EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research

iMeta, Год журнала: 2023, Номер 2(1)

Опубликована: Янв. 27, 2023

It is difficult for beginners to learn and use amplicon analysis software because there are so many tools choose from, all of them need multiple steps operation. Herein, we provide a cross-platform, open-source, community-supported pipeline EasyAmplicon. EasyAmplicon has most the modules needed an analysis, including data quality control, merging paired-end reads, dereplication, clustering or denoising, chimera detection, generation feature tables, taxonomic diversity compositional biomarker discovery, publication-quality visualization. includes more than 30 cross-platform R packages commonly used in field. All integrated into RStudio, which reduces learning costs, keeps flexibility process, facilitates personalized analysis. The maintained updated by authors editors WeChat official account "Meta-genome." Our team will regularly release latest tutorials both Chinese English, read feedback from users, help GitHub. can be deployed on various platforms, installation time less half hour. On ordinary laptop, whole process dozens samples completed within 3 h. available at GitHub (https://github.com/YongxinLiu/EasyAmplicon) Gitee (https://gitee.com/YongxinLiu/EasyAmplicon).

Язык: Английский

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Effects of Probiotics on Gut Microbiota: An Overview

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(11), С. 6022 - 6022

Опубликована: Май 30, 2024

The role of probiotics in regulating intestinal flora to enhance host immunity has recently received widespread attention. Altering the human gut microbiota may increase predisposition several disease phenotypes such as inflammation and metabolic disorders. converts dietary nutrients into metabolites that serve biologically active molecules modulating regulatory functions host. Probiotics, which are microorganisms, play a versatile restoring composition microbiota, helping improve prevent phenotypes. This comprehensive review provides firsthand information on their influence health, effects diet how alter function along with corresponding building healthy intestine. We also discuss implications some most important diseases. In summary, significant boosting overall immunity, increasing abundance beneficial bacteria, ameliorate symptoms multiple

Язык: Английский

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Harnessing the plant microbiome for sustainable crop production

Nature Reviews Microbiology, Год журнала: 2024, Номер unknown

Опубликована: Авг. 15, 2024

Язык: Английский

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Broadening oncological boundaries: the intratumoral microbiota

Trends in Microbiology, Год журнала: 2024, Номер 32(8), С. 807 - 822

Опубликована: Фев. 3, 2024

The microbiota of solid tumors was identified >100 years ago; however, heterogeneous composition and diversity have been revealed only recently. Growing evidence has suggested that several functional mechanisms the intratumoral affect tumorigenesis progression, suggesting is a promising biomarker for multiple cancers. low biomass poses major challenge to related research, thus necessitating use multiple-modality integrated framework resolve this dilemma. Advanced techniques such as single-cell sequencing provide significant clues, gradual optimization experiments culture-based methods enables deeper investigation underlying involved. In review, we outline current state research on describe challenges comprehensive strategies future research.

Язык: Английский

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Beneficial microorganisms: Regulating growth and defense for plant welfare

Plant Biotechnology Journal, Год журнала: 2024, Номер unknown

Опубликована: Дек. 20, 2024

Beneficial microorganisms (BMs) promote plant growth and enhance stress resistance. This review summarizes how BMs induce promotion by improving nutrient uptake, producing growth-promoting hormones stimulating root development. How disease resistance help protect plants from abiotic stresses has also been explored. Growth-defense trade-offs are known to affect the ability of survive under unfavourable conditions. discusses studies demonstrating that regulate growth-defense through microbe-associated molecular patterns multiple pathways, including leucine-rich repeat receptor-like kinase pathway, abscisic acid signalling pathway specific transcriptional factor regulation. multifaceted relationship underscores significance in sustainable agriculture. Finally, need for integration artificial intelligence revolutionize biofertilizer research highlighted. elucidates cutting-edge advancements potential plant-microbe synergistic microbial agents.

Язык: Английский

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Harnessing of Artificial Intelligence for the Diagnosis and Prevention of Hospital-Acquired Infections: A Systematic Review

Diagnostics, Год журнала: 2024, Номер 14(5), С. 484 - 484

Опубликована: Фев. 23, 2024

Healthcare-associated infections (HAIs) are the most common adverse events in healthcare and constitute a major global public health concern. Surveillance represents foundation for effective prevention control of HAIs, yet conventional surveillance is costly labor intensive. Artificial intelligence (AI) machine learning (ML) have potential to support development HAI algorithms understanding risk factors, improvement patient stratification as well prediction timely detection infections. AI-supported systems so far been explored clinical laboratory testing imaging diagnosis, antimicrobial resistance profiling, antibiotic discovery prediction-based decision tools terms HAIs. This review aims provide comprehensive summary current literature on AI applications field HAIs discuss future potentials this emerging technology infection practice. Following PRISMA guidelines, study examined articles databases including PubMed Scopus until November 2023, which were screened based inclusion exclusion criteria, resulting 162 included articles. By elucidating advancements field, we aim highlight report related issues shortcomings directions.

Язык: Английский

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A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions

Frontiers in Microbiology, Год журнала: 2024, Номер 15

Опубликована: Фев. 13, 2024

Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition functional potential. However, a critical challenge in this field is the lack standard comprehensive metadata associated with raw data, hindering ability to perform robust data stratifications consider confounding factors. In review, we categorize publicly available microbiome five types: shotgun sequencing, amplicon metatranscriptomic, metabolomic, metaproteomic data. We explore importance for reuse address challenges collecting standardized metadata. also, assess limitations collection existing public repositories metagenomic This review emphasizes vital role interpreting comparing datasets highlights need protocols fully leverage data's Furthermore, future directions implementation Machine Learning (ML) retrieval, offering promising avenues deeper understanding ecological roles. Leveraging these tools will enhance capabilities dynamics diverse ecosystems. Finally, emphasize crucial ML models development.

Язык: Английский

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Recent advances in deep learning and language models for studying the microbiome

Frontiers in Genetics, Год журнала: 2025, Номер 15

Опубликована: Янв. 7, 2025

Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein genomic sequences, like natural languages, form of life, enabling the adoption LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications learning analyzing We focus problem formulations, necessary datasets, integration modeling techniques. provide an extensive overview protein/genomic their contributions studies. also discuss such as novel viromics modeling, biosynthetic gene cluster prediction, knowledge for

Язык: Английский

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Evolving approaches to profiling the microbiome in skin disease

Frontiers in Immunology, Год журнала: 2023, Номер 14

Опубликована: Апрель 4, 2023

Despite its harsh and dry environment, human skin is home to diverse microbes, including bacteria, fungi, viruses, microscopic mites. These microbes form communities that may exist at the surface, deeper layers, within microhabitats such as hair follicle sweat glands, allowing complex interactions with host immune system. Imbalances in microbiome, known dysbiosis, have been linked various inflammatory disorders, atopic dermatitis, acne, psoriasis. The roles of abundant commensal bacteria belonging Staphylococcus Cutibacterium taxa fungi Malassezia , where particular species or strains can benefit cause disease, are increasingly appreciated disorders. Furthermore, recent research suggests between microorganisms host’s system on distant systemic effects body, gut brain, “skin-gut” “skin-brain” axes. Studies microbiome disease typically relied 16S rRNA gene sequencing methods, which cannot provide accurate information about skin. However, advancing technologies, metagenomics other functional ‘omic’ approaches, great potential more comprehensive detailed health disease. Additionally, inter-species multi-kingdom cascading shifts towards dysbiosis crucial but yet-to-be-explored aspects many Better understanding these dynamics will require meta-omic studies complemented experiments clinical trials confirm function. Evolving how we profile alongside technological advances essential exploring relationships. This review presents current emerging methods their findings for profiling advance our

Язык: Английский

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How to Provide Nitrite Robustly for Anaerobic Ammonium Oxidation in Mainstream Nitrogen Removal

Environmental Science & Technology, Год журнала: 2023, Номер 57(51), С. 21503 - 21526

Опубликована: Дек. 14, 2023

Innovation in decarbonizing wastewater treatment is urgent response to global climate change. The practical implementation of anaerobic ammonium oxidation (anammox) treating domestic the key reconciling carbon-neutral management with sustainable development. Nitrite availability prerequisite anammox reaction, but how achieve robust nitrite supply and accumulation for mainstream systems remains elusive. This work presents a state-of-the-art review on recent advances anammox, paying special attention available pathways (forward-going (from nitrite) backward-going nitrate nitrite)), controlling strategies, physiological ecological characteristics functional microorganisms involved supply. First, we comprehensively assessed nitrite-oxidizing bacteria control methods, outlining that these technologies are transitioning possessing multiple selective pressures (such as intermittent aeration membrane-aerated biological reactor), integrating side stream free ammonia/free nitrous acid suppression recirculated sludge treatment), maintaining high activity ammonia-oxidizing competing oxygen bacteria. We then highlight emerging strategies supply, including production driven by novel microbes (ammonia-oxidizing archaea complete ammonia bacteria) reduction (partial denitrification nitrate-dependent methane oxidation). resources requirement different analyzed, hybrid pathway combining partial nitrification encouraged. Moreover, data-driven modeling process well proactive microbiome proposed hope achieving application. Finally, existing challenges further perspectives highlighted, i.e., investigation nitrite-supplying bacteria, scaling-up from laboratory under real conditions, stable performance fundamental insights this aim inspire advance our understanding about provide robustly shed light important obstacles warranting settlement.

Язык: Английский

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