Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(5), P. 745 - 757

Published: June 29, 2023

Language: Английский

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Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle

Cell, Journal Year: 2023, Volume and Issue: 186(22), P. 4803 - 4817.e13

Published: Sept. 7, 2023

Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute disproportionately large fraction microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow epibionts on host Actinobacteria. Due lack suitable tools, genetic basis this lifestyle and other unique features Patescibacteira remain unexplored. Here, we show Saccharibacteria exhibit natural competence, exploit property for their manipulation. Imaging fluorescent protein-labeled provides high spatiotemporal resolution phenomena accompanying epibiotic growth, transposon-insertion sequencing (Tn-seq) genome-wide screen reveals contribution enigmatic Saccharibacterial genes growth hosts. Finally, leverage metagenomic data provide cutting-edge protein structure-based bioinformatic resources support strain Southlakia epibionticum its corresponding host, Actinomyces israelii, model system unlocking molecular underpinnings lifestyle.

Language: Английский

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“ Candidatus Nealsonbacteria” Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture

Applied and Environmental Microbiology, Journal Year: 2023, Volume and Issue: 89(5)

Published: April 26, 2023

The Candidate Phyla Radiation (CPR), also referred to as superphylum

Language: Английский

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Unlocking the Interactions Between the Whole-Body Microbiome and HPV Infection: A Literature Review

Pathogens, Journal Year: 2025, Volume and Issue: 14(3), P. 293 - 293

Published: March 18, 2025

The human microbiome plays a vital role in maintaining homeostasis, acting as key regulator of host immunity and defense mechanisms. However, dysbiotic microbial communities may cause disruption the symbiotic relationship between local microbiota, leading to pathogenesis various diseases, including viral infections cancers. One most common infectious agents causing cancer is papilloma virus (HPV), which accounts for more than 90% cervical In cases, immune system activated clears HPV, whereas some infection persists can lead precancerous lesions. Over last two decades, advent next-generation sequencing (NGS) technology bioinformatics has allowed thorough in-depth analysis composition anatomical niches, allowing researchers unveil interactions underlying mechanisms through microbiota could affect HPV establishment, persistence, progression. Accordingly, present narrative review aims shed light on our understanding context its progression, mainly cancer. Furthermore, we explore by balance exert potential pathogenic or protective effects, either persistence disease outcomes clearance. Special interest given how modulate infection. Lastly, summarize latest findings therapeutic efficacy probiotics prebiotics preventing and/or treating vaginal transplantation while highlighting significance personalized medicine approaches emerging from NGS-based profiling artificial intelligence (AI) optimal management HPV-related diseases.

Language: Английский

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Nannochloropsis oceanica IMET1 and its bacterial symbionts for carbon capture, utilization, and storage: biomass and calcium carbonate production under high pH and high alkalinity

Applied and Environmental Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

ABSTRACT To combat the increasing levels of carbon dioxide (CO 2 ) released from combustion fossil fuels, microalgae have emerged as a promising strategy for biological capture, utilization, and storage. This study used marine microalgal strain, Nannochloropsis oceanica IMET1, which thrives in high CO concentrations. A high-pH, high-alkalinity culture was designed capture through algal biomass production well permanent sequestration calcium carbonate (CaCO 3 precipitation. accomplished by timed pH elevation addition sodium bicarbonate to cultures N. grown at lab scale (1 L) pilot (500 with 10% 5% , respectively. Our data showed that 0.02 M NaHCO promoted growth sparging ambient air after 12 days raised created favorable CaCO formation conditions. At 1 L scale, we reached 1.52 g −1 an extra 9.3% captured form precipitates. 500 60% (Day 40) maximum rate 63.2 m −2 day 35). Bacterial communities associated were dominated two novel Patescibacteria. Functional analysis revealed genes several plant growth-promotion traits (PGPTs) enriched within this group. The microalgal-bacterial coculture system offers advantages enhanced mitigation simultaneous precipitation recalcitrant long-term IMPORTANCE Capturing fuel is utmost importance impacts climate change continue worsen. Microalgae can remove their natural photosynthetic pathways are additionally able convert into stable, ). We demonstrate microalgae-based systems be greatly improved alkalinity providing optimal conditions results microalga, strain show (pilot) scale. optimized provides approach mechanisms: (i) organic (ii) inorganic stored permanently 3.

Language: Английский

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Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode

Systematic and Applied Microbiology, Journal Year: 2024, Volume and Issue: 47(2-3), P. 126506 - 126506

Published: April 9, 2024

Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island Balearic archipelago, harbours variety thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding regional average). The metagenomes two in centre southern showed Pseudomonadota to be most represented phylum when using extracted 16S rRNA gene sequences. However, structures within between were remarkably diverse but similar their metabolic profiles as revealed by metagenome-assembled genomes (MAGs) pointing prevalence aerobic chemolithoautotrophic heterotrophic metabolisms, especially Llucmajor aquifer. Also, some evidences anaerobic lifestyles detected, which would indicate that these environments either could suffer episodes oxygen depletion or anaerobes had been transported from deeper waters. We believe local environmental factors (temperature, external inputs chemistry) seem more relevant than connection and, eventually, transport cells aquifer determining highly divergent structures. Notably, reconstructed belonged undescribed bacterial lineages them high-quality MAGs classified novel taxa named following rules Code Nomenclature Prokaryotes Described Sequence Data (SeqCode). Accordingly, we propose new species genus Costitxia debesea gen. nov., sp. affiliated with family Costitxiaceae fam. order Costitxiales ord. nov. class Costitxiia class. nov.; Lloretia Lloretiaceae

Language: Английский

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Cell envelope diversity and evolution across the bacterial tree of life

Nature Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 18, 2024

Language: Английский

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Effects of spent substrate of oyster mushroom (Pleurotus ostreatus) on ruminal fermentation, microbial community and growth performance in Hu sheep

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Oct. 23, 2024

Introduction The study aimed to evaluate the effects of Pleurotus Spent Mushroom Substrate (P.SMS) on rumen microbiota, encompassing bacteria and fungi, as well their interactions in Hu sheep. Methods A total forty-five 3-month-old sheep were randomly assigned five groups. Each group was fed diets which whole-plant corn silage (WPCS) substituted with P.SMS at varying levels: 0% (CON), 5% (PSMS5), 10% (PSMS10), 15% (PSMS15), or 20% (PSMS20). Results results indicated that higher proportions during experimental period might have a detrimental effect feed utilization efficiency, kidney function, blood oxygen-carrying capacity. Notably, moderate levels P.SMS, specifically below 15%, associated improvements NH 3 -N absorption (1) PSMS20 exhibited significantly feed-to-gain ratio compared CON ( P < 0.05); (2) PSMS15 showed content than CON, PSMS5, PSMS20. Additionally, PSMS10 had elevated concentrations PSMS5 (3) length width papillae greater (4) Creatinine (5) By conclusion experiment, hemoglobin concentration significant increase 0.05). Furthermore, addition influenced microorganisms both phylum genus At level, prevalence Patescibacteria lower other groups; relative abundances Basidiomycota PSMS10, while also demonstrated Candidatus_Saccharimonas PSMS15. Conversely, Phanerochaete notably it Correlation analysis no correlation between changes structure bacterial fungal communities. Discussion Considering these findings, high percentage negatively impacted oxygen carrying capacity, promotes indicating feeding is optimal.

Language: Английский

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Anaerobic Thermodesulfovibrio and Aerobic Meiothermus Coexist in Deep Thermal Water

Microbiology, Journal Year: 2023, Volume and Issue: 92(3), P. 324 - 333

Published: June 1, 2023

Language: Английский

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Preliminary landscape of Candidatus Saccharibacteria in the human microbiome

Frontiers in Cellular and Infection Microbiology, Journal Year: 2023, Volume and Issue: 13

Published: July 27, 2023

Introduction Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR reported in gastrointestinal urogenital tracts. However, exploration new niches has limited to date. Methods In this study, we performed a prospective retrospective screening TM7 samples using standard PCR, real-time scanning electron microscopy (SEM) shotgun metagenomics. Results Using Real-time PCR presented highest prevalence followed by fecal samples, breast milk vaginal urine samples. Surprisingly, were also detected infectious namely cardiac valves blood cultures at low (under 3%). Moreover, observed CPR-like structures SEM all sample types except valves. The reconstruction genomes from metagenomics reads further confirmed their high some Conclusion This study confirmed, through detection multiple that are commensals can be found clinical settings. Their warrants studies explore role pathological setting.

Language: Английский

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