Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Nature Biotechnology, Год журнала: 2023, Номер 41(11), С. 1633 - 1644

Опубликована: Фев. 23, 2023

Abstract Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms most metagenomes. Here we present MetaPhlAn 4, which integrates information metagenome assemblies and isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference metagenome-assembled genomes, define unique marker genes 26,970 species-level genome bins, 4,992 them taxonomically unidentified at the species level. 4 explains ~20% reads in international human gut microbiomes >40% less-characterized environments such as rumen microbiome proves accurate than available alternatives on synthetic evaluations while also reliably quantifying with no cultured isolates. Application method to >24,500 metagenomes highlights previously undetected be strong biomarkers host conditions lifestyles mouse shows that even uncharacterized genetically profiled resolution single strains.

Язык: Английский

---

Short-Chain Fatty-Acid-Producing Bacteria: Key Components of the Human Gut Microbiota

Nutrients, Год журнала: 2023, Номер 15(9), С. 2211 - 2211

Опубликована: Май 6, 2023

Short-chain fatty acids (SCFAs) play a key role in health and disease, as they regulate gut homeostasis their deficiency is involved the pathogenesis of several disorders, including inflammatory bowel diseases, colorectal cancer, cardiometabolic disorders. SCFAs are metabolites specific bacterial taxa human microbiota, production influenced by foods or food supplements, mainly prebiotics, direct fostering these taxa. This Review provides an overview SCFAs’ roles functions, SCFA-producing bacteria, from microbiological characteristics taxonomy to biochemical process that lead release SCFAs. Moreover, we will describe potential therapeutic approaches boost levels treat different related diseases.

Язык: Английский

---

The person-to-person transmission landscape of the gut and oral microbiomes

Nature, Год журнала: 2023, Номер 614(7946), С. 125 - 135

Опубликована: Янв. 18, 2023

Abstract The human microbiome is an integral component of the body and a co-determinant several health conditions 1,2 . However, extent to which interpersonal relations shape individual genetic makeup its transmission within across populations remains largely unknown 3,4 Here, capitalizing on more than 9,700 metagenomes computational strain-level profiling, we detected extensive bacterial strain sharing individuals (more 10 million instances) with distinct mother-to-infant, intra-household intra-population patterns. Mother-to-infant gut was considerable stable during infancy (around 50% same strains among shared species (strain-sharing rate)) remained detectable at older ages. By contrast, oral occurred horizontally enhanced by duration cohabitation. There substantial cohabiting individuals, 12% 32% median strain-sharing rates for microbiomes, time since cohabitation affected age or genetics did. Bacterial additionally recapitulated host population structures better species-level profiles Finally, taxa appeared as efficient spreaders modes were associated different predicted phenotypes linked out-of-host survival capabilities. microorganism that describe underscores relevance in studies 5 , especially those non-infectious, microbiome-associated diseases.

Язык: Английский

---

The gut–liver axis and gut microbiota in health and liver disease

Nature Reviews Microbiology, Год журнала: 2023, Номер 21(11), С. 719 - 733

Опубликована: Июнь 14, 2023

Язык: Английский

---

Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases

Signal Transduction and Targeted Therapy, Год журнала: 2024, Номер 9(1)

Опубликована: Фев. 16, 2024

Abstract The human gastrointestinal tract is populated with a diverse microbial community. vast genetic and metabolic potential of the gut microbiome underpins its ubiquity in nearly every aspect biology, including health maintenance, development, aging, disease. advent new sequencing technologies culture-independent methods has allowed researchers to move beyond correlative studies toward mechanistic explorations shed light on microbiome–host interactions. Evidence unveiled bidirectional communication between central nervous system, referred as “microbiota–gut–brain axis”. microbiota–gut–brain axis represents an important regulator glial functions, making it actionable target ameliorate development progression neurodegenerative diseases. In this review, we discuss mechanisms As provides essential cues microglia, astrocytes, oligodendrocytes, examine communications microbiota these cells during healthy states Subsequently, diseases using metabolite-centric approach, while also examining role microbiota-related neurotransmitters hormones. Next, targeting intestinal barrier, blood–brain meninges, peripheral immune system counteract dysfunction neurodegeneration. Finally, conclude by assessing pre-clinical clinical evidence probiotics, prebiotics, fecal transplantation A thorough comprehension will foster effective therapeutic interventions for management

Язык: Английский

---

Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial

Nature Medicine, Год журнала: 2023, Номер 29(8), С. 2121 - 2132

Опубликована: Июль 6, 2023

Язык: Английский

---

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic

Cell Host & Microbe, Год журнала: 2023, Номер 31(5), С. 712 - 733

Опубликована: Май 1, 2023

Язык: Английский

---

Artificial intelligence, machine learning and deep learning: Potential resources for the infection clinician

Journal of Infection, Год журнала: 2023, Номер 87(4), С. 287 - 294

Опубликована: Июль 17, 2023

BackgroundArtificial intelligence (AI), machine learning and deep (including generative AI) are increasingly being investigated in the context of research management human infection.ObjectivesWe summarise recent potential future applications AI its relevance to clinical infection practice.Methods1,617 PubMed results were screened, with priority given trials, systematic reviews meta-analyses. This narrative review focusses on studies using prospectively collected real-world data validation, translational potential, such as novel drug discovery microbiome-based interventions.ResultsThere is some evidence utility applied laboratory diagnostics (e.g. digital culture plate reading, malaria diagnosis, antimicrobial resistance profiling), imaging analysis pulmonary tuberculosis diagnosis), decision support tools sepsis prediction, prescribing) public health outbreak COVID-19). Most date lack any validation or metrics. Significant heterogeneity study design reporting limits comparability. Many practical ethical issues exist, including algorithm transparency risk bias.ConclusionsInterest development AI-based for undoubtedly gaining pace, although appears much more modest.

Язык: Английский

---

The role of diet in shaping human gut microbiota

Best Practice & Research Clinical Gastroenterology, Год журнала: 2023, Номер 62-63, С. 101828 - 101828

Опубликована: Фев. 1, 2023

Gut microbiota plays a fundamental role within human health, and exerts key functions the body. Diet is one of most powerful modulators gut composition. This complex interplay involves also immune system intestinal barrier, highlighting central diet in pathogenesis treatment multiple diseases. In this review article we will paint landscape effects specific dietary nutrients, detrimental or beneficial outcomes different patterns, on composition microbiota. Moreover, discuss potential application as therapeutic modulator microbiota, including cutting-edge ways exploitation, use components adjuvants to promote microbial engraftment after fecal transplantation, personalized nutritional approaches, targeted patient microbiome.

Язык: Английский

---

Machine learning for microbiologists

Nature Reviews Microbiology, Год журнала: 2023, Номер 22(4), С. 191 - 205

Опубликована: Ноя. 15, 2023

Язык: Английский

---