With increasing global travel, individuals are frequently exposed to new diets, environments, and microbial communities that may influence gut microbiota dynamics and facilitate the acquisition of antimicrobial resistance genes (ARGs). At present, studies characterising day-to-day microbiota and ARGs dynamics during travel are lacking. This study aimed to elucidate the short-term effects of travel on gut microbiota dynamics and ARG acquisition using a high-frequency sampling approach. A cohort of eleven Dutch travellers to Asia self-collected 254 fecal swabs before, during, and after travel for microbiota and resistome profiling. Samples were analysed using qPCR targeting clinically relevant ARGs (qnrB, qnrS and blaCTX-M) and profiled by 16S rRNA gene amplicon sequencing. Longitudinal analyses revealed pronounced inter- and intra-individual variation, with rapid shifts in microbiota composition observed within the first days of travel. An increase in Enterobacterales and a decline in commensal taxa were detected during early travel, coinciding with swift ARG acquisition. These findings underscore the key role of travel in global ARG dissemination.

Gut microbiota can modulate the tumor microenvironment and influence therapeutic outcomes in breast cancer. We hypothesized that similar interactions occur between the breast microbiota and tumor microenvironment. This exploratory study evaluated whether in situ microbial and macrophage densities differ between good and poor neoadjuvant chemotherapy responders and compared microbial density and composition post treatment with surgery-only controls. In 20 postmenopausal estrogen receptor-positive breast cancer patients, bacterial density was quantified by fluorescence in situ hybridization and macrophages density by multiplexed immunofluorescence in pre and post treatment tissue. Bacterial composition was analyzed by 16S rRNA sequencing of post-treatment resection specimens. Nine surgery-only patients served as controls. Neoadjuvant chemotherapy significantly reduced CD68 macrophage density, but not CD163 macrophages or bacterial density. Macrophages and bacterial densities were not correlated, and bacterial densities did not differ between good and poor responders. Higher pretreatment CD68 and CD163 macrophage densities predicted good response. Post treatment resections showed reduced bacterial density and alpha-diversity compared to surgery-only controls. These findings suggest that neoadjuvant chemotherapy affects local breast microbiota and macrophages, with macrophages as promising biomarkers to predict treatment response. The interaction between breast microbiota and local immunity deserves more attention in future research.

Early-life microbial exposures shape immune development and allergy risk. Food allergen sensitization, reflected by the presence of food allergen-specific immunoglobulin E (IgE), is an early indication of impaired immune tolerance. Here we show that early-life transmission of aromatic lactate-producing bifidobacteria strains in 147 children followed from birth to 5 years of age, facilitated by vaginal delivery, exposure to older siblings and exclusive breastfeeding for the first 2 months, led to increased levels of aromatic lactates in the infant gut. This microbiota–metabolite signature was inversely associated with the development of food allergen-specific IgE until 5 years and atopic dermatitis at 2 years. The observed effect was mediated by 4-hydroxy-phenyllactate, which inhibited IgE, but not IgG, production in ex vivo human immune cell cultures. Together, these findings define an early-life microbiota–metabolite–immune axis linking microbial transmission and feeding practices with reduced allergic sensitization. Vaginal birth, exclusive breastfeeding and early contact with siblings promote colonization of the infant gut with bifidobacteria capable of producing aromatic lactates, a microbial and metabolite signal that is inversely related to the risk of allergen-specific sensitization and dermatitis later in life.

Abstract Background The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures. Methods Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures. Results Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value = 0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism. Conclusions This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.

Abstract Background Crohn’s disease (CD) is a chronic, relapsing–remitting gastrointestinal inflammatory condition with a multifactorial etiology. At present, drug therapy is the most important treatment option. However, a substantial number of CD patients experience side effects and/or nonresponse to medical drugs. In part, this might be attributed to the interaction of the intestinal microbiome with xenobiotics, such as medical drugs. The aim of this study was to explore the effect of the common CD drugs budesonide, 6-mercaptopurine (6-MP), as well as tofacitinib on the CD patient’s microbiome in vitro. Results We performed 16S rRNA gene-based bacterial community profiling and metaproteomic analyses on anaerobic ex vivo incubations of CD patient-derived fecal microbiota (FM) that were exposed to CD drugs or control conditions. Both bacterial community profiling and metaproteomics revealed larger differences in 24-h FM incubations between the five donor-derived FM samples than between the various drug incubations. Incubation of the FM of one of the donors with 6-MP or tofacitinib resulted in a significant alteration in the metaproteome when compared to the control condition, whereas no effect could be observed upon incubation with budesonide. Considering only bacterial proteins detected in at least 80% of either the drug or control FM incubations, 33 proteins were consistently more abundant and 93 less abundant in all five donor-derived samples with 6-MP incubation, distinguishing 6-MP from control conditions. In contrast to metaproteomic analyses, bacterial community profiling only detected a significantly lower relative abundance of Colidextribacter in 15 µg/ml tofacitinib FM incubations. No alterations were detected in overall bacterial richness, diversity, or community structure in response to incubation with any of the drugs. Conclusions Tofacitinib and especially 6-MP significantly affect microbial function, but barely microbial composition in vitro. These drug-induced functional changes may subsequently influence host physiology and potentially inflammation in CD. Our findings emphasize the relevance to include functional microbial studies when investigating drug–microbiota interactions. Further research is needed to elucidate the impact of 6-MP-induced microbial alterations on intestinal physiology and inflammation in CD.

Abstract Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2′-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.

Cervical cancer remains one of the most common malignancies among women worldwide, and treatment of locally advanced disease is often associated with substantial toxicity that negatively affects the quality of life. Therefore, strategies aimed at improving survival while minimizing treatment-related side effects are essential. Emerging evidence suggests that the gut and vaginal microbiomes influence cervical carcinogenesis, treatment response, and treatment-related adverse effects. This narrative review aims to summarize current evidence regarding the role of the gut and vaginal microbiomes in locally advanced cervical cancer and explores their potential clinical implications, including interactions with immunological mechanisms. Dysbiosis has been associated with chronic inflammation, impaired antitumor immune responses, reduced treatment efficacy, and increased toxicity, whereas a beneficial microbial composition appears to support improved therapeutic outcomes and reduced toxicity. In addition, microbiome-targeted interventions, including probiotics, show promise in modulating microbial composition, optimizing treatment outcomes, and mitigating treatment-related toxicity. Longitudinal studies integrating analyses of both the gut and vaginal microbiomes with immune infiltrates, patient-reported outcomes, and clinical treatment results are essential to clarify the therapeutic potential of microbiome-targeted interventions in personalized cervical cancer care. Particular attention should be given to interactions between the microbiome and immunotherapy, as immune checkpoint inhibitors are increasingly being incorporated into treatment strategies for locally advanced disease.

Several studies demonstrated curative responses of combined radio-immunotherapy, although not standard-of-care for most cancers. Increased fiber intake has been associated with improved radiotherapy and immunotherapy outcomes, but fiber compositions’ impact remains unclear. This study aimed to explore whether dietary fiber composition influences the therapeutic outcome of combined radio-immunotherapy in a preclinical cancer model. A syngeneic mouse model of colon cancer (CT26) (female BALB/cOla Hsd) was used. Mice were randomized into three groups ( n = 12) of iso-caloric diets with different fiber compositions. Five instances of local radiotherapy on tumors, combined with injections of anti-PD-L1, were administered over 5 and 10 days. Diets’ impact was assessed on progression-free survival, SCFA levels in fecal and cecal samples, gut microbiome composition, and immunological profile. Progression-free survival was different between compositions, as well as their gut microbiota community structure, at all measured time-points. Therapeutic outcome (cure) was negatively associated with the relative abundance of Bacteroides and positively with Atopobiaceae Family . There was no association with SCFA levels. Cured mice displayed smaller spleens containing increased proportions of CD8+ T-cells and decreased proportions of myeloid-derived suppressor cells. Our data suggest that fiber composition may influence therapeutic outcome of combined radio-immunotherapy treatment in vivo.

There is growing evidence for the relationship between the gut microbiota and the effect of chemotherapy. Therefore, this systematic review provides an overview of the current evidence on the effects of the gut microbiota on chemotherapy response, efficacy and toxicity in patients with cancer. PubMed, Web of Science, and EMBASE were searched to collect studies on cancer patients treated with chemotherapy that evaluated tumor response, efficacy, or toxicity, and included microbiome analysis through fecal samples. A total of 22 studies were included. Bacteria associated with better response in lung tumors were, amongst others, a relatively higher abundance of Streptococcus mutans, Enterococcus casseliflavus, and Bacteroides, while bacteria linked to response in gastrointestinal tumors included, among others, higher relative abundances of Lactobacillaceae, Bacteroides fragilis, and Roseburia faecis. Distinctive bacterial taxa were associated with clinical therapy, although causality was not proven. Targeting the gut microbiota during chemotherapy is considered to be a promising approach to enhance the response and to prevent toxicity of chemotherapy.

The gut microbiota ferments dietary fibers, producing short-chain fatty acids (SCFA). Enhanced SCFA production in the distal colon has been linked to improved cardiometabolic health. However, most fibers are fermented proximally, resulting in increased protein fermentation distally, producing metabolites putatively harmful to metabolic health. This 12-week randomized, placebo-controlled trial aimed to improve metabolic health through increasing distal SCFA production while inhibiting proteolytic fermentation using a fiber supplement that increased distal SCFA production in vitro. We assessed the effects of daily potato fiber/sugar beet pectin supplementation (fiber, n = 19) versus maltodextrin (placebo, n = 21), both added to a high-protein diet (25E% protein, ±45% plant-based), on peripheral insulin sensitivity (IS) in adults with overweight/obesity. Secondary outcomes included tissue-specific IS, body composition, microbial composition and functionality, substrate metabolism, and gut permeability. Peripheral IS tended to decrease after fiber supplementation compared to placebo (p = 0.081), while whole-body IS significantly decreased (p = 0.034). Fiber mitigated the increase in insulin-mediated carbohydrate oxidation (p = 0.027) and decrease in fat oxidation (p = 0.006) that occurred in the placebo group. Additionally, fiber prevented an increase in protein oxidation (p = 0.048), while increasing colonic gut permeability (p = 0.046) and plasma interleukin-6 (p = 0.025). Body composition, microbial composition, and fecal and circulating metabolites remained unchanged. In conclusion, fibers combined with a high-protein diet reduced (peripheral) IS and decreased metabolic flexibility compared to placebo. Reduced protein oxidation after fiber may reflect diminished amino acid bioavailability. Additionally, coadministration of fiber and protein may compromise gut barrier function and inflammatory responses. More research investigating the interplay between dietary fibers and proteins is needed.

When profiling the human gut microbiome, technical biases introduced by analytical approaches impede translational research, reducing data reliability and study comparability. Here, through a global study involving 23 labs, we analyzed a wide range of sequencing and bioinformatic approaches for the taxonomic profiling of two well-defined DNA reference reagents (RRs) comprised of 20 common gut bacteria. Through both shotgun and 16S rRNA gene amplicon sequencing, we aimed to isolate sources of bias and understand their impact on microbiome profiling accuracy. Importantly, minimum quality criteria (MQC) were established and are used to evaluate profiling performance. We found that the variability of shotgun sequencing data sets was greater than that of 16S rRNA gene amplicon sequencing and isolated sources of bias in wet and dry lab steps, such as sequencing depth, primer and database choices, rarefaction, and 16S copy number adjustment. This study presents well-defined RRs and MQC to combat technical bias, paving the way for reliable and comparable microbiome research.IMPORTANCEThis benchmark paper highlights the true level of variability in microbiome data across the world and across sectors, underscoring the critical need for the use of WHO International DNA Gut Reference Reagents (RRs) to elevate the quality of data in microbiome research. This global study is the first of its kind, revealing the reality of the bias in the field, comprehensively testing methodologies used by leading laboratories across the world, but also providing avenues for workflow optimization, to accelerate innovation and translational research and move the field forward.

Background: Respiratory infections in early life are an identified risk factor for asthma. We hypothesized that infection-prevention measures during the coronavirus disease 2019 (COVID-19) pandemic influenced the risk of respiratory morbidity and aeroallergen sensitization in early childhood. Objective: We compared respiratory morbidity and aeroallergen sensitization in children born before and during the pandemic. Methods: We compared a COVID-19 category (exposed children; n = 1661) to a pre-COVID-19 category (nonexposed children; n = 1676) by using data from the prospective population-based NorthPop Birth Cohort study in Sweden. Data on respiratory morbidity and concomitant medication were retrieved from national registers. Prospectively collected data on respiratory morbidity using web-based questionnaires at 9 and 18 months of age were applied. At age 18 months, serum IgE levels to aeroallergens were determined (n = 1702). Results: The risk of developing any respiratory tract infection (adjusted odds ratio [aOR] = 0.33 [95% CI, 0.26-0.42]), bronchitis (aOR = 0.50 [95% CI, 0.27-0.95]) and croup (aOR = 0.59 [95% CI, 0.37-0.94]) were decreased in the COVID-19 category. The risk of wheeze in the first 9 months was lower in the COVID-19 category (aOR = 0.70 [95% CI, 0.55-0.89]). There were also fewer prescriptions of antibiotics in the COVID-19 category. The prevalence of aeroallergen sensitization was similar between categories. Conclusion: Children born during the COVID-19 pandemic demonstrated significantly decreased risks of respiratory infections and prescribed antibiotics until 18 months of age compared to children born before the COVID-19 pandemic. Whether this will affect the risk of developing asthma in childhood is being followed.

Vaccine responses vary across populations and are influenced by numerous intrinsic and extrinsic factors, including the gut microbiota. However, studies linking microbiota composition to vaccine immunogenicity in low- and middle-income countries are sparse. In this study, we examined the gut microbiota of 143 healthy rural and urban living Tanzanians who participated in a yellow fever vaccine (YF-17D) trial. We found significant differences in gut microbiota profiles between rural and urban participants. Rural-associated microbiota showed higher diversity and enrichment of taxa like Prevotella and Succinivibrio, which were linked to dietary intake patterns. Yellow fever neutralizing antibody titers were higher in rural compared to urban participants. Interestingly, a subset of urban individuals with a rural-like microbiota had higher antibody titers and faster antibody waning than those with a more industrialized microbiota. These findings suggest that gut microbiota composition might be linked to vaccine immunogenicity, potentially outweighing the influence of living location.

The gut microbiota plays a pivotal role in human life and undergoes dynamic changes throughout the human lifespan, from infancy to old age. During our life, the gut microbiota influences health and disease across life stages. This review summarizes the discussions and presentations from the symposium "Gut microbiota development from infancy to old age" held in collaboration with the Journal of Internal Medicine. In early infancy, microbial colonization is shaped by factors such as mode of delivery, antibiotic exposure, and milk-feeding practices, laying the foundation for subsequent increased microbial diversity and maturation. Throughout childhood and adolescence, microbial maturation continues, influencing immune development and metabolic health. In adulthood, the gut microbiota reaches a relatively stable state, influenced by genetics, diet, and lifestyle. Notably, disruptions in gut microbiota composition have been implicated in various inflammatory diseases-including inflammatory bowel disease, Type 1 diabetes, and allergies. Furthermore, emerging evidence suggests a connection between gut dysbiosis and neurodegenerative disorders such as Alzheimer's disease. Understanding the role of the gut microbiota in disease pathogenesis across life stages provides insights into potential therapeutic interventions. Probiotics, prebiotics, and dietary modifications, as well as fecal microbiota transplantation, are being explored as promising strategies to promote a healthy gut microbiota and mitigate disease risks. This review focuses on the gut microbiota's role in infancy, adulthood, and aging, addressing its development, stability, and alterations linked to health and disease across these critical life stages. It outlines future research directions aimed at optimizing the gut microbiota composition to improve health.

The development of the human gut microbiota during infancy is marked by frequent colonization of Enterobacteriaceae, a bacterial family notoriously associated with various diseases. Yet, despite their prominence in the absence of illness, their exact ecological role during healthy maturation of the infant gut remains poorly explored. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed neonates (n=41) at two, six, and eleven months post-delivery, as well as microbiota of related mothers (n=30) with shotgun metagenomic sequencing, complemented by novel computational approaches and experimentation. Strain-resolved profiling indicates that dominant Bifidobacterium are frequently shared between infants and parenting mothers, while Escherichia coli originate from other sources, yet often persist within individuals. Despite their ecological differences, these genera co-exist, and both display evolutionary adaptations related to the utilization of human milk oligosaccharide (HMO) degradation products. We demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating the cooperative degradation of 2′-fucosyllactose (2′FL), the predominant HMO. In turn, the liberated monosaccharides support E. coli proliferation and niche occupation. These findings reveal a fundamental cross-feeding interaction during development of healthy infant gut microbiota. ### Competing Interest Statement The authors have declared no competing interest.

Environmental factors like diet and antibiotics modulate the gut microbiota in early life. During weaning, gut microbiota progressively diversifies through exposure to non-digestible carbohydrates (NDCs) from diet, while antibiotic perturbations might disrupt this process. Supplementing an infant's diet with prebiotic NDCs may mitigate the adverse effects of antibiotics on gut microbiota development. This study evaluated the influence of supplementation with 2-fucosyllactose (2'-FL), galacto-oligosaccharides (GOS), or isomalto/malto-polysaccharides containing 87% of α(1→6) linkages (IMMP-87), on the recovery of antibiotic-perturbed microbiota. The TIM-2 in vitro colon model inoculated with fecal microbiota of 9-month-old infants was used to simulate the colon of weaning infants exposed to the antibiotics amoxicillin/clavulanate or azithromycin. Both antibiotics induced changes in microbiota composition, with no signs of recovery in azithromycin-treated microbiota within 72 h. Moreover, antibiotic exposure affected microbiota activity, indicated by a low valerate production, and azithromycin treatment was associated with increased succinate production. The IMMP-87 supplementation promoted the compositional recovery of amoxicillin/clavulanate-perturbed microbiota, associated with the recovery of Ruminococcus, Ruminococcus gauvreauii group, and Holdemanella. NDC supplementation did not influence compositional recovery of azithromycin-treated microbiota. Irrespective of antibiotic exposure, supplementation with 2'-FL, GOS, or IMMP-87 enhanced microbiota activity by increasing short-chain fatty acids production (acetate, propionate, and butyrate).

Gastrointestinal symptoms are common during infancy, including infantile colic. Colic can be loosely defined as prolonged and recurrent crying without obvious cause. The cause indeed remains unclear despite much research. Results on infant nutrition are inconclusive, but prior work has linked maternal mental health to infant crying. Recently, several small studies have described associations between gut microbiota and colic. We used a larger cohort to examine the role of the microbiota in infant gastrointestinal health, while also accounting for other biopsychosocial factors. Using fecal 16S rRNA gene amplicon sequencing data from 1,012 infants in the KOALA birth cohort, we examined associations between the 1-month gut microbiota and parent-reported functional gastrointestinal symptoms throughout infancy, including colic, constipation, and cramps. These analyses were adjusted for biopsychosocial factors that were associated with symptoms in a broader analysis involving 2,665 participants. In 257 infants, we also explored associations between breastmilk human milk oligosaccharides (HMOs) and gastrointestinal symptoms. Higher relative abundance of Staphylococcus at one month was associated with less constipation in the first three months of life. Conversely, Ruminococcus gnavus group abundance was associated with more colicky symptoms, particularly between four and seven months. Breastmilk concentrations of the HMOs lacto-N-hexaose (LNH) and lacto-N-neohexaose (LNnH) were associated with less constipation in the first three months. Our results support the conclusion that gut microbiota are relevant in infantile colic and constipation. However more work is needed to elucidate the underlying mechanisms, and explore their interplay with other relevant biopsychosocial factors such as maternal mental health.

Antibiotic-induced perturbations of the gut microbiome can be long-lasting and potentially affect host metabolic health. Strategies supporting microbial resilience are needed to mitigate the negative impact of antibiotics. We investigated the potential of 2 '-fucosyllactose (2 '-FL) supplementation after vancomycin use in a double-blind placebo-controlled randomized intervention among adults with overweight/obesity. Participants received oral vancomycin for seven days followed by 2 '-FL or placebo for eight weeks. At baseline, after vancomycin use and after supplementation, glucose tolerance, insulin sensitivity, plasma lipids, glucagon-like peptide 1, inflammatory cytokines, fecal short-chain fatty acids (SCFAs) and branched-chain fatty acids were analyzed. Gut microbial diversity, composition and resilience were analyzed using 16S rRNA gene sequencing. Vancomycin use decreased gut microbial richness and diversity and disrupted microbiota composition and fecal SCFA concentrations. 2 '-FL improved gut microbial resilience compared to placebo (pTreatment*Time = 0.043) after two weeks of supplementation, but differences were no longer observed at the end of the intervention. Two-week 2 '-FL supplementation also differentially impacted specific bacterial taxa. Eight-week 2 '-FL supplementation decreased fasting plasma interleukin-6 (IL-6) concentrations (pTreatment*Time = 0.041). 2 '-FL intake led to transient improvements in gut microbial resilience after vancomycin use, indicating its beneficial potential to limit antibiotic-induced perturbations. Subsequent effects on metabolic health were limited and require further study.

Shallow metagenomics promises taxonomic and functional insights into samples at an affordable price.To determine the depth of sequencing required for specific analysis, benchmarking is required using defined communities. We used complex mixtures of DNA from cultured gut bacteria and analysed taxonomic composition, strain-level resolution, and functional profiles at nine sequencing depths (0.1-10.0 Gb). Reference-based analysis provided accurate taxonomic, and strain-level insights at 0.5-1.0 Gb. In contrast, de-novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb). Furthermore, it was found that even high-quality MAGs were chimeric, with few (54.5 %) accurately representing the original strains. Functionally, 2 Gb provided reliable insights at the pathway level, but sufficient proteome coverage was only achieved at 10 Gb. Library preparation and host-DNA were identified as confounders in shallow metagenomic analysis. This comprehensive analysis using complex mock communities provides guidance to an increasing community of scientists interested in using shallow metagenomics, and highlights the limitations of MAGs in capturing strain-level diversity. ### Competing Interest Statement The authors have declared no competing interest.

Dose-limiting toxicities pose a major barrier to cancer treatment. While preclinical studies show that the gut microbiota influences and is influenced by anticancer drugs, data from patients paired with careful side effect monitoring remains limited. Here, we investigate capecitabine (CAP)-microbiome interactions through longitudinal metagenomic sequencing of stool from 56 advanced colorectal cancer patients. CAP significantly altered the gut microbiome, enriching for menaquinol (vitamin K2) biosynthesis genes. Transposon library screens, targeted gene deletions, and media supplementation revealed that menaquinol biosynthesis protects Escherichia coli from drug toxicity. Stool menaquinol gene and metabolite levels were associated with decreased peripheral sensory neuropathy. Machine learning models trained in this cohort predicted toxicities in an independent cohort. Taken together, these results suggest treatment-associated increases in microbial vitamin biosynthesis serve a chemoprotective role for bacterial and host cells. Further, our findings provide a foundation for in-depth mechanistic dissection, human intervention studies, and extension to other cancer treatments.IMPORTANCESide effects are common during the treatment of cancer. The trillions of microbes found within the human gut are sensitive to anticancer drugs, but the effects of treatment-induced shifts in gut microbes for side effects remain poorly understood. We profiled gut microbes in colorectal cancer patients treated with capecitabine and carefully monitored side effects. We observed a marked expansion in genes for producing vitamin K2 (menaquinone). Vitamin K2 rescued gut bacterial growth and was associated with decreased side effects in patients. We then used information about gut microbes to develop a predictive model of drug toxicity that was validated in an independent cohort. These results suggest that treatment-associated increases in bacterial vitamin production protect both bacteria and host cells from drug toxicity, providing new opportunities for intervention and motivating the need to better understand how dietary intake and bacterial production of micronutrients like vitamin K2 influence cancer treatment outcomes.