Critical Assessment of Metagenome Interpretation: the second round of challenges

Nature Methods, Journal Year: 2022, Volume and Issue: 19(4), P. 429 - 440

Published: April 1, 2022

Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative Critical Assessment Metagenome Interpretation (CAMI). The CAMI II challenge engaged community to assess methods on realistic complex datasets with long- short-read sequences, created computationally from around 1,700 new known genomes, as well 600 plasmids viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due long-read data. Related strains still challenging assembly genome recovery through binning, was quality latter. Profilers markedly matured, taxon profilers binners excelling at higher bacterial ranks, but underperforming viruses Archaea. Clinical pathogen detection revealed a need improve reproducibility. Runtime memory usage analyses identified efficient programs, including top performers other metrics. identify challenges guide researchers selecting analyses.

Language: Английский

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Time of sample collection is critical for the replicability of microbiome analyses

Nature Metabolism, Journal Year: 2024, Volume and Issue: 6(7), P. 1282 - 1293

Published: July 1, 2024

Language: Английский

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Integration of 168,000 samples reveals global patterns of the human gut microbiome

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

Published: Jan. 1, 2025

The factors shaping human microbiome variation are a major focus of biomedical research. While other fields have used large sequencing compendia to extract insights requiring otherwise impractical sample sizes, the field has lacked comparably sized resource for 16S rRNA gene amplicon commonly quantify composition. To address this gap, we processed 168,464 publicly available gut samples with uniform pipeline. We use compendium evaluate geographic and technical effects on variation. find that regions such as Central Southern Asia differ significantly from more thoroughly characterized microbiomes Europe Northern America composition alone can be predict sample's region origin. also strong associations between primers DNA extraction. anticipate growing work, Human Microbiome Compendium, will enable advanced applied methodological

Language: Английский

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A Comparison of Six DNA Extraction Protocols for 16S, ITS and Shotgun Metagenomic Sequencing of Microbial Communities

BioTechniques, Journal Year: 2022, Volume and Issue: 73(1), P. 34 - 46

Published: June 17, 2022

Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems potentially members human microbiome, beyond those that can cause disease. To expand our analysis microbial to include data from fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against standardized protocol for archaea using 16S rRNA gene amplicon- shotgun metagenomics sequencing. The results presented considering diverse panel host-associated environmental sample types comparing cost, processing time, well-to-well contamination, yield, limit detection community composition among protocols. Across all criteria, MagMAX Microbiome kit was found perform best. PowerSoil Pro performed comparably but with increased cost per overall time. Zymo MagBead, NucleoMag Food Norgen Stool included.

Language: Английский

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Evolving approaches to profiling the microbiome in skin disease

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 14

Published: April 4, 2023

Despite its harsh and dry environment, human skin is home to diverse microbes, including bacteria, fungi, viruses, microscopic mites. These microbes form communities that may exist at the surface, deeper layers, within microhabitats such as hair follicle sweat glands, allowing complex interactions with host immune system. Imbalances in microbiome, known dysbiosis, have been linked various inflammatory disorders, atopic dermatitis, acne, psoriasis. The roles of abundant commensal bacteria belonging Staphylococcus Cutibacterium taxa fungi Malassezia , where particular species or strains can benefit cause disease, are increasingly appreciated disorders. Furthermore, recent research suggests between microorganisms host’s system on distant systemic effects body, gut brain, “skin-gut” “skin-brain” axes. Studies microbiome disease typically relied 16S rRNA gene sequencing methods, which cannot provide accurate information about skin. However, advancing technologies, metagenomics other functional ‘omic’ approaches, great potential more comprehensive detailed health disease. Additionally, inter-species multi-kingdom cascading shifts towards dysbiosis crucial but yet-to-be-explored aspects many Better understanding these dynamics will require meta-omic studies complemented experiments clinical trials confirm function. Evolving how we profile alongside technological advances essential exploring relationships. This review presents current emerging methods their findings for profiling advance our

Language: Английский

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The emerging potential of microbiome transplantation on human health interventions

Computational and Structural Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20, P. 615 - 627

Published: Jan. 1, 2022

The human microbiome has been the subject of intense research over past few decades, in particular as a promising area for new clinical interventions. microbiota colonizing different body surfaces are benefit multiple physiological and metabolic processes host increasing evidence suggests an association between disturbances composition functionality several pathological conditions. This provided rationale beneficial modulation microbiome. One approach being explored modulating diseased individuals is transferring or constituents from healthy donors via transplantation. great success fecal transplantation treatment Clostridioides difficile infections encouraged application this procedure other diseases such vaginal disorders microbiota, skin pathologies microbiota. Microbiome could even become novel strategy improving efficacy cancer therapies. review discusses principle, advantages limitations well contexts where applied.

Language: Английский

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Gut microbiome signatures and host colonization with multidrug-resistant bacteria

Trends in Microbiology, Journal Year: 2022, Volume and Issue: 30(9), P. 853 - 865

Published: Feb. 18, 2022

Language: Английский

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Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 22, 2023

Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to physiology. Gut have been shown impact dietary digestion, mediate infection, and even modify behavior cognition. Given large physiological pathophysiological contribution provide their host, it is reasonable assume that vertebrate gut microbiome may also fitness, health ecology wildlife. In accordance with this expectation, an increasing number investigations considered role wildlife ecology, health, conservation. To help promote development nascent field, we need dissolve technical barriers prohibitive performing research. The present review discusses 16S rRNA gene landscape, clarifying best practices data generation analysis, particular emphasis on unique situations arise during investigations. Special consideration given topics relevant for from sample collection molecular techniques generation, analysis strategies. Our hope article not only calls greater integration analyses into studies but provides researchers framework needed successfully conduct such

Language: Английский

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Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease

npj Metabolic Health and Disease, Journal Year: 2024, Volume and Issue: 2(1)

Published: July 1, 2024

Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only few studies have explored KD's impact, especially on blood cerebrospinal fluid (CSF). Our study involved participants at for AD, either cognitively normal or with mild cognitive impairment. The consumed both modified Mediterranean Ketogenic Diet (MMKD) American Heart Association (AHAD) 6 weeks each, separated 6-week washout period. We employed nuclear magnetic resonance (NMR)-based metabolomics to profile serum CSF metagenomics profiling fecal samples. AHAD induced no notable changes, MMKD led significant alterations CSF. These changes included improved like increased HDL-C reduced BMI, reversed disturbances linked such as microbiome-mediated increase valine levels, reduction systemic inflammation. Additionally, was amino acid levels CSF, breakdown branched-chain acids (BCAAs), decreased levels. Importantly, we observed strong correlation between serum, suggesting regulation metabolism. findings highlight that can improve AD-related reverse some associated align across blood-CSF barrier.

Language: Английский

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Multi-omics analysis of a fecal microbiota transplantation trial identifies novel aspects of acute graft-versus-host disease pathogenesis

Cancer Research Communications, Journal Year: 2024, Volume and Issue: 4(6), P. 1454 - 1466

Published: May 20, 2024

Abstract Acute GVHD (aGVHD) is a major complication of allogeneic hematopoietic cell transplantation (alloHCT) associated with gut microbiota disruptions. However, whether therapeutic modulation prevents aGVHD unknown. We conducted randomized, placebo-controlled trial third-party fecal (FMT) administered at the peak injury in 100 patients acute myeloid leukemia receiving induction chemotherapy and alloHCT recipients. Despite improvements microbiome diversity, expansion commensals, shrinkage potential pathogens, occurred more frequently after FMT than placebo. Although this unexpected finding could be explained by clinical differences between two arms, we asked explanation might also present. To end, performed multi-omics analysis preintervention postintervention serum metabolome. found that Faecalibacterium, commensal genus gut-protective anti-inflammatory properties under homeostatic conditions, predicted higher risk for aGVHD. Faecalibacterium predominantly was due to engraftment unique donor taxa, suggesting Faecalibacterium-derived antigens have stimulated immune cells. ursodeoxycholic acid (an secondary bile acid) were negatively correlated, offering an alternative mechanistic explanation. In conclusion, demonstrate context dependence effects where normally beneficial bacteria may become detrimental disease. While broad, community-level intervention, it need precision engineering ecologically complex settings multiple perturbations (e.g., antibiotics, intestinal damage, alloimmunity) are concurrently effect. Significance: Post-FMT engraftment, our findings suggest pathogenic setting alloHCT. Our results support future product used as prophylaxis

Language: Английский

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