Biology subjects

Richter, A.

Publications and source records attributed to Richter, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Dietary omega-3 polyunsaturated fatty acids interact with select gut microbes to produce bioactive metabolites found in infant gut metabolomes

Gut microbes metabolize nutrients in infant diets, producing compounds that play roles in host health. Long-chain polyunsaturated fatty acids (LCPUFAs) are an important component of infant diets, supporting neurological development and immune regulation. Emerging evidence demonstrates that gut microbes, alongside the host, participate in the metabolism of dietary lipids, highlighting an underexplored avenue for LCPUFA biology. In this work, alkyne-tagged eicosapentaenoic acid (EPAALK) was used to investigate interactions between LCPUFAs and the gut microbiota. Flow cytometry and comparative metabolomics identified gut microbial EPA interactors in the ileum of mice. Further comparative metabolomics analysis identified the conversion of EPA to N-acyl amino acids, including attachment to phenylalanine (EP-Phe) and leucine (EP-Leu). Targeted analysis of ex vivo stool cultures determined that EP-Phe and EP-Leu are produced by gut bacteria. A survey of lipid-relevant infant gut bacteria determined various flow cytometry-confirmed EPA-microbe interactions and identified Enterococcus faecalis, Bacteroides thetaiotaomicron, and Clostridium bifermentans as competent producers of EP-Phe or EP-Leu. Thus, both novel metabolites from diet-derived inputs and microbial producers of these metabolites were identified. Together, this highlights important microbiome-centric and mechanistic consequences of LCPUFA consumption and emphasizes that the gut microbiome may be an important consideration in targeted supplementation strategies.

microbiology↗

bioRxiv2026

Chromosomal mutational signatures of DNA damaging agents at single cell resolution

The chromosomal-scale mutational spectrum of small molecules that interact with DNA has been hard to study at scale, as mutational events are distributed in location and occur in parallel in different cells. Here, we present a framework that pairs phylogenetic ancestry reconstruction with mutational signature decomposition to characterise recent, cell-private copy number alteration (CNA) mutational patterns at single-cell resolution. We used this framework to characterise the cell-wise mutational spectrum of contemporaneous CNAs generated by double-strand-break-inducing chemotherapeutic drugs. We demonstrate that platinum salts, G-quadruplex stabilizers and topoisomerase II inhibitors, although mechanistically distinct, converge on a mutational signature dominated by telomere-bounded copy-number gains and losses. This signature is observed in different genetic backgrounds and in vivo in drug-treated patient-derived xenografts. We also observe a high rate of endogenous telomere-bounded mutational foreground in BRCA1 deficient cells. We show that the single cell genome derived signature exposures are drug dose-dependent, and use this to identify the decay of mutational load after drug withdrawal. We observe that both cisplatin and a G4 binder molecule (CX5461) exhibit foreground mutational signature persistence for at least 3 weeks after drug withdrawal, suggesting that residual effects of exposure may last longer than anticipated. Finally, extending the framework to serially drug-treated patient-derived xenograft (PDX) models, we show that telomere-bounded CNA signature exposure is associated with tumoural response to drug, consistent with loss of mutational activity on the genome after acquired resistance emerges. Together, our results show that our framework applied on scWGS identifies contemporaneous chromosomal mutation patterns induced by small molecules in human tissues.

cancer biology↗

bioRxiv2026

Defining a New Standard: Human Platelet Lysate Supports Proliferation and Differentiation of Primary Respiratory Epithelial Cells

Air-liquid interface (ALI) cultures consisting of well-differentiated primary respiratory epithelial cells (PRECs) provide a versatile in vitro model for pharmacological studies and to investigate host-pathogen interactions. Proliferation and differentiation of PRECs require complex media containing several growth factors, hormones, and nutrients. Usually, some of these essential components are provided by the addition of fetal calf serum (FCS). However, several disadvantages of FCS and, most importantly, ethical concerns regarding the method of serum collection have encouraged researchers to find alternatives. Human platelet lysate (hPL) has emerged as a promising alternative to FCS for supporting cell expansion in vitro. In the present study, we investigated the effects of different concentrations of hPL on the proliferation of porcine PRECs and their subsequent differentiation under ALI conditions. Cell morphology was assessed by phase-contrast microscopy, while cell proliferation was evaluated using the ClickTech EdU Cell Proliferation Kit and visualization of proliferating cells by fluorescence microscopy. Differentiation under ALI conditions was monitored by immunofluorescence staining of ciliated cells and the establishment of an intact epithelial barrier was confirmed by measuring transepithelial electrical resistance (TEER). We found that 5% hPL supported efficient cell growth and the subsequent formation of a functional, well-differentiated airway epithelium comparable to or even better than 10% FCS. Thus, hPL offers a reproducible, ethically sound, and scalable alternative to FCS for complex cell culture models in respiratory research, drug development, and host-pathogen interaction studies. LO_SCPLOWAYC_SCPLOW SO_SCPLOWUMMARYC_SCPLOWRespiratory epithelial cells from the lungs of slaughtered animals, such as pigs, can be used for cell culture models to study respiratory diseases and drug development. Air-liquid interface (ALI) cultures closely mimic the natural environment of the airways by exposing the cells to air, making them a valuable alternative to animal experiments. To grow and mature properly, these cells require nutrients and growth factors that are commonly supplied by serum from unborn calves (FCS). However, for ethical and scientific reasons, the use of FCS should be avoided. Therefore, we evaluated whether human platelet lysate (hPL) derived from expired blood donations could replace FCS in ALI cultures. We found that adding 5% hPL to the medium supported efficient cell growth and the development of a well-differentiated airway epithelium. This approach enables the use of an improved and ethically superior model of the (porcine) respiratory tract in accordance with the 3Rs principle.

cell biology↗

bioRxiv2026

Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies

Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable, in part because existing computational models do not fully capture the metabolic compatibility between donor and recipient communities. Here, we present a metagenome-scale metabolic modeling framework that quantifies metabolic niche complementarity between donor and recipient microbiomes to predict transplantation outcomes. Using MICOM-derived community metabolic models, we show that donor taxa whose metabolic flux profiles are more dissimilar from the recipient community engraft at significantly higher rates in both murine and human FMT cohorts. In a human IBS trial, metabolic models accurately predicted post-FMT community composition via leave-one-out cross-validation and recapitulated disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to demonstrate a platform for personalized donor screening. This screen identified super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition, as quantified by a flux-derived ecological network balance index that strongly predicted engraftment potential. This framework provides a mechanistic, scalable tool for rational donor-recipient matching that could guide personalized microbiome-based therapies.

microbiology↗

bioRxiv2026

Who and how much? Quantifying the role of trophic guilds in soil organic carbon mineralization

Understanding the biotic processes that drive soil organic carbon (SOC) mineralization is essential for predicting the climate warming-carbon cycle feedback. Here, we combined Tree-of-life sequencing (TOLseq; cross-domain profiling using ribosomal RNA) with quantitative conversion factors linking rRNA transcript abundance to biomass, to understand how soil food web changes affect SOC mineralization in an in situ soil warming experiment. Field observations showed that warming reduced SOC stocks, but after decades of warming SOC mineralization had acclimated. An energetic soil food web model revealed both bottom-up and top-down controls in the trophic cascades, shifting C flows from fungal and plant-associated channels towards the bacterial channel. This caused an increase in SOC mineralization rate in warmed soils of 30% per-unit biomass across the year.

microbiology↗

bioRxiv2026

Successful dendritic cell vaccines require lasting in-situ TNF α secretion to license antitumor CD8 + T cell cytotoxicity

Dendritic cells (DCs) are central to activating cytotoxic CD8 T cells, yet DC-based vaccines have achieved limited success against established tumors. To address this gap, we analyzed the transcriptomic and functional changes CD8 T cells undergo following interactions with DC subsets in lymphoid organs and tumor sites. This approach allowed us to map their trajectory from naive to fully cytotoxic effector cells. We found that classical DCs in lymphoid organs provide essential antigen presentation but fail to elicit cytotoxicity. Instead, antigenexperienced CD8 T cells require additional inflammatory signals, primarily through TNF, delivered at tumor sites by infiltrating myeloid DCs. Effective cytotoxic responses therefore depend on the synchronization of these distinct, temporally separated signals. Notably, tumor antigen-pulsed DC vaccines rapidly lose TNF expression after infiltrating tumors, limiting their efficacy. These findings establish a sequential model of T cell activation and suggest strategies to enhance the potency of DC-based immunotherapies.

immunology↗

bioRxiv2026

Smad6-mediated inhibition of BMP/TGF-β signaling disrupts midbrain growth in chick embryos

Bone morphogenetic proteins (BMPs) play an important role in dorsal spinal cord patterning. Their presence in the roof plate of the midbrain indicates a role in its development. We examined whether the BMP signaling contributes to dorsal midbrain size expansion in chick embryos by missexpressing pathway activators and inhibitors. Overactivation of BMP4 did not affect midbrain development, whereas GDF7 reduced midbrain growth. In contrast, expression of a truncated dominant-negative BMP receptor type 1b or the extracellular inhibitor Chordin had no detectable effect. Ectopic expression of SMAD6, the intracellular inhibitor of the BMP/ TGF-{beta} pathway, significantly reduced midbrain size, which correlated with decreased proliferation rates of SMAD6-overexpressing cells. In some cases, SMAD6 also disrupted MTN axon trajectory. These results indicate an important role for SMAD-dependent signaling pathways in early dorsal midbrain growth.

developmental biology↗

bioRxiv2026

Altered theta distribution and coherence during set-shifting in older age

Cognitive flexibility is an executive function that enables adapting behaviour to a changing environment and is thus critical for daily life. The degree of its preservation upon healthy aging and the neural mechanisms underlying it are still a matter of debate. To investigate the electrophysiological correlates of cognitive flexibility in older age, we measured cognitive flexibility in 99 young (24.75 {+/-} 4.45 years) and 83 older adults (69.19 {+/-} 6.25) using electroencephalography (EEG). Compared to young adults, older adults showed a more conservative response pattern with longer reaction times, but lower error rates (speed-accuracy tradeoff). In the EEG, both age groups exhibited increased theta-power during set-shifting, with a fronto-central peak in the young, but a more fronto-lateral topography in older adults. Importantly, both groups displayed increases in theta coherence and global efficiency during set-shifting, but coherence modulations were restricted in frontocentral areas in the young but were diminished and distributed across the scalp in the older. Better set-shifting performance was most strongly associated with high coherence and global efficiency irrespective of age group. These results point to an age-related change of cortical processing underlying cognitive flexibility which involves the employment of more distributed neural resources for successful task completion.

neuroscience↗

bioRxiv2025

An inositol pyrophosphate interaction screen provides insight into the regulation of plant casein kinase II

Inositol pyrophosphates (PP-InsPs) are key nutrient messengers in plants, but their protein receptors remain poorly defined. Using a systems-level affinity screen with biotinylated InsP, InsP, and InsP in Arabidopsis thaliana, we identify multiple conserved PP-InsP-interacting complexes involved in mRNA metabolism, translation, and cell signaling, including the nuclear -subunits of casein kinase II (CK2). The CK2 subunit AtCKA1 associates with the PP-InsP kinase AtVIH2, and its 1.9 [A] crystal structure with InsP6 reveals two conserved PP-InsP binding sites located in the N-and C-terminal lobes. AtCKA1 binds InsP6, InsP7, and InsP8 with micromolar affinity. Mutation of both binding sites in the AtCKA6xmut mutant abolishes PP-InsP binding in vitro. AtCKA6xmut partially rescues the flowering phenotype of ck2a1/2/3 mutants, and equivalent mutations inactivate the yeast orthologs ScCka1 and ScCka2. InsP6 competitively inhibits phosphorylation of canonical CK2 substrates by occupying a basic substrate-binding groove. Although incorporating {beta}-subunits strongly enhances the phosphorylation of substrates by the AtCK2 holoenzyme, ck2b1/2/3/4 mutants exhibit only mild growth defects in Arabidopsis. In Marchantia, loss of the single ck2a gene severely impairs growth, whereas deletion of the {beta} subunit has no effect. Together, our findings suggest that InsP6/PP-InsPs modulate the activity of the isolated CK2 -subunit by regulating access to its substrate-binding site.

plant biology↗

bioRxiv2025

High-throughput phenomics of global ant biodiversity

The big data era in biology is underway, but the study of organismal form has been slow to capitalize on advances in imaging and computation. Modern imaging can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Within the open science initiative Antscan, we applied high-throughput synchrotron X-ray microtomography to capture phenotypes across a diverse and ecologically dominant insect group -- ants. We provide 2193 whole-body 3D ant datasets from 792 species to broadly cover the ant phylogeny with a global scope, also pairing phenomic data with genome sequencing projects. Scans acquired with standardized parameters facilitate automated analysis and free access to data can broaden the audience and incentivize methods development. Antscan presents a scalable approach to create libraries of diverse anatomies, heralding a new era of studies on the evolution, structure, and function of organismal phenotypes.

zoology↗

bioRxiv2025

Soil trace gas oxidizers divergently respond to short- and long-term warming

The upland soil microbiome is dominated by aerobic bacteria that oxidize atmospheric trace gases, including CO, H2, and CH4. As a result, soils are the largest biological sink for these climate-active gases. Whether global warming will enhance or suppress these processes remains unclear. Here, we studied the warming responses of soil trace gas oxidizers by profiling natural geothermal gradients in a subarctic grassland with over 60 years of field warming at +6{degrees}C. We integrate field flux measurements, ex situ biogeochemical assays, metagenomics, and metatranscriptomics to determine ecosystem and cellular-level responses. Our results show that the oxidation of atmospheric CO and H2, but not CH4, increased with long-term warming due to higher cell numbers. However, at the cellular level, trace gas oxidizers, especially methanotrophs, tended to reduce gas consumption and transcription of gas-metabolizing enzymes in response to long-term warming. Our findings suggest that soils may remain a robust sink for trace gases despite lower per-cell activity. This work establishes a framework for interpreting the relationships between temperature and microbial trace gas oxidation on timescales relevant to Earths climate system.

microbiology↗

bioRxiv2025

Pumping Venom: Valvilli Architecture and Implications for Stinger Functionality

The internal structure of the insect stinger plays a central role in venom delivery, yet critical components in this process remain poorly understood. Of these, the valvilli, a pair of articulated structures within the valve chamber that act as flaps, have often been overlooked or described only superficially. Here, we use high-resolution micro-computed tomography (micro-CT), histological sectioning, and confocal laser scanning microscopy (CLSM) to characterize the fine morphology and material composition of the cuticle of ant valvilli. We report structural differentiation within the valvilli, including sharply delimited material zones that may correspond to distinct mechanical properties. CLSM imaging highlights variation in sclerotization, resilin distribution, and ultrastructure, indicating that the valvilli are not uniform flap-like elements but rather complex, partially deformable structures. Furthermore, comparative micro-CT scans of stingers fixed in different actuation states indicate the involvement of a non-antiphasic pattern of valvilli movement during stinger deployment, challenging the current understanding of valvilli-assisted pumping based on rhythmic, alternating movements, as inferred from European honeybees. These findings offer new anatomical insight into the architecture of the ant stinger and provide a refined morphological basis for future studies of venom delivery mechanisms in Hymenoptera; to also foster our understanding of the complex functionality of micro-scale injection and pumping systems in insects.

zoology↗

bioRxiv2025

Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration

Peatlands are water-logged ecosystems that limit microbial decomposition making them effective carbon sinks. However, drainage or erosion removes these constraints on decomposition, switching them to carbon sources. Restoration aims to reverse these trends. Microbial ecophysiology influences carbon fluxes but how it responds to peatland degradation and restoration is poorly understood. Here we used metagenomics to study microbial functions and quantified growth rates using isotope labelling across seven sites in Britain, each with restored, degraded, and near-natural peatlands. We found that growth rates in restored treatments were comparable to the near-natural, but were significantly higher in degraded. This growth rate reduction in restored peatlands was dependent on the scale of degradation and the length of restoration, and was underpinned by a shift towards energetically less favourable metabolic pathways such as anaerobic respiration, fermentation, and carbon fixation. A peatland ecosystem health index estimated based on measurements of peat moisture, oxygen, pH, organic matter chemistry, and moss cover, explained a significant amount of variation in microbial ecophysiology across the gradient. We demonstrate that microbial ecophysiology changes with peatland ecosystem health in a predictable manner. This knowledge can inform restoration targets and monitoring of recovery to maximise the return of carbon accrual functions of peatlands.

microbiology↗

bioRxiv2025

Differential Effects of Short-term and Long-term Deep Brain Stimulation on Striatal Neuronal Excitability in a Dystonia Animal Model

Deep brain stimulation (DBS) is, by now, one of the standard treatment options for movement disorders like dystonia or Parkinsons Disease. Although its clinical effectiveness is established, the exact mechanisms by which DBS influences neural motor networks are not fully understood. The present study explores the development of adaptive network mechanisms with DBS in the dtsz hamster model, an in-vivo model exhibiting spontaneous dystonic episodes, by comparing functional impacts of short-term and long-term DBS on medium spiny neurons (MSNs) and synaptic transmission in the striatum. In this electrophysiological study, we uncovered contrasting changes in neuronal excitability and synaptic dynamics following short-term versus long-term DBS. Short-term DBS enhanced neuronal firing responses, while long-term DBS diminished them. Regarding synaptic alterations, both short-term and long-term DBS significantly shifted spontaneous EPSC occurrences to longer intervals, with this effect, however, being more pronounced in short-term DBS, leading to a significant decrease in mEPSC frequency. Notably, acetylcholine application effectively reversed this effect, restoring mEPSC frequency more efficiently again in tissue subjected to short-term DBS compared to long-term DBS. These observations indicate that the therapeutic benefits of DBS in dystonia may involve both immediate and adaptive mechanisms, which has implications for improving stimulation parameters and treatment protocols. The findings shed light on the temporal specificity of DBS effects and highlight the importance of understanding synaptic mechanisms to enhance therapeutic outcomes for dystonia patients.

neuroscience↗

bioRxiv2025

Flexibility and Neural Correlates of Action-Sound Predictions

To interact efficiently with our environment, our brain predicts the sensory effects of our actions and compares them with the actual outcomes. This allows us to adapt our actions when predictions and sensory outcomes mismatch. While this process is generally well understood for action-sound predictions, it is an open question how flexibly these predictions can adapt in frequently changing environments, as they occur in real life. To investigate the flexibility of top-down predictions, we asked participants (N = 41) to press one of two buttons, a left-hand and a right-hand button, and switch hands autonomously. One button frequently produced a sound (80%) and rarely no sound. The other button frequently generated no sound (80%) and rarely produced a sound. In a third, separate condition, each button produced a sound in 50% of the trials. Unexpected sounds and unexpected sound omissions elicited a series of error-related brain responses in the electroencephalogram (EEG) at different levels of auditory processing, including a mismatch negativity (MMN) and the P3 complex for unexpected sounds, and the oN1, oN2, and oP3 complex for unexpected omissions. Moreover, unexpected sounds elicited an equivalent MMN--regardless of whether silence was expected (80%) or no reliable expectation was possible (50%), while later P3 components showed different amplitudes. Our results demonstrate flexible action-sound predictions at sensory and higher cortical levels. Furthermore, they indicate that predicted silence does not have an explicit sensory representation at lower levels but emerges at later stages, when higher-level information has been integrated.

neuroscience↗

bioRxiv2025

Sulfoquinovose is differently degraded by the mouse and human gut microbiota and not metabolized by the host

BackgroundSulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for few human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism. Results13CO2 breath tests with germ-free C57BL/6 mice gavaged with 13C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the mouse gut. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain. ConclusionsOur findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.

microbiology↗

bioRxiv2025

In the face of competition, imperfect knowledge can lead to sustainable exploitation of a shared resource.

Overexploitation of a shared resource is a frequent phenomenon among groups of selfish consumers, known as the tragedy of the commons. To avoid "self-damage through self-interest", humans may either defend exclusive access to resources, or collectively adopt advanced cooperative behaviour and carefully designed spatial harvesting strategies to exploit a shared resource sustainably. However, why do many non-human species that are neither social nor territorial also appear to avoid overexploiting resources? This study shows that, even under highly competitive scenarios, cooperation is not necessary to sustainably exploit shared resources if individuals have imperfect knowledge about the distribution of those resources. Poorly informed individuals are more likely to inadvertently exploit resources in peripheral habitats, which may allow for higher resource renewal in the nearby and low-cost habitats, enhancing the sustainability of resource use. As a result, those consumers can achieve a long-term yield that approaches that of cooperative consumers and is higher than omniscient consumers. Ironically, while there might be an evolutionary drive for individuals to make well-informed decisions, consumers of shared resources may be collectively more prosperous when they make decisions based on less information. These findings might explain why apparently sub-optimal consumer behaviour appears so prevalent in nature.

ecology↗

bioRxiv2025

Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences

Metatranscriptome (MetaT) sequencing is a critical tool for profiling the dynamic metabolic functions of microbiomes. In addition to taxonomic information, MetaT also provides real-time gene expression data of both host and microbial populations, thus permitting authentic quantification of the functional (enzymatic) output of the microbiome and its host. The main challenge to effective and accurate MetaT analysis is the removal of highly abundant rRNA transcripts from these complex mixtures of microbes, which can number in the thousands of individual species. Regardless of methodology for rRNA depletion, the design of rRNA removal probes based solely upon taxonomic content of the microbiome typically requires very large numbers of individual probes, making this approach complex to commercially manufacture, costly, and frequently technically infeasible. In previous work [1], we designed a set of depletion probes for human stool samples using a design strategy based solely on sequence abundance, completely agnostic of the microbiomal species present. Here, we show that the human-based probes are less effective when used with mouse cecal samples. However, adapting additional rRNA depletion probes specifically to cecal content provides both greater efficiency and consistency for MetaT analysis of mouse samples. ImportanceSequencing total RNA from microbiome samples is seriously impaired by the overwhelming proportion of rRNA to mRNA content. As much as 99% of sequencing reads can be assigned to the rRNA content, thus removal of these abundant transcripts is critical to MetaT analysis. The use of Ribo Zero Plus rRNA depletion probes designed for human gut microbiomes proved to be less effective and more inconsistent across mouse cecal donor samples, a common experimental system for microbiome studies. In the present work, we have extended and refined a taxonomically-neutral probe design method for mouse cecal content. The additional probes were carefully chosen to limit the number needed for effective depletion to reduce both the cost and risk of introducing bias to MetaT analysis. Our results demonstrate this method as efficient and consistent for rRNA removal in mouse cecal samples, thus providing a significant increase in the number of mRNA-rich sequencing reads for MetaT analysis.

genomics↗