Folia Microbiologica, Год журнала: 2022, Номер 67(4), С. 573 - 590
Опубликована: Март 19, 2022
Язык: Английский
ISME Communications, Год журнала: 2022, Номер 2(1)
Опубликована: Окт. 6, 2022
Abstract The many microbial communities around us form interactive and dynamic ecosystems called microbiomes. Though concealed from the naked eye, microbiomes govern influence macroscopic systems including human health, plant resilience, biogeochemical cycling. Such feats have attracted interest scientific community, which has recently turned to machine learning deep methods interrogate microbiome elucidate relationships between its composition function. Here, we provide an overview of how latest studies harness inductive prowess artificial intelligence methods. We start by highlighting that data – being compositional, sparse, high-dimensional necessitates special treatment. then introduce traditional novel discuss their strengths applications. Finally, outlook pipelines, focusing on bottlenecks considerations address them.
Язык: Английский
Процитировано
138
Environment International, Год журнала: 2021, Номер 154, С. 106560 - 106560
Опубликована: Апрель 16, 2021
The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats human health, it is urgent develop efficient strategies eliminate them from Bacteria-driven PAE biodegradation been considered as an inexpensive yet effective strategy restore the contaminated Despite great advances in bacterial culturing and sequencing, inherent complexity indigenous microbial community hinders us mechanistically understand situ efficiently harness degrading power bacteria. synthetic ecology provides a simple controllable model system address this problem. In review, we focus on current progress mediated by isolates communities, discuss prospective PAE-degrading communities research. It anticipated that theories approaches will revolutionize study bacteria-driven provide novel insights for developing bioremediation solutions.
Язык: Английский
Процитировано
121
Nature Communications, Год журнала: 2022, Номер 13(1)
Опубликована: Дек. 22, 2022
Abstract The role of rhizosphere microbiota in the resistance tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that FWD incidence was significantly negatively correlated with diversity both bacterial and fungal communities. Using microbiological culturomic approach, selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free seedlings, their roles suppressing monitored using omics approach. Cross-kingdom (fungi bacteria) SynComs most effective than those Fungal or Bacterial alone. This effect underpinned by a combination molecular mechanisms related immunity microbial interactions contributed study provides new insight dynamics pathogen suppression host interactions. Also, formulation manipulation for functional complementation constitute beneficial strategy controlling disease.
Язык: Английский
Процитировано
120
Advanced Science, Год журнала: 2022, Номер 9(21)
Опубликована: Май 23, 2022
Microbes with complex functions have been found to be a potential component in tumor microenvironments. Due their low biomass and other obstacles, intratumor microbiota is poorly understood. Mucosal sites normal adjacent tissues are important sources of microbiota, while hematogenous spread also leads the invasion microbes. Intratumor affects progression tumors through several mechanisms, such as DNA damage, activation oncogenic pathways, induction immunosuppression, metabolization drugs. Notably, different types tumors, composition abundance highly heterogeneous may play roles tumors. Because concern this field, techniques omics immunological methods used study microbiota. Here, recent progress field reviewed, including related heterogeneity. Techniques that can discussed. Moreover, research summarized into development strategies antitumor treatment prospects for possible future field.
Язык: Английский
Процитировано
118
Nature Microbiology, Год журнала: 2023, Номер 8(12), С. 2244 - 2252
Опубликована: Ноя. 23, 2023
Язык: Английский
Процитировано
83
Environmental Research, Год журнала: 2023, Номер 222, С. 115298 - 115298
Опубликована: Янв. 13, 2023
Язык: Английский
Процитировано
60
Nature Ecology & Evolution, Год журнала: 2023, Номер 7(5), С. 768 - 781
Опубликована: Апрель 3, 2023
Abstract Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although classical concept ecology, niche breadth has remained challenging quantify for microorganisms because it depends on an objective definition of the Here, by defining environment microorganism as community resides in, we integrated information from over 22,000 environmental sequencing samples derive quantitative measure niche, which call social breadth. At level genera, explored range strategies throughout prokaryotic tree life. We found that generalists include opportunists stochastically dominate local communities, stable but low abundance. Social have more diverse and open pan-genome than specialists, no global correlation between genome size. Instead, observed two distinct evolutionary strategies, whereby relatively small genomes habitats with diversity, large high diversity. Together, our analysis shines data-driven light microbial strategies.
Язык: Английский
Процитировано
59
Nature Communications, Год журнала: 2023, Номер 14(1)
Опубликована: Ноя. 11, 2023
Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct large-scale excavation soil matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 metagenomes. We identify 16,530 21,077 species-level (SGBs) unknown SGBs (uSGBs), which expand archaeal bacterial diversity across the tree life. also illustrate pivotal role uSGBs in augmenting microbiome’s functional landscape intra-species diversity, providing large proportions 43,169 biosynthetic gene clusters 8545 CRISPR-Cas genes. Additionally, determine that contributed 84.6% previously unexplored viral-host associations catalogue. The catalogue provides useful genomic resource for further studies investigating resources.
Язык: Английский
Процитировано
57
npj Biofilms and Microbiomes, Год журнала: 2023, Номер 9(1)
Опубликована: Сен. 22, 2023
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir microbial biodiversity, yet majority desert microorganisms remain uncharacterized are seen as "microbial dark matter". Here, we introduce multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, shotgun metagenomic sequencing. The results showed CBM captured amount taxonomic functional diversity missed in direct sequencing by increasing recovery amplicon sequence variants (ASVs) high/medium-quality metagenome-assembled genomes (MAGs). Importantly, allowed post hoc microbes interest (e.g., novel or specific taxa), even those with extremely low abundance culture. Furthermore, strain-level analyses based on revealed soils harbored considerable number bacterial candidates (1941, 51.4%), which 1095 (from CBM) were culturable. However, would not exactly reflect relative true composition pathways situ environment, its use coupled could provide greater insight into microbiomes. Overall, this study exemplifies strategy high-resolution is an ideal way to deeply explore untapped resources soils, substantially expands our knowledge matter hidden vast expanse deserts.
Язык: Английский
Процитировано
46
Food Research International, Год журнала: 2023, Номер 173, С. 113249 - 113249
Опубликована: Июль 19, 2023
Язык: Английский
Процитировано
43