Fecal microbiota transplantation: current challenges and future landscapes

Clinical Microbiology Reviews, Год журнала: 2024, Номер 37(2)

Опубликована: Май 8, 2024

SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest developing innovative therapeutic strategies for restoring microbiota. One such approach, fecal microbiota transplantation (FMT), is main "whole microbiome replacement" strategy and integrated into clinical practice guidelines treating recurrent

Язык: Английский

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The overlooked evolutionary dynamics of 16S rRNA revises its role as the “gold standard” for bacterial species identification

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Апрель 20, 2024

Abstract The role of 16S rRNA has been and largely remains crucial for the identification microbial organisms. Although could certainly be described as one most studied sequences ever, current view it somewhat ambiguous. While some consider to a variable marker with resolution power down strain level, others them living fossils that carry information about origin domains cellular life. We show is clearly an evolutionarily very rigid sequence, making unique irreplaceable marker, but its applicability beyond genus level highly limited. Interestingly, seems evolutionary rigidity not driven by functional constraints sequence (RNA–protein interactions), rather results from characteristics host organism. Our suggest that, at least in lineages, Horizontal Gene Transfer (HGT) within genera plays important non-dynamics (stasis) rRNA. Such exhibit apparent lack diversification comparison rest genome. However, why limited specifically solely enigmatic.

Язык: Английский

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Genome-resolved metagenomics: a game changer for microbiome medicine

Experimental & Molecular Medicine, Год журнала: 2024, Номер 56(7), С. 1501 - 1512

Опубликована: Июль 1, 2024

Abstract Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain biomedical research: microbiome medicine. This emerging field aims understand and leverage the microbiota derivative molecules for disease prevention treatment. Despite complex hierarchical organization of this ecosystem, most research over years relied on 16S amplicon sequencing, legacy bacterial phylogeny taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis entire microbiota, translating relatively short nucleotide information into functional taxonomic posed challenges until recently. In last decade, genome-resolved metagenomics, which reconstruct microbial genomes directly from whole-metagenome data, made significant strides continues unveil mysteries various human-associated communities. There been rapid increase volume whole metagenome data compilation novel metagenome-assembled protein sequences public depositories. review provides an overview capabilities methods metagenomics studying microbiome, with focus investigating prokaryotic gut. Just as decoding genome its variations marked beginning genomic medicine era, unraveling microbes their sequence is ushering us era Genome-resolved stands pivotal tool transition can accelerate our journey toward achieving these scientific medical milestones.

Язык: Английский

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Building a genome-based understanding of bacterial pH preferences

Science Advances, Год журнала: 2023, Номер 9(17)

Опубликована: Апрель 28, 2023

The environmental preferences of many microbes remain undetermined. This is the case for bacterial pH preferences, which can be difficult to predict a priori despite importance as factor structuring communities in systems. We compiled data on distributions from five datasets spanning gradients soil and freshwater systems (1470 samples), quantified taxa across these datasets, genomic representative taxa. While taxonomic phylogenetic information were generally poor predictors we identified genes consistently associated with preference environments. then developed validated machine learning model estimate alone, that could aid selection microbial inoculants, improve species distribution models, or help design effective cultivation strategies. More generally, demonstrate value combining biogeographic infer diverse

Язык: Английский

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Response surface methodology as a statistical tool for optimization and FAME profile by GC-MS for assessing microalgae Scenedesmus quadricauda as a potential biodiesel feedstock

Journal of the Taiwan Institute of Chemical Engineers, Год журнала: 2024, Номер 166, С. 105415 - 105415

Опубликована: Март 5, 2024

Язык: Английский

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Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis

Molecular Phylogenetics and Evolution, Год журнала: 2025, Номер 204, С. 108284 - 108284

Опубликована: Янв. 6, 2025

Multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly rRNA genes, to discriminate closely related species nematode genus Heterorhabditis. In addition, conflicting tree topologies are often obtained using different which limits our understanding phylo- and co-phylogenetic relationships biogeography entomopathogenic Here we carried out phylogenomic reconstructions whole nuclear mitochondrial genomes, ribosomal operon sequences, as well multiple various single genes. Using inferred phylogenies, then investigated between Heterorhabditis their Photorhabdus bacterial symbionts biogeographical patterns. Robust, well-resolved, highly congruent were reconstructed both genomes. Similarly, sequences proved valuable for reconstructions, though they value species. two cytochrome c oxidase subunit I (cox-1) NADH dehydrogenase 4 (nad-4), housekeeping fanconi-associated nuclease 1 (fan-1) serine/threonine-protein phosphatase regulatory (ppfr-1), provided most robust compared other individual According findings, and/or genomes strongly recommended reconstructing If unavailable, a combination genes can be an alternative. Under these circumstances, conspecific isolates in context should analyzed avoid artefactual over-splitting driven by high intraspecific sequence divergence lumping low interspecific some On hand, observed that genera exhibit diverse biogeographic patterns, ranging from cosmopolitan potentially endemic species, show congruence, although host switches also occurred. Our study contributes better biodiversity important group biological control agents advances efforts develop more tools compatible with sustainable eco-friendly agricultural practices.

Язык: Английский

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Lactic acid bacteria: Nature, Characterization, Mode of action, Products and Applications

Process Biochemistry, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

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Population genomics meets the taxonomy of cyanobacteria

Algal Research, Год журнала: 2023, Номер 72, С. 103128 - 103128

Опубликована: Май 1, 2023

Язык: Английский

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Accurately clustering biological sequences in linear time by relatedness sorting

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Апрель 8, 2024

Clustering biological sequences into similar groups is an increasingly important task as the number of available continues to grow exponentially. Search-based approaches clustering scale super-linearly with input sequences, making it impractical cluster very large sets sequences. Approaches in linear time currently lack accuracy super-linear approaches. Here, I set out develop and characterize a strategy for complexity that retains less scalable The resulting algorithm, named Clusterize, sorts by relatedness linearize problem. Clusterize produces clusters rivaling popular programs (CD-HIT, MMseqs2, UCLUST) but exhibits asymptotic scalability. generates higher oftentimes much larger than Linclust, fast algorithm. demonstrate utility accurately solving different problems involving millions nucleotide or protein

Язык: Английский

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Research progress on the application of 16S rRNA gene sequencing and machine learning in forensic microbiome individual identification

Frontiers in Microbiology, Год журнала: 2024, Номер 15

Опубликована: Фев. 2, 2024

Forensic microbiome research is a field with wide range of applications and number protocols have been developed for its use in this area research. As individuals host radically different microbiota, the human expected to become new biomarker forensic identification. To achieve an effective procedure understanding factors which can alter determinations stable changing elements will be critical selecting appropriate targets investigation. The 16S rRNA gene, notable conservation specificity, represents potentially ideal marker Gene sequencing involving currently method choice investigating microbiomes. While involved generate large multi-dimensional datasets that difficult analyze interpret, machine learning methods useful surmounting analytical challenge. In review, we describe related technologies available application gene addition, assess potential value science.

Язык: Английский

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