@article{mclaren_nearing_willis_lloyd_callahan_2022, title={Implications of taxonomic bias for microbial differential-abundance analysis}, url={https://doi.org/10.1101/2022.08.19.504330}, DOI={10.1101/2022.08.19.504330}, abstractNote={AbstractDifferential-abundance (DA) analyses enable microbiome researchers to assess how microbial species vary in relative or absolute abundance with specific host or environmental conditions, such as health status or pH. These analyses typically use sequencing-based community measurements that are taxonomically biased to measure some species more efficiently than others. Understanding the effects that taxonomic bias has on the results of a DA analysis is essential for achieving reliable and translatable findings; yet currently, these effects are unknown. Here, we characterized these effects for DA analyses of both relative and absolute abundances, using a combination of mathematical theory and data analysis of real and simulated case studies. We found that, for analyses based on species proportions, taxonomic bias can cause significant errors in DA results if the average measurement efficiency of the community is associated with the condition of interest. These errors can be avoided by using more robust DA methods (based on species ratios) or quantified and corrected using appropriate controls. Wide adoption of our recommendations can improve the reproducibility, interpretability, and translatability of microbiome DA studies.This manuscript was rendered from commit 7412a36 of https://github.com/mikemc/differential-abundance-theory. Supporting data analyses can be found in the accompanying computational research notebook. Please post comments or questions on GitHub. The manuscript is licensed under a CC BY 4.0 License. See the GitHub Releases or Zenodo record for earlier versions.}, author={McLaren, Michael R. and Nearing, Jacob T. and Willis, Amy D. and Lloyd, Karen G. and Callahan, Benjamin J.}, year={2022}, month={Aug} }
 @article{fletcher_pike_parsons_rivera_foley_mclaren_montgomery_theriot_2021, title={Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota}, volume={12}, ISSN={["2041-1723"]}, url={https://doi.org/10.1038/s41467-020-20746-4}, DOI={10.1038/s41467-020-20746-4}, abstractNote={AbstractClostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation.}, number={1}, journal={NATURE COMMUNICATIONS}, author={Fletcher, Joshua R. and Pike, Colleen M. and Parsons, Ruth J. and Rivera, Alissa J. and Foley, Matthew H. and McLaren, Michael R. and Montgomery, Stephanie A. and Theriot, Casey M.}, year={2021}, month={Jan} }
 @article{thanissery_mclaren_rivera_reed_betrapally_burdette_winston_jacob_callahan_theriot_2020, title={Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota}, volume={66}, ISSN={["1095-8274"]}, DOI={10.1016/j.anaerobe.2020.102279}, abstractNote={The relationship between the gut microbiota and Clostridioides difficile, and its role in the severity of C. difficile infection in humans is an area of active research. Intestinal carriage of toxigenic and non-toxigenic C. difficile strains, with and without clinical signs, is reported in animals, however few studies have looked at the risk factors associated with C. difficile carriage and the role of the host gut microbiota. Here, we isolated and characterized C. difficile strains from different animal species (predominantly canines (dogs), felines (cats), and equines (horses)) that were brought in for tertiary care at North Carolina State University Veterinary Hospital. C. difficile strains were characterized by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16S rRNA gene sequencing was done on animal feces to investigate the relationship between the presence of C. difficile and the gut microbiota in different hosts. Here, we show that C. difficile was recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes including ones known to cause CDI in humans. The presence of C. difficile results in a shift in the fecal microbial community structure in both canines and equines. Commensal Clostridium hiranonis was negatively associated with C. difficile in canines. Further experimentation showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts.}, journal={ANAEROBE}, author={Thanissery, R. and McLaren, M. R. and Rivera, A. and Reed, A. D. and Betrapally, N. S. and Burdette, T. and Winston, J. A. and Jacob, M. and Callahan, B. J. and Theriot, C. M.}, year={2020}, month={Dec} }
 @misc{nguyen_bakerlee_mckelvey_rose_norman_joseph_manheim_mclaren_jiang_barnes_et al._2021, title={Evaluating Use Cases for Human Challenge Trials in Accelerating SARS-CoV-2 Vaccine Development}, volume={72}, ISSN={["1537-6591"]}, DOI={10.1093/cid/ciaa935}, abstractNote={Abstract
               Human challenge trials (HCTs) have been proposed as a means to accelerate SARS-CoV-2 vaccine development. We identify and discuss 3 potential use cases of HCTs in the current pandemic: evaluating efficacy, converging on correlates of protection, and improving understanding of pathogenesis and the human immune response. We outline the limitations of HCTs and find that HCTs are likely to be most useful for vaccine candidates currently in preclinical stages of development. We conclude that, while currently limited in their application, there are scenarios in which HCTs would be extremely beneficial. Therefore, the option of conducting HCTs to accelerate SARS-CoV-2 vaccine development should be preserved. As HCTs require many months of preparation, we recommend an immediate effort to (1) establish guidelines for HCTs for COVID-19; (2) take the first steps toward HCTs, including preparing challenge virus and making preliminary logistical arrangements; and (3) commit to periodically re-evaluating the utility of HCTs.}, number={4}, journal={CLINICAL INFECTIOUS DISEASES}, author={Nguyen, Linh Chi and Bakerlee, Christopher W. and McKelvey, T. Greg and Rose, Sophie M. and Norman, Alexander J. and Joseph, Nicholas and Manheim, David and McLaren, Michael R. and Jiang, Steven and Barnes, Conor F. and et al.}, year={2021}, month={Feb}, pages={710–715} }
 @article{mclaren_callahan_2020, title={Pathogen resistance may be the principal evolutionary advantage provided by the microbiome}, volume={375}, url={https://doi.org/10.1098/rstb.2019.0592}, DOI={10.1098/rstb.2019.0592}, abstractNote={To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life.This article is part of the theme issue ‘The role of the microbiome in host evolution’.}, number={1808}, journal={Philosophical Transactions of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={McLaren, Michael R. and Callahan, Benjamin J.}, year={2020}, month={Sep}, pages={20190592} }
 @article{thanissery_mclaren_rivera_reed_betrapally_burdette_winston_jacob_callahan_theriot_2019, title={Characterization of C. difficile strains isolated from companion animals and the associated changes in the host fecal microbiota}, url={http://europepmc.org/abstract/PPR/PPR100283}, DOI={10.1101/822577}, abstractNote={AbstractBackgroundClostridioides difficileis an enteric pathogen historically known to cause hospital associated (HA)-infections in humans. A major risk factor for CDI in humans is antibiotic usage as it alters the gut microbiota and there is a loss of colonization resistance againstC. difficile. In recent years there has been an increase in community associated (CA)-C. difficileinfection that does not have the same risk factors as HA-CDI. Potential sources of CA-CDI have been proposed and include animals, food, water, and the environment, however these sources remain poorly investigated. Here, we define the prevalence ofC. difficilestrains found in different companion animals (canines, felines, and equines) to investigate a potential zoonotic link.C. difficilestrains were identified by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16s rRNA gene sequencing was done on animal feces to investigate the relationship between the presence ofC. difficileand the gut microbiota in different hosts.ResultsHere, we show thatC. difficilewas recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes, with overlap between HA- and CA-CDI cases in humans. The presence ofC. difficileresults in a shift in the fecal microbial community structure in both canines and equines. Commensal ClostridiaC. hiranoniswas negatively associated withC. difficilein canines. Further experimentation showed a clear antagonistic relationship between the two strainsin vitro, suggesting that commensalClostridiamight play a role in colonization resistance againstC. difficilein different hosts.ConclusionsIn this study we investigated a potentially important source ofC. difficiletransmission: the companion animal population.C. difficilecarriage was common in dogs, cats, and horses.C. difficileisolates from companion animals included many of the same ribotypes known to cause HA- and CA-CDI in humans, and had similar antimicrobial resistance profiles as those isolated from human populations. These data contribute to our understanding of non-hospital exposure toC. difficilein the human population and suggest new avenues for reducingC. difficileprevalence in companion animals and, perhaps, thereby reducing CA-CDI in humans.}, author={Thanissery, R and McLaren, M and Rivera, A and Reed, AD and Betrapally, N and Burdette, T and Winston, J and Jacob, M and Callahan, B and Theriot, C}, year={2019}, month={Oct} }
 @article{mclaren_willis_callahan_2019, title={Consistent and correctable bias in metagenomic sequencing experiments}, url={https://doi.org/10.7554/eLife.46923}, DOI={10.7554/eLife.46923}, abstractNote={Marker-gene and metagenomic sequencing have profoundly expanded our ability to measure biological communities. But the measurements they provide differ from the truth, often dramatically, because these experiments are biased toward detecting some taxa over others. This experimental bias makes the taxon or gene abundances measured by different protocols quantitatively incomparable and can lead to spurious biological conclusions. We propose a mathematical model for how bias distorts community measurements based on the properties of real experiments. We validate this model with 16S rRNA gene and shotgun metagenomics data from defined bacterial communities. Our model better fits the experimental data despite being simpler than previous models. We illustrate how our model can be used to evaluate protocols, to understand the effect of bias on downstream statistical analyses, and to measure and correct bias given suitable calibration controls. These results illuminate new avenues toward truly quantitative and reproducible metagenomics measurements.}, journal={eLife}, author={McLaren, Michael R and Willis, Amy D and Callahan, Benjamin J}, year={2019}, month={Sep} }
 @article{mclaren_willis_callahan_2019, title={Consistent and correctable bias in metagenomic sequencing measurements}, volume={2}, url={https://www.biorxiv.org/content/10.1101/559831v1}, DOI={10.1101/559831}, abstractNote={AbstractMeasurements of biological communities by marker-gene and metagenomic sequencing are biased: The measured relative abundances of taxa or their genes are systematically distorted from their true values because each step in the experimental workflow preferentially detects some taxa over others. Bias can lead to qualitatively incorrect conclusions and makes measurements from different protocols quantitatively incomparable. A rigorous understanding of bias is therefore essential. Here we propose, test, and apply a simple mathematical model of how bias distorts marker-gene and metagenomics measurements: Bias multiplies the true relative abundances within each sample by taxon-and protocol-specific factors that describe the different efficiencies with which taxa are detected by the workflow. Critically, these factors are consistent across samples with different compositions, allowing bias to be estimated and corrected. We validate this model in 16S rRNA gene and shotgun metagenomics data from bacterial communities with defined compositions. We use it to reason about the effects of bias on downstream statistical analyses, finding that analyses based on taxon ratios are less sensitive to bias than analyses based on taxon proportions. Finally, we demonstrate how this model can be used to quantify bias from samples of defined composition, partition bias into steps such as DNA extraction and PCR amplification, and to correct biased measurements. Our model improves on previous models by providing a better fit to experimental data and by providing a composition-independent approach to analyzing, measuring, and correcting bias.}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory}, author={McLaren, Michael R. and Willis, Amy D. and Callahan, Benjamin J.}, year={2019}, month={Feb}, pages={559831} }
 @article{sakowski_uritskiy_cooper_gomes_mclaren_meisel_mickol_mintz_mongodin_pop_et al._2019, title={Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.}, volume={10}, url={http://europepmc.org/abstract/med/31594828}, DOI={10.1128/mSystems.00392-19}, abstractNote={Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses.}, journal={mSystems}, author={Sakowski, E and Uritskiy, G and Cooper, R and Gomes, M and McLaren and Meisel, JS and Mickol, RL and Mintz, CD and Mongodin, EF and Pop, M and et al.}, year={2019}, month={Oct} }
 @article{berman_mclaren_callahan_2020, title={Understanding and interpreting community sequencing measurements of the vaginal microbiome}, volume={127}, url={https://doi.org/10.1111/1471-0528.15978}, DOI={10.1111/1471-0528.15978}, abstractNote={Community‐wide high‐throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: (1) amplicon sequencing, (2) shotgun metagenomic sequencing, and (3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally, and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome.Tweetable abstractWe review the advantages and limitations of amplicon sequencing, metagenomics, and metatranscriptomics methods for the study of the vaginal microbiome.}, number={2}, journal={BJOG: An International Journal of Obstetrics & Gynaecology}, publisher={Wiley}, author={Berman, HL and McLaren and Callahan, BJ}, year={2020}, month={Jan}, pages={139–146} }
 @article{mclaren_callahan_2018, title={In Nature, There Is Only Diversity}, volume={9}, ISSN={["2150-7511"]}, url={http://www.ncbi.nlm.nih.gov/pubmed/29295915}, DOI={10.1128/mbio.02149-17}, abstractNote={ABSTRACT
          
            Microbial ecology has been transformed by the advent of high-throughput marker gene and metagenomic sequencing methods. These tools provide expansive descriptions of microbial communities, but the descriptions are framed in terms of molecular objects, such as 97% ribosomal operational taxonomic units (OTUs), rather than biological objects, such as species. A recent study by A. B. Chase and colleagues (mBio 8:e01809-17, 2017,
            https://doi.org/10.1128/mBio.01809-17
            ) explores the so-called microdiversity within the
            Curtobacterium
            OTU, the most abundant OTU in a leaf litter community. Perhaps unsurprisingly, they find that some important ecologic traits, such as drought response, are coherent within the OTU, but that others vary significantly. Here we discuss their findings in relation to the more general issue of how molecular tools can be effectively used to study microbial ecology. We specifically note the need for investigators to choose the right molecular methods for their biological problem, as nature does not respect the limitations and conventions associated with our methods.
          }, number={1}, journal={MBIO}, publisher={American Society for Microbiology}, author={McLaren, Michael R. and Callahan, Benjamin J.}, year={2018} }
 @article{mclaren_2016, title={Fitness-valley crossing in subdivided asexual populations}, url={http://biorxiv.org/content/early/2016/10/08/079624}, DOI={10.1101/079624}, abstractNote={AbstractAdaptations may require multiple mutations that are beneficial only in combination. To adapt, a lineage must acquire mutations that are individually neutral or deleterious before gaining the beneficial combination, thereby crossing a plateau or valley, respectively, in the mapping from genotype to fitness. Spatial population structure can facilitate plateau and valley crossing by allowing neutral and deleterious lineages to survive longer and produce more beneficial mutants. Here, we analyze adaptation across a two-mutation plateau or valley in an asexual population that is subdivided into discrete subpopulations, or demes, connected by migration. We describe how subdivision alters the dynamics of adaptation from those in an equally sized unstructured population and give a complete quantitative description of these dynamics for the island migration model. Subdivision can significantly decrease the waiting time for the adaptation if demes and migration rates are small enough that single-mutant lineages fix in one or more demes before producing the beneficial double mutant. But, the potential decrease is small in very large populations and may also be limited by the slow spread of the beneficial mutant in extremely subdivided populations. Subdivision has a smaller effect on the probability that the population adapts very quickly than on the mean time to adapt, which has important consequences in some applications, such as the development of cancer. Our results provide a general and intuitive framework for predicting the effects of spatial structure in other models and in natural populations.}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory Press}, author={McLaren, Michael R.}, year={2016} }
 @article{the atacama cosmology telescope: cosmological parameters from three seasons of data_2013, volume={2013}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84888090276&partnerID=MN8TOARS}, DOI={10.1088/1475-7516/2013/10/060}, abstractNote={We present constraints on cosmological and astrophysical parameters from high-resolution microwave background maps at 148 GHz and 218 GHz made by the Atacama Cosmology Telescope (ACT) in three seasons of observations from 2008 to 2010. A model of primary cosmological and secondary foreground parameters is fit to the map power spectra and lensing deflection power spectrum, including contributions from both the thermal Sunyaev-Zeldovich (tSZ) effect and the kinematic Sunyaev-Zeldovich (kSZ) effect, Poisson and correlated anisotropy from unresolved infrared sources, radio sources, and the correlation between the tSZ effect and infrared sources. The power ℓ2Cℓ/2π of the thermal SZ power spectrum at 148 GHz is measured to be 3.4±1.4 μK2 at ℓ = 3000, while the corresponding amplitude of the kinematic SZ power spectrum has a 95% confidence level upper limit of 8.6 μK2. Combining ACT power spectra with the WMAP 7-year temperature and polarization power spectra, we find excellent consistency with the LCDM model. We constrain the number of effective relativistic degrees of freedom in the early universe to be Neff = 2.79±0.56, in agreement with the canonical value of Neff = 3.046 for three massless neutrinos. We constrain the sum of the neutrino masses to be Σmν < 0.39 eV at 95% confidence when combining ACT and WMAP 7-year data with BAO and Hubble constant measurements. We constrain the amount of primordial helium to be Yp = 0.225±0.034, and measure no variation in the fine structure constant α since recombination, with α/α0 = 1.004±0.005. We also find no evidence for any running of the scalar spectral index, dns/dln k = −0.004±0.012.}, number={10}, journal={Journal of Cosmology and Astroparticle Physics}, year={2013} }
 @article{hand_appel_battaglia_richard bond_das_devlin_dunkley_dünner_essinger-hileman_fowler_et al._2011, title={The Atacama cosmology telescope: Detection of Sunyaev-Zel'dovich decrement in groups and clusters associated with luminous red galaxies}, volume={736}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80051485713&partnerID=MN8TOARS}, DOI={10.1088/0004-637X/736/1/39}, abstractNote={We present a detection of the Sunyaev–Zel'dovich (SZ) decrement associated with the luminous red galaxy (LRG) sample of the Sloan Digital Sky Survey. The SZ data come from 148 GHz maps of the equatorial region made by the Atacama Cosmology Telescope. The LRG sample is divided by luminosity into four bins, and estimates for the central SZ temperature decrement are calculated through a stacking process. We detect and account for a bias of the SZ signal due to weak radio sources. We use numerical simulations to relate the observed decrement to Y200 and clustering properties to relate the galaxy luminosity to halo mass. We also use a relation between brightest cluster galaxy luminosity and cluster mass based on stacked gravitational lensing measurements to estimate the characteristic halo masses. The masses are found to be around 1014 M☉.}, number={1}, journal={Astrophysical Journal}, author={Hand, N. and Appel, J.W. and Battaglia, N. and Richard Bond, J. and Das, S. and Devlin, M.J. and Dunkley, J. and Dünner, R. and Essinger-Hileman, T. and Fowler, J.W. and et al.}, year={2011} }