Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes

Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology, Journal Year: 2024, Volume and Issue: 296, P. 111690 - 111690

Published: July 2, 2024

Language: Английский

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Model systems to study tumor-microbiome interactions in early-onset colorectal cancer

EMBO Molecular Medicine, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 13, 2025

Abstract Colorectal cancer (CRC) is a major health problem, with an alarming increase of early-onset CRC (EO-CRC) cases among individuals under 50 years age. This trend shows the urgent need for understanding underlying mechanisms leading to EO-CRC development and progression. There significant evidence that gut microbiome acts as key player in by triggering molecular changes colon epithelium, tumorigenesis. However, comprehensive collection comparison methods study such tumor-microbiome interactions context sparse. review provides overview available vivo, ex vivo well vitro approaches model assess effect microbes on tumor growth. By comparing advantages limitations each system, it highlights that, while no single perfect, suitable studying specific aspects microbiome-induced Taken together, multifaceted can simulate human body’s complexity, aiding effective treatment prevention strategies EO-CRC.

Language: Английский

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Gut microbiota: our fellow travellers in health & disease

FEBS Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

The last two decades have seen a major increase in our understanding of the role microbiome health and disease. We now realise that these fellow travellers are really important regulators various systems body across lifespan. In this Special Issue, we bring together collection articles from leading authors who summarise current state art host-microbe interactions. While celebrate breakthroughs science, also acknowledge challenges-variability microbiota composition, complexities interactions need for standardised methodologies. As research progresses, harnessing power may pave way novel diagnostic therapeutic strategies, reaffirming notion never alone-our microbial accompany us through life, better or worse.

Language: Английский

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New thoughts on the gut–immune axis of arthritis

Trends in Immunology, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

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The microbiome: what a neurologist needs to know

Practical Neurology, Journal Year: 2025, Volume and Issue: unknown, P. pn - 004400

Published: March 12, 2025

The gastrointestinal tract is inhabited by trillions of micro-organisms that form the gut microbiome, which serves various functions can influence neurological pathways. It release metabolites could affect nervous system. bidirectional communication between intestine and central system known as gut–brain axis. This be impacted microbiota in direct indirect ways. There has been a suggested connection microbiome many disorders, including epilepsy, Alzheimer’s disease, Parkinson’s disease multiple sclerosis. explored human animal studies. While no microbial biomarkers have identified yet, alterations several taxa to associated with states. potential modulate function sparked clinical trials using gut-altering treatments, some positive preliminary results.

Language: Английский

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Integrating host and microbiome biology using holo-omics

Molecular Omics, Journal Year: 2024, Volume and Issue: 20(7), P. 438 - 452

Published: Jan. 1, 2024

Holo-omics is the use of omics data to study a host and its inherent microbiomes – biological system known as “holobiont”.

Language: Английский

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The breath volatilome is shaped by the gut microbiota

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 3, 2024

ABSTRACT The gut microbiota is widely implicated in host health and disease, inspiring translational efforts to implement our growing body of knowledge clinical settings. However, the need characterize by its genomic content limits feasibility rapid, point-of-care diagnostics. produces a diverse array xenobiotic metabolites that disseminate into tissues, including volatile organic compounds (VOCs) may be excreted breath. We hypothesize breath contains microbe-derived VOCs inform composition metabolic state microbiota. To explore this idea, we compared volatilome fecal microbiomes 27 healthy children found VOC correlated with microbiomes. experimentally interrogate finding, devised method for capturing exhaled from gnotobiotic mice. Breath volatiles are then profiled gas-chromatography mass-spectrometry (GC-MS). Using novel methodology, murine profile markedly shaped also find produced microbes pure culture can identified vivo mice monocolonized same bacteria. Altogether, studies identify support mechanism which bacterial metabolism directly contributes mammalian profiles.

Language: Английский

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Role of Gut Microbiota in Immune System Regulation

Pakistan Journal of Health Sciences, Journal Year: 2024, Volume and Issue: unknown, P. 02 - 12

Published: Aug. 31, 2024

The human gut is a densely populated organ system that bears hundreds of microbial species, including bacteria, viruses, and various protozoans. microbiome expresses enormous functional diversity based on community collection. However, this has remained unexplored for long time, but in the recent past researches have revealed its immense significance host metabolism immunity. Gut microbiota metabolize undigested substances release metabolites response to significant effect immune system. balance stability within body are achieved maintained through complex interaction between mucosal Upon loss control by system, dysbiosis occurs, modulation community, which leads different disorders, inflammatory bowel disease colorectal cancer. Moreover, also associated with autoimmune diseases such as rheumatoid arthritis, diabetes mellitus, multiple sclerosis. Despite intricate mechanism diseases, therapeutic strategies utilized treat chronic prebiotics treatment, personalized probiotics therapy, fecal transplantation, narrow-spectrum antibiotic treatment. This review discusses how association becomes dysregulated, outcomes form interventions cope it.

Language: Английский

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Gut microbiome and inflammation in cardiovascular drug response: trends in therapeutic success and commercial focus

Inflammopharmacology, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 2, 2024

Language: Английский

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An urgent need for longitudinal microbiome profiling coupled with machine learning interventions

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Nov. 11, 2024

Our understanding of the role gut microbes in human health and disease has come a long way since John M. Whipps colleagues first defined term 'microbiome'. Since early 2000s, with gradual lowering cost commercial DNA sequencing, science been flooded 16S rRNA data. Unfortunately, despite plethora preclinical clinical publications on gutliver axis, majority our microbiota-liver reciprocal interaction basically remains limited to correlation analysis. The most exciting part such metagenomic studies is sheer amount 'big data' generated which rather easy correlate physiological variables; bigger data number independent variables, more chances find 'significant' associations. Notably, gut-liver axis derived from microbiome, not microbiota. Therefore, conclusions obtained through microbiome-related often do reflect causation, are representative universal phenomenon, there almost no true microbial markers dysbiosis linked chronic liver disease.Translational potentials pre-clinical associations prediction treatment have much successful enormous numbers interventional observational studies. In fact, relevance utilizing rodents' signatures diseases criticized due massive difference between both species, attributed gastrointestinal biogeography genetic makeup (Nguyen et al., 2015). Especially high-fat diet model metabolic disease, lack consistency good bad microbes. also associated strains belonging probiotics (e.g., Lactobacillus) commensals Akkermansia, Faecalibacterium) (Dey Ray Chaudhuri, 2023). Added this fact that confounding results chemicalinduced models physiologically mostly irrelevant (Dey, 2020) germ-free mice possess innate defect various processes (Jans Vereecke, 2024). Clinical progression distinct terms timeline, cellular phenotype, pathological complexity, immune responses, machinery (Liu 2013). Further, general differences animal as biological makeup, organ anatomy, functional capacity), extent complexity specificity, co-influence comorbidities), ability perform controlled experiments, predictive validity, etc. make it challenging conclude phenotypes based Although emerging reports vitro distal intestine (Qi 2023), these given their host nature. Due advent culturomics techniques studies, patterns were initially considered conditions, Firmicutesto-Bacteroides ratio, enrichment energy-harvesting specific functions, seem be falling apart. For instance, -proteobacteria presence lipopolysaccharide (LPS) previously thought simply cause hepatic inflammation. However, identified LPS-TLR4-inflammation cannot generalized huge LPS structure dictating response (Picarello, 2022), luminal LPS-supplying Bacteroides, displays an immunosuppressive characteristics (d'Hennezel 2017). Today, being strongly recognized good, bad, ugly nature microbiota conditionspecific. Factors availability preferred nutrients, pathoadaptive mutations, evade mucosal critical factors define species commensal or pathobiont 2023;Dey, bottom line proper definition eubiosis features. only one aspect universally accepted loss diversity when we talk about diversity, it's community effects, causation by single species.A recent systematic review meta-analysis 54 indicated substantial inter-study heterogeneity taxonomic identification, inflammation-inducing genera closely non-alcoholic fatty but provide long-term risk value (Su To date, than 100 cross-sectional identify predominant yet absolute core microbiome related progressive identified. longitudinal superior informed pathogenesis can former one, few undertaken order link health. One study Kyoto (Japan) evaluated alterations pre-transplantation two months post-surgery 38 transplant patients (Kato Data show initial decline later increase along overall Enterobacteriaceae, Streptococcaceae, Bifidobacteriaceae, while depletion abundance Lactobacillaceae, Enterococcaceae, Clostridiaceae, Peptostreptococcaceae Ruminococcaceae was noted. authors acknowledged variations antibiotic regimes, food, synbiotics, patient donors underlying diseases) likely influence study's findings. Confounding variables relative among limitations. line, relatively National Institutes Health, USA, investigated hepatitis C patients, taking into account varied degrees fibrosis severity (Ali investigation done six after HCV undetectable (n=23) before (n=29) attaining durable virologic response. suggest increased correlated Anaerostipes hadrus, Bacteroides vulgatus portal inflammation HCV. A prolonged Methanobrevibacter smithii may beneficial effect indicators disease. made possible compare HCV-infected individuals supposedly improved viral clearance state, they unable report healthy controls unavailability samples. Another Stanford examines composition at body site (including gut) multi-omics, immunological, hepatic) (n=86) over 6-year period comprehend dynamic microbiomes throughout illness (Zhou Despite, identifying compositional parameters metabolites, temporal measured liver-specific transaminases). Emerging although claims causative effects oral including (Gupta Dey, till date. Thus, dynamics under course remission largely unknown.Beyond data, fundamental difficulty analyzing large-scale big-data lie high dimensionality (Advani Ganguli, 2016). classically designed small carefully selected (V) test hypothesis, large measurements (M) for each variable. measurement density very (M/V → ∞). Such datasets referred low-dimensional, classical statistics operates within framework. contrast scenario, technological capacity high-throughput sequencing led different statistical regime. It commonplace simultaneously measure many hundreds taxa individual level. constraints time resources, simultaneous measurements. M V large, (M/V) smaller conventional experiments. dimensional, i.e., consist points high-dimensional space. Microbiome thousands gut. Hence, requires us employ machine learning (ML) approaches dissect dataset. Utilizing enhances complex host-microbe reciprocal, helping tracking monitoring valuable personalized medicine.In years, ML widely used shed light how impact diseases. These biomarkers (Ruuskanen 2021;Zhang 2021;Liu 2022;Park nature, suffer First, extremely difficult detect sets useful insight translational value. High dimensional analysis PCA, ICA, t-SNE, reducing detecting patterns. resulting axes represent linear combinations features abundance), interpreting making experimental predictions (Donoho Tanner, 2009) (Furchtgott Identifying becomes even proportion relevant decreases, higher levels 2009). decades research shown This indicate subset accurate computational inferences. need develop novel methods sparse datasets.The second challenge extract meaningful predict outcomes guide implications Building describing networks involve parameters. cases remain completely unknown. As Von Neumann once said: "with four I fit elephant, five him wiggle his trunk." challenges involving clearly exacerbated simplest would require available always never constrain space completely. Given under-constrained problem, exist infinite successfully replicate underconstrained proven challenging. Moreover, trained Western Chinese generalize populations, limiting applicability. Often employed population size. Some suffered absence lifestyle information diet, socioeconomic status, tobacco, alcoholism, etc.). Also, some case, clinical, metabolomic profiles, hampered garnering comprehensive causal aspects disease.The its function character disorders well captured investigations. We using cutting-edge conjunction address issues. imperative then train models. By addressing limitations building new approaches, fully harness potential deepen microbiome's other areas. doing this, pinpoint certain advancement development potent preventative therapeutic approaches. reach full potential, must included.

Language: Английский

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