**Background:** The human microbiome—the collection of microorganisms living in and on the body—influences health through pathways including nutrient metabolism and metabolite production, and has been linked to chronic diseases such as allergies, inflammatory bowel disease, obesity, heart disease, and HIV. The physical environment, including neighbourhood characteristics, may shape microbiome composition. Neighbourhood socioeconomic status (SES) is a recognised determinant of health, with lower SES neighbourhoods associated with increased cardiovascular disease and mortality independent of individual SES. Potential mechanistic links between neighbourhood and microbiome include greenspace exposure, diet quality, environmental pollutants, and disparities in healthcare access. The authors note that no published review has yet synthesised the evidence on neighbourhood–microbiome relationships.
**Methods:** This scoping review follows the Arksey and O’Malley framework and will adhere to PRISMA-ScR reporting guidelines. The search strategy was developed by an interdisciplinary team (medicine, public health, nursing, molecular biology, biological anthropology) and a clinical research librarian. Six databases will be searched: PubMed/Medline (NLM), Embase (Elsevier), Web of Science Core Collection (Clarivate Analytics), Scopus (Elsevier), medRxiv preprint server, and Open Science Framework server. No date or language restrictions will be applied; translation services are available through the authors' institutional library. Reference lists of included studies and pre-identified sentinel papers will also be screened.
Inclusion criteria require studies to evaluate the relationship between microbiome diversity and neighbourhood, include at least one human microbiome site, provide a measurement of neighbourhood (e.g., self-perception, geographical location), and include an analysis linking neighbourhood measurement to microbiome diversity. Studies of any design (primary, secondary, reviews, grey literature) with human subjects of any age are eligible. Postmortem studies are included if premortem health factors are reported. Exclusion criteria include secondary literature reviews without primary data, studies missing either microbiome diversity measurement or neighbourhood measurement, and postmortem populations without known health factors.
Screening will be conducted independently by two reviewers, with a third reviewer (KM) arbitrating disagreements. Covidence software will manage the screening process. Data extraction will use a piloted form capturing citation details, research team characteristics (disciplines, funding), study design, participant demographics and health status, microbiome diversity type (relative abundance, alpha/beta diversity, metabolites), genetics, neighbourhood measurement type (residential, occupational, school; urban/suburban/rural), and mechanistic factors (food environment, pollutant exposure, greenspace).
Risk of bias will be assessed using ROBINS-I for non-randomised studies, ROBINS-E for observational studies, and the Cochrane Risk of Bias Tool for randomised studies, with two independent assessors and third-author resolution of disagreements.
**Key Results:** This is a protocol paper; no results are reported. The review will use both qualitative thematic analysis and quantitative descriptive statistics to summarise findings. A consultation phase will involve focus groups with stakeholders including individuals from neighbourhoods facing structural inequities and topic experts, recruited through a Washington, DC-based community advisory board. Focus group feedback will be analysed thematically and integrated into the final interpretation.
**Clinical Implications:** The authors anticipate that this scoping review will identify gaps in the literature and provide a framework for future studies on microbial diversity, microbial metabolites, and health disparities in structurally disadvantaged neighbourhoods. Findings are intended to inform translational community-based research and will be disseminated through peer-reviewed publication and stakeholder engagement. The protocol explicitly notes that no ethical approval is required as it uses public literature databases, and stakeholder consultation will not collect personal information.