Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton DOI Creative Commons
Harriet Alexander, Sarah K. Hu, Arianna I. Krinos

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: July 25, 2021

Abstract Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools processing metagenomic data are not designed to consider eukaryotes, nor they built an increasing amount sequence data. EukHeist automated pipeline retrieve eukaryotic prokaryotic metagenome assembled genomes (MAGs) from large-scale datasets. We developed workflow specifically process large amounts both and/or metatranscriptomic in reproducible fashion. Here, we applied large-size fraction (0.8-2000 µm ) Tara Oceans recover MAGs, which refer as TOPAZ ( Particle-Associated MAGs). The MAGs consisted >900 environmentally-relevant >4,000 bacterial archaeal MAGs. expand known marine phylogenetic diversity through increase coverage likely particle- host-associated taxa. also demonstrate approach infer putative functional mode recovered A global survey enabled identification cohorts, driven by specific environmental factors, host-microbe associations. Importance Despite importance single-celled organisms environments, majority difficult cultivate lab. Sequencing genetic material extracted samples enables researchers document naturally-occurring protistan However, conventional sequencing methodologies cannot separate out individual organisms. To more completely capture entire genomic content community, can create bins sequences that represent same organism. scientists bin reads, show results provide exciting insights into what communities present ocean play ecosystem. Accessible scalable computational tools, such EukHeist, accelerate meaningful signatures datasets, ultimately expanding tree life.

Language: Английский

ESHRE good practice recommendations on recurrent implantation failure DOI Creative Commons
Danilo Cimadomo, María José de los Santos, Georg Griesinger

et al.

Human Reproduction Open, Journal Year: 2023, Volume and Issue: 2023(3)

Published: Jan. 1, 2023

Abstract STUDY QUESTION How should recurrent implantation failure (RIF) in patients undergoing ART be defined and managed? SUMMARY ANSWER This is the first ESHRE good practice recommendations paper providing a definition for RIF together with on how to investigate causes contributing factors, improve chances of pregnancy. WHAT IS KNOWN ALREADY challenge clinic, multitude investigations interventions offered applied clinical practice, often without biological rationale or unequivocal evidence benefit. DESIGN, SIZE, DURATION document was developed according predefined methodology recommendations. Recommendations are supported by data from literature, if available, results previously published survey expertise working group. A literature search performed PubMed Cochrane focussing ‘recurrent reproductive failure’, ‘repeated failure’. PARTICIPANTS/MATERIALS, SETTING, METHODS The Working Group Recurrent Implantation Failure included eight members representing Special Interest Groups Early Pregnancy, Reproductive Endocrinology, Embryology, an independent chair expert statistics. were formulated based opinion group, while taking into consideration uptake practice. draft then open online peer review revised light comments received. MAIN RESULTS AND THE ROLE OF CHANCE group recommends considering as secondary phenomenon ART, it can only observed IVF, that following description adopted: ‘RIF describes scenario which transfer embryos considered viable has failed result positive pregnancy test sufficiently specific patient warrant further and/or interventions'. It agreed recommended threshold cumulative predicted chance identify purposes initiating investigation 60%. When couple have not had successful certain number embryo transfers associated greater than 60%, they counselled treatment options. term defines actions considered. Nineteen when suspected, 13 interventions. colour-coded whether investigations/interventions (green), (orange), recommended, i.e. routinely (red). LIMITATIONS, REASONS FOR CAUTION While awaiting studies trials, identifying individual restrict treatments those clear indicating their likely WIDER IMPLICATIONS FINDINGS article provides advice but also highlights need research. research, well-conducted, will key making progress management RIF. FUNDING/COMPETING INTEREST(S) meetings technical support this project funded ESHRE. N.M. declared consulting fees ArtPRED (The Netherlands) Freya Biosciences (Denmark); Honoraria lectures Gedeon Richter, Merck, Abbott, IBSA; being co-founder Verso Biosense. He Co-Chief Editor Biomedicine Online (RBMO). D.C. Associate Human Reproduction Update, honoraria Organon, IBSA, Fairtility; attending Cooper Surgical, Fujifilm Irvine Scientific. G.G. he his institution received financial non-financial lectures, workshops, advisory roles, travelling Ferring, Gedeon-Richter, PregLem, Vifor, MSD, Coopersurgical, ObsEVA, ReprodWissen. journals Archives Obstetrics Gynecology Online, Chief Journal Gynäkologische Endokrinologie. involved guideline developments quality control national international level. G.L. Vianex/Organon, MSD. immediate past Coordinator Endocrinology been Guideline Development fertility authorities. D.J.M. Open statistical Advisor Online. B.T. shareholder Reprognostics she her roles Exeltis, Merck Serono, Bayer, Teva, Theramex Novartis, Astropharm, Ferring. other authors nothing disclose. DISCLAIMER Good Practice (GPR) represents views ESHRE, consensus between relevant stakeholders scientific available at time preparation. GPRs used information educational purposes. They interpreted setting standard care deemed inclusive all proper methods care, exclusive reasonably directed obtaining same results. do replace application judgement each presentation, variations locality facility type. Furthermore, constitute imply endorsement, favouring, any technologies

Language: Английский

Citations

94

The Endometrial Microbiome and Its Impact on Human Conception DOI Open Access
Bruno Toson, Carlos Simón, Inmaculada Moreno

et al.

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(1), P. 485 - 485

Published: Jan. 1, 2022

Changes in the female genital tract microbiome are consistently correlated to gynecological and obstetrical pathologies, dysbiosis can impact reproductive outcomes during fertility treatment. Nonetheless, a consensus regarding physiological core inside uterine cavity has not been reached due myriad of study limitations, such as sample size experimental design variations, influence endometrial bacterial communities on human reproduction remains debated. Understanding healthy microbiota how changes its composition affect would potentially allow personalized treatment through management assisted therapies, ultimately leading improvement clinical outcomes. Here, we review current knowledge it relates conception.

Language: Английский

Citations

80

Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity DOI
Amanda M. Achberger, Rose M. Jones, John W. Jamieson

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(3), P. 657 - 668

Published: Jan. 29, 2024

Language: Английский

Citations

16

Metagenome-guided culturomics for the targeted enrichment of gut microbes DOI Creative Commons

Jeremy Armetta,

Simone S. Li,

Troels Holger Vaaben

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 14, 2025

The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, bioactive compounds. Whole-metagenome identified medium additives, like caffeine, that enhance often associated healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact on composition cultured communities establish link between preference microbial phylogeny. Leveraging these insights, demonstrate combinations media can further targeted enrichment metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks potential selective enrichment, advancing research by understanding different parameters microbes.

Language: Английский

Citations

2

The impact of the female genital tract microbiome in women health and reproduction: a review DOI Open Access
Paula Punzón-Jiménez, Elena Labarta

Journal of Assisted Reproduction and Genetics, Journal Year: 2021, Volume and Issue: 38(10), P. 2519 - 2541

Published: June 10, 2021

Language: Английский

Citations

90

The female reproductive tract microbiotas, inflammation, and gynecological conditions DOI Creative Commons

Mahsa Gholiof,

Emma Adamson-De Luca, Jocelyn M. Wessels

et al.

Frontiers in Reproductive Health, Journal Year: 2022, Volume and Issue: 4

Published: Aug. 9, 2022

The intricate interactions between the host cells, bacteria, and immune components that reside in female reproductive tract (FRT) are essential maintaining homeostasis. Much of our current knowledge surrounding FRT microbiota relates to vaginal microbiota, where ‘health’ has long been associated with low bacterial diversity Lactobacillus dominance. This concept recently challenged as women can have a diverse microbial composition absence symptomatic disease. structures upper (the endocervix, uterus, Fallopian tubes, ovaries) distinct, lower biomass microbiotas than vagina; however, existence permanent at these sites is disputed. During homeostasis, balance exists bacteria system maintains quiescence. Alterations system, or local environment may result perturbances defined dysbiosis. inflammatory signature perturbed “dysbiotic” characterized by elevated concentrations pro-inflammatory cytokines cervical fluid. It appears homeostasis be disrupted two different mechanisms: first, shift toward increased trigger inflammation, second, immunity altered some manner, which disrupts response an environmental change. dysbiosis negative effects on health. review will examine increasing evidence for involvement inflammation gynecologic conditions such endometriosis, infertility, endometrial ovarian cancer; precise mechanisms involved remains speculative present. While only their infancy, use antibiotics probiotics therapeutically alter being studied discussed herein. Our understanding intimate relationship its early days, more research needed deepen mechanistic this assess how present harnessed assist diagnosis treatment conditions.

Language: Английский

Citations

63

Microorganisms in the reproductive system and probiotic's regulatory effects on reproductive health DOI Creative Commons
Tao Feng, Yan Liu

Computational and Structural Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20, P. 1541 - 1553

Published: Jan. 1, 2022

The presence of microbial communities in the reproductive tract has been revealed, and this resident microbiota is involved maintenance health. Intentional modulation via probiotics proposed as a possible strategy to enhance health reduce risk diseases. male seminal suggested an important factor that influences couple's health, pregnancy outcomes, offspring Probiotics have reported play role fertility affect mothers offspring. While female more complicated identified both upper lower systems, they together contribute maintenance. shown regulatory effects on tract, thereby contributing homeostasis influencing Further, through transmission bacteria or other indirect mechanisms, parent's probiotic intervention influence infant gut colonization immunity development, with potential consequences. In vitro vivo studies explored mechanisms underlying benefits administration intervention, array positive results, such composition, regulation metabolism, promotion epithelial barrier, improvement immune function, observed. Herein, we review state art system its reproduction, well beneficial their contributions prevention associated

Language: Английский

Citations

50

Current findings in endometrial microbiome: impact on uterine diseases DOI Open Access
Diana Medina-Bastidas, Ignacio Camacho‐Arroyo, Elizabeth García-Gómez

et al.

Reproduction, Journal Year: 2022, Volume and Issue: 163(5), P. R81 - R96

Published: Feb. 23, 2022

Microbiome or microbiota is essential to regulate many mammalian physiological processes, including reproduction. Like other organs tissues, the upper female reproductive tract used be considered as devoid of microorganisms; however, a non-infection-related bacterial community was discovered in uterus from humans and mammals, its composition related success. The dysbiosis endometrial associated with benign malign uterine diseases. Hence, this review addressed current knowledge about alterations their association common diseases, polyposis, endometriosis, myomatosis, hyperplasia, cancer. There specific endometrium most-analyzed However, constant finding consists reduced abundance Firmicutes Lactobacillus , while there an increased Proteobacteria (such Escherichia coli Enterococcus ), Bacteroidetes ( Prevotella for example), Actinobacteria (as Gardnerella contrast healthy endometrium. Besides, we discussed future usefulness components biomarkers diagnose diseases probable clinical outcomes. In addition, analyzed potential use probiotics since they could provide alternative complement existing therapies.

Language: Английский

Citations

45

Gut and genital tract microbiomes: Dysbiosis and link to gynecological disorders DOI Creative Commons
Hoda Elkafas,

Melinique Walls,

Ayman Al‐Hendy

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2022, Volume and Issue: 12

Published: Dec. 16, 2022

Every year, millions of women are affected by genital tract disorders, such as bacterial vaginosis (BV), endometrial cancer, polycystic ovary syndrome (PCOS), endometriosis, and uterine fibroids (UFs). These disorders pose a significant economic burden on healthcare systems have serious implications for health fertility outcomes. This review explores the relationships between gut, vaginal, dysbiosis pathogenesis various diseases female tract. In recent years, reproductive clinicians scientists focused microbiome to investigate its role in prevention diseases. Recent studies microbiomes identified patterns composition changes across individuals' lives associated with specific healthy diseased states, particularly regarding effects estrogen-gut axis estrogen-driven (such UFs) estrogen deficiency PCOS). Furthermore, this discusses contribution vitamin D gut altered metabolism well how these play key roles UFs. More research influences is vital.

Language: Английский

Citations

42

Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study DOI Creative Commons
Pirkko Peuranpää, Tiina Holster, Schahzad Saqib

et al.

Reproductive BioMedicine Online, Journal Year: 2022, Volume and Issue: 45(5), P. 1021 - 1031

Published: June 17, 2022

Is the composition of endometrial or vaginal microbiota associated with recurrent pregnancy loss (RPL)?Endometrial and samples were collected from 47 women two more consecutive losses 39 healthy control without a history loss, between March 2018 December 2020 at Helsinki University Hospital, Helsinki, Finland. The compositions microbiota, analysed using 16S rRNA gene amplicon sequencing, compared RPL women, individual samples. mycobiota was internal transcribed spacer 1 sequencing for descriptive summary. models adjusted body mass index, age parity. False discovery rate-corrected P-values (q-values) used to define nominal statistical significance q < 0.05.Lactobacillus crispatus less abundant in controls (mean relative abundance 17.2% versus 45.6%, = 0.04). Gardnerella vaginalis group than both (12.4% 5.8%, 0.001) (8.7% 5.7%, 0.002) microbial correlated strongly (R 0.85, P 0.001). Fungi detected 22% 36% samples.Dysbiosis reproductive tract is may represent novel risk factor losses.

Language: Английский

Citations

39