Autoimmune gastritis (AIG) in its advanced atrophic stage is characterized by reduced acid secretion, dysbiosis, and gastric cancer (GC) risk. Swallowed oral bacteria surviving in increased intragastric pH may play a carcinogenic role. Oral microbiota was linked to increased GC risk. In AIG, the concomitant assessment of oral and gastric microbiota has not yet been performed. This study aimed to investigate the oral and gastric microbiota in AIG patients to clarify the role of oral bacteria in gastric dysbiosis. A case–control study on n = 20 histologically diagnosed AIG patients and n = 20 controls without AIG is conducted. Saliva samples were obtained from subjects who were fasting and without toothbrushing. Within 1 h, gastroscopy with biopsies (for histopathology and DNA extraction) was performed. Saliva (n = 40) and biopsy (n = 40) samples were frozen at −20 °C. DNA was extracted and prepared; paired-end sequencing was performed (IlluminaMiSeq-sequencer, San Diego, CA, USA). Bacterial abundance in biopsies was higher in AIG than in controls (p = 0.06), but was not different in the saliva (p = 0.54) samples. In biopsies, AIG showed a lower Shannon-Index than controls (p = 0.001). In saliva studies, AIG showed a higher Shannon-Index than controls (p = 0.0). In biopsies, Streptococcus oralis, Fusobacterium pseudoperiodonticum, Veillonella rogosae, and Gemella sanguinis were more frequent in AIG (p < 0.03). The most abundantly shared taxa between saliva and biopsy were S. oralis and Prevotella histicola; Gemella sanguinis, Fusobacterium pseudoperidonticum, and Veillonella rogosae were shared in AIG patients only. This study confirmed gastric dysbiosis in AIG. Oral taxa were more commonly associated with AIG and shared between the mouth and the stomach. In AIG, the oral microbiota is associated with gastric dysbiosis, highlighting the importance of oral eubiosis in patients with impaired gastric acid secretion.

Gut dysbiosis, an imbalance in gut microbiota, is increasingly linked to depression through the microbiota-gut-brain axis. Stress is an important risk factor for both gut dysbiosis and depression. Despite evidence of altered gut microbiota composition in patients with depression, little is known about how stress and specific gut microbiota features interact to influence depressive symptoms in healthy individuals. This study examined 398 healthy adults (241 women) who provided stool samples and completed validated questionnaires on perceived stress (PSS) and depressive symptoms (CES-D), with a focus on sex differences. In this sample, men and women were characterised by similar gut microbiota composition and diversity. Women reported higher PSS scores than men, whereas no differences were found in CES-D scores. Using Bayesian analyses, results showed that perceived stress predicted depressive symptoms in both sexes. Notably, in women, the genus Eubacterium moderated this relationship: higher perceived stress combined with lower Eubacterium abundance predicted more severe depressive symptoms. In contrast, no moderations by gut bacteria were found in men. The current results warrant further sex-specific investigations of the interaction between stress and specific gut microbiota features in influencing depressive symptoms and suggest that the genus Eubacterium might be a promising microbial biomarker associated with depressive symptoms, particularly in women under higher stress levels.

Fecal calprotectin is a biomarker for intestinal inflammatory conditions, while specific taxa of gut microbiota are proposed as biomarkers for inflammatory bowel disease. However, the relationship between microbiota and calprotectin levels is still largely unexplored. Using shallow shotgun metagenomics, we investigate microbial taxonomic and functional patterns correlated with calprotectin levels in fecal samples of 515 adult individuals without known intestinal pathologies, enrolled within the Parma Microbiota Project. The median value of calprotectin was 23.6 μg/g, but levels higher than the normal threshold of 50 μg/g were measured in 20% of participants. While no changes were detected in alpha- and beta-diversities, calprotectin levels were negatively associated with butyrate-producing bacteria, while positively correlated with several opportunistic pathogens. Functional analysis showed significant correlations between calprotectin levels and the predicted microbial enzymatic functions. If confirmed in longitudinal studies, these findings could indicate early microbial biomarkers of gut inflammatory conditions.

Background: Bifidobacteria are recognized as one of the most influential bacterial groups inhabiting the human gut, capable of modulating the host's health. To understand how these bacteria interact with their hosts, it is essential to investigate their extracellular structures, such as pili. While the presence of sortase-dependent pili has already been investigated in the Bifidobacterium genus, limited information is available on Type IV pili (T4P), which have previously been identified in a few species as tight adherence (Tad) loci. Methods: Here, we explored the T4P distribution across the currently 117 (sub)species representing all described taxa of the Bifidobacterium genus, revealing two distinct loci unevenly distributed within the genus through in silico genomic analyses supported by in vitro validation. Results: Our analysis identified a conserved Type IVc pili (T4cP) structure across all bifidobacterial taxa, with minor predicted structural variations in members of the Bifidobacterium longum and Bifidobacterium boum phylogenetic groups. This T4cP structure, also known as Tad, exhibited an ancestral, non-retractile architecture typically associated with stable colonization and long-term persistence. In addition, a secondary Type IVa pili (T4aP) structure was detected in 13 bifidobacterial species. These species are associated with specific ecological niches, including primate, bovine, and porcine hosts, suggesting a link between this locus and host-associated adaptation. Conclusion: Notably, twitching motility assays demonstrated that Bifidobacterium adolescentis strains harboring the T4aP locus exhibit motility in response to specific environmental signals, observed upon starch supplementation of the growth medium, thereby challenging the traditional view of bifidobacteria as a strictly non-motile bacterial genus.

Background: Bifidobacterium bifidum (B. bifidum) is an infant gut symbiont specialized in degrading host-derived glycans. Despite its relevance in early life, the species’ genomic diversity has not yet been comprehensively surveyed, and current reference collections capture only a fraction of the global B. bifidum pangenome. Methods: In this study, we reconstructed the first comprehensive pangenome of B. bifidum using 1,351 high-quality genomes, including metagenome-assembled genomes. This dataset was used for in silico comparative genomics analyses to identify species-specific genetic and functional features. In vitro transcriptomics analyses were further performed to validate and functionally characterize selected species-specific traits. Results: Comparative genomic analysis with other human-associated bifidobacteria species identified 667 B. bifidum-specific clusters of orthologous genes mostly involved in carbohydrate utilization, osmotic regulation, and host interaction. Notably, B. bifidum displays the most extensive enzymatic repertoire for host-glycan degradation, dedicating 43% of its conserved glycoside hydrolases to these substrates. We identified significant gain-of-function events, including two unique phosphotransferase systems (PTS) for disaccharide uptake. Transcriptomic profiling corroborated the functional relevance of these PTS clusters, which were significantly up-regulated during growth on human milk oligosaccharides, mucin, and N-acetylglucosamine. While the species exhibits high genomic stability, a localized divergence (average nucleotide identitiy, ANI < 98.5%) was identified in rural, non-Westernized populations, reflecting niche-specific adaptations. Conclusion: The identified genomic framework highlighted a distinct evolutionary path of B. bifidum, placing this taxon as a metabolic cornerstone in the neonatal gut via extensive metabolic specialization toward glycan hosts.

Bifidobacterium adolescentis is one of the most frequently encountered bifidobacterial species present in the adult human gut microbiota, with a prevalence of approximately 60%. Despite its high prevalence, B. adolescentis has not been extensively studied and characterized, and our understanding of its physiological traits, genetic diversity, and potential interactions with other members of the human gut microbiota or with its host is therefore fragmentary. In the current study, a data set comprising 1,682 B. adolescentis genomes was compiled by combining publicly available data and metagenome assemblies from 131 projects to uncover the unique genetic characteristics of this species. A pangenome analysis of B. adolescentis identified 203 clusters of orthologous genes absent from the other five human-associated Bifidobacterium species, six of which were in silico predicted to encode functions unique to this taxon. Furthermore, 2,597 genes were predicted to have been acquired by horizontal gene transfer, including genes encoding extracellular structures involved in interaction with the host and other microorganisms, and phage defense mechanisms against bacteriophages. Detailed phylogenetic analysis revealed seven clusters within the B. adolescentis species, each partially associated with the origin of strain isolation, suggesting phylogenetic differentiation shaped by geographical strain origin. Moreover, a large-scale metagenomic analysis of over 10,000 human gut metagenomes from healthy adults revealed that B. adolescentis co-occurs with 36 putative beneficial commensals and butyrate-producing taxa, highlighting its role as a key bifidobacterial species involved in microbial networking within the adult human gut microbiota.IMPORTANCETo comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversity of Bifidobacterium adolescentis by retrieving a large number of genomes from human gut metagenomic samples. The complete overview of the B. adolescentis pangenome enabled us to investigate the genetic features that distinguish this gut commensal from other bifidobacterial species residing in the human intestinal microbiota.

Ventilator-associated pneumonia (VAP) remains a leading complication in mechanically ventilated patients, yet the contribution of the respiratory microbiota remains poorly understood. The PULMIVAP study is a multicenter, longitudinal cohort investigation of respiratory microbiota composition and host immune responses in critically ill adults intubated for non-pulmonary conditions. A total of 146 intubated adult patients were enrolled across eight Italian ICUs, forming matched groups of 73 with VAP and 73 without. Oropharyngeal swabs and endotracheal aspirates were collected at intubation and either at VAP diagnosis or at a matched point in controls for a total of 584 biological samples. Metataxonomic analyses revealed substantial temporal shifts in microbial communities across both upper and lower respiratory compartments, with a trend toward reduced microbial richness in patients who developed VAP. Several genera, such as Corynebacterium, were more abundant in no-VAP patients, whereas Escherichia-Shigella and Peptoniphilus were enriched in VAP samples. Cytokine-microbiota correlation analysis suggested a pro-inflammatory signature in VAP patients, with Citrobacter positively associated with IFN-γ and TNF-α, while several commensal genera were inversely correlated with inflammatory mediators. Additionally, taxa associated with VAP correlated with lower PaO2/FiO2 ratios, implicating them in disease severity. Consistently, several bacteria, such as Corynebacterium, appeared to be linked to better respiratory outcomes, suggesting protective or risk-associated microbial profiles. Overall, these findings highlight the complex interplay between microbial communities and mucosal immunity in the pathogenesis of VAP. The identification of condition-associated microbial and immunological signatures may inform future strategies for risk stratification and targeted prevention.IMPORTANCEVentilator-associated pneumonia (VAP) remains a major complication of mechanical ventilation, yet most microbiome studies have focused on late-stage infection or single airway compartments, limiting insight into early microbial dynamics associated with VAP risk. By longitudinally characterizing upper and lower airway microbiota before and during VAP development, this study provides new insights into microbial and immune patterns associated with susceptibility and disease severity in humans. These findings contribute to the current understanding of VAP pathogenesis by suggesting a role for early airway dysbiosis and local immune responses alongside clinical factors. Remarkably, the identification of taxa associated with risk or protection supports the potential for microbiota-informed monitoring and future risk stratification strategies during mechanical ventilation.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT04849039.

Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.

Aim: Plant-derived proteins have emerged as promising alternatives to animal-based proteins, offering not only environmental and nutritional benefits to the human host but also potential effects on the gut microbiota. Yellow pea (Pisum sativum) represents an attractive source due to its balanced amino acid composition and suitability for food applications. This preliminary study was designed to evaluate the effects of two commercial pea-derived protein preparations - a wet-extracted protein isolate (PPI) and a dry-fractionated protein concentrate (PPC) - on the human gut microbiota using a dual in vitro approach. Methods: We combined monoculture assays on selected representative intestinal bacterial strains with in vitro cultivation models of stabilized microbial communities derived from human fecal samples. Results: Monoculture experiments revealed selective growth responses in certain taxa, such as Bacteroides thetaiotaomicron and Bifidobacterium spp. Moreover, in silico genomic predictions of amino acid biosynthesis and proteolytic capabilities further supported these findings, highlighting functional differences among the tested strains. Furthermore, analysis based on stabilized microbial communities revealed moderate shifts in microbial richness and composition. Notably, PPC was associated with greater variation in taxonomic profiles across samples. Both protein ingredients exhibited similar directional effects on specific taxa, including increases in the load of Bifidobacterium longum and Faecalibacterium duncaniae, and decreases in members of Bacteroides, Parabacteroides, and Phocaeicola. Conclusion: These findings indicate that pea-derived proteins, especially when used as concentrates, exert selective pressure on gut microbial communities.

Bifidobacteria are key members of the human gut, especially during infancy. The ability of bifidobacteria to outcompete other members of the microbial communities encountered in this highly competitive human gut environment represents a key example of their evolutionary and ecological success. In the current report, we investigated the highly conserved bifidobacterial upp gene, which encodes the uracil phosphoribosyltransferase and which is involved in the pyrimidine salvage pathway. Phylogenetic analysis incorporating 107 bifidobacterial upp sequences, representing all currently known Bifidobacterium taxa, indicates that this gene followed an evolutionary route that apparently deviates from that of the 16S rRNA gene. In addition, the upp gene may support bifidobacterial survival in environments with limited uracil availability, potentially providing a competitive advantage under nutrient-restricted conditions.

SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.

During the first year after birth, the infant gut microbiome undergoes a rapid and profound compositional and functional transformation, impelled by an intricate network of intrinsic and extrinsic factors. This process results in increased taxonomic and functional diversification, alongside greater interindividual variability. To better understand this early-life ecosystem, this study assessed the interindividual variability of the infant gut microbiome using a comprehensive infant gut microbiome database of 5288 fecal metagenomic data from healthy, full-term infants across various geographical locations. Our study identified six reference microbial communities, termed Early-Life Community State Types (ELi-CSTs), which not only capture specific compositional profiles and heterogeneity of the infant gut microbiome, but also record the extensive transformation experienced by this developing microbial community during the first year of human life. Indicative Species analysis and Random Forest modeling assisted the precise identification of unique, key taxonomic signatures that are critical to the structure of each ELi-CST, highlighting microbial taxa with pivotal roles in shaping the infant gut microbiota. To complement these findings, we established a bacterial biobank through dedicated cultivation efforts of the infant microbiota, comprising 182 genome-sequenced isolates corresponding to key taxa involved in early life gut microbiota assembly. This biobank provided the basis for co-cultivation experiments combined with transcriptome analyses, thereby enabling in vitro investigations into microbial cross-talk among key modulators, and yielding novel insights into the molecular interactions and cooperative dynamics behind early microbiome development.

B-group vitamins and vitamin K are essential micronutrients required for numerous cellular processes in both microbial and human physiology. While traditionally considered to originate predominantly from dietary sources, the biosynthetic capacity of the human gut microbiota has recently been recognized as a valuable, though historically underappreciated, endogenous source of these vitamins. In particular, the microbial contribution to the host vitamin pool is increasingly acknowledged as a functionally relevant aspect of vitamin homeostasis, especially in the colon, where microbiota-derived vitamins may be absorbed via specific transport mechanisms. This review provides a comprehensive overview of our current understanding of the biosynthesis of B-group vitamins and vitamin K by human gut-associated bacteria, with particular emphasis on key methodologies employed to assess if, how and to what extent members of the gut microbiota supply their host with such micronutrients. Through an integrated overview of available evidence, we highlight both the progress made and the outstanding challenges in elucidating the microbial contribution to the host vitamin metabolism.

Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production. IMPORTANCE:The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.

Plastic pollution is a major environmental challenge, with millions of tonnes produced annually and accumulating in ecosystems, causing long-term harm. Conventional disposal methods, such as landfilling and incineration, are often inadequate, emphasising the need for sustainable solutions like bioremediation. However, the bacterial biodiversity involved in plastic biodegradation remains poorly understood. To address this gap, we present the Plastic-Microbial BioRemediation (Plastic-MBR) database, a curated multi-omics resource that integrates publicly available genetic and enzymatic data related to putative plastic-degrading microorganisms. This database supports in silico analyses of metagenomic data from plastic-contaminated environments and comparative genomics, aiming to identify microbial taxa with potential plastic-degrading functions. We validated the functionality of the Plastic-MBR database by applying it to metagenomic datasets from plastic-contaminated soil and river water, successfully identifying numerous putative plastic-degrading genes across diverse microbial taxa. These results support the use of the Plastic-MBR database as a tool to identify candidate bacteria for future experimental validation, strain isolation, and functional studies, ultimately contributing to a deeper understanding of microbial potential in plastic bioremediation. While this study focuses on database development and computational validation, future studies will be essential to confirm and translate these genomic predictions into effective bioremediation strategies.

The microbiota–gut–brain axis is a complex communication system that plays a crucial role in influencing various aspects of our physical and mental health. The goal of this study was to determine the extent to which individual differences in resting measures of vagally-mediated heart rate variability (HRV) and cortisol levels were associated with psychometric and specific gut microbiota characteristics in seventy-five (38 females) healthy individuals. Participants were assessed for vagally-mediated HRV, daily salivary cortisol levels, psychometric characteristics, and gut microbiota composition. Using a categorical approach based on the median split of HRV and cortisol values, we identified an association between low vagally-mediated HRV, greater depressive symptomatology, and altered gut microbiota (e.g., a higher abundance of Prevotella and a smaller abundance of Faecalibacterium, Alistipes, and Gemmiger). This suggests that vagally-mediated HRV may be a useful biomarker of microbiota-gut brain axis function, and that low vagally-mediated HRV may play an important role in the bidirectional link between gut dysbiosis and depression. On the other hand, daily cortisol parameters (e.g., cortisol awakening response, diurnal cortisol slope) were associated either with higher anxiety and perceived stress, or with a specific gut microbiota profile. Therefore, their utility as biomarkers of microbiota-gut-brain axis function needs further scrutiny.

Over millions of years, humans and their gut microbes have developed a symbiotic relationship that benefits both organisms. Many plants and herbs consumed as food by humans, such as aloe vera gel and dandelion root extracts, contain bioactive compounds with recognized therapeutic or preventive effects. However, the impact of these botanicals on the composition and functionality of the human gut microbiota is not yet understood. In this study, the molecular impact of these botanicals on reconstructed human gut microbiota was assessed by in-vitro bioreactor experiments followed by metagenomics and transcriptomic approaches, highlighting both taxonomic and functional changes in the human gut microbiome. Furthermore, cross-feeding activities established by common human gut microbial taxa like Bacteroides spp. when cultivated on these extracts were assessed. In conclusion, the results show that botanicals affect intestinal populations that are highly dependent on the microbial taxa present and that trophic interactions are established in few key gut members.

Increasing evidence shows that the onset of the host cytoskeleton changes during the viral infection process. The attainment of in-depth knowledge about the molecular pathways coopted by viruses to induce cytoskeleton remodeling represents a useful premise for designing broad-spectrum antivirals. Current investigations suggest that viruses coopt specific host factors to induce cell type-related cytoskeleton modifications for successful cell invasion and viral progeny spread to neighboring cells. On the other hand, it has been argued that cytoskeletal dynamics represent the first line of innate antiviral response activation. Here, we highlight the role of the main cytoskeletal regulatory mechanisms responsible for modulating the structure/function of specific cytoskeletal proteins at the global and local levels, which may affect the outcome of virus infection.

In vitro fecal fermentation models are essential for studying gut microbiota-mediated metabolism of dietary flavan-3-ols. Current methodologies typically limit fermentation periods to 24 h, potentially overlooking the complete kinetics of catabolites. This study aims to extend in vitro fecal fermentation of dietary (poly)phenols up to 48 h to improve the physiological relevance of the model. Fermentation dynamics were assessed through the simultaneous monitoring of polyphenol catabolites, pH, and microbiota composition. One flavan-3-ol monomer ((-)-epicatechin) and two oligomers (procyanidin B2 and procyanidin A2) were fermented using human fecal slurry. Fourteen catabolites were quantified at five time points, revealing that flavan-3-ol polymerization and procyanidin linkage influence bioaccessibility and catabolism. The extended fermentation provided a more complete view of flavan-3-ol metabolism, with stable pH (5-6) and unaffected microbial composition. Substrate-specific effects on microbial alpha diversity suggest distinct resilience patterns, and putative associations between microbial taxa and phenolic catabolites were identified. This study demonstrates that 48 h incubation maintains physiological relevance, capturing late-stage catabolites, making the colonic model more reliable, with significant implications for understanding the colonic fate of undigested dietary (poly)phenols and the microorganisms possibly involved in their transformation.