High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients

Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup

Diet significantly influences the human gut microbiota, a key player in health. We analyzed shotgun metagenomic sequencing data from healthy individuals with long-term dietary patterns-vegan, flexitarian, or omnivore-and included detailed dietary surveys and blood biomarkers. Dietary patterns notably affected the bacterial community composition by altering the relative abundances of certain species but had a minimal impact on microbial functional repertoires. However, diet influenced microbial functionality at the strain level, with diet type linked to strain genetic variations. We also found molecular signatures of selective pressure in species enriched by specific diets. Notably, species enriched in omnivores exhibited stronger positive selection, such as multiple iron-regulating genes in the meat-favoring bacterium Odoribacter splanchnicus, an effect that was also validated in independent cohorts. Our findings offer insights into how diet shapes species and genetic diversity in the human gut microbiota.

RFW captures species-level metagenomic functions by integrating genome annotation information

Functional profiling of whole-metagenome shotgun sequencing (WMS) enables our understanding of microbe-host interactions. We demonstrate microbial functional information loss by current annotation methods at both the taxon and community levels, particularly at lower read depths. To address information loss, we develop a framework, RFW (reference-based functional profile inference on WMS), that utilizes information from genome functional annotations and taxonomic profiles to infer microbial function abundances from WMS. Furthermore, we provide an algorithm for absolute abundance change quantification between groups as part of the RFW framework. By applying RFW to several datasets related to autism spectrum disorder and colorectal cancer, we show that RFW augments downstream analyses, such as differential microbial function identification and association analysis between microbial function and host phenotype. RFW is open source and freely available at https://github.com/Xingyinliu-Lab/RFW.

Guilds as guides for health vs. disease

In a recent Cell paper, Wu et al. identified microbiome guilds based on bacterial co-occurrence among type 2 diabetes patients. Two competing guilds, associated with high-fiber vs. control diets, correlated with healthy biomarkers. The potential of this approach was further verified across 15 diseases in 26 studies.

The gut microbiome and the brain

PURPOSE OF REVIEW

The importance of the gut microbiome for human health and well-being is generally accepted, and elucidating the signaling pathways between the gut microbiome and the host offers novel mechanistic insight into the (patho)physiology and multifaceted aspects of healthy aging and human brain functions.

RECENT FINDINGS

The gut microbiome is tightly linked with the nervous system, and gut microbiota are increasingly emerging as important regulators of emotional and cognitive performance. They send and receive signals for the bidirectional communication between gut and brain via immunological, neuroanatomical, and humoral pathways. The composition of the gut microbiota and the spectrum of metabolites and neurotransmitters that they release changes with increasing age, nutrition, hypoxia, and other pathological conditions. Changes in gut microbiota (dysbiosis) are associated with critical illnesses such as cancer, cardiovascular, and chronic kidney disease but also neurological, mental, and pain disorders, as well as chemotherapies and antibiotics affecting brain development and function.

SUMMARY

Dysbiosis and a concomitant imbalance of mediators are increasingly emerging both as causes and consequences of diseases affecting the brain. Understanding the microbiota's role in the pathogenesis of these disorders will have major clinical implications and offer new opportunities for therapeutic interventions.

Scalable log-ratio lasso regression for enhanced microbial feature selection with FLORAL

Identifying predictive biomarkers of patient outcomes from high-throughput microbiome data is of high interest, while existing computational methods do not satisfactorily account for complex survival endpoints, longitudinal samples, and taxa-specific sequencing biases. We present FLORAL, an open-source tool to perform scalable log-ratio lasso regression and microbial feature selection for continuous, binary, time-to-event, and competing risk outcomes, with compatibility for longitudinal microbiome data as time-dependent covariates. The proposed method adapts the augmented Lagrangian algorithm for a zero-sum constraint optimization problem while enabling a two-stage screening process for enhanced false-positive control. In extensive simulation and real-data analyses, FLORAL achieved consistently better false-positive control compared to other lasso-based approaches and better sensitivity over popular differential abundance testing methods for datasets with smaller sample sizes. In a survival analysis of allogeneic hematopoietic cell transplant recipients, FLORAL demonstrated considerable improvement in microbial feature selection by utilizing longitudinal microbiome data over solely using baseline microbiome data.

The intestinal microbiota and cellular therapy: implications for impact and mechanisms

ABSTRACT

The microbiota, comprising bacteria, fungi, and viruses residing within our bodies, functions as a key modulator in host health and states, including immune responses. Studies have linked microbiota and microbiota-derived metabolites to immune cell functions. In this review, we probe the complex relationship between the human microbiota and clinical outcomes of cellular therapies that leverage immune cells to fight various cancers. With a particular emphasis on hematopoietic cell transplantation and chimeric antigen receptor T-cell therapy, we explore the potential mechanisms underpinning this interaction. We also highlight the interventional applications of the microbiota in cellular therapy while outlining future research directions in the field.

Ensemble learning algorithms to elucidate the core microbiome's impact on carbon content and degradation properties at the soil aggregate level

Soil aggregates are crucial for soil organic carbon (OC) accumulation. This study, utilizing a 32-year fertilization experiment, investigates whether the core microbiome can elucidate variations in carbon content and decomposition across different aggregate sizes more effectively than broader bacterial and fungal community analyses. Employing ensemble learning algorithms that integrate machine learning with network inference, we found that the core microbiome accounts for an average increase of 26 % and 20 % in the explained variance of PCoA and Adonis analyses, respectively, in response to fertilization. Compared to the control, inorganic and organic fertilizers decreased the decomposition index (DDI) by 31 % and 38 %, respectively. The fungal core microbiome predominantly influenced OC content and DDI in larger macroaggregates (>2000 μm), explaining over 35 % of the variance, while the bacterial core microbiome had a lesser impact, explaining <30 %. Conversely, in smaller aggregates (<2000 μm), the bacterial core microbiome significantly influenced DDI (R2 > 0.2), and the fungal core microbiome more strongly affected OC content (R2 > 0.3). Mantel tests showed that pH is the most significant environmental factor affecting core microbiome composition across all aggregate sizes (Mantel's r > 0.8, P < 0.01). Linear correlation analysis further confirmed that the core microbiome's community structure could accurately predict OC content and DDI in aggregates (R2 > 0.8, P < 0.05). Overall, our findings suggested that the core microbiome provides deeper insights into the variability of aggregate organic carbon content and decomposition, with the bacterial core microbiome playing a particularly pivotal role within the soil aggregates.

Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants

Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three neonatal intensive care units using shotgun metagenomics of 2,512 stools and metatranscriptomics of 1,381 stools. Strain tracking, taxonomic and functional profiling, and comprehensive clinical metadata identify Enterobacteriaceae, enterococci, and staphylococci as primarily exploiting available niches to populate the gut microbiome. Clostridioides difficile lineages persist between individuals in single centers, and Staphylococcus epidermidis lineages persist within and, unexpectedly, between centers. Collectively, antibiotic and non-antibiotic medications influence gut microbiome composition to greater extents than maternal or baseline variables. Finally, we identify a persistent low-diversity gut microbiome in neonates who develop necrotizing enterocolitis after day of life 40. Overall, we comprehensively describe gut microbiome dynamics in response to medical interventions in preterm, hospitalized neonates.

Maladaptive weight control and eating behaviours in female adolescents/young adults are associated with increased risk of irritable bowel syndrome in adulthood: Results from the Growing Up Today Study (GUTS)

BACKGROUND

Irritable bowel syndrome (IBS) is common among individuals with eating disorders. The relationship between these conditions is likely bidirectional. However, data on the risk of IBS among those with prior eating disorders is largely limited to cross-sectional studies.

AIM

To prospectively evaluate the association between maladaptive weight control/eating behaviours in females during adolescence/young adulthood with subsequent IBS using the Growing Up Today Study (GUTS).

METHODS

Starting in 1996 (age: 9-14) and during follow-up, participants reported frequency of maladaptive eating/weight control behaviours during the past year to lose weight: self-induced vomiting (n = 5740), laxative use (n = 5438), and fasting (n = 5522) in addition to reporting binge eating (n = 4459). Starting in 2001 and during follow-up, participants reported if they had ever been diagnosed with an eating disorder (n = 5316). Incident IBS cases were identified from four questionnaire cycles (2013, 2014, 2016, 2019), with participants specifying the year of diagnosis if occurring before the questionnaire date. Multivariable logistic regressions adjusting for age, body mass index, and depressive symptoms estimated the associations of interest.

RESULTS

Maladaptive weight control/eating behaviours were associated with increased IBS risk [ORs (95% CIs) for laxatives to lose weight = 3.67 (2.52-5.35), vomiting to lose weight = 1.83 (1.29-2.60), fasting to lose weight = 2.62 (1.86-3.70), and bingeing = 2.25 (1.54-3.28)] as was history of eating disorder diagnosis [OR (95% CI) = 3.42 (2.38-4.90)]. The magnitude of IBS risk increased with the frequency of maladaptive behaviours.

CONCLUSIONS

There is evidence for the potential role of early maladaptive weight control/eating behaviours in the development of adult IBS among females.

Mismatch repair-proficient tumor footprints in the sands of immune desert: mechanistic constraints and precision platforms

Mismatch repair proficient (MMRp) tumors of colorectal origin are one of the prevalent yet unpredictable clinical challenges. Despite earnest efforts, optimal treatment modalities have yet to emerge for this class. The poor prognosis and limited actionability of MMRp are ascribed to a low neoantigen burden and a desert-like microenvironment. This review focuses on the critical roadblocks orchestrated by an immune evasive mechanistic milieu in the context of MMRp. The low density of effector immune cells, their weak spatiotemporal underpinnings, and the high-handedness of the IL-17-TGF-β signaling are intertwined and present formidable challenges for the existing therapies. Microbiome niche decorated by Fusobacterium nucleatum alters the metabolic program to maintain an immunosuppressive state. We also highlight the evolving strategies to repolarize and reinvigorate this microenvironment. Reconstruction of anti-tumor chemokine signaling, rational drug combinations eliciting T cell activation, and reprograming the maladapted microbiome are exciting developments in this direction. Alternative vulnerability of other DNA damage repair pathways is gaining momentum. Integration of liquid biopsy and ex vivo functional platforms provide precision oncology insights. We illustrated the perspectives and changing landscape of MMRp-CRC. The emerging opportunities discussed in this review can turn the tide in favor of fighting the treatment dilemma for this elusive cancer.

Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome

Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.

Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes

The detection of oral bacteria in faecal samples has been associated with inflammation and intestinal diseases. The increased relative abundance of oral bacteria in faeces has two competing explanations: either oral bacteria invade the gut ecosystem and expand (the 'expansion' hypothesis), or oral bacteria transit through the gut and their relative increase marks the depletion of other gut bacteria (the 'marker' hypothesis). Here we collected oral and faecal samples from mouse models of gut dysbiosis (antibiotic treatment and DSS-induced colitis) and used 16S ribosomal RNA sequencing to determine the abundance dynamics of oral bacteria. We found that the relative, but not absolute, abundance of oral bacteria increases, reflecting the 'marker' hypothesis. Faecal microbiome datasets from diverse patient cohorts, including healthy individuals and patients with allogeneic haematopoietic cell transplantation or inflammatory bowel disease, consistently support the 'marker' hypothesis and explain associations between oral bacterial abundance and patient outcomes consistent with depleted gut microbiota. By distinguishing between the two hypotheses, our study guides the interpretation of microbiome compositional data and could potentially identify cases where therapies are needed to rebuild the resident microbiome rather than protect against invading oral bacteria.

Critical role of the gut microbiota in immune responses and cancer immunotherapy

The gut microbiota plays a critical role in the progression of human diseases, especially cancer. In recent decades, there has been accumulating evidence of the connections between the gut microbiota and cancer immunotherapy. Therefore, understanding the functional role of the gut microbiota in regulating immune responses to cancer immunotherapy is crucial for developing precision medicine. In this review, we extract insights from state-of-the-art research to decipher the complicated crosstalk among the gut microbiota, the systemic immune system, and immunotherapy in the context of cancer. Additionally, as the gut microbiota can account for immune-related adverse events, we discuss potential interventions to minimize these adverse effects and discuss the clinical application of five microbiota-targeted strategies that precisely increase the efficacy of cancer immunotherapy. Finally, as the gut microbiota holds promising potential as a target for precision cancer immunotherapeutics, we summarize current challenges and provide a general outlook on future directions in this field.

Fecal microbiota transplantation in capsules for the treatment of steroid refractory and steroid dependent acute graft vs. host disease: a pilot study

Acute graft-versus-host disease (aGvHD) is a serious complication of allogeneic hematopoietic stem-cell transplantation with limited treatment options. The gut microbiome plays a critical role in aGvHD pathogenesis. Fecal microbiota transplantation (FMT) has emerged as a potential therapeutic approach to restore gut microbial diversity. In this prospective pilot study, 21 patients with steroid-resistant or steroid-dependent lower gastrointestinal aGvHD received FMT in capsule form. At 28 days after the first FMT, the overall response rate was 52.4%, with 23.8% complete and 28.6% partial responses. However, sustained responses were infrequent, with only one patient remaining aGvHD-free long-term. FMT was generally well-tolerated. Microbiome analysis revealed dysbiosis in pre-FMT patient stool samples, with distinct microbial characteristics compared to donors. Following FMT, there was an increase in beneficial Clostridiales and a decrease in pathogenic Enterobacteriales. These findings highlight the potential of FMT as a treatment option for steroid-resistant aGvHD. Trial registration number NCT #03214289.

The gut microbiome: Bridging medications and clinical outcomes post stem cell transplantation

Anti-cancer therapies are usually intertwined with prolonged use of drugs, which may lead to different clinical outcomes. Recently in Cell and Cell Host & Microbe, Nguyen et al. and Vallet et al., respectively, deconvolute the drug effects on gut microbiome dynamics underpinning clinical outcomes after allogeneic hematopoietic stem cell transplantation.

Medication effects on the gut microbiome in allo-HCT

Decreased gut microbiome diversity has been associated with negative outcome in allogeneic hematopoietic stem cell transfer (HCT). A study published in this issue of Cell identifies associations between non-antibiotic drug administration, microbiome state transitions, and response to HCT, highlighting the potential impact of such drugs on microbiome and HCT outcome.

Rationale behind phosphate therapy to modulate the gut microbiome and protect against surgery-related infection

Despite major advances in infection control and the ever increasing use of broader spectrum antibiotics in surgery, postoperative infections continue to occur under the best of care and in the best institutions. Postoperative infections, also termed "surgical site infections (SSIs), can range from superficial wound infections to deep organ space infections. SSIs can be superficial and only require medical treatment (i.e antibiotics), whereas others such as deep organ space infections resulting from an anastomotic leak can require multiple surgeries leading to sepsis and occasionally shock and death. Many if not most stakeholders in the field including surgeons, infectious disease specialists, infection control nurses, etc., in general advocate the use of prophylactic antibiotics and the enforcement of greater levels of sterility reasoning that all postoperative infections must arise from some type of direct contamination event. In this piece, the alternative view is presented that today, in the era of mandated asepsis protocols, enhanced recovery programs, and enforcement of prophylactic antibiotics in all cases, many if not most postoperative infections and SSIs occur from pathogens endogenous to the patient not from sources exogenous to the patient. It is also suggested that applying broader antibiotic coverage in elective surgery is neither an evolutionarily stable strategy nor inexorable in the context of emerging knowledge in the field of gut ecology. Here this concept is reviewed and the rationale behind using agents that preserve the gut microbiome and attenuate pathogen virulence in lieu of applying broader spectrum antibiotics and greater levels of sterility.