Microbiome Monthly: March 2026
Contents
- Trends This Month — topic volume trends across January–March
- Papers of the Month — the six highest field-weighted-impact microbiome papers from March
- Decomposition Dump — March literature from decomposition ecology, forensic entomology, and necrobiome research
- Top 100 Papers — all March microbiome papers ranked by FWCI, searchable by title, author, journal, or topic
- Most Cited Papers from March 2026 Literature — the foundational papers March’s literature was citing most
Trends This Month
OpenAlex indexed roughly 200 microbiome-related articles published in March 2026. Cancer & Immunotherapy and Gut-Brain Axis have climbed steadily since January, with the gut-brain category nearly doubling over the quarter, and not driven by a single megapaper. Spatial & Single-Cell had a flat January and February before jumping to three papers in March, tracking with the growing push to bring spatial transcriptomics to host-microbe interfaces. IBD & Gut Inflammation dropped sharply this month after a modest February, while Methods & Bioinformatics continues its slow upward grind as the field’s dominant category by volume.
Microbiome publication volume by topic area, January–March 2026. Pulsing points mark the current month's data, still accumulating as the literature settles. Data from OpenAlex.
Methods & Bioinformatics remains the dominant category by volume, a consistent pattern that probably reflects both genuine activity and the fact that methods papers tend to accumulate citations faster than narrowly scoped empirical work.
Papers of the Month
The six highest field-weighted-impact microbiome papers from March, drawn from a broad keyword search and targeted journal queries across ten major microbiome venues. FWCI normalizes citation counts by field and paper age, which makes it useful for comparing very recent work before raw citation counts have had time to accumulate.
FWCI scores for the six highlighted papers. A score of 1.0 is the field average for papers of this age; all six are far above it. Data from OpenAlex.
Microbial metabolism of food allergens determines severity of IgE-mediated anaphylaxis
Abstract not available from publisher.
Prediction of eukaryotic cellular complexity in Asgard archaea
Asgard archaea played a key role in the origin of the eukaryotic cell, with extant genomes encoding relatives of diverse eukaryotic signature proteins (ESPs) involved in cellular organization. However, their often punctuated distribution and the absence of detectable homologues for many eukaryotic proteins limit our ability to reconstruct the cellular complexity of the Asgard archaeal ancestor of eukaryotes. Here we used de novo protein structure modelling and sequence similarity detection across an expanded Asgard archaeal genomic dataset to build a structural catalogue of the Asgard archaeal pangenome. We identified 908 'isomorphic' ESPs—Asgard archaeal proteins with statistically enriched structural matches to eukaryotic proteins, often bridging deep sequence divergence. These isomorphic ESPs are enriched in information storage and processing roles and contain key components of the eukaryotic Vault (MVP) and Commander (COMMD) complexes, with potential roles in cellular compartmentalization and endosomal processing. These findings expand the repertoire of eukaryotic-like proteins in Asgard archaea and suggest a higher degree of eukaryote-like cellular complexity in the archaeal ancestor of eukaryotes.
Intestinal interoceptive dysfunction drives age-associated cognitive decline
Ageing is accompanied by declining memory function, with extremely heterogeneous manifestation in the human population. Brain-extrinsic factors influencing cognitive decline, such as gastrointestinal signals, have emerged as attractive targets for peripheral interventions, but the underlying mechanisms remain largely unclear. Here, by charting a high-resolution map of microbiome ageing and its functional consequences throughout the lifespan of mice, we identify a mechanism by which inhibition of gut-brain signalling during ageing results in impaired neuronal activation in the hippocampus and loss of memory encoding. Specifically, accumulation of gut bacteria that produce medium-chain fatty acids, such as Parabacteroides goldsteinii, can drive peripheral myeloid cell inflammation through GPR84 signalling. As a result, the function of vagal afferent neurons is impaired, the interoceptive signal received by the brain is weakened and hippocampal function declines. We leverage this pathway to define interventions that enhance memory in aged mice, such as phage targeting of Parabacteroides, GPR84 inhibition and restoration of vagal activity. These findings indicate a key role for interoceptive dysfunction in brain ageing and suggest that interoceptomimetics that stimulate gut-brain communication may counteract age-associated cognitive decline.
AMR governance across 193 countries: a One Health assessment
Antimicrobial resistance (AMR) poses a major global health threat, yet the effectiveness of national action plans (NAPs) remains uncertain. Here we developed a multidimensional One Health governance index through a structured Delphi expert consultation to evaluate AMR governance across 193 countries (2017–2022), integrating 269 policy documents, expert-weighted indicators and multinational survey and surveillance datasets. Difference-in-differences and joinpoint regression analyses were used to link governance to antimicrobial use, AMR prevalence and AMR-related mortality. Global governance scores improved from 30.7 to 44.5/100, although implementation and monitoring lagged behind policy design, particularly in animal and environmental sectors. A significant increase in AMR prevalence scores was observed only 5 years after NAP adoption (two-stage difference-in-differences, β = 2.43, 95% confidence interval (CI) 1.02–3.85, P < 0.05), underscoring the delayed impact of policy. Multisector engagement and antimicrobial use surveillance systems showed the strongest associations with improvement in AMR outcomes. As the 2026 Global Action Plan update approaches, sustained financing and integrated One Health surveillance, with stronger environmental and agricultural engagement, are essential for translating NAPs into sustained reductions in resistance.
Spatial transcriptomics maps host–gut microbiome biogeography at 1 µm resolution
Intermicrobial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong intermicrobial interactions at short length scales and tumour-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.
Atlas of one-carbon metabolism in conventional and germ-free mice: folate as a key microbiome-dependent determinant
Folates participate in the one-carbon metabolism (OCM) cycle, supporting many biochemical pathways. Existing methods to profile folate are limited in the diversity of vitamers they measure and the samples they profile. Here we present a metabolomics workflow for stable extraction, separation and measurement of folates, along with precursors and products of OCM-associated pathways. We profile these metabolites in 37 mouse tissues to chart an interactive 'OCM atlas', revealing vast heterogeneity across organs and an uncharacterized folate derivative. We discover that, in adult mice, the gut microbiota is a consumer of folate and folate polyglutamylation in the host is not regulated by folate availability. Germ-free mice show tissue-specific shifts in methyl donor abundances relative to conventionally raised mice, indicative of altered DNA methylation. Correlation analyses uncover the central roles of folates in potentially modulating other biochemical pathways in tissues, thus linking microbial folate consumption directly to its global impacts on host metabolism.
Decomposition Dump
Papers from March 2026 at the intersection of decomposition ecology, forensic microbiology, and forensic entomology. Sourced from separate targeted searches for necrobiome, thanatomicrobiome, necrophagous, forensic entomology, blow fly microbiome, Ignatzschineria, and PMI estimation literature, separate from the broader microbiome sweep above. FWCI is unavailable for all of these; papers published days or weeks ago have had no time to accumulate citations relative to field baselines, so 0.0 is expected and says nothing about quality.
Necromass chemistry drives the functional diversity of the necrobiome, resulting in microbe–organic matter feedbacks
In temperate European forests, soil fungal communities, dominated by saprotrophic and ectomycorrhizal (ECM) species, represent almost 25% of soil organic carbon (C) in the soil. However, the decomposition dynamics of fungal necromass, the bioavailability of its associated elements and its role in soil C stabilisation remain poorly understood. We investigated how intrinsic chemical properties—particularly melanin content, nitrogen (N) and phosphorus (P) levels—influence the microbial decomposition of fungal necromass in a temperate oak forest. We compared two types of fungal necromass: Laccaria bicolor (low melanin content) and Fomitiporia robusta (high melanin content). We monitored mass loss, stoichiometric ratios and microbial enzymatic activity over a six-month period in soil. Additionally, we analysed bacterial and fungal community structures via DNA metabarcoding, and estimated microbial biomass using qPCR during the decomposition process. The highly melanised necromass showed limited mass loss and reduced enzymatic activity, indicating greater recalcitrance. Contrasting C:P and C:N ratio profiles during the decomposition of the two types of substrate suggest that melanin plays a key role in the decomposition dynamics of the fungal necromass, while P and N do not appear to be determining factors in this process. Copiotrophic bacteria and saprotrophic fungi dominated the early stages of decomposition, while in later stages, oligotrophic bacteria and certain ECM genera became dominant. Our findings confirm that fungal necromass decomposition is strongly influenced by its intrinsic chemical properties, and particularly by its melanin content. This substrate constitutes a unique ecological niche, shaping the succession of specialised microbial guilds (i.e. the fungal necrobiome).
FWCI not available — paper too recent for field-normalized citation data.
Interactions between necrobiome communities and soil chemistry in penguin carrion decomposition
Abstract not available from publisher.
FWCI not available — paper too recent for field-normalized citation data.
Bioactive Natural Products Produced by Streptomyces from the Microbiome of Cadaveric Fly Larvae
Streptomyces are prolific producers of bioactive compounds and increasingly recognized as members of insect microbiomes, yet the microbiome of cadaveric fly larvae remain an overlooked system for discovering metabolically versatile Streptomyces species. Here, we conduct targeted bacterial isolations from the microbiome of fly larvae collected from pig cadavers, generating 42 Streptomyces isolates of interest, and systematically evaluated their metabolic potential through genomic analysis, antimicrobial screening, biosynthetic gene cluster assessment, untargeted LC-MS/MS metabolomics, and compound purification. The Streptomyces isolates spanned nine species, including underrepresented lineages for which we added genomic representatives. Streptomyces from carrion fly larvae exhibited broad-spectrum antimicrobial activity and substantial BGC diversity, supported by metabolomic detection of antimycins, surugamides, and macrotetrolides. From a deep phylogenetic lineage, we purified JBIR-68 and Simamycin and demonstrated their potent anthelmintic activity against Brugia malayi microfilariae. GNPS molecular networking revealed three additional JBIR-68 analogs, establishing the first taxonomically resolved Streptomyces lineage capable of producing these rare metabolites. Our findings position cadaveric fly larvae as a rich ecological reservoir for discovering Streptomyces with the potential to produce chemically diverse natural products with biomedical applications.
FWCI not available — preprint, no citation data.
Dietary Specialisation Shapes Gut Bacterial Diversity in Dung Beetles: Insights From Coprophagy to Millipede Carnivory
Dung beetles are ecosystem engineers, providing ecosystem services like nutrient cycling, waste degradation and parasite suppression. Their gut microbiome is essential for exploiting specialised diets, yet the eco-evolutionary factors driving microbial composition across diverse feeding strategies remain ambiguous. Here, we show that diet strongly influences gut bacterial composition across seven dung beetle species specialising in coprophagy, necrophagy, detritophagy, fungivory and carnivory. Most dietary specialisations grouped separately, though fungivores clustered with carrion and millipede feeders. The millipede-feeding species, Sceliages brittoni and S. hippias, hosted the most distinct and least diverse gut microbiomes. Taxonomically, differences were driven by distinct marker taxa, many of which are consistently isolated across taxonomic orders with similar diets. For example, the indicative bacterial species I. indica has been identified in various flesh-feeding insect taxa. Crucially, this pattern of shared bacterial communities suggests that diet is a dominant structuring factor which promotes community convergence regardless of host phylogeny. This study highlights the role of diet in shaping the dung beetle gut microbiome and provides the first characterisation of the gut microbiota in millipede-feeding dung beetles.
FWCI not available — paper too recent for field-normalized citation data.
The Blowfly Chrysomya megacephala as a Vector of Pathogens Associated with Infectious Diseases
Chrysomya megacephala is a synanthropic fly with a high potential to act as a mechanical vector of pathogenic bacteria, surpassing Musca domestica in both bacterial load and diversity. Native to Asia and Africa, it has become a cosmopolitan species, successfully adapting to a wide range of environments, including natural ecosystems. In Colombia, studies on its role as a vector are limited and have largely relied on traditional culturing methods. This study aimed to characterize the pathogenic bacterial microbiota associated with C. megacephala using 16S rRNA gene sequencing in urban, rural, and forest settings of a coastal tourist city. Flies were collected using Van Someren Rydon traps with attractants and sterile materials. Bacterial identification was performed through Oxford Nanopore MinION sequencing. A total of 49 bacterial species were identified, with urban environments showing the highest taxonomic richness. The forest environment was characterized by a highly dominant community structure, led by Vagococcus carniphilus. Notably, 20 bacterial species of public health relevance were detected, including Clostridium botulinum, Clostridium perfringens, Ignatzschineria ureiclastica, Escherichia coli, and Streptococcus agalactiae. These findings indicate that bacterial community composition varies by environment and underscore the potential role of C. megacephala as a mechanical vector, highlighting the importance of surveillance for its public health implications.
FWCI not available — paper too recent for field-normalized citation data.
Ecophysiological Profiling of Ignatzschineria larvae Isolated from an Aquatic Insect: pH, Salinity, Thermal, Radiation, and Antibiotic Tolerance
Ignatzschineria larvae are a recently characterized bacterium with limited ecophysiological data and are proposed as a potential microbial biomarker for insect colonization. We isolated I. larvae (strain MW602513) from the gut of an aquatic insect and assessed their tolerance and antibiotic susceptibility (Kirby-Bauer, CLSI/EUCAST) to pH (3–11), NaCl salinity (0.5–10%), temperature (4–55°C) and ultraviolet radiation. Inhibition zones were interpreted according to current breakpoints. The isolate exhibited robust growth at pH 6–7, low salinity (≤ 2%) and moderate temperatures (30–37°C); there was no growth at 10°C or 50–55°C, and a significant growth reduction was observed at ≥ 5% NaCl. Bacteria were observed to not grow under UV radiation applied for 5 minutes. Resistance to various antibiotic groups tested was observed. The results demonstrate that the bacteria can adapt to mesophilic environments with low salinity and neutral to alkaline pH, highlighting their ecological resilience and potential impact on ecosystems.
FWCI not available — paper too recent for field-normalized citation data.
Comparative Effects of Snake Envenomation on Rabbit Carcass Decomposition and Insect Succession in a Forensic Context
Snake envenomation significantly influenced decomposition kinetics and arthropod colonization patterns. Envenomation with C. cerastes venom produced more pronounced alterations than envenomation with N. haje venom.
FWCI not available — paper too recent for field-normalized citation data.
Endogenous and Exogenous Small RNA Signatures as Novel Tools for Postmortem Interval Determination
These findings highlight the potential of integrated endogenous and exogenous sRNA analysis in PMI estimation, providing a high-precision, rapid diagnostic tool and revealing complex postmortem molecular processes.
FWCI not available — paper too recent for field-normalized citation data.
Top 100 Papers
All microbiome-related papers from March 2026 ranked by FWCI, searchable by title, author, journal, or topic. The broad keyword sweep picks up some off-topic results; the FWCI ranking and journal filter are the most reliable way to find relevant work.
Most Cited Papers from March 2026 Literature
These are the papers most frequently cited by March 2026’s microbiome literature. Not papers published this month, but the foundational work the field was actively referencing. Citation counts here mean “how many of March’s papers cited this work,” not cumulative lifetime citations.
The list skews heavily toward methods tools, which tracks with Methods & Bioinformatics being the dominant topic. DADA2, QIIME2, fastp, Bowtie2, phyloseq. This is essentially a snapshot of the standard methods stack the field is running on right now. Bar color reflects overall FWCI (log scale); the tools at the top aren’t just widely cited this month, they’re among the most field-normalized papers in all of biology.
Papers most frequently cited by March 2026 microbiome publications. Bar length = times cited within this month's corpus; color = overall FWCI on a log scale. Hover for full title. Data from OpenAlex.
Publication data sourced from OpenAlex. Topic classifications are automated keyword-based groupings and may not perfectly reflect each paper’s primary focus. FWCI (Field-Weighted Citation Impact) normalizes citation counts by research field and paper age. A score of 1.0 is average; higher values indicate above-expected citation rates for papers of that age.