Prokaryote-prokaryote symbiotic relationships influence interactions within microbial communities, affecting colonization, survival, and organization. Unlike competition, consortium species facilitate growth via metabolite cross-feeding. This study explored interactions between two early human gut colonizers: partially aerotolerant Bifidobacterium spp. and strict anaerobic Bacteroides spp., using omics techniques. Promotion of Bacteroides spp. growth by Bifidobacterium animalis subsp. lactis was demonstrated through co-culture experiments in anaerobic conditions. Metabolomic analysis revealed over 150 unique metabolites present in B. animalis subsp. lactis supernatants are absent in other Bifidobacterium species, including 3-hydroxycapric acid, D-alanyl-D-alanine, 2-isopropylmalic acid, and D-glucose 2-phosphate. These compounds served as nutritional substrates, including carbon and nitrogen sources, significantly enhancing Bacteroides spp. growth. In murine models, early colonization by B. animalis subsp. lactis consolidated Bacteroides fragilis colonization (1.7 × 104 to 9.7 × 106 copy number/g fecal sample) by providing these metabolites as a niche. These findings highlight B. animalis subsp. lactis plays a critical role in gut colonization of Bacteroides spp. via its exclusive metabolic profile, offering insights into partitioned metabolic activity within gut communities and emphasizing the importance of specific metabolites in early microbial establishment.

Intestinal crypts harbour a specific microbiota but whether and how these bacteria regulate intestinal stem cells (ISCs) or influence colorectal cancer (CRC) development is unclear. Here we screened crypt-resident bacteria in organoids and found that indole acetic acid (IAA) secreted by Acinetobacter radioresistens inhibits ISC turnover. A. radioresistens inhibited cellular proliferation in tumour slices from CRC patients and inhibited intestinal tumorigenesis and spheroid initiation in APCMin/+ mice. Targeted clearance of A. radioresistens from colonic crypts using bacteriophage increased EphB2 expression and consequently promoted cellular proliferation, ISC turnover and tumorigenesis in mouse models of CRC. The protective effects of A. radioresistens were abrogated upon deletion of trpC to prevent IAA production, or upon intestine-specific aryl hydrocarbon receptor (AhR) knockout, identifying an IAA-AhR-Wnt-beta-catenin signalling axis that promotes ISC homeostasis. Our findings reveal a protective role for an intestinal crypt-resident microbiota member in tumorigenesis.

Background/Objectives: We conducted an untargeted metabolomic study in serum, urine, and fecal water in colorectal cancer (CRC) patients compared to healthy controls. The aim was to define the interactions between metabolites and microbiota. Methods: Effluents were collected before colonoscopy. Metabolites were analyzed using LC-HRMS. Bioinformatics analyses included Limma test, along with spectral house and public databases for annotations. Whole-genome shotgun sequencing was performed on fecal samples. Species-metabolite interactions were calculated using Spearman correlation. Interleukins and inflammatory proteins were measured. Results: Fifty-three patients (11 stage I, 10 stage II, 10 stage III, and 22 stage IV) and twenty controls were included. Derivatives of deoxycholic acid, cholic acid, and fatty acids were lower in serum, while urinary bile acids were higher in stage IV CRC patients (versus controls). Metabolites related to tryptophan and glutamate were found significantly altered in stage IV: upregulation of kynurenine and downregulation of indole pathways. This was linked to increased inflammatory protein and microbial metabolites and to the imbalance between virulent pro-inflammatory bacteria (Escherichia and Desulfovibrio) and symbiotic (Ruminococcus and Bifidobacterium) bacteria. Conclusions: E. coli-related tryptophan catabolism shift is shown through stage IV CRC as compared to controls. As a consequence, tryptophan/kynurenine metabolite may become a promising marker for detecting the failure to immune response during therapy.

Human enteric α-defensin 5 (HD5) is an immune system peptide that acts as an important antimicrobial factor but is also known to promote pathogen infections by enhancing adhesion of the pathogens. The mechanistic basis of these conflicting functions is unknown. Here we show that HD5 induces abundant filopodial extensions in epithelial cells that capture Shigella, a major human enteroinvasive pathogen that is able to exploit these filopodia for invasion, revealing a mechanism for HD5-augmented bacterial invasion. Using multi-omics screening and in vitro, organoid, dynamic gut-on-chip and in vivo models, we identify the HD5 receptor as P2Y11, a purinergic receptor distributed apically on the luminal surface of the human colonic epithelium. Inhibitor screening identified cAMP-PKA signalling as the main pathway mediating the cytoskeleton-regulating activity of HD5. In illuminating this mechanism of Shigella invasion, our findings raise the possibility of alternative intervention strategies against HD5-augmented infections. HD5 induces filopodial extensions in epithelial cells that the pathogen Shigella exploits to facilitate invasion and infection.

Introduction. Child stunting is still a major concern worldwide with 148 million under-5 children affected in 2022. Stunting is likely to affect brain development and prevent children from reaching their full potential. This study aimed at evaluating the contribution of stunting, the fecal microbiota and other related factors in brain development in children from Madagascar. Methods. Severely stunted, moderately stunted and non-stunted 2-5 years old children from the AFRIBIOTA cross-sectional study in Madagascar were submitted to the Ages and Stages Questionnaire version III, covering 5 developmental domains (communication, personal-social, problem-solving, fine motor and gross motor). Fecal samples were used for 16S rRNA gene amplicon sequencing for fecal microbiota characterization. A Structural Equation Modelling (SEM) approach was used to evaluate statistical associations, including latent variables, with direct and indirect effects. Results. In all models, stunting was negatively associated with neurodevelopment, as well as low socioeconomic status. β-diversity of the microbiota was neither directly nor indirectly associated with cognitive performance but α-diversity was, in one of the tested models. Socioeconomic status, branched-chain amino acids and hemoglobin levels were associated with stunting in the SEM models tested. Conclusion. Neurodevelopment was associated in this cross-sectional study with socioeconomic status and stunting. The gut microbiota α- and β-diversity were not associated with neurodevelopmental score, except for the Shannon diversity index in the complex SEM model tested. In the future, longitudinal studies assessing not only taxonomic composition but also the functional potential of the microbiome at different timepoints throughout the first years of life could shed better light on a possible, maybe also transient, role of the microbiome and metabolites released thereof on neurodevelopment. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The Afribiota project was funded by the Total Foundation, Institut Pasteur, the Bill and Melinda Gates Foundation (OPP1204689, INV-004352 and INV-002525), the Fondation Petram and a donation by the Odyssey Re-Insurance company. PV was supported by an Early Postdoctoral Fellowship (P2EZP3\_152159), an Advanced Postdoctoral Fellowship (P300PA\_177876) as well as a Return Grant (P3P3PA\_177877), an Eccellenza Professorial Fellowship (PCEFP3\_194545) and a SNSF Starting Grant (TMSGI3_218455) from the Swiss National Science Foundation. This study has been further supported as a part of the NCCR Microbiome, a National Center of Competence and research, funded by the Swiss National Science Foundation (Grant number 180575). JT is a Marie Curie Slodowska Actions Global Fellow. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study protocol of AFRIBIOTA was approved by the Institutional Review Board of the Institut Pasteur (2016-06/IRB) and the National Ethical Review Boards of Madagascar (55/MSANP/CE, 19 May 2015). All participants received oral and written information about the study. The legal representatives of the children provided written consent to participate in the study. The present analysis (AfriGutBrain) was approved by the Swiss CER-VD (BASEC-ID 2023-01834). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors

The COVID-19 pandemic accelerated research and innovation across numerous fields of medicine. It emphasized how disease concepts must reflect dynamic and heterogeneous interrelationships between physical characteristics, genetics, co-morbidities, environmental exposures, and socioeconomic determinants of health throughout life. This article explores how scientists and other stakeholders must collaborate in novel, interdisciplinary ways at these new frontiers of medicine, focusing on communicable diseases, precision/personalized medicine, systems medicine, and data science. The pandemic highlighted the critical protective role of vaccines against current and emerging threats. Radical efficiency gains in vaccine development (through mRNA technologies, public and private investment, and regulatory measures) must be leveraged in the future together with continued innovation in the area of monoclonal antibodies, novel antimicrobials, and multisectoral, international action against communicable diseases. Inter-individual heterogeneity in the pathophysiology of COVID-19 prompted the development of targeted therapeutics. Beyond COVID-19, medicine will become increasingly personalized via advanced omics-based technologies and systems biology—for example targeting the role of the gut microbiome and specific mechanisms underlying immunoinflammatory diseases and genetic conditions. Modeling proved critical to strengthening risk assessment and supporting COVID-19 decision-making. Advanced computational analytics and artificial intelligence (AI) may help integrate epidemic modeling, clinical features, genomics, immune factors, microbiome data, and other anthropometric measures into a “systems medicine” approach. The pandemic also accelerated digital medicine, giving telehealth and digital therapeutics critical roles in health system resilience and patient care. New research methods employed during COVID-19, including decentralized trials, could benefit evidence generation and decision-making more widely. In conclusion, the future of medicine will be shaped by interdisciplinary multistakeholder collaborations that address complex molecular, clinical, and social interrelationships, fostering precision medicine while improving public health. Open science, innovative partnerships, and patient-centricity will be key to success.

The COVID-19 pandemic was a challenging time—many people got sick and even died, most people had to stay home from school and work, and fun things like going to the movies, traveling, and visiting friends and family were discouraged. However, the pandemic also taught us some key lessons. We learned that it is important for scientists and doctors to work together closely to understand health threats. Collaboration led to fast production of a safe, effective, COVID-19 vaccine. We learned that diseases can quickly spread all over the world, which taught us about the need for global cooperation and equal access to vaccination and other health services. The pandemic also showed us how critical it is to understand health information, so that we can tell accurate information apart from false claims. These lessons will shape our future, hopefully leading to even greater advances in science and healthcare that will create a healthier world.

The deleterious effects of human activities on biodiversity in the vegetal and animal world, and on climate changes are now well-established facts. However, little is yet known on the impact of human activities on microbial diversity on the planet and more specifically on the human microbiota Large implementation of metagenomics allows exaustive microbial cataloguing with broad spatio-temporal resolution of human microbiota. A reduction in bacterial richness and diversity in the human microbiota, particularly in the intestinal tract, is now established and particularly obvious in the most industrialized regions of the planet. Massive, uncontrolled use of antibiotics, drastic changes in traditional food habits and some elements of the "global exposome" that remain to identify are usually considered as stressors accounting for this situation of "missing microbes". As a consequence, a dysbiotic situation develops, a "dysbiosis" being characterized by the erosion of the central core of shared bacterial species across individuals and the development of opportunistic "pathobionts" in response to a weaker barrier capacity of these impoverished microbiota. The current challenge is to establish a causality link between the extension of these dysbiotic situations and the steady emergence of epidemic, non-communicable diseases such as asthma, allergy, obesity, diabetes, autoimmune diseases and some cancers. Experimental animal models combined with controlled, prospective clinical interventions are in demand to consolidate causality links, with the understanding that in the deciphering of the mechanisms of alteration of the human-microbiome symbiosis resides a novel exciting chapter of medicine: "microbial medicine".

The transformation of DNA into cells is the basis of molecular biology. Commonly employed techniques include heat shock transformation, electro-transformation, conjugation, transduction, and protoplast fusion. Recently, ultrasonic transformation technology has been developed to transfer DNA into competent cells. The transformation conditions, such as temperature and ultrasonic power, were preliminarily studied. However, this technique has not been widely applied because competent cells must be prepared de novo. In this study, various factors, such as ultrasonic frequency and power, were optimized for the ultrasonic transformation of Escherichia coli. The study found that the optimal conditions for ultrasonic transformation with a defined ultrasonic transformation vial were a frequency of 28 kHz and a power of 80 W. Meanwhile, this research demonstrated that combining the 42°C heat shock conditions with ultrasonic transformation is the most efficient method compared to using only heat shock. Furthermore, the cryoprotective agent ratio for ultrasonic competent cells was investigated and optimized. These findings provide new insights into enhancing transformation efficiency and lay a foundation for the broader application of ultrasonic transformation. IMPORTANCE:Plasmid transformation is widely applicable in gene expression and modification. As an efficient, non-invasive, and gentle method of transformation, ultrasonic transformation provides a novel approach for strain modification. This research presents new strategies for enhancing transformation efficiency and lays the groundwork for expanding the utilization of ultrasonic transformation.

Phenol and p-cresol are two common toxic small molecules related to various diseases. Existing reports confirmed that high l-tyrosine in the daily diet can increase the concentration of phenolic compounds in blood and urine. L-tyrosine is a common component of protein-rich foods. Some anaerobic bacteria in the gut can convert non-toxic l-tyrosine into these two toxic phenolic compounds, phenol and p-cresol. Existing methods have been constructed for measuring the concentration of phenolic compound in feces. However, there is still a lack of direct visual evidence to measure the phenolic compounds in the intestine. In this study, we aimed to construct a whole-cell biosensor for phenolic compounds detection based on the dmpR, the regulator from the phenol metabolism cluster. The commensal bacterium Citrobacter amalonaticus PS01 was selected and used as the chassis. Compared with the biosensor based on ECN1917, the biosensor PS01[dmpR] could better implant into the mouse gut through gavage and showed a higher sensitive to phenolic compound. And the concentration of phenolic compounds in the intestines could be observed with the help of in vivo imaging system using PS01[dmpR]. This paper demonstrated endogenous phenol synthesis in the gut and the strategy of using commensal bacteria to construct whole-cell biosensors for detecting small molecule compounds in the intestines.

Sixty years elapsed between the discovery of messenger RNA (mRNA) and the use of this molecule in an unprecedented global vaccination campaign that brought the Covid-19 pandemic under control. Sixty years of doubts for some and certainties for others about the possibility of using mRNA-an example of synthetic biology-in therapeutic medicine and vaccinology. Years of "translational" research and development have culminated in the success of anti-Covid-19 mRNA vaccines and the promise of more to come against emerging pathogens. A new paradigm in vaccinology, enabling pandemics to be tackled as they emerge. A lesson to be learned: medical progress is less a question of time than of the critical nature of the biological discovery that underpins it. Before leaving us, François Gros, who played a key role in the discovery of mRNA, was able to appreciate the relevance of this obvious fact.

Intestinal mucins play a crucial role in the mucosal barrier, serving as the body’s initial defense against microorganisms. However, how the host regulates the secretion and glycosylation of these mucins in response to bacterial invasion remains unclear. Our study demonstrates that when exposed to Streptococcus gallolyticus ( SGG ), a gut pathobiont, the host mucosa promptly adjusts the behavior of specialized goblet cells (GCs) located in the middle of the crypts. A subset of these cells undergoes a transformation, becoming intercrypt goblet cells (icGCs), which do not detach from the surface but instead migrate along intercrypt spaces while secreting mucins. These mucins form a dense layer covering the epithelial cell surface and filling the gaps between mucus plumes secreted from crypt openings, thereby forming a continuous protective mucus layer. Notably, the mucins produced by icGCs exhibit a distinct glycosylation pattern that makes them impermeable to bacterial pathogens. Significantly, a non-piliated SGG mutant unable to bind to mucus fail to induce icGCs, allowing its translocation through the mucosa and submucosa. Intriguingly, a closely related mucus-adherent bacterium, SGM , which is considered non-pathogenic, also triggers the differentiation of GCs into icGCs. This discovery opens new avenues for treating patients with intestinal diseases characterized by mucus layer deficiencies, such as inflammatory bowel diseases and metabolic disorders. Utilizing mucus-adherent probiotics to induce icGCs represents a promising strategy for reinforcing the mucosal barrier. ![Figure][1] In brief We demonstrate here that, upon oral infection by a gut pathobiont, namely Streptococcus gallolyticus , the murine intestinal mucosa displays a novel type of goblet cells recently described as intercrypt goblet cells (icGCs). These icGCs are not shed at the surface of epithelial cells, in contrast to differentiated goblet cells, and produce a continuous protective mucus layer, with a specific pattern of glycosylation rendering it impenetrable to bacteria. No icGCs were induced in response to a non-mucus binding SGG mutant, thus allowing bacterial translocation into the mucosa and submucosa, highlighting the essential role played by icGCs in the protective mucus barrier function. Importantly, SGM , a commensal mucus-adherent bacterium recognized as safe, is also able to stimulate production of icGCs, opening avenues in the treatment of patients with a “leaky gut”. Highlights ### Competing Interest Statement The authors have declared no competing interest. [1]: pending:yes

Sixty years elapsed between the discovery of messenger RNA (mRNA) and the use of this molecule in an unprecedented global vaccination campaign that brought the Covid-19 pandemic under control. Sixty years of doubts for some and certainties for others about the possibility of using mRNA—an example of synthetic biology—in therapeutic medicine and vaccinology. Years of “translational” research and development have culminated in the success of anti-Covid-19 mRNA vaccines and the promise of more to come against emerging pathogens. A new paradigm in vaccinology, enabling pandemics to be tackled as they emerge. A lesson to be learned: medical progress is less a question of time than of the critical nature of the biological discovery that underpins it. Before leaving us, François Gros, who played a key role in the discovery of mRNA, was able to appreciate the relevance of this obvious fact.

Intestinal mucins play a crucial role in the mucosal barrier, serving as the body’s initial defense against microorganisms. However, how the host regulates the secretion and glycosylation of these mucins in response to bacterial invasion remains unclear. Our study demonstrates that when exposed to Streptococcus gallolyticus (SGG), a gut pathobiont, the host mucosa promptly adjusts the behavior of specialized goblet cells (GCs) located in the middle of the crypts. A subset of these cells undergoes a remodeling, becoming intercrypt goblet cells (icGCs), which do not detach from the surface but instead migrate along intercrypt spaces while secreting a mucus impermeable to bacterial pathogens. Significantly, a non-piliated SGG mutant unable to bind to mucus fails to induce icGCs, allowing its translocation through the mucosa and submucosa. Interestingly, a closely related nonpathogenic bacterium, SGM, able to bind to mucus, also triggers the differentiation of GCs into icGCs. This discovery opens new avenues for treating patients with a “leaky gut” as observed in intestinal diseases such as inflammatory bowel diseases and metabolic disorders, but also patients with a history of repeated antibiotic use. Utilizing mucus-adherent probiotics to induce icGCs represents a promising strategy for reinforcing the mucosal barrier.

The human gut bacteriome is believed to have pivotal influences on human health and disease while the particular roles associated with the gut phageome have not been fully characterized yet with few exceptions. It is argued that gut microbiota can have a potential role in autism spectrum disorders (ASD). The public microbiota database of ASD and typically developing (TD) Chinese individuals were analyzed for phage protein-coding units (pPCU) to find any link between the phageome and ASD. The gut phageome of ASD individuals showed a wider diversity and higher abundance compared to TD individuals. The ASD phageome was associated with a significant expansion of Caudoviricetes bacteriophages. Phages infecting Bacteroidaceae and prophages encoded within Faecalibacterium were more frequent in ASD than in TD individuals. The expansion and diversification of ASD phageome can influence the bacterial homeostasis by imposing pressure on the bacterial communities. In conclusion, the differences of phages community in in ASD and TD can be used as potential diagnosis biomarkers of ASD. Further investigations are needed to verify the role of gut phage communities in the pathogenesis of ASD.

In this work, we investigated the oncogenic role of Streptococcus gallolyticus subsp. gallolyticus ( SGG ), a gut bacterium associated with colorectal cancer (CRC). We showed that SGG UCN34 accelerates colon tumor development in a chemically induced CRC murine model. Full proteome and phosphoproteome analysis of murine colons chronically colonized by SGG UCN34 revealed that 164 proteins and 725 phosphorylation sites were differentially regulated. Ingenuity Pathway Analysis (IPA) indicates a pro-tumoral shift specifically induced by SGG UCN34, as ~ 90% of proteins and phosphoproteins identified were associated with digestive cancer. Comprehensive analysis of the altered phosphoproteins using ROMA software revealed up-regulation of several cancer hallmark pathways such as MAPK, mTOR and integrin/ILK/actin, affecting epithelial and stromal colonic cells. Importantly, an independent analysis of protein arrays of human colon tumors colonized with SGG showed up-regulation of PI3K/Akt/mTOR and MAPK pathways, providing clinical relevance to our findings. To test SGG ’s capacity to induce pre-cancerous transformation of the murine colonic epithelium, we grew ex vivo organoids which revealed unusual structures with compact morphology. Taken together, our results demonstrate the oncogenic role of SGG UCN34 in a murine model of CRC associated with activation of multiple cancer-related signaling pathways.