for effective disease control, and this study provides insights into the microbial composition of the surface of lemon and the role of C. lusitaniae 146.

Gut bacteria Prevotellaceae related lithocholic acid metabolism promotes colonic inflammation

BackgroundThe conversion of primary bile acids to secondary bile acids by the gut microbiota has been implicated in colonic inflammation. This study investigated the role of gut microbiota related bile acid metabolism in colonic inflammation in both patients with inflammatory bowel disease (IBD) and a murine model of dextran sulfate sodium (DSS)-induced colitis.MethodsBile acids in fecal samples from patients with IBD and DSS-induced colitis mice, with and without antibiotic treatment, were analyzed using ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). The composition of the microbiota in fecal samples from IBD patients and DSS-colitis mice was characterized via Illumina MiSeq sequencing of the bacterial 16S rRNA gene V3-V4 region. Metagenomic profiling further identified metabolism-related gene signatures in stool samples from DSS-colitis mice. Histological analysis, quantitative PCR (qPCR) and Western Blotting were conducted on colonic samples from DSS-induced colitis mice to assess colonic inflammation, mucosal barrier integrity, and associated signaling pathways. The multivariate analysis of bile acids was conducted using Soft Independent Modelling of Class Analogy (SIMCA, Umetrics, Sweden). The relation between the relative abundance of specific phyla/genera and bile acid concentration was assess through Spearman's correlation analyses. Finally, lithocholic acid (LCA), the key bile acid, was administered via gavage to evaluate its effect on colonic inflammation and mucosal barrier integrity.ResultsIn patients with IBD, the composition of colonic bile acids and gut microbiota was altered. Moreover, changes in the gut microbiota further modulate the composition of bile acids in the intestine. As the gut microbiota continues to shift, the bile acid profile undergoes additional alterations. The aforementioned alterations were also observed in mice with DSS-induced colitis. The study revealed a correlation between dysbiosis of the gut microbiota and modifications in the profile of colonic bile acids, notably LCA observed in both patients with IBD and mice with DSS-induced colitis. Through multivariate analysis, LCA was identified as the key bile acid that significantly affects colonic inflammation and the integrity of mucosal barrier. Subsequent experiments confirmed that LCA supplementation effectively mitigated the inhibitory effects of gut microbiota on colitis progression in mice, primarily through the activation of the sphingosine-1-phosphate receptor 2 (S1PR2)/NF-κB p65 signaling pathway. Analysis of the microbiome and metagenomic data revealed changes in the gut microbiota, notably an increased abundance of an unclassified genus within the family Prevotellaceae in DSS-induced colitis mice. Furthermore, a positive correlation was observed between the relative abundance of Prevotellaceae and bile acid biosynthesis pathways, as well as colonic LCA level.ConclusionsThese findings suggest that LCA and its positively correlated gut bacteria, Prevotellaceae, are closely associated with intestinal inflammation. Targeting colonic inflammation may involve inhibiting LCA and members of the Prevotellaceae family as potential therapeutic strategies.

A Systematic Review of Microbiota in Cirrhosis: A Change Towards a More Pathogenic Predisposition

The microbiome of the human intestine is a regulator of health that modulates immune response and plays an important role in metabolism. The diversity, and abundance of microbiota communities in the gut have been shown to change in cirrhosis and its complications. We aimed to review the current knowledge regarding microbiota alterations in cirrhosis, its potential differences according to etiology, and its role in the development of cirrhosis complications. A systematic search of the online bibliographic database up to July 2024 was performed. Randomized controlled trials and observational and cohort studies that included a total or at least a cohort of cirrhotic adult patients were enlisted for data extraction and analysis. A total of 73 publications were included for data extraction. Alpha diversity was found to decrease in cirrhotic patients in 30/38 (78%) of the studies, while beta diversity in 20/22 (90%) presented significant differences between healthy and cirrhotic groups. Proteobacteria significantly increased in 20/27 (74%) studies, followed by Actinobacteria and Fusobacteria, while 22/25 (88%) studies found either a reduction in cirrhotic patients or increased abundance in healthy controls for Firmicutes and Bacteroidetes. The most abundant genera in hepatic encephalopathy groups were pathobionts such as Enterococcus and Streptococcus, followed by Vellionella and Escherichia. Heterogeneity was found among studies regarding Alpha diversity in hepatocellular carcinoma (HCC) as it was decreased in three studies, indifferent in five, and increased in three studies in comparison to cirrhotic non-HCC patients. The dysbiosis of the gut microbiota is associated with cirrhosis and the development of complications such as hepatic encephalopathy and hepatocellular carcinoma.

Metagenomic analysis of microbial diversity in sucuk, a traditional Turkish dry-fermented sausage, and its relationship with organic acid compounds

Sucuk is a traditional Turkish fermented meat product that is widely consumed in Türkiye. The aim of this study was to determine the microbial diversity and organic acid profile and to elucidate their mutual relationship. The most abundant phylum in sucuk was Firmicutes, followed by Proteobacteria and Cyanobacteria phyla. The most abundant genera in sucuk were Lactobacillus, Pediococcus, and Staphylococcus. Acetic, lactic, and tartaric acids were found in all sucuk samples. Tartaric and lactic acids were positively correlated with microbial diversity parameters. Furthermore, tartaric acid was found to be an indicator of the presence of a rare genus, while lactic acid was found to be an indicator of a balanced distribution among genus and the dominance of some genus. This study for the first time showed that the microbiota of fermented Turkish sausage will be an important contribution to future studies.

A novel immobilized bacteria consortium enhanced remediation efficiency of PAHs in soil: Insights into key removal mechanism and main driving factor.

The remediation of sites co-contaminated with polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) poses challenges for efficient and ecofriendly restoration methods. In this study, three strains (Pseudomonas sp. PDC-1, Rhodococcus sp. RDC-1, and Enterobacter sp. EDC-1) were isolated from sites contaminated with PAHs and HMs. The constructed bacteria consortium was then immobilized using biochar, bentonite, and peat. The immobilized bacteria consortium (IBC) demonstrated efficient removal ability of phenanthrene (58.1 %-73.4 %) and benzo[a]pyrene (69.6 %-83.5 %) during 60 days. Additionally, the IBC decreased soil bacterial richness and diversity, but increased the relative abundance of Proteobacteria phylum and Ochrobactrum genus, which were capable of degrading PAHs. Soil microbial co-occurrence network with IBC was classified into three main modules, and 14 genera were identified as keystone taxa linked to PAHs degradation and HMs resistance. The IBC enhanced the dioxygenase metabolic pathways for PAHs degradation, including phthalic acid and salicylic acid pathways, which became the main driving factor affecting PAHs removal efficiency based on the structural equation modeling analysis. This study confirmed the potential application of the constructed IBC in the bioremediation of soil co-contaminated with PAHs-HMs, and provides insights into key removal mechanism and main driving factor of the enhanced elimination of PAHs.

Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems.

Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is Rhodoferax, an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of Rhodoferax species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of "Rhodoferax" revealed that species previously assigned to Rhodoferax in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the Rhodoferax genus.

Soil Microbial Responses to Varying Environmental Conditions in a Copper Belt Region of Africa: Phytoremediation Perspectives

The mining industry in the copper belt region of Africa was initiated in the early 1900s, with copper being the main ore extracted to date. The main objectives of the present study are (1) to characterize the microbial structure, abundance, and diversity in different ecological conditions in the cupriferous city of Lubumbashi and (2) to assess the metal phytoextraction potential of Leucaena leucocephala, a main plant species used in tailing. Four ecologically different sites were selected. They include a residential area (site 1), an agricultural dry field (site 2), and an agricultural wetland (site 3), all located within the vicinity of a copper/cobalt mining plant. A remediated tailing was also added as a highly stressed area (site 4). As expected, the highest levels of copper and cobalt among the sites studied were found at the remediated tailing, with 9447 mg/kg and 2228 mg/kg for copper and cobalt, respectively. The levels of these metals at the other sites were low, varying from 41 mg/kg to 579 mg/kg for copper and from 4 mg/kg to 110 mg/kg for cobalt. Interestingly, this study revealed that the Leucaena leucocephala grown on the remediated sites is a copper/cobalt excluder species as it accumulates soil bioavailable metals from the rhizosphere in its roots. Amplicon sequence analysis showed significant differences among the sites in bacterial and fungal composition and abundance. Site-specific genera were identified. Acidibacter was the most abundant bacterial genus in the residential and remediated tailing sites, with 11.1% and 4.4%, respectively. Bacillus was predominant in both dry (19.3%) and wet agricultural lands (4.8%). For fungi, Fusarium exhibited the highest proportion of the fungal genera at all the sites, with a relative abundance ranging from 15.6% to 20.3%. Shannon diversity entropy indices were high and similar, ranging from 8.3 to 9 for bacteria and 7.0 and 7.4 for fungi. Β diversity analysis confirmed the closeness of the four sites regardless of the environmental conditions. This lack of differences in the microbial community diversity and structures among the sites suggests microbial resilience and physiological adaptations.

Characterization of the Rhizobiome of the Yellow Pitcher Plant (Sarracenia flava) in Wild and Restored Habitats of Virginia

The yellow pitcher plant, Sarracenia flava, is an insectivorous perennial distributed extensively in southeastern North America. In Virginia, it is restricted to a few wetland ecosystems, with only one natural site known to remain. To uncover whether there were microbial differences in the rhizospheres across natural and reintroduced sites of pitcher plant restoration, shotgun metagenome sequencing was undertaken to characterize the microbiomes of the healthy rhizosphere in the last remaining natural stand in Virginia compared to rhizospheres sampled in two restored habitats where pitcher plants were reintroduced and a nearby control habitat without pitcher plants. Statistical analysis showed no significant differences in rhizobiome communities among the natural, reintroduced, and control sites. Comparison of test rhizobiomes with those of other soil types revealed no significant difference in S. flava habitats versus wildland soil types but significant difference from agricultural soils. Indicator species analysis found Pseudomonas was a significantly more abundant genus in the S. flava habitats. The control site was enriched with iron-reducing bacteria compared to the rest of the sites. Further studies based on gene expression could better facilitate an understanding of the role of Pseudomonas in S. flava rhizosphere specific to habitats, which will provide better knowledge for local conservation of this plant.

Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.

The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where pediatric antibiotic consumption is exceptionally common. We characterized the effects of antibiotics commonly used by Peruvian children (i.e., amoxicillin, azithromycin, cefalexin, sulfa-trimethoprim) on gut diversity, genera, and antibiotic resistance gene (ARG) abundance from 3-16 months. This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-2019. Stool collected at 3, 6, 7, 9, 12, and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40,662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, the association of recent antibiotic use with species richness, diversity, gut genera, and ARG abundance over time was examined. Most children were vaginally delivered (73%), received breastmilk almost daily over the study period, and belonged to socioeconomically diverse households. Amoxicillin, azithromycin, cefalexin, and sulfa-trimethoprim did not impact gut diversity or genera abundance. Azithromycin use significantly impacted ARGs from the macrolide, aminoglycoside, and folate pathway antagonist classes. Amoxicillin use significantly increased total ARGs. Antibiotics' effects on ARGs appeared to be independent of gut microbiome changes. Common antibiotics like amoxicillin and azithromycin may be key drivers of the gut resistome but not the microbiome during early childhood in this setting with frequent breastfeeding.

The Role of Bacteria in Pink Stone Discoloration: Insights from Batalha Monastery

The colonization of historical buildings and monuments by fungi, algae, and bacteria is a common phenomenon. This often leads to deterioration processes that cause either visual or structural harm. The Batalha Monastery in Portugal, a UNESCO World Heritage Site, currently shows significant surface changes to the stone architectural elements within both the Founder’s Chapel and the church, including a widespread pink discoloration on the walls and columns. The main goal of this study was to analyze the biological colonization and assess the influence of bacterial communities on the biodeterioration of Ançã limestone, providing valuable insights to help conservators and restorers select the best preservation strategies for the monastery. The prokaryote population was characterized using both high-throughput DNA sequencing and culture-dependent methods and several orange-pink pigment-producing bacteria were identified, for example, Bacillus, Gordonia, Serratia and Methylobacterium, as well as Halalkalicoccus, an abundant archaeal genus. The pink discoloration observed could be due to biofilms created by bacteria that produce pigments, namely carotenoids. Biocolonization tests were performed using stone mock-ups, which were prepared and inoculated with the bacteria isolated in this study. These tests were designed to replicate the natural conditions of the monastery and monitor the colonization process to understand the discoloration phenomenon.

Co-metabolic Biotransformation of Bisphenol AF by a Bisphenol A-Growing Bacterial Enrichment Culture.

The fluorinated bisphenol A (2,2-bis[4-hydroxyphenyl]propane, BPA) substitute bisphenol AF (BPAF) could be more persistent and toxic than BPA, but little is known about its environmental fate. In this study, we established a co-metabolic BPAF-degrading bacterial enrichment culture with BPA as the growth substrate. BPAF degradation by the enrichment culture was dependent on BPA, and BPAF could be eliminated to below the detection limit with successive additions of BPA. BPAF was mainly degraded via phenolic ring hydroxylation and sequential ring cleavage, which are minor BPA transformation pathway. Conjugated BPAF products were also identified based on the characteristic CF3- fragment and were found to accumulate during BPAF degradation. Sphingopyxis was the key BPA and BPAF degrader in the aerobic enrichment cultures, which was the most abundant genera in only BPA-added and BPA and BPAF-added cultures and was proven to be able to degrade BPA and BPAF by isolation. The aerobic co-metabolic BPAF degrading community also contain non-BPA and BPAF degraders, such as Pandoraea, which may play a supporting role in the community.

Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.

Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.

Mycobiome analysis of leaf, root, and soil of symptomatic oil palm trees (Elaeis guineensis Jacq.) affected by leaf spot disease.

Recently, attention has been shifting toward the perspective of the existence of plants and microbes as a functioning ecological unit. However, studies highlighting the impacts of the microbial community on plant health are still limited. In this study, fungal community (mycobiome) of leaf, root, and soil of symptomatic leaf-spot diseased (SS) oil palm were compared against asymptomatic (AS) trees using ITS2 rRNA gene metabarcoding. A total of 3,435,417 high-quality sequences were obtained from 29 samples investigated. Out of the 14 phyla identified, Ascomycota and Basidiomycota were the most dominant accounting for 94.2 and 4.7% of the total counts in AS, and 75 and 21.2% in SS, respectively. Neopestalotiopsis is the most abundant genus for AS representing 8.0% of the identified amplicons compared to 2.0% in SS while Peniophora is the most abundant with 8.6% of the identified amplicons for SS compared to 0.1% in AS. The biomarker discovery algorithm LEfSe revealed different taxa signatures for the sample categories, particularly soil samples from asymptomatic trees, which were the most enriched. Network analysis revealed high modularity across all groups, except in root samples. Additionally, a large proportion of the identified keystone species consisted of rare taxa, suggesting potential role in ecosystem functions. Surprisingly both AS and SS leaf samples shared taxa previously associated with oil palm leaf spot disease. The significant abundance of Trichoderma asperellum in the asymptomatic root samples could be further explored as a potential biocontrol agent against oil palm disease.

Effect of Dietary Astragalus Fermentation Products on Growth, Intestinal Microflora and Disease Resistance in Largemouth Bass Micropterus salmoides.

Fermentation of Astragalus by Lactobacillus plantarum and Bacillus coagulans can increase the release of active components and degrade its macromolecular substances. This study investigated the effect of fermentation products (Astragalus + L. plantarum + B. coagulans, ALB) on largemouth bass. We specifically focused on growth performance, serum biochemical indices, intestinal microbial diversity, intestinal enzyme activity, immune gene expression and resistance to infections by Aeromonas hydrophila and largemouth bass ranavirus (LMBRaV). The largemouth bass were divided into five groups based on the amount of ALB added to the feed as following, (1) ALB0 (no ALB, ALB0.5 [0.5% addition of ALB], ALB1 [1% addition of ALB], ALB3 [3% addition of ALB], ALB5 [5% addition of ALB]). The feeding trial spanned 28 days. Comprehensively comparing the feeding results of different ALB concentration, the ALB0.5 group showed the best effect. The ALB0.5 group had significantly increased weight gain rate, alkaline phosphatase, total protein, albumin, digestive enzymes activities of lipase, trypsin and increased intestinal villi and thickness of muscularis propria. And it decreased feed conversion ratio, aspartate aminotransferase and alanine aminotransferase of largemouth bass. Furthermore, the ALB0.5 group improved the richness and diversity of the intestinal microbiota. Increased abundance of dominant phylum and genus in the intestine of largemouth bass included Fusobacteria and Cetobacterium, which promoted the growth and immune performance of largemouth bass. After infection with A. hydrophila and LMBRaV, the survival rates were higher in ALB addition experimental groups than in the ALB0 group, respectively. And the survival rate of ALB0.5 group was higher than other groups. Meanwhile, the ALB added to the feed could regulated the immune gene expression (Mx, IRF-3, TNF-α, IL-1β and IL-10), which also promoted the largemouth bass resistance to disease. In summary, adding 0.5% ALB to the diet of largemouth bass can boost its growth performance, immune genes expression, intestinal health and disease resistance.

Differences in Gut Microbial Composition and Characteristics Among Three Populations of the Bamboo Pitviper (Viridovipera stejnegeri).

The gut microbiota contributes to host health by facilitating nutrient uptake, digestion, energy metabolism, intestinal development, vitamin synthesis, and immunomodulation, and plays an important role in the growth and reproduction of the animal itself. Considering the paucity of research on the gut microbiota of wild snakes, this study focused on bamboo pitviper (Viridovipera stejnegeri) populations from Anhui, Guizhou, and Hunan, with multiple fecal samples collected from each population (six, five, and three, respectively). Total microbial DNA was extracted from the fecal samples using metagenomic next-generation sequencing and differences in gut microbial composition, abundance, and carbohydrate-active enzymes (CAZymes) were analyzed and compared among the three populations. Results showed no significant variance in the α-diversity of the gut microbes across the three populations, while principal coordinate analysis revealed significant differences in gut microbe composition. The four most abundant phyla in the gut microbiota of V. stejnegeri were Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota, while the four most abundant genera were Salmonella, Citrobacter, Bacteroides, and Yokenella. Linear discriminant analysis effect size demonstrated notable differences in gut microbial abundance among the three populations. Marked differences in CAZyme abundance were also observed across the microbial communities. Future studies should incorporate diverse ecological factors to evaluate their influence on the composition and function of gut microbiota.

Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences

Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.

Antibiotic resistance in the Ganga River: Investigation of antibiotic resistant bacteria and antibiotic resistance genes, and public health risk assessment

The Ganga River, sacred to India and supporting 440 million people, faces a severe threat from antibiotic resistance. Here, we have investigated the abundance of antibiotic resistant bacteria (ARB), antibiotic resistant genes (ARGs), and mobile genetic elements (MGEs) in water and sediment samples at 16 different sites across the Ganga River biannually. Furthermore, we investigated the presence of potentially pathogenic ARB at genus level in the Ganga River and conducted a risk assessment for human exposure to ESKAPE pathogens during swimming activities. Among the sites studied, a notably higher abundance of ARB, ARGs, and MGEs was observed downstream of the pristine sites (G1 and G2) due to anthropogenic inputs. A significant positive correlation (p < 0.05) was observed between ARB, ARGs, MGEs, and coliforms, suggesting a close association between faecal contamination and MGEs in the spread of antibiotic resistance in the river. Of the identified, 10,340 isolates, Pseudomonas, Bacillus, Acinetobacter, Pseudoxanthomonas, and Aeromonas were the top five most abundant genera. The dominant potentially pathogenic ARB were Pseudomonas, Acinetobacter, Aeromonas, Stenotrophomonas, and Brevundimonas. The results of the Quantitative Microbial Risk Assessment (QMRA) and the analysis of disability-adjusted life years (DALYs) indicated that Enterobacter cloacae posed the highest risk, followed by Acinetobacter baumannii and Klebsiella pneumoniae. Overall, this study provides quantitative data on antibiotic resistance and human health risks in the Ganga River. The data from this study can serve as a foundational basis for guiding crucial actions and policy recommendations for safeguarding the Ganga River and the well-being of its users.

Seasonal and Spatial Dynamics of Fungal Leaf Endophytes in Eucalyptus crebra (Narrow-Leaved Ironbark)

Fungal endophytes play an important role in improving the health and productivity of native and cultivated plant species. Despite their ecological and industrial importance, few eucalypt species have been studied in terms of their endophyte communities. We examined the seasonal and spatial dynamics of fungal leaf endophytes in the model species, Eucalyptus crebra (narrow-leaved ironbark), using ITS-based amplicon sequencing. Alpha and beta diversity analyses revealed significantly higher species richness in summer compared to autumn and spring. Similarly, two-way ANOVA analysis showed significantly higher species diversity in summer compared to autumn (observed p < 0.001, Chao1 p < 0.005) and spring (observed p < 0.005, Chao1 p < 0.005). No difference in Shannon index was observed among different canopy levels across the season. Beta-diversity showed differences in fungal composition across the seasons and at various canopy levels based on unweighted UniFrac distance metric (PERMANOVA season p < 0.001, canopy p < 0.05), signifying distinct separation of fungi based on presence-absence. Ascomycota was the most abundant and diverse phylum and was present throughout the year. In contrast, Basidiomycota was only observed during cooler and drier seasons. Neofusicoccum was the most abundant genus, but distribution fluctuated significantly across the seasons. Pestalotiopsis and Neopestalotiopsis were most abundant in the low leaf canopy, whereas Pseudosydowia was most abundant in the high canopy. This study indicates that the diversity and abundance of endophytic fungi in the leaves of healthy E. crebra trees fluctuate seasonally and across canopy levels. The data generated can be used as a baseline for assessing and potentially modulating the health of E. crebra and other important Eucalyptus spp.

Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy.

The prevalence of food allergy (FA) in children is increasing. Dysbiosis of the microbiome has been linked to FA but needs to be better understood. We aimed to characterize the gut and skin microbiome of young food-allergic children over time and within different types of immunoglobulin E (IgE)-mediated FA. We studied 23 patients, as a pilot study of an ongoing prospective multicenter cohort study including children < 2y with newly diagnosed IgE-mediated FA. Samples (feces/skin swabs) were collected at enrollment and at 1-year follow-up and sequenced for the bacterial 16S rRNA gene (hypervariable v1-v2 region). Gut and skin bacterial diversity was significantly higher in patients compared with controls and increased over time (beta test, Shannon diversity, p < 0.01). Within different types of IgE-mediated FA, bacterial diversity was similar. Community composition differed significantly over time and within IgE-mediated FA types (PERMANOVA: p < 0.01). Several significantly different genus abundances were revealed. We observed a positive correlation between high total IgE and a high abundance of the genus Collinsella in patients with a higher number of allergies/sensitizations (≥3), and patients with tree nut and/or peanut allergy. This study revealed an increased bacterial diversity in children with FA compared with non-atopic children. Importantly, the gut and skin microbiome differed in their composition over time and within different types of IgE-mediated FA. These findings contribute to the understanding of microbiome changes in children with FA and indicate the potential of the genus Collinsella as a biomarker for tree nut and/or peanut allergy and possibly for allergy persistence.

Assessing functional properties of diet protein hydrolysate and oil from fish waste on canine immune parameters, cardiac biomarkers, and fecal microbiota.

Locally produced fish hydrolysate and oil from the agrifood sector comprises a sustainable solution both to the problem of fish waste disposal and to the petfood sector with potential benefits for the animal's health. This study evaluated the effects of the dietary replacement of mainly imported shrimp hydrolysate (5%) and salmon oil (3%; control diet) with locally produced fish hydrolysate (5%) and oil (3.2%) obtained from fish waste (experimental diet) on systemic inflammation markers, adipokines levels, cardiac function and fecal microbiota of adult dogs. Samples and measurements were taken from a feeding trial conducted according to a crossover design with two diets (control and experimental diets), six adult Beagle dogs per diet and two periods of 6 weeks each. The experimental diet, with higher docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids contents, decreased plasmatic triglycerides and the activity of angiotensin converting enzyme, also tending to decrease total cholesterol. No effects of diet were observed on serum levels of the pro-inflammatory cytokines interleukin (IL)-1β, IL-8, and IL-12/IL-23 p40, and of the serum levels of the anti-inflammatory adipokine adiponectin. Blood pressure, heart rate and echocardiographic measurements were similar between diets with the only exception of left atrial to aorta diameter ratio that was higher in dogs fed the experimental diet, but without clinical relevance. Diet did not significantly affect fecal immunoglobulin A concentration. Regarding fecal microbiome, Megasphaera was the most abundant genus, followed by Bifidobacterium, Fusobacterium, and Prevotella, being the relative abundances of Fusobacterium and Ileibacterium genera positively affected by the experimental diet. Overall, results from the performed short term trial suggest that shrimp hydrolysate and salmon oil can be replaced by protein hydrolysate and oil from fish by-products without affecting systemic inflammatory markers, cardiac structure and function, but potentially benefiting bacterial genera associated with healthy microbiome. Considering the high DHA and EPA contents and the antioxidant properties of fish oil and hydrolysate, it would be worthwhile in the future to assess their long-term effects on inflammatory markers and their role in spontaneous canine cardiac diseases and to perform metabolomic and metagenomics analysis to elucidate the relevance of microbiota changes in the gut.