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Results for “scientific communication and education”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2026

Evaluating Large Language Models as Tools to Navigate Researchers in Rapidly Evolving Research Landscapes: A Case Study in Cancer Drug Response Prediction

Large Language Models (LLMs) have emerged as promising tools for assisting researchers in automating and accelerating the synthesis of literature reviews. However, their reliability is a significant concern due to issues like factual inaccuracies and hallucinations. The key question is whether LLMs can reliably provide comprehensive, up-to-date overviews and analyses. This study evaluates the performance of three leading LLMs (OpenAI's ChatGPT, Google's Gemini, and DeepSeek) on the complex task of generating a comprehensive survey paper on deep learning for cancer Drug Response Prediction (DRP). By testing both standard and Deep Research (DR) / Deep Think (DT) modes of LLMs with prompts of varying detail, this paper assesses key academic dimensions, including reference management, content quality, and analytical depth. Key findings reveal that while DR modes of LLMs significantly improve reliability by eliminating hallucinations, performance variations exist across models and prompts. A trade-off between reference quantity and integration quality was observed, and even the best-performing models lacked the analytical depth of human experts, often requiring extensive human supervision. The study concludes that LLMs currently serve as powerful assistive tools but still cannot replace the critical validation and synthesis provided by human researchers. Choosing the best LLM to use depends on the task in hand, while several strategies can be implemented to improve the produced output.

scientific communication and education↗

bioRxiv2026

From Prompt to Provenance: BloClaw, a Capability-Gated AI4S Workstation for Auditable Computational Biology

Scientific agents can produce plausible answers while remaining unable to establish whether the computation behind an answer is executable, recoverable, or reproducible. We present BloClaw, an AI4S workstation built around a simple principle: a scientific agent should know what it can do, show how it did it, and state what remains unvalidated. Each capability declares an execution state, input constraints, dependencies, expected outputs, and scientific limitations. Natural-language requests are translated into structured tasks, validated against this registry, executed through scientific tools, and recorded in a provenance-aware Living Lab Notebook. The system is designed to detect invalid inputs, failed tool calls, missing dependencies, and remote timeouts, and to route them to repair, retry, or escalation. The implemented and tested scope comprises RDKit-based molecular property and rule screening, protein structure analysis, docking-pose inspection, 3D visualization, and structured reporting. We demonstrate the workflow on a PubChem-retrieved osimertinib structure and a supplied 6LU7 docking artifact: the former yields deterministic descriptors (molecular weight 499.619 Da, cLogP 4.5098, TPSA 87.55 A^2), while the latter contains 2,387 protein ATOM records, 309 residues, and nine pose records. These examples are workflow demonstrations, not efficacy or affinity studies. Beyond retrospective prediction, the manuscript specifies a prior-minimized constructive mode in which a desired function is compiled into explicit physical, chemical, and systems constraints, candidate mechanisms are simulated, and observations are reintroduced for calibration and falsification; this is a proposed extension rather than a result of the present case studies. We describe an evaluation protocol that compares BloClaw with a standard single-agent workflow and fixed-script execution using task completion, scientific correctness, recovery success, provenance completeness, reproducibility, human review time, latency, and cost. This manuscript reports the system design, verified capability boundary, deterministic software artifacts, and a reproducible evaluation protocol; it does not claim benchmark improvements before those experiments are run. BloClaw is an execution and accountability layer for AI-assisted research, complementing expert review and experimental validation rather than replacing them.

bioinformatics↗

bioRxiv2026

The Anti-Cancer Effects of Selected Indigenous Medicinal Plants of the Arid Bioregion

Ethnopharmacological relevance: Australian Indigenous medicinal plants represent a valuable yet underexplored source of bioactive compounds with potential therapeutic relevance. The Iningai community of Central Queensland has traditionally used native plants to manage conditions associated with inflammation, pain, infection, and general illness. Scientific evaluation of these plants may provide evidence for their customary applications and identify bioactivities relevant to anticancer biodiscovery. Aim of the study: This study evaluated leaf and stem extracts of seven medicinal plants-Pittosporum angustifolium, Alphitonia excelsa, Calytrix microcoma, Geijera parviflora, Melaleuca uncinata, Gossypium australe, and Eucalyptus similis-traditionally used by the Iningai community, focusing on three biological processes relevant to cancer: oxidative stress, inflammation, and cellular proliferation. Materials and methods: Antioxidant activity was assessed using DPPH radical-scavenging and ferric reducing antioxidant power (FRAP) assays. Anti-inflammatory activity was evaluated in lipopolysaccharide (LPS)-stimulated THP-1 macrophage-like cells by profiling IFN-, TNF-, IL-6, IL-12, IL-18, and IL-23. Antiproliferative activity was assessed using MTT-based viability assays in human and murine liver cancer cell lines (Huh7, Hep3B, Hep-55.1c, and A52). Results: The extracts exhibited distinct biological activity profiles. G. parviflora stem and C. microcoma leaf extracts showed the strongest antioxidant activities, whereas P. angustifolium stem exhibited the weakest radical-scavenging capacity. Cytokine responses were extract-specific, with E. similis leaf extract demonstrating broad and pronounced suppression of multiple LPS-induced pro-inflammatory cytokines. Several extracts produced concentration-dependent reductions in liver cancer cell viability, with P. angustifolium stem exhibiting the most consistent and potent antiproliferative activity across the cell lines tested. Notably, strong antioxidant or anti-inflammatory activity did not necessarily correspond with antiproliferative activity. Conclusion: Australian Indigenous medicinal plant extracts demonstrated distinct antioxidant, immunomodulatory, and antiproliferative activities rather than uniform bioactivity across experimental systems. The divergent activities of G. parviflora, C. microcoma, E. similis, and P. angustifolium highlight the importance of integrated biological screening and support the value of Indigenous knowledge-guided biodiscovery. These plants represent promising sources for further investigation of selective bioactive compounds with potential relevance to anticancer drug discovery.

cancer biology↗

bioRxiv2026

Automatic bioinformatic software named entity recognition from literature

Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale. The lack of a comprehensive and up-to-date catalog of bioinformatics resources hinders efforts toward automated biomedical knowledge extraction and streamlined data analysis. Here we present SNAIL, a hybrid named entity recognition framework designed to automatically identify bioinformatics software and database (SW/DB) names from biomedical texts. SNAIL integrates complementary lexical and semantic modeling strategies. The lexical component captures orthographic patterns and contextual cues characteristic of SW/DB names, while the semantic component leverages contextual embeddings generated by transformer-based language models such as SciBERT, combined with an explicit token-masking strategy to enhance entity-focused representations. A large training corpus was constructed automatically through a hybrid pipeline that integrates citation-hinted extraction with large language model-assisted distillation. Evaluation on two independent benchmark datasets and real-world research articles demonstrates that SNAIL substantially outperforms existing approaches, including domain-specific methods such as bioNerDS2 and general-purpose large language models such as ChatGPT, Gemini, Grok and Claude. Applying SNAIL to large-scale literature analysis further reveals distinct journal-level preferences across bioinformatics subfields. These results demonstrate that SNAIL provides an accurate and scalable solution for identifying bioinformatics resources in scientific texts and enables systematic meta-analysis of tool usage and research trends.

bioinformatics↗

bioRxiv2026

Persistent but variable effect of experimental laboratory burns on microbial community resistance, resilience, and function across contrasting boreal forest soils

Boreal forests stretch across vast swaths of the northern hemisphere, are shaped by wildfire, and play an important role in the global carbon cycle. Microorganisms play a critical role in soil nutrient cycling in these ecosystems, yet there are many open questions about the impacts of wildfire on microbially mediated soil biogeochemical cycles. In this study, we used laboratory burns and soil incubations of intact soil cores collected from two distinct soil types -- Histosols and Gleysols -- from boreal forest within Wood Buffalo National Park, Alberta, Canada, to assess burn effects on soil bacterial and fungal community composition and function. We compared resistance and resilience to burning for microbial communities vs. resistance and resilience to burning for soil pH and soil respiration to assess the relationships between burn-induced shifts in microbial community composition, the soil environment, and microbial activity. To link shifts in microbial community composition to potential community function, we measured glucose-specific carbon use efficiency (CUE) and assessed its relationship with weighted mean predicted 16S rRNA gene copy numbers for bacterial communities and FUNGuild-estimated relative abundance of putative symbiotrophic and saprotrophic fungi in burned and unburned soils. Microbial community resistance and resilience to burning varied across soil type with higher resistance of both bacterial and fungal communities from Histosols compared to the O horizons of Gleysols. This may be explained by a larger impact of burning on microbes in the thinner Gleysol O horizons. The relatively low resilience of bacterial and fungal communities to burning as well as the failure of resilience to increase with time since burning supports previous reports of post-burn microbial community recovery occurring over years rather than months. Burning caused a decrease in CUE with larger decreases following longer, hotter burns, which correlated with an increase in weighted mean predicted 16S rRNA gene copy number, raising the possibility that copy number could serve as a proxy for post-fire CUE in boreal forest soils, though more research is needed to constrain the effects of environmental conditions, substrates, and time since fire on this relationship. These findings suggest several ways in which burn-induced shifts in microbial community composition reflect altered microbial community function in meaningful ways for soil carbon cycling.

ecology↗

bioRxiv2026

OMICON: a community resource for studying gene coexpression networks in normal and neoplastic human brain samples

Genome-wide coexpression analysis of intact tissue samples is a powerful approach for identifying reproducible signatures of cell types and states, since it can survey vast numbers of individuals, cells, and transcripts. However, it can be difficult to optimize gene coexpression network construction and compare results from independent analyses. To address these challenges, we developed OMICON (theomicon.ucsf.edu) for research on human brain gene coexpression networks. OMICON contains gene expression data from >17K normal and neoplastic human brain samples with standardized metadata. Systematic analysis of independent datasets identified >250K gene coexpression modules, which were characterized and compared via enrichment analysis with >40K gene sets. All modules are discoverable via an advanced search engine that can filter by genes, metadata, and enrichment results. Analyses can also be browsed with an interactive workflow visualization tool, and users can communicate within OMICON using @mention functionality to support communal research on human brain gene coexpression networks.

neuroscience↗

bioRxiv2026

Cross-species analysis links cell-cell communication rewiring to NOTCH2 during serous endometrial carcinogenesis

Cell-cell interactions shape the fate of mutant cells during cancer initiation but how these interactions evolve during progression to pathologically recognizable lesions remain poorly understood. Here, we investigated cell-cell communication during serous endometrial carcinoma (SEC; also known as uterine serous carcinoma) development using a lineage-traceable mouse model and cross-species analyses of the mouse and human neoplastic endometrium. In mice, the early, pre-dysplastic stage was marked by a global decrease in inferred cell-cell interactions, followed by extensive communication network rewiring during neoplastic progression. Pathway-specific analysis revealed a similar pattern for NOTCH signaling, with NOTCH2 emerging as the dominant NOTCH receptor in Trp53/Rb1-mutant immature epithelial cells. Functionally, NOTCH2 promoted the outgrowth of more proliferative mutant organoids. Cross-species transcriptomic analysis identified conserved immature epithelial states in mouse and human neoplastic endometrial epithelium. In human tissues, NOTCH2 was overexpressed in serous endometrial intraepithelial carcinoma, a precursor of SEC, and in overt SEC. Furthermore, elevated NOTCH2 expression was associated with poor patient survival. These findings link cell-cell communication rewiring during experimental SEC development to conserved neoplastic epithelial states and identify NOTCH2 as an early marker and a potential target of disease interception.

cancer biology↗

bioRxiv2026

Mitochondrial transfer mediates metabolic communication between beta cells and islet macrophages

Pancreatic islet macrophages support islet homeostasis and adapt their metabolic program in response to environmental cues, including beta cell released factors. Intercellular mitochondrial transfer is a biological process that modulates cellular responses. To test whether beta cells, which are strongly secretory, transfer mitochondria to islet macrophages, we generated mice with beta cell-specific expression of mitochondrial GFP (PhAMfloxIns1Cre). We demonstrate that beta cells transfer mitochondria to islet macrophages in vivo and in vitro. Diabetogenic stressors did not alter the frequency of mitochondrial transfer and macrophages containing beta cell-derived GFP exhibit increased protein synthesis rates. RNA-seq identified upregulation of activity-regulated cytoskeleton associated protein (Arc) in macrophages receiving beta cell-derived mitochondria, while disruption of actin cytoskeleton dynamics prevented mitochondrial transfer. Together, these findings identify mitochondrial transfer as a previously unrecognized mechanism of beta cell-macrophage communication that may contribute to islet homeostasis and immune regulation.

cell biology↗

bioRxiv2026

Plaque microbial community restructuring in rampant dental caries after exclusion of a confirmed Streptococcus mutans ASV: an analysis of public 16S rRNA sequencing data

Background: Dental caries is increasingly understood as an ecological biofilm disorder rather than the consequence of a single organism. Although Streptococcus mutans is strongly implicated in cariogenesis, it remains unclear whether caries-associated plaque-community differences persist beyond this organism. Methods: We reanalysed publicly available supragingival-plaque 16S rRNA sequencing data from 88 preschool children with rampant caries (n=44) or who were caries-free (n=44; BioProject PRJNA1141721). Single-end DADA2 processing yielded 25,669 amplicon sequence variants (ASVs), including one ASV confirmed as S. mutans by an eHOMD reference-window procedure. The pre-specified primary analysis compared Bray-Curtis community composition after exclusion of this ASV. Results: Non-S. mutans community composition differed between groups (PERMANOVA pseudo-R2=0.0462, pseudo-F=4.16, P<0.001), without evidence of unequal multivariate dispersion (P=0.796); rarefaction produced a nearly identical result. Shannon diversity did not differ (P=0.486). The confirmed S. mutans ASV was detected in 8/44 rampant-caries and 42/44 caries-free samples and was lower in abundance in rampant caries. Among 758 prevalence-filtered non-S. mutans ASVs, 239 showed conventional FDR-significant differential abundance, with more showing lower than higher bias-corrected abundance in rampant caries (176 versus 63); 239 additional ASVs were classified as structural zeros. Individual ASV findings were sensitive to prevalence filtering. Adjustment for S. mutans abundance attenuated the global caries-group association (marginal pseudo-R2=0.0149, P=0.085) in the presence of strong collinearity. Conclusions: Rampant caries was associated with modest but reproducible plaque-community restructuring after exclusion of a confirmed S. mutans ASV, without a corresponding Shannon-diversity difference. These findings support a community-level ecological interpretation but do not establish statistical independence from S. mutans or a causal role for individual taxa.

microbiology↗

bioRxiv2026

VLCFA-mediated inter-cell layer communication controls cellular pluripotency in Arabidopsis callus

Plants have remarkable capacity to reconstruct entire organ systems from tissue explants. In Arabidopsis two-step tissue culture system, pluripotency regulators are specifically expressed in the middle-cell layer of the stratified callus tissue. However, regulatory mechanisms underlying the radial patterning of callus remained unclear. Here, we found that very-long-chain fatty acids (VLCFAs) synthesized in the epidermis-like outermost layer are essential for pluripotency acquisition and successful shoot regeneration. Our genetic and transcriptomic analyses revealed that the regulatory roles of VLCFAs on pluripotency acquisition involve inter-cell layer signaling in callus tissue, while they are at least partly independent of ATML1/PDF2 functions and cuticular wax synthesis in the outermost layer. VLCFAs spatially restrict procambium cell identity by non-cell-autonomously suppressing cytokinin signaling, thereby allowing for establishment of the middle-cell layer. We propose that the inhibitory relationships between layer-specific regulators underlie the intricate balance of cellular fate determination in pluripotent callus.

plant biology↗

bioRxiv2026

From Bile Acids to a Gas-Producing Microbiome Phenotype: A Novel Mechanism of Host-Microbiome Communication

Background Microbiome-derived metabolites regulate host physiology, yet bacterial gaseous metabolites remain largely overlooked. Traditionally regarded as fermentation end-products, bacterial gases may act as biologically active mediators of host-microbiome communication. We hypothesized that bile acids regulate bacterial gaseous metabolism and influence host epithelial responses. Methods A high gas-producing clinical Escherichia coli isolate from a patient with moderately severe acute pancreatitis was cultured with selected primary and secondary bile acids. Gas production was assessed by pressure measurements, GC-TCD and GC-MS. Biological activity was evaluated by indirect exposure of Caco-2 and PANC-1 epithelial cells, followed by apoptosis/necrosis assays and whole-transcriptome RNA sequencing. Results Bile acids markedly reshaped bacterial gaseous metabolism. Cholic acid and deoxycholic acid promoted intense gas production, whereas chenodeoxycholic acid almost completely abolished it. Despite minimal apoptosis and necrosis, bacterial gaseous metabolites induced extensive transcriptional remodeling. Caco-2 cells showed stronger responses than PANC-1 cells, particularly to deoxycholic acid-derived gases, involving inflammatory signaling, extracellular matrix remodeling, epithelial plasticity, stress responses, and cancer-associated genes including PTGS2, MMP1, PLAUR, NR4A2, and SERPINE1. PANC-1 cells exhibited a more restricted response involving oxidative stress, proteostasis, and autophagy-associated pathways. Conclusions Our findings indicate that bacterial gases are a previously underrecognized class of microbiome-derived signaling molecules capable of modulating host gene expression independently of direct bacterial contact. We identify a gas-producing microbiome phenotype regulated by bile acid composition, linking microbial metabolism with epithelial signaling. These findings expand the concept of host-microbiome communication and provide a framework for investigating bacterial gaseous metabolites in intestinal and pancreatic diseases.

microbiology↗

bioRxiv2026

Spatial profiling and neurovascular communication in the developing and adolescent cortex following prenatal alcohol exposure

Fetal alcohol spectrum disorders (FASD) constitute a wide range of developmental, cognitive, and behavioral impairments caused by prenatal alcohol exposure (PAE). Although neuronal and vascular consequences of PAE have been studied, how alcohol affects the cerebrovasculature within the framework of the neurovascular unit (NVU) across development remains poorly understood. At minimum, the NVU comprises neurons, astrocyte endfeet, and endothelial cells (ECs), which coordinate to maintain brain homeostasis. Here, we used the NanoString Digital Spatial Profiling platform to characterize spatial transcriptomic data from neurons, astrocytes, and ECs from PAE and saccharin (SAC) control cortices at embryonic day 18 (E18) and postnatal day 28 (P28). Differentially expressed genes were then used for Ingenuity Pathway Analysis (IPA) to identify altered biological pathways and perform comparison analyses across developmental time points, while CellChat was used to infer cell cell communication networks. We uncovered thousands of differentially expressed genes and numerous altered pathways and biological processes in PAE cortices across development. Both IPA and CellChat analyses implicated dysregulation of vascular and extracellular matrix (ECM) remodeling, cell adhesion, and neuroinflammatory signaling. CellChat further predicted the loss of several key bidirectional relationships and altered ligand-receptor interactions among neurovascular cell types at E18 and P28. Overall, these findings identify PAE associated alterations in neurovascular gene expression and intercellular signaling across development, providing potential mechanisms by which PAE may disrupt neurodevelopment.

molecular biology↗

bioRxiv2026

Warm temperature impedes the spread of a heritable manipulative symbiont community in spider populations

Heritable bacterial symbionts are pervasive in terrestrial arthropods, often imposing reproductive manipulations to promote their own spread within host populations. Co-infections are common, potentially allowing symbiont co-infectors to hitchhike through a host population. However, adverse thermal conditions can disrupt these communities, particularly when co-infectors vary in their thermal sensitivity. We used a multi-generation experiment to test whether warm (29 {degrees}C) conditions disrupted spread of heritable symbionts through uninfected populations of the spider, Mermessus fradeorum. We tested two common infection combinations: a single infection with a cytoplasmic incompatibility (CI) inducing Rickettsiella or a feminizing co-infection that included a feminizing Wolbachia, the same Rickettsiella, and up to three apparent hitchhikers (two additional Wolbachia strains and Tisiphia). We initiated replicate populations with 1/3 of one infection type and 2/3 uninfected spiders, evaluating population infection rate over 5 spider generations under different temperature regimes. Under cool (21{degrees}C) conditions, Wolbachia feminization drove co-infection to 88% and Rickettsiella CI drove single infection to 83% of host populations. Vertical transmission for all symbionts was high (97-99%) and hitchhiking symbionts also spread effectively. Under warm conditions, feminization and CI efficacy were reduced, and symbionts suffered variably reduced vertical transmission. Warm conditions ultimately destroyed the co-infecting symbiont consortium and impeded symbiont spread. On its own, though, Rickettsiella was still able to increase, despite reduced strength of CI. We hypothesize that contrasting tensions between feminizing spread of the symbiont consortium versus environmentally driven loss of function and transmission may explain observed patterns of mixed infections in field populations of this spider.

ecology↗

bioRxiv2026

Developments in the European parasitoid community of Dryocosmus kuriphilus

The invasive gallwasp Dryocosmus kuriphilus was first detected in Italy in 2002, although likely to have initially arrived in the late 90s. Its ability to utilise sweet chestnut species non-native to its original Chinese range has allowed it to spread rapidly, and throughout Europe via European sweet chestnut Castanea sativa. Given the severity of its impact on C. sativa crop production, particularly in Mediterranean countries, previous studies have aimed to assess damage levels caused by D. kuriphilus, the efficacy of and potential non-target effects of the introduced biocontrol agent Torymus sinensis, and the possibility of regulation by native parasitoids. As yet a broad overview and analytical synthesis of these native parasitoid communities are absent. This review focuses on important aspects of the D. kuriphilus invasion. In particular, the invasion history and currently known distribution of D. kuriphilus, and several aspects of its associated parasitoid community. For native species to plausibly suppress D. kuriphilus, we might expect rates of parasitoid attack to increase with establishment time as native populations adapt to exploit the new resource, and this is a key focus of the review. We answer the following questions: 1) What is the distribution of D. kuriphilus in Europe, and has D. kuriphilus fully utilised the available niche space within its 20+ years in Europe? 2) Which species of native parasitoids attack D. kuriphilus in Europe and what are their ecological characteristics? 3) How consistent is the parasitoid community of D. kuriphilus across its range, and are there signs of convergence over time? 4) What effect does establishment time have on the species richness and abundance of parasitoid communities? We report the following: 1) D. kuriphilus has expanded its range throughout Europe and is present in nearly every major region where sweet chestnut is present. Native and non-native naturalised chestnut forests may be less susceptible to invasion than areas of industry due to differing socioeconomic and ecological factors, though areas with large chestnut industries also tend to be in the most heavily forested areas in the non-native range of sweet chestnut. D. kuriphilus has reportedly been eradicated from some countries, and effectively eradicated in a number of countries implementing biocontrol with T. sinensis, although successive invasions from neighbouring regions are still possible, and eradication may be transient. 2) 72 parasitoid species are identified attacking D. kuriphilus in Europe (far more species than any other gallwasp in the Western Palearctic). Its members are predominantly oak gallwasp parasitoids (82% of species), followed by gall-specialists of different host plants, leaf miner parasitoids and a minority of others with differing host life stages and ecologies. Parasitoids attacking D. kuriphilus are dominated by idiobiont ectoparasitoids of the superfamily Chalcidoidea (>96%). 3) The parasitoid community is highly variable, both temporally and spatially, although the vast proportion (>95%) of parasitoids at any one time are composed of locally common generalist oak gall parasitoids. The most common members include Bootanomyia dorsalis, Eupelmus urozonus, Eurytoma brunniventris, Mesopolobus sericeus and Torymus flavipes. 4) The length of establishment time has minimal effect on the species richness, abundance, and composition of the community, suggesting that regulation by natives, if it occurs, may take longer than the 20+ years that D. kuriphilus has persisted. While little evidence of increasing parasitoid attack of D. kuriphilus is apparent, we exercise caution by stating that the heterogeneity in available data are large, and that common biocontrol interventions using T. sinensis interrupt the natural process of community development dramatically. D. kuriphilus has been present in Europe for nearly three decades and few localities have repeated years of data collection. Even fewer studies have communities with establishment times exceeding ten years. Proper biocontrol by natives may not occur within short timeframes, although studies of other gallwasp invaders find similar results over periods exceeding 40 years. Given that many countries have chosen to implement T. sinensis for biocontrol, the focus may be better spent monitoring native gall communities for potential non-target effects.

ecology↗

bioRxiv2026

Convergent stochastic assembly governs reef biofilm microbiomes across ecologically distinct benthic substrates

Understanding the processes that shape microbial biodiversity and community structure is a key objective of the field of microbial ecology. The processes driving assembly of benthic biofilm bacteria on functionally important reef substrates, such as crustose coralline algae (CCA) and calcium carbonate, are not well understood, despite their critical contributions to the maintenance of biodiversity and ecosystem function on reefs. To characterize the patterns of community assembly and biogeography on these substrates, climax biofilm bacterial communities from 11 reef sites were collected, and full 16S small subunit rRNA genes were sequenced. Though CCA- and carbonate-associated communities demonstrated different diversity, composition, and correlations with environmental conditions, communities on both substrates were assembled according to similar processes. Stochastic processes dominated assembly on both substrates, primarily drift with moderate influence from dispersal limitation and selection. Sub-communities of habitat generalists and specialists, as well as rare and abundant taxa, experienced disparate patterns of assembly that remained consistent between substrates, highlighting the importance of individual taxa traits in shaping community assembly. These results provide insight into the factors shaping benthic biofilm bacterial assembly and biogeography in a tropical reef ecosystem and contribute to understanding of reef resilience in the face of environmental change.

ecology↗

bioRxiv2026

Taxonomic classification cost tracks neither sequencing depth nor community richness at single-sample scale: a measured resource protocol for 16S rRNA amplicon pipelines

Marker-gene amplicon workflows are routinely run on shared compute, yet the cores, memory and wall time they are given are chosen by convention and not by measurement. We present a protocol for measuring them, applied to the two dominant stages of a QIIME 2 16S rRNA pipeline, DADA2 denoising and Naive Bayes taxonomic classification, across nine upper-respiratory samples from a paediatric otitis media cohort. The two stages do not consume the same input: denoising reads every sequence, classification only those surviving it. Subsampling one library across a 27-fold range of sequencing depth, denoising wall time rose 14.3-fold while classification changed by 1% and its peak memory not at all (3.11 GiB). Amplicon sequence variant (ASV) richness rose 2.8-fold over that range, so this is not richness saturating: the stage is dominated by a fixed per-invocation cost. Across a body-site gradient of 5 to 70 ASVs, denoising followed read count (exponent 0.75) while classification followed neither: a 5-ASV effusion and a 70-ASV adenoid community cost 40.81 s and 40.79 s. One ASV took 36.20 s and 218 took 37.27 s, 97% fixed cost. Thread-level parallelism offered little benefit. Denoising peaked at 1.18x near 8 threads and then declined; classification was slower at every setting above one job, consuming 10.5 times the CPU at 40. Representative sequences and their taxonomic assignments were identical at 1, 4 and 40 threads, so a reduced allocation changes what the analysis costs, not what it reports. Extending the query set to 10,000 sequences located two distinct boundaries: eight jobs first beat one at roughly 5,000 queries, and fitted fixed and per-query costs become equal at 15,248. Both lie roughly two orders of magnitude above the richest single sample measured. Practically: size denoising by read count, calibrate classification once against the reference in use, request one job for classification below a few thousand sequences, and take throughput from sample-level parallelism. Protocol, data and analysis code are released with the pipeline.

bioinformatics↗

bioRxiv2026

A strong-to-weak interaction shift during microbiome succession is coupled to colonizer-dependent antimicrobial resistance

The outcome of ecological succession is often attributed to the characteristics of the invader or the resident community, but rarely to how the community's interaction network reorganizes during assembly. Here, we track intraspecific lineage dynamics and infer time-resolved community interaction networks using Dynamic Covariance Mapping during ecological invasion of the mouse gut by a chromosomally barcoded, spectinomycin-resistant Escherichia coli K12 colonizer. The network is initially dominated by strong, predominantly inhibitory interactions, but as community diversity recovers, the distribution of interaction strengths contracts toward zero, producing a community increasingly dominated by weak and near-neutral interactions. The dominant eigenvalue of the DCM-inferred interaction matrix moves toward marginal stability predicted for dynamically assembling ecological networks. This pattern replicates across eight independent mice in two experimental cohorts, at both inter- and intra-species resolution. The ecological transition coincides with the reproducible resurgence of Paenibacillaceae to high relative abundance and persistent coexistence with E. coli under continued spectinomycin pressure. Whole-genome sequencing of recovered Paenibacillus macerans isolates identifies recurrent mutations in ribosomal protein S5 region associated with spectinomycin binding and strongly implicating this variant in resistance. Strikingly, under antibiotic pressure but without E. coli K12 invasion, resident Paenibacillaceae never blooms, indicating that expansion of the resistant population depends on the ecological context established by the colonizer. These findings show that gut microbiome succession is accompanied by a reproducible transition from strong toward weak interactions and link this network reorganization to the colonizer-dependent ecological benefit of antimicrobial resistance.

ecology↗

bioRxiv2026

Increased substrate complexity drives re-diversification and functional reorganization in simplified methanogenic consortia

Anaerobic digestion is a sustainable process for methane production that relies on complex microbial networks. While simplified enriched consortia offer a promising strategy to improve process control, excessive simplification can disrupt key functions and microbial partnerships, reducing community resilience. In this study, we investigated whether simplified methanogenic communities could re-diversify and maintain methane production when exposed to more complex substrates, namely butyrate and glucose. We also evaluated the effect of vitamin and amino acid supplementation on sustaining key methanogens and beneficial microbial partners. Three methanogenic communities were monitored over three months for methane production and microbial diversity while receiving butyrate and/or glucose, with different vitamin or amino acid supplements. Exposure to more complex substrates successfully restored the diversity of acidogenic and acetogenic populations, even after prolonged feeding with simple substrates, highlighting both the resilience of the simplified communities and the ecological importance of low-abundance taxa. However, the transition reduced process stability and methane production, likely due to substrate overloading. The results further suggest that substrate complexification should be introduced stepwise, promoting acetogenesis before acidogenesis. This fundamental study brings new light on which factors must be considered in the long-term goal of designing tailored-made consortia for anaerobic digestion.

bioengineering↗