Search Results (5,400)

Bacterial cell morphology might result from natural selection to gain a competitive advantage under environmentally stressful conditions such as nutrient limitation. In nutrient-limited conditions, a higher surface-to-volume ratio is crucial for cell survival because it allows for a more efficient exchange of nutrients and waste products. A bacterial strain YC6860^T isolated from the rhizosphere of rice (Oryza sativa L.) showed pleomorphic behavior with smooth cell morphology and wrinkled surface rods depending upon nutritional conditions. Based on scanning and transmission electron microscopy studies, we hypothesized that the surface-to-volume ratio of cells would increase with decreasing nutrient concentrations and tested this quantitatively. The transition from smooth to wrinkled cell surface morphology could be one of the adaptation strategies by which YC6860^T maximizes its ability to access available nutrients. To characterize the properties of the wrinkled strain, we performed taxonomic and phylogenetic analyses. 16S rRNA gene sequencing results showed that the strain represented a novel, deep-rooting lineage within the order Rhizobiales with the highest similarity of 94.2% to Pseudorhodoplanes sinuspersici RIPI 110^T. Whole-genome sequencing was also performed to characterize its genetic features. The low phylogenetic and genetic similarity is probably related to the wrinkled morphology of the strain. Therefore, we propose that the strain YC6860^T might belong to a new genus and species, named Rugositalea oryzae. In addition, taxonomic analysis showed that YC6860^T is Gram-negative, aerobic, and rod-shaped with regular surface wrinkles under nutrient-limiting conditions, resembling a delicate twist of fusilli, with groove depths of 48.8 ± 3.7 nm and spacing of 122.5 ± 16.9 nm. This unique cell structure with regular rugosity could be the first finding that has not been reported in the existing bacterial morphology. Full article

Multiple sclerosis (MS) is an autoimmune and neurodegenerative disease affecting approximately 1 million people in the United States. Despite extensive research into the mechanisms of disease development, many aspects of the biological changes during MS progression and the varying symptoms among patients remain unclear. In the era of high-throughput sequencing, transcriptome databases are flooded with data. However, bulk RNA sequencing (RNA-seq) data are typically used only for differential gene expression analysis. Alternative splicing, a key process that alters the transcriptome, can also be identified from bulk data. Here, we accessed 11 studies with bulk RNA-seq data of postmortem MS patients’ brain samples via NCBI’s Gene Expression Omnibus (GEO). We extracted additional information from these data by identifying exclusively alternatively spliced genes via replicate multivariate analysis of transcript splicing (rMATS) analysis. Our analyses revealed that changes in RNA splicing mediate distinct biological signals compared to those driven by differential gene expression. Gene ontology and protein do-main analyses of genes exclusively regulated by alternative splicing revealed distinct molecular differences between progressive and relapsing–remitting MS as well as among lesions from different brain regions and between white and gray matter. These findings highlight the critical role of alternative splicing and its associated pathways in MS disease development and progression. Full article

The progression of metabolic dysfunction-associated steatotic liver disease (MASLD) to severe forms, including metabolic dysfunction-associated steatohepatitis (MASH) and liver fibrosis, involves metabolic dysfunction, genetics, and gut dysbiosis. People with HIV (PWH) represent a high-risk group for MASLD, but the role of gut microbiota alterations in disease severity within this population remains poorly understood. We prospectively recruited PWH with MASLD, defined as the controlled attenuation parameter (CAP) ≥ 238 dB/m, and excluded those with viral hepatitis coinfection or alcohol abuse. Severe MASLD was defined as the presence of MASH (cytokeratin-18 ≥ 130.5 U/L) and/or significant liver fibrosis (liver stiffness ≥ 7.1 kPa). Stool samples were collected for 16S rRNA gene sequencing to characterize gut microbiota composition. Functional predictions were generated using PICRUSt. The differential abundance of bacterial taxa and predicted functions were analyzed using a generalized linear model with a negative binomial distribution. Among 34 PWH with MASLD, 18 (53%) met the criteria for severe MASLD. Microbiota profiling revealed significant differences in bacterial genera between the PWH with and without severe MASLD. Enrichment was observed in the Ruminococcus gnavus group, Negativibacillus, Holdemanella, Subdoligranulum, the Eubacterium hallii group, and Butyricicoccus, while depletion was seen in Prevotella, Alloprevotella, Dialister, Catenibacterium, the Christensenellaceae R 7 group, Clostridium sensu stricto, Olsenella, Oscillospiraceae UCG-005, Libanicoccus, and the Eubacterium siraeum group. Predicted functional pathways related to fatty acid degradation, folate biosynthesis, and amino acids metabolism did not differ between groups. MASLD severity in PWH is associated with a distinct gut microbiota signature, though not with functional pathway alterations. Microbial profiling may complement existing non-invasive biomarkers for risk stratification in this high-risk population. Full article

Background: Edentulism, or toothlessness, is a significant public health issue with profound implications for physical and systemic health, especially during pregnancy, when hormonal and behavioral changes increase the risk of oral diseases. Indigenous populations are particularly vulnerable due to socioeconomic and cultural factors that limit access to dental care. Methods: This pilot study assessed the oral microbiota of nine women, both pregnant and non-pregnant, aged 18–35 from the Salasaca indigenous community in Ecuador, using 16S rRNA gene sequencing. Samples were collected from dentin, saliva, and oral mucosa, and analyzed for alpha and beta diversity levels, taxonomic composition, and ecological metrics using the DADA2 pipeline and a canonical correspondence analysis. Results: Pregnant participants exhibited significantly lower microbial diversity compared to non-pregnant individuals, with notable differences in species richness and community structure. Dominant phyla included Bacillota, Bacteroidota, and Pseudomonadota. Prevotella sp., Neisseria sp., and Haemophilus sp. were among the prevalent genera, with the canonical correspondence analysis highlighting associations between microbial profiles and variables such as gestational status, marital status, and BMI. Conclusion: The findings suggest that pregnancy influences the oral microbiota composition, potentially predisposing women to dysbiosis and dental pathology. This study highlights the need for targeted oral health strategies during pregnancy and serves as a foundation for larger studies in underserved indigenous populations. Full article

The gut microbiota plays a pivotal role in developing colorectal cancer (CRC) through interactions with host immunity, metabolism, and inflammation. However, microbiome-based studies remain scarce in Middle Eastern populations, limiting regional insights into microbial signatures associated with CRC. This study aimed to characterize the gut microbiota profiles of Jordanian CRC patients using 16S rRNA gene sequencing and compare them to those of healthy controls from the GutFeeling KnowledgeBase (GutFeelingKB). Stool samples from 50 CRC patients were analyzed using Illumina iSeq targeting the V3–V4 region. Taxonomic profiling was conducted with a standardized 16S metagenomics pipeline and compared with GutFeelingKB reference data. CRC samples were enriched in Streptococcus, Enterococcus, Klebsiella, Escherichia, Citrobacter, Veillonella, Megamonas, and Eggerthella, while beneficial butyrate-producing genera such as Roseburia, Ruminococcus, Akkermansia, Faecalibacterium, and Bacteroides were significantly depleted. The absence of Fusobacterium nucleatum and Bacteroides fragilis—commonly seen in global studies—suggests region-specific microbial patterns. This study is the first metagenomic study profiling CRC-associated microbiota in Jordan. The findings reveal a dysbiotic microbial signature that reflects both global changes associated with CRC and local ecological influences. This research emphasizes the importance of population-specific microbiome studies and highlights the need to include appropriately matched controls in future investigations. Full article

The crown-of-thorns starfish (CoTS, Acanthaster spp.), is responsible for a considerable amount of coral loss in the tropical Indo-Pacific region. After decimating coral populations through predation, it is expected that CoTS will face food scarcity before coral recovery. It is unclear how CoTS respond to starvation stress. Therefore, we conducted a four-month starvation stress experiment on CoTS, and analyzed the response characteristics of its stomach bacterial communities using high-throughput 16S rRNA sequencing. The results showed no significant differences in the α-diversity of the stomach bacterial community, but the β-diversity differed significantly between fed and starved CoTS. The bacterial community composition in the CoTS stomach changed dramatically, manifesting mainly from Tenericutes to Proteobacteria at the phylum level, and from a community dominated by digestive bacteria (Mycoplasma) to beneficial bacteria (Endozoicomonas) at the genus level. Furthermore, co-occurrence network analysis revealed that starvation reduced the network stability of the bacteria community, but improved network modularity, which may have contributed to the CoTS adaptation to chronic starvation. This study provides a basis for elucidating the mechanism of starvation resistance in the crown-of-thorns starfish. Full article

The coastal waters of Qinhuangdao are a major hotspot for harmful algal blooms (HABs) in the Bohai Sea, with Noctiluca scintillans being one of the primary algal species responsible for these events. A comprehensive understanding of the microbial community structure and functional responses to N. scintillans bloom events is crucial for elucidating their underlying mechanisms and ecological impacts. This study investigated the microbial community dynamics, metabolic shifts, and the environmental drivers associated with a N. scintillans bloom in the coastal waters of Qinhuangdao, China, using high-throughput sequencing of 16S and 18S rRNA genes, co-occurrence network analysis, and metabolic pathway prediction. The results revealed that the proliferation of autotrophic phytoplankton, such as Minutocellus spp., likely provided a nutritional foundation and favorable conditions for the N. scintillans bloom. The bloom significantly altered the community structures of prokaryotes and microeukaryotes, resulting in significantly lower α-diversity indices in the blooming region (BR) compared to the non-blooming region (NR). Co-occurrence network analyses demonstrated reduced network complexity and stability in the BR, with keystone taxa primarily belonging to Flavobacteriaceae and Rhodobacteraceae. Furthermore, the community structures of both prokaryotes and microeukaryotes correlated with multiple environmental factors, particularly elevated levels of NH₄⁺-N and PO₄³⁻-P. Metabolic predictions indicated enhanced anaerobic respiration, fatty acid degradation, and nitrogen assimilation pathways, suggesting microbial adaptation to bloom-induced localized hypoxia and high organic matter. Notably, ammonia assimilation was upregulated, likely as a detoxification strategy. Additionally, carbon flux was redirected through the methylmalonyl-CoA pathway and pyruvate-malate shuttle to compensate for partial TCA cycle downregulation, maintaining energy balance under oxygen-limited conditions. This study elucidates the interplay between N. scintillans blooms, microbial interactions, and functional adaptations, providing insights for HAB prediction and management in coastal ecosystems. Full article

Extreme environments, such as hypersaline habitats, hot springs, deep-sea hydrothermal vents, glaciers, and permafrost, provide diverse ecological niches for studying microbial evolution. However, knowledge of microbial communities in extreme environments at high southern latitudes remains limited, aside from Antarctica. Laguna Timone is a hypersaline crater lake located in a Pleistocene maar of the Pali Aike Volcanic Field, southern Patagonia; the lake was formed during basaltic eruptions in a periglacial setting. Here, we report the first integrative characterization of microbial communities from biofilms and microbial mats in this lake using high-throughput 16S rRNA and ITS gene sequencing, along with mineralogical and hydrochemical analyses of water, sediments, and carbonates. Bacterial communities were dominated by the genera Enterobacterales ASV1, Pseudomonas, Oscillatoria, Nodularia, and Belliella, with site-specific assemblages. Fungal communities included Laetinaevia, Ilyonectria, Thelebolus, Plectosphaerella, and Acrostalagmus, each showing distinct distribution patterns. These baseline data contribute to understanding microbial dynamics in hypersaline maar environments and support future investigations. This integrative approach highlights key microbe–mineral relationships and underscores the potential of Laguna Timone as a natural laboratory for exploring biosignature formation and microbial adaptation in chemically extreme environments, both on early Earth and potentially beyond. Full article

In this study, we assessed soil pollutants and surveyed the bacterial communities using 16S rRNA sequencing to better understand how to improve rehabilitation strategies for nickel-laterite mines in the Philippines. Representative soil samples and rhizospheres from Saccharum spontaneum L. in three post-mining sites rehabilitated in 2015, 2017, and 2019 were collected and analyzed. X-ray diffraction (XRD) identified iron oxyhydroxides, silicates, and clays as major soil components. Based on the pollution load index and contamination degree, the 2015A and 2015B sites were classified as “pristine” and had a “low degree of pollution”, while the remaining sites (2017A, 2017B, 2019A, and 2019B) were considered “moderately contaminated” with nickel, chromium, cobalt, lead, zinc, and copper. An analysis of the bacterial community composition revealed that the phyla Proteobacteria and Actinobacteria, along with the genus Ralstonia, were the most abundant groups across both control and rehabilitated sites. Our results showed that the soil pH and organic matter contents were strongly linked to specific bacterial community composition. These taxa have potential for inoculation in nickel-laterite soils to promote the growth of hyperaccumulator plants. Our results also showed a significant correlation between the structure of the bacterial communities and nickel, chromium, and manganese soil contents, but not with rehabilitation time. Furthermore, we identified the genera Diaphorobacter as potential bioindicators because they are sensitive to nickel and chromium. This study provides valuable baseline data on heavy metal pollution and microbial diversity in a rehabilitated Ni-laterite mine site. Full article

Coffee pulp, the primary residue generated during the wet processing of Coffea arabica L., is frequently applied directly to fields as a crude soil amendment. However, this practice often lacks proper microbial stabilization, limiting its agronomic potential and posing risks due to the presence of phytotoxic compounds. In Colombia, disease-resistant varieties such as Coffea arabica L. var. Castillo and var. Cenicafé 1, developed by the National Coffee Research Center (Cenicafé), are the amongst the most widely cultivated varieties in the country; however, despite their widespread adoption, the microbial ecology of postharvest residues from these varieties remains poorly characterized. This study aimed to isolate and functionally characterize native microbial communities from the pulp of Coffea arabica var. Castillo and var. Cenicafé 1, and to evaluate their role in postharvest processing and organic waste management. Fresh pulp samples were collected from a wet-processing facility located in tropical mid-elevation zones. A total of 53 microbial isolates were recovered using culture-dependent techniques on selective media targeting yeasts, lactic acid bacteria (LAB), and filamentous fungi. Amplicon sequencing of the 16S rRNA gene (V3–V4 region) and ITS1 region was conducted to profile bacterial and fungal communities, revealing diverse microbial consortia dominated by Aspergillus, Lactobacillus, Leuconostoc, Pichia, and Saccharomyces species. Enzymatic screening indicated high pectinolytic and cellulolytic activity. Composting trials using inoculated pulp showed a ~40% reduction in composting time and improved nutrient content. These findings support the use of native microbiota to enhance composting efficiency and postharvest valorization, contributing to more sustainable and circular coffee systems. Full article

The endangered Bengal slow loris (Nycticebus bengalensis) relies heavily on captive/rescue populations for conservation. This study investigated the critical link between Major Histocompatibility Complex (MHC) class II DRB1 exon 2 (DRB1e2) genetic variation and gut microbiota in 46 captive individuals, aiming to improve ex situ management. Using standardized conditions across three enclosure types, we characterized DRB1e2 polymorphism via targeted sequencing and analyzed fecal microbiota using 16S rRNA gene amplicon sequencing. Results demonstrated that high DRB1e2 polymorphism significantly reduced microbial community evenness. Specific genotypes showed distinct microbial associations: G9 strongly correlated with beneficial short-chain fatty acid producers like Fructobacillus, and G2 positively correlated with Bifidobacterium spp., while G2, G3, and G4 correlated negatively with Buchnera (a nutrient-provisioning symbiont). Genotypes and polymorphism collectively explained 9.77% of microbiota variation, exceeding the weaker (5.15%), though significant, influence of enclosure type on β-diversity. These findings reveal that host DRB1e2 variation is a primary driver shaping gut microbiota structure and taxon abundance in captive slow lorises, providing evidence for MHC-mediated host–microbe co-adaptation. This offers a genetically informed framework for optimizing conservation strategies, such as tailoring diets or probiotics to specific genotypes, to enhance gut health and population viability. Full article

Weaning is one of the most challenging stages in a piglet’s life, with multiple stressors contributing to poor gut health. For several years, zinc oxide (ZnO) was the preferred means of promoting a healthy gut and preventing post-weaning diarrhea (PWD). However, with the banning of its use at medicinal levels in the EU since 2022, alternatives are needed. Berberine (BBR), an isoquinoline alkaloid, has been used for centuries in Chinese medicine to treat diarrhea and has pharmacological properties that could make this molecule an attractive alternative to ZnO. The aim of this study was to investigate how berberine is metabolized in the intestinal tract and liver of weaned piglets; determine which metabolites are detected in intestinal contents and plasma; and whether a low dose can alter histomorphological parameters, short-chain fatty acid (SCFA) production, and gut microbiota composition. A total of 60 piglets weaned at 4 weeks were divided into two groups (Control and BBR), each consisting of six pens of five animals. After two weeks of feeding with a normal diet or a berberine-supplemented diet (30 mg berberine/kg feed), berberine and its metabolites were quantified in intestinal contents and plasma by ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) on 12 animals per group (2 male piglets per pen). Moreover, villus length and crypt depth were measured in small-intestinal tissue, and 16S rRNA gene sequencing was performed to examine jejunal, cecal, and colonic gut microbiota composition. Our findings show that piglets metabolize berberine into phase I and II metabolites; however, a low dose does not affect their histomorphology, microbiota composition, or SCFA production. Full article

The gut microbiota is recognized as one of the extrinsic factors that modulate the clinical outcomes of immune checkpoint inhibitors (ICIs), such as inhibitors targeting programmed cell death protein 1 (PD-1), in cancer patients. However, the link between intestinal barrier, which mutually interacts with the gut microbiota, and therapeutic effects has not been extensively studied so far. Therefore, the primary goal of this study was to investigate the relationship between intestinal barrier functionality and clinical outcomes of anti-PD-1 therapy in patients with advanced melanoma. Fecal samples were collected from 64 patients before and during anti-PD-1 therapy. The levels of zonulin, calprotectin, and secretory immunoglobulin A (SIgA), which reflect intestinal permeability, inflammation, and immunity, respectively, were measured in fecal samples (n = 115) using an Enzyme-Linked Immunosorbent Assay (ELISA). Moreover, the composition of the immunoglobulin (Ig)-bound (n = 108) and total stool microbiota (n = 117) was determined by the V3–V4 region of 16S rRNA gene sequencing. ELISA indicated a higher baseline concentration of fecal SIgA in patients with favorable clinical outcomes than those with unfavorable ones. Moreover, high baseline concentrations of intestinal barrier state biomarkers correlated with survival outcomes. In the cases of fecal zonulin and fecal SIgA, there was a positive correlation, while in the case of fecal calprotectin, there was a negative correlation. Furthermore, there were differences in the microbial profiles of the Ig-bound stool microbiota between patients with favorable and unfavorable clinical outcomes and their changes during treatment. Collectively, these findings indicate an association between intestinal barrier functionality and clinical outcomes of anti-PD-1 therapy in advanced melanoma patients. Full article

Background: Iron is an essential nutrient for many bacterial pathogens and normal cellular function and homeostasis of their hosts. Studies suggest that iron deficiency or overload may contribute to the pathogenesis of several chronic conditions and modify host–microbial interactions. In this study, we assessed the impact of varying dietary iron intakes on the microbiota of the intestinal tract and lungs of wild-type mice. Methods: Male C57BL/6J mice were fed either a standard pellet chow (high iron diet), a ferrous ammonium sulfate (FeAS)-supplemented diet or an iron-deficient diet for four weeks. Tissue from the lung, duodenum and colon was collected, and 16S rRNA gene fragments were pyrosequenced. Results: Total serum iron levels were negatively associated with richness of the lung microbiome (p = 0.035). In the murine lungs, there was no association between the iron diet and the overall lung microbiota community composition, but Bacteroides spp. were significantly enriched in the lungs of mice fed the FeAS diet (LDA score > 4, p < 0.05). The community composition of the intestinal microbiota changed significantly depending on the iron diet, with increased richness in the low-iron compared to the iron-supplemented groups (p = 0.053). In the duodenum, Prevotella spp. were reduced (Mean = 7.869, SEM = 3.464, p < 0.05), and Desulfovibrio species increased (Mean = 5.343, SEM = 1.362, p < 0.001) in iron-supplemented groups compared to the low-iron-diet group. In the colon, Bifidobacterium and Bacteroides species were reduced (Mean = 7.175, SEM = 2.246, p < 0.01 and Mean = 6.967, SEM = 1.834, p < 0.01 respectively), and Pseudomonas increased (Mean = 24.03, SEM = 8.919, p < 0.05) in mice on higher-iron diets compared to the low-iron diet. Discussion: This study demonstrates that dietary iron intake significantly impacts the intestinal microbiota and has a small, yet significant, effect on the lung microbiome in C57BL/6J mice. Whilst dietary iron content per se did not significantly modulate the composition of the lung microbiota, serum iron levels had subtle impacts on the community composition of the lung microbiota. Full article

Tropical forage crops vary widely in biochemical composition, resulting in inconsistent silage quality. Understanding how plant traits shape microbial and metabolic networks during ensiling is crucial for optimizing fermentation outcomes. Eight tropical forages—Sorghum bicolor (sweet sorghum), Sorghum × drummondii (sorghum–Sudangrass hybrid), Sorghum sudanense (Sudangrass), Pennisetum giganteum (giant Napier grass), Pennisetum purpureum cv. Purple (purple elephant grass), Pennisetum sinese (king grass), Leymus chinensis (sheep grass), and Zea mexicana (Mexican teosinte)—were ensiled under uniform conditions. Fermentation quality, bacterial and fungal communities (16S rRNA and ITS sequencing), and metabolite profiles (untargeted liquid chromatography–mass spectrometry, LC-MS) were analyzed after 60 days. Sweet sorghum and giant Napier grass showed optimal fermentation, with high lactic acid levels (111.2 g/kg and 99.4 g/kg, respectively), low NH₄⁺-N (2.4 g/kg and 3.1 g/kg), and dominant Lactiplantibacillus plantarum. In contrast, sheep grass and Mexican teosinte exhibited poor fermentation, with high NH₄⁺-N (6.7 and 6.1 g/kg) and Clostridium dominance. Fungal communities were dominated by Kazachstania humilis (>95%), while spoilage-associated genera such as Cladosporium, Fusarium, and Termitomyces proliferated in poorly fermented silages. Metabolomic analysis identified 15,827 features, with >3000 significantly differential metabolites between silages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed divergence in flavonoid biosynthesis, lipid metabolism, and amino acid pathways. In the sweet sorghum vs. sheep grass comparison, oxidative stress markers ((±) 9-HODE, Agrimonolide) were elevated in sheep grass, while sweet sorghum accumulated antioxidants like Vitamin D3. Giant Napier grass exhibited higher levels of antimicrobial flavonoids (e.g., Apigenin) than king grass, despite both being dominated by lactic acid bacteria. Sorghum–Sudangrass hybrid silage showed enrichment of lignan and flavonoid derivatives, while Mexican teosinte accumulated hormone-like compounds (Gibberellin A53, Pterostilbene), suggesting microbial dysbiosis. These findings indicate that silage fermentation outcomes are primarily driven by forage-intrinsic traits. A “forage–microbiota–metabolite” framework was proposed to explain how plant-specific properties regulate microbial assembly and metabolic output. These insights can guide forage selection and development of precision inoculant for high-quality tropical silage. Full article