Antimicrobial resistance crisis: could artificial intelligence be the solution?

Military Medical Research, Journal Year: 2024, Volume and Issue: 11(1)

Published: Jan. 23, 2024

Abstract Antimicrobial resistance is a global public health threat, and the World Health Organization (WHO) has announced priority list of most threatening pathogens against which novel antibiotics need to be developed. The discovery introduction are time-consuming expensive. According WHO’s report antibacterial agents in clinical development, only 18 have been approved since 2014. Therefore, critically needed. Artificial intelligence (AI) rapidly applied drug development its recent technical breakthrough dramatically improved efficiency antibiotics. Here, we first summarized recently marketed antibiotics, antibiotic candidates development. In addition, systematically reviewed involvement AI utilization, including small molecules, antimicrobial peptides, phage therapy, essential oils, as well mechanism prediction, stewardship.

Language: Английский

---

Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 11, 2024

Spaceflight induces an immune response in astronauts. To better characterize this effect, we generated single-cell, multi-ome, cell-free RNA (cfRNA), biochemical, and hematology data for the SpaceX Inspiration4 (I4) mission crew. We found that 18 cytokines/chemokines related to inflammation, aging, muscle homeostasis changed after spaceflight. In I4 single-cell multi-omics data, identified a "spaceflight signature" of gene expression characterized by enrichment oxidative phosphorylation, UV response, function, TCF21 pathways. confirmed presence signature independent datasets, including NASA Twins Study, skin spatial transcriptomics, 817 GeneLab mouse transcriptomes. Finally, observed (1) T cells showed up-regulation FOXP3, (2) MHC class I genes exhibited long-term suppression, (3) infection-related pathways were associated with microbiome shifts. summary, study reveals conserved distinct disruptions occurring details roadmap potential countermeasures preserve astronaut health.

Language: Английский

---

Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(7), P. 1661 - 1675

Published: June 11, 2024

Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes. However, documenting microbial shifts has been difficult due to mission constraints that lead limited sampling profiling. Here we executed a six-month longitudinal study quantify the high-resolution human microbiome response three days in orbit for four individuals. Using paired metagenomics metatranscriptomics alongside single-nuclei immune cell profiling, characterized time-dependent, multikingdom changes across 750 samples 10 body sites before, after at eight timepoints. We found most alterations were transient sites; example, viruses increased skin mostly flight. longer-term observed oral microbiome, including plaque-associated bacteria (for Fusobacteriota), which correlated with gene expression. Further, genes associated phage activity, toxin-antitoxin systems stress enriched multiple sites. In total, this reveals in-depth characterization experienced by astronauts short-term living environment, can help guide future missions, spacecraft design space habitat planning.

Language: Английский

---

Sequencing-based analysis of microbiomes

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(12), P. 829 - 845

Published: June 25, 2024

Language: Английский

---

Viroid-like colonists of human microbiomes

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

Published: Jan. 21, 2024

Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA ~1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing entire genome, and (iii) open reading frames coding for novel protein superfamily, which call "Oblins". We find Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, are prevalent tested microbiome metatranscriptomes representatives detected ~7% analysed stool (29/440) ~50% oral (17/32). Obelisk compositions appear differ between anatomic sites capable persisting individuals, continued presence over >300 days observed one case. Large scale searches 29,959 (clustered at 90% nucleotide identity), examples from all seven continents diverse ecological niches. From this search, subset code Obelisk-specific variants hammerhead type-III self-cleaving ribozyme. Lastly, case bacterial species (Streptococcus sanguinis) defined laboratory strains harboured specific population. As such, comprise RNAs have colonised, gone unnoticed in, human, global microbiomes.

Language: Английский

---

Longitudinal phage–bacteria dynamics in the early life gut microbiome

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Language: Английский

---

Expanding the human gut microbiome atlas of Africa

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

Published: Jan. 29, 2025

Population studies provide insights into the interplay between gut microbiome and geographical, lifestyle, genetic environmental factors. However, low- middle-income countries, in which approximately 84% of world's population lives1, are not equitably represented large-scale research2-4. Here we present AWI-Gen 2 Microbiome Project, a cross-sectional study sampling 1,801 women from Burkina Faso, Ghana, Kenya South Africa. By engaging with communities that range rural horticultural to post-industrial urban informal settlements, capture far greater breadth diversity. Using shotgun metagenomic sequencing, identify taxa geographic lifestyle associations, including Treponema Cryptobacteroides species loss Bifidobacterium gain populations. We uncover 1,005 bacterial metagenome-assembled genomes, antibiotic susceptibility as factor might drive succinifaciens absence Finally, find an HIV infection signature defined by several previously associated HIV, Dysosmobacter welbionis Enterocloster sp. This represents largest population-representative survey metagenomes African individuals so far, paired extensive clinical biomarkers demographic data, provides opportunity for microbiome-related discovery.

Language: Английский

---

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

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

Published: March 20, 2024

Summary The prototypic crAssphage ( Carjivirus communis ) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured its lifestyle uncharacterized. For last decade, has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain widespread success. Through genomic analyses culturing, we find uses a phage-plasmid persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, use plaque-free approach measure replication culture with Phocaeicola vulgatus, dorei, Bacteroides stercoris , revealing broad host range. We demonstrate persists hosts without causing major cell lysis events or integrating into chromosomes. ability switch between plasmid within wide range contributes prolific nature human microbiome.

Language: Английский

---

Viroid-like colonists of human microbiomes

Cell, Journal Year: 2024, Volume and Issue: 187(23), P. 6521 - 6536.e18

Published: Oct. 31, 2024

Language: Английский

---

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(11)

Published: March 10, 2025

The long-term success of introduced populations depends on both their initial size and ability to compete against existing residents, but it remains unclear how these factors collectively shape colonization dynamics. Here, we investigate population (propagule) shapes the outcome community coalescence by systematically mixing eight pairs in vitro microbial communities at ratios that vary over six orders magnitude, compare our results neutral ecological theory. Although composition resulting cocultures deviated substantially from expectations, each coculture contained species whose relative abundance depended propagule even after ~40 generations growth. Using a consumer–resource model, show this dose-dependent can arise when resident have high niche overlap consume shared resources similar rates. Strain isolates displayed longer-lasting dose dependence into diverse than pairwise cocultures, consistent with model’s prediction should larger, more persistent effects communities. Our model also successfully predicted resource-utilization profiles, as inferred growth spent media untargeted metabolomics, would stronger coculture. This work demonstrates transient, dynamics emerge resource competition exert outcomes coalescence.

Language: Английский

---