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This paper proposes an instrument to allow instructional designers and subject matter experts (SMEs) to balance gender and ethnicity categories from inception of mobile courses throughout the complete design of the course. This instrument can also be used to analyze the matter of gender and ethnicity in all Technology Enhanced Learning courses. [ABSTRACT FROM AUTHOR]

Abstract Background We present an innovative approach to healthcare worker (HCW) training using mobile phones as a personal learning environment. Twenty physicians used individual Smartphones (Nokia N95 and iPhone), each equipped with a portable solar charger. Doctors worked in urban and peri-urban HIV/AIDS clinics in Peru, where almost 70% of the nation's HIV patients in need are on treatment. A set of 3D learning scenarios simulating interactive clinical cases was developed and adapted to the Smartphones for a continuing medical education program lasting 3 months. A mobile educational platform supporting learning events tracked participant learning progress. A discussion forum accessible via mobile connected participants to a group of HIV specialists available for back-up of the medical information. Learning outcomes were verified through mobile quizzes using multiple choice questions at the end of each module. Methods In December 2009, a mid-term evaluation was conducted, targeting both technical feasibility and user satisfaction. It also highlighted user perception of the program and the technical challenges encountered using mobile devices for lifelong learning. Results With a response rate of 90% (18/20 questionnaires returned), the overall satisfaction of using mobile tools was generally greater for the iPhone. Access to Skype and Facebook, screen/keyboard size, and image quality were cited as more troublesome for the Nokia N95 compared to the iPhone. Conclusions Training, supervision and clinical mentoring of health workers are the cornerstone of the scaling up process of HIV/AIDS care in resource-limited settings (RLSs). Educational modules on mobile phones can give flexibility to HCWs for accessing learning content anywhere. However lack of softwares interoperability and the high investment cost for the Smartphones' purchase could represent a limitation to the wide spread use of such kind mLearning programs in RLSs.

The link between the oral microbiome and neurodevelopmental disorders remains a compelling hypothesis, still requiring confirmation in large-scale datasets. Leveraging over 7000 whole-genome sequenced salivary samples from 2025 US families with children diagnosed with autism spectrum disorders (ASD), our cross-sectional study shows that the oral microbiome composition can discriminate ASD subjects from neurotypical siblings (NTs, AUC = 0.66), with 108 differentiating species (q < 0.005). The relative abundance of these species is highly correlated with cognitive impairment as measured by Full-Scale Intelligence Quotient (IQ). ASD children with IQ < 70 also exhibit lower microbiome strain sharing with parents (p < 10 -6 ) with respect to NTs. A two-pronged functional enrichment analysis suggests the contribution of enzymes from the serotonin, GABA, and dopamine degradation pathways to the distinct microbial community compositions observed between ASD and NT samples. Although measures of restrictive eating diet and proxies of oral hygiene show relatively minor effects on the microbiome composition, the observed associations with ASD and IQ may still represent unaccounted-for underlying differences in lifestyle among groups. While causal relationships could not be established, our study provides substantial support to the investigation of oral microbiome biomarkers in ASD., Competing Interests: Competing interests The authors do not have any competing interests to declare., (© 2024. The Author(s).)

Multiple clinical trials targeting the gut microbiome are being conducted to optimize treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these interventions, understanding gut microbiome changes during ICB is urgently needed. Here through longitudinal microbiome profiling of 175 patients treated with ICB for advanced melanoma, we show that several microbial species-level genome bins (SGBs) and pathways exhibit distinct patterns from baseline in patients achieving progression-free survival (PFS) of 12 months or longer (PFS ≥12) versus patients with PFS shorter than 12 months (PFS <12). Out of 99 SGBs that could discriminate between these two groups, 20 were differentially abundant only at baseline, while 42 were differentially abundant only after treatment initiation. We identify five and four SGBs that had consistently higher abundances in patients with PFS ≥12 and <12 months, respectively. Constructing a log ratio of these SGBs, we find an association with overall survival. Finally, we find different microbial dynamics in different clinical contexts including the type of ICB regimen, development of immune-related adverse events and concomitant medication use. Insights into the longitudinal dynamics of the gut microbiome in association with host factors and treatment regimens will be critical for guiding rational microbiome-targeted therapies aimed at enhancing ICB efficacy., (© 2024. The Author(s).)

Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains., (© 2023. The Author(s).)

An operational research study was conducted in 2019 to assess the quality of data submitted by antimicrobial resistance (AMR) surveillance sites in the Bagmati Province of Nepal to the National Public Health Laboratory for Global Antimicrobial Resistance and Use Surveillance System (GLASS). Measures were implemented to enhance the quality of AMR surveillance by strengthening capacity, improving infrastructure, implementing data sharing guidelines, and supervision. The current study examined reports submitted by surveillance sites in the same province in 2022 to assess whether the data quality had improved since 2019. The availability of infrastructure at the sites was assessed. Of the nine surveillance sites in the province, seven submitted reports in 2022 versus five in 2019. Completeness in reporting improved significantly from 19% in 2019 to 100% in 2022 ( p < 0.001). Timely reports were received from two sites in 2019 and only one site in 2022. Specimen-pathogen consistency in accordance with the GLASS guidelines for urine, feces, and genital swab specimens improved, with ≥90% consistency at all sites. Overall, the pathogen-antibacterial consistency improved significantly for each GLASS priority pathogen. The study highlights the importance of dedicated infrastructure and institutional arrangements for AMR surveillance. Similar assessments covering all provinces of the country can provide a more complete country-wide picture.

Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Statistical methods, especially machine learning, learning(ML), are pivotal for the analyses of large data generated by multiomics human gut microbiota study. These analyses lead to the discovery of microbe-disease associations. Furthermore, recent efforts for more data transparency and accessible analytical tools improved data availability and study reproducibility. Our recent accumulated knowledge on microbe-disease associations brings light to the next questions: what is the role of microbes in disease progression and how can we apply our knowledge of microbiome in clinical settings? Here, we introduce recent studies that implemented ML to answer the questions of causal inference and clinical translation., (Copyright © 2022. Published by Elsevier Ltd.)

The human microbiome is an integral component of the human body and a co-determinant of several health conditions 1,2 . However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown 3,4 . Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies 5 , especially those on non-infectious, microbiome-associated diseases., (© 2023. The Author(s).)

The identification of the protospacer adjacent motif (PAM) sequences of Cas9 nucleases is crucial for their exploitation in genome editing. Here we develop a computational pipeline that was used to interrogate a massively expanded dataset of metagenome and virome assemblies for accurate and comprehensive PAM predictions. This procedure allows the identification and isolation of sequence-tailored Cas9 nucleases by using the target sequence as bait. As proof of concept, starting from the disease-causing mutation P23H in the RHO gene, we find, isolate and experimentally validate a Cas9 which uses the mutated sequence as PAM. Our PAM prediction pipeline will be instrumental to generate a Cas9 nuclease repertoire responding to any PAM requirement., (© 2022. The Author(s).)

Introduction : Qualitative studies are often inadequately reported, making it difficult to judge their appropriateness for decision making in public health. We assessed the publication characteristics and quality of reporting of qualitative and mixed-method studies from the Structured Operational Research and Training Initiative (SORT IT), a global partnership for operational research capacity building. Methods: A cross-sectional analysis of publications to assess the qualitative component using an adapted version of the Consolidated Criteria for Reporting Qualitative Research (COREQ) checklist. Results: In 67 publications involving 18 countries, 32 journals and 13 public health themes, 55 were mixed-methods studies and 12 were qualitative studies. First authorship from low-and-middle-income (LMIC) countries was present in 64 (96%), LMIC last authorship in 55 (82%), and female first authorship in 30 (45%). The mean LMIC institutions represented per publication was five (range 1-11). Sixty-three (94%) publications were open access. Reporting quality was graded as 'good' to 'excellent' in 60 (89%) publications, 'fair' in five (8%) and 'poor' in two (3%). Conclusion: Most SORT IT publications adhered to COREQ standards, while supporting gender equity in authorship and the promotion of LMIC research leadership. SORT IT plays an important role in ensuring quality of evidence for decision making to improve public health.

With safely managed water accessible to only 19% of the population in Ghana, the majority of its residents are at risk of drinking contaminated water. Furthermore, this water could be a potential vehicle for the transmission of antimicrobial-resistant bacteria. This study assessed the presence of bacteria and the antibiotic resistance profile of Escherichia coli and Pseudomonas aeruginosa in drinking-water sources using membrane filtration and Kirby-Bauer disc diffusion methods. A total of 524 water samples were analyzed for total coliforms, total heterotrophic bacteria, E. coli and P. aeruginosa . Samples included sachets, bottled water, tap water, borehole and well water. Most of the sachet and bottled water samples were within the limits of Ghana's standards for safe drinking water for the parameters tested. Over 50% of tap and borehole water was also free of E. coli and P. aeruginosa . Overall, of 115 E. coli isolates from tap and ground water samples, most were resistant to cefuroxime (88.7%), trimethoprim-sulfamethoxazole (62.6%) and amoxicillin-clavulanate (52.2%). P. aeruginosa isolates were most resistant to aztreonam (48%). Multidrug resistance was predominantly seen among E. coli isolates (58%). Evidence from this study calls for routine antimicrobial resistance surveillance in drinking water across the country and additional treatment of water sources at household levels.

Introduction: Timely and appropriate management of snakebites in the tropics is a lifesaver. Many snakebite patients are being bitten in remote rural areas and do not manage to get in due time to healthcare facilities. This study assessed the clinical features and the risk factors associated with treatment outcomes of snakebite patients admitted at two hospitals in the Northwest of Ethiopia., Methodology: In a retrospective cohort study, routinely collected data from 250 patients' medical charts at University of Gondar Hospital and Metema Hospital, between September 2012 and August 2020, were reviewed., Results: The median age of the snakebite cases was 24 years (95% CI = 22-26), with 80.8% male patients. At admission 148/250 patients presented in Clinical stage 1 or 2 (local symptoms only) and 73.7% presented more than 12 hours after the bite, 80.2% received antibiotics and 79.0% antivenom. The median duration of hospitalization was 3 days (95% CI = 3-4); 72% of the patients recovered and were discharged, 10.8% died and 0.5% underwent an amputation. On logistic regression analysis, residence in rural areas (AOR = 2.52, 95 % CI = 1.2-5.3), sign of bacterial superinfection on the bite site (AOR = 4.69. 95% CI = 1.4-15.4), clinical stage 3 or 4 with systemic symptoms or toxic signs at admission (AOR = 4.84, 95% CI = 1.3-18.0) and no treatment with antivenoms (AOR = 6.65, 95% CI = 1.6-27.7) were associated with bad outcome (death, amputation and/or referred/ went against medical advice)., Conclusions: Timely presentation at early clinical stage, appropriate clinical management and availability of antivenoms are cornerstones to reduce snakebite morbidity and mortality., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2022 Rezika Mohammed, Johan van Griensven, Addisu Alemu Ambaw, Tesfaye Yesuf Yimer, Kudakwashe Collin Takarinda, Edward Mberu Kamau, Maria Zolfo, Veerle Vanlerberghe.)

Introduction: In Sub-Saharan Africa, snakebites are a public health problem. In Ethiopia, clinical cases have been described, but little information exists on snakebites burden and its geographical distribution. The aim of this study was to document the spatial distribution of venomous snakes and snakebites in Ethiopia., Methodology: In a cross-sectional observational study, venomous snakes were collected during snake catching activities in six Ethiopian hotspot areas between April 2015 and September 2020. Species and habitat were described. In the hotspot areas, routine health information data on reported snakebites was collected in 78 districts and subsequently used to map annual incidence per district., Results: A total of 333 snakes were collected and 14 species were identified. The most prevalent species were Bitis arietans, Bitis arietanus somalica, Echis pyramidum, known as vipers, and Naja pallida, known as cobra. The highest number of snakes (75) was observed in the Northwest and Eastern parts of Ethiopia, mostly in cultivation and man-made farm land, wooded and moist dry savanna. In each hotspot a wide variety of species was observed, although composition was different. The highest snakebite incidence overlapped with the high snakes densities in Northwest Ethiopia. The snakebite annual average incidence at district level was very heterogeneous and ranged from < 15 cases/100,000 inhabitants (44% of the districts) to 309.2 cases/100,000 inhabitants., Conclusions: Snake diversity and distribution, linked to high incidence of snakebites in the hotspots, suggests a close interconnection between human, animal and environmental systems and could inform the need for antivenoms per geographical locality., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2022 Gashaw Gebrewold, Timothy J Colston, Ashebir Abebe, Karifa Kourouma, Robinah Najjemba, Demise Mulugeta, Hailu Lumma, Sintayehu Abdella, Tamrat Haile, Maria Zolfo, Veerle Vanlerberghe.)

Introduction: Trachomatous trichiasis (TT) is the advanced stage of trachoma where lashes touch the globe of the eye causing permanent damage. Without eyelid surgery, TT can lead to irreversible blindness. In 2015 the Ethiopian Ministry of Health launched the Fast Track Initiative with the aim of enhancing the provision of surgical services for TT. The aims of this study were to determine the productivity of individual surgeons during the 2017 Initiative, to compare this productivity with the Ministry's annual target indicator of ≥ 200 surgeries, and to assess the factors associated with surgical output., Methodology: This retrospective cross-sectional study utilized programmatic data on surgical output from 140 surgeons active from January 2017 through December 2017 in the eastern half of Amhara region, Ethiopia. Data were collected from a surgery monitoring dataset, analyzed, and compared to the performance targets set by the Ministry., Results: The mean annual number of surgeries carried out per surgeon was 169 (standard deviation: 111) for a total of 23,616 surgeries. Among the 140 surgeons, 38% achieved the target set by the Ministry. Location of surgical training site and estimated surgical backlog were signficantly associated with a higher surgery output., Conclusions: An increase in surgical output was observed compared to productivity prior to the Initiative, although the average annual output during the 2017 Fast Track Initiative was lower than the Ministry's target. Using data driven approaches to setting annual productivity goals should be considered, particularly in light of fewer remaining TT cases as a result of the successful Initiative., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2022 Begashaw Hailemariam, Eshetu Sata, Mengesha Halefom, Andrew R Deathe, Mulat Zerihun, Kimberly A Jensen, E Kelly Callahan, Melkamu Beyene, Wim Adriaensen, Philip Owiti, Mbazi Senkoro, Maria Zolfo, Scott D Nash.)

The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on the specific microbiome characteristics linked to the clinical benefits of ICIs. We performed shotgun metagenomic sequencing of stool samples collected before ICI initiation from five observational cohorts recruiting ICI-naive patients with advanced cutaneous melanoma (n = 165). Integrating the dataset with 147 metagenomic samples from previously published studies, we found that the gut microbiome has a relevant, but cohort-dependent, association with the response to ICIs. A machine learning analysis confirmed the link between the microbiome and overall response rates (ORRs) and progression-free survival (PFS) with ICIs but also revealed limited reproducibility of microbiome-based signatures across cohorts. Accordingly, a panel of species, including Bifidobacterium pseudocatenulatum, Roseburia spp. and Akkermansia muciniphila, associated with responders was identified, but no single species could be regarded as a fully consistent biomarker across studies. Overall, the role of the human gut microbiome in ICI response appears more complex than previously thought, extending beyond differing microbial species simply present or absent in responders and nonresponders. Future studies should adopt larger sample sizes and take into account the complex interplay of clinical factors with the gut microbiome over the treatment course., (© 2022. The Author(s).)

Background: Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored., Results: We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon., Conclusions: We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria., (© 2021. The Author(s).)

Antimicrobials help in the prevention and treatment of infections and are crucial for animal production, but overuse can result in antimicrobial resistance. Hence, understanding data quality on livestock antimicrobial use is essential. We assessed frequency of reporting, completeness, and concordance of reported data and availability of human resources and infrastructure in 14 districts in Sierra Leone. This was a cross-sectional study involving a review of district and sub-district animal treatment forms submitted from January 2016 to August 2019. Out of the 14 districts, only 3 had filled forms available for review: A total of 6 (0.97% of 616 expected) district forms and 79 (1.15% of 6840 expected) sub-district forms. Data between district and sub-district treatment forms were fully discordant. Hence, completeness of data could not be assessed. All districts had livestock officers (barring one) and livestock assistants but no veterinarians. The gap in community animal health workers ranged from 14 to 100% per district. No districts had a functional computer or internet access. Reporting was non-existent in 11 districts and poor in the other 3. Resources are urgently needed to address critical gaps in human resources and capacity and computer and Internet connectivity to develop critical One Health surveillance functions at the national and sub-national levels.

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii , previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies., Competing Interests: FB, LM, AB, LD, FA, SM, AM, PM, MS, AT, MV, GW, YZ, MZ, CH, EF, NS No competing interests declared, (© 2021, Beghini et al.)

Globally, 5-15% of hospitalized patients acquire infections (often caused by antimicrobial-resistant microbes) due to inadequate infection prevention and control (IPC) measures. We used the World Health Organization's (WHO) 'Infection Prevention and Control Assessment Framework' (IPCAF) tool to assess the IPC compliance at Lira University hospital (LUH), a teaching hospital in Uganda. We also characterized challenges in completing the tool. This was a hospital-based, cross-sectional study conducted in November 2020. The IPC focal person at LUH completed the WHO IPCAF tool. Responses were validated, scored, and interpreted per WHO guidelines. The overall IPC compliance score at LUH was 225/800 (28.5%), implying a basic IPC compliance level. There was no IPC committee, no IPC team, and no budgets. Training was rarely or never conducted. There was no surveillance system and no monitoring/audit of IPC activities. Bed capacity, water, electricity, and disposal of hospital waste were adequate. Disposables and personal protective equipment were not available in appropriate quantities. Major challenges in completing the IPCAF tool were related to the detailed questions requiring repeated consultation with other hospital stakeholders and the long time it took to complete the tool. IPC compliance at LUH was not optimal. The gaps identified need to be addressed urgently.

Antimicrobial resistance (AMR) is a global problem, and Nepal is no exception. Countries are expected to report annually to the World Health Organization on their AMR surveillance progress through a Global Antimicrobial Resistance Surveillance System, in which Nepal enrolled in 2017. We assessed the quality of AMR surveillance data during 2019-2020 at nine surveillance sites in Province 3 of Nepal for completeness, consistency, and timeliness and examined barriers for non-reporting sites. Here, we present the results of this cross-sectional descriptive study of secondary AMR data from five reporting sites and barriers identified through a structured questionnaire completed by representatives at the five reporting and four non-reporting sites. Among the 1584 records from the reporting sites assessed for consistency and completeness, 77-92% were consistent and 88-100% were complete, with inter-site variation. Data from two sites were received by the 15th day of the following month, whereas receipt was delayed by a mean of 175 days at three other sites. All four non-reporting sites lacked dedicated data personnel, and two lacked computers. The AMR surveillance data collection process needs improvement in completeness, consistency, and timeliness. Non-reporting sites need support to meet the specific requirements for data compilation and sharing.

Dental implants are installed in an increasing number of patients. Mucositis and peri-implantitis are common microbial-biofilm-associated diseases affecting the tissues that surround the dental implant and are a major medical and socioeconomic burden. By metagenomic sequencing of the plaque microbiome in different peri-implant health and disease conditions (113 samples from 72 individuals), we found microbial signatures for peri-implantitis and mucositis and defined the peri-implantitis-related complex (PiRC) composed by the 7 most discriminative bacteria. The peri-implantitis microbiome is site specific as contralateral healthy sites resembled more the microbiome of healthy implants, while mucositis was specifically enriched for Fusobacterium nucleatum acting as a keystone colonizer. Microbiome-based machine learning showed high diagnostic and prognostic power for peri-implant diseases and strain-level profiling identified a previously uncharacterized subspecies of F. nucleatum to be particularly associated with disease. Altogether, we associated the plaque microbiome with peri-implant diseases and identified microbial signatures of disease severity.