Biology subjects

Langenfeld, K.

Publications and source records attributed to Langenfeld, K..

7 recordsLinked to original sources

bioRxiv2025

Novel Machine Learning-based Approach to Identify Viral Biomarkers of Human Respiratory Emissions from Oral and Nasal Metagenomes

Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes and prevalence was further increased to 77-81% by combining two or three biomarkers. Quantitative PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling. IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and thus exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.

microbiology↗

bioRxiv2023

Benchmarking combined informatics approaches for virus discovery: Caution is needed when combining in silico identification methods

BackgroundThe identification of viruses from environmental metagenomic samples using informatics tools has offered critical insights in microbiome studies. However, it remains difficult for researchers to know for their specific study which tool(s) and settings are best suited to maximize capture of viruses while minimizing false positives. Studies are increasingly combining multiple tool outputs attempting to recover more viruses, but no combined approach has been benchmarked for accuracy. Here, we benchmarked 63 viral identification rulesets against mock metagenomes composed of publicly available viral, bacterial, archaeal, fungal, and protist sequences. These rulesets are based on combinations of four single-tool rules and two multi-tool tuning rules. We applied these rulesets to various aquatic metagenomes and filtering strategies to evaluate the impact of habitat and viral enrichment on individual and combined tool performance. We provide a packaged pipeline for researchers that want to replicate our process. ResultsWe found that combining rules increased viral recall, but at the expense of increased false positives. Six of the 63 combinations tested had equivalent accuracies to the highest one (MCC=0.77, padj [≥] 0.05). All of the six high accuracy rulesets included VirSorter2, five included our "tuning removal" rule, and no high performing rulesets used more than four of our six rules. DeepVirFinder, VIBRANT, and VirSorter were each found once in these high accuracy rulesets, but never in combination with each other. Our validation suggests that the MCC plateau at 0.77 is caused by inaccurate labeling of the data that viral identification tools rely on for training and validation. In the aquatic metagenomes, our "highest MCC" ruleset identified a higher proportion of viral sequences in the virus-enriched samples (44-46%) than the non-enriched, cellular metagenomes (7-19%). ConclusionWhile improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with curating accurately labeled viral gene and sequence databases. For most applications, we recommend the use of the ruleset that uses VirSorter2 and our empirically derived tuning removal rule. By providing a rigorous overview of the behavior of in silico viral identification strategies, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.

bioinformatics↗

bioRxiv2022

Evaluating limitations of quantitative metagenomics with synthetic dsDNA and ssDNA standards

Quantitative metagenomic methods are maturing but continue to lack clearly-defined analytical limits. Here, we developed a computational tool, QuantMeta, to determine the absolute abundance of targets in metagenomes spiked with synthetic DNA standards. The tool establishes (1) entropy-based detection thresholds to confidently determine the presence of targets, and (2) an approach to identify and correct read mapping or assembly errors and thus improve the quantification accuracy. Together this allows for an approach to confidently quantify absolute abundance of targets, be they microbial populations, genes, contigs, or metagenome assembled genomes (MAGs). We applied the approach to quantify single- and double-stranded DNA viruses in wastewater viral metagenomes, including pathogens and bacteriophages. Concentrations of total DNA viruses in wastewater influent and effluent were greater than 108 copies/mL using QuantMeta. Human-associated DNA viruses were detected and quantifiable with QuantMeta thresholds, including polyomavirus, papillomavirus, and crAss-like phages, at concentrations similar to previous reports that utilized quantitative PCR-based assays. Our results highlight the higher detection thresholds of quantitative metagenomics ([~]500 copies/L) as compared to PCR-based quantification ([~]10 copies/L) despite a sequencing depth of 200 million reads per sample. The QuantMeta approach, applicable to both viral and cellular metagenomes, advances quantitative metagenomics by improving the accuracy of measured target absolute abundances.

genomics↗

bioRxiv2022

Pilotins are mobile T3SS components involved in assembly and substrate specificity of the bacterial type III secretion system

In animal pathogens, assembly of the type III secretion system injectisome requires the presence of so-called pilotins, small lipoproteins that assist the formation of the secretin ring in the outer membrane. Using a combination of functional assays, interaction studies, proteomics, and live-cell microscopy, we determined the contribution of the pilotin to the assembly, function, and substrate selectivity of the T3SS and identified potential new downstream roles of pilotin proteins. In absence of its pilotin SctG, Yersinia enterocolitica forms few, largely polar injectisome sorting platforms and needles. In line, most export apparatus subcomplexes are mobile in these strains, suggesting the absence of fully assembled injectisomes. Remarkably, while absence of the pilotin all but prevents export of early T3SS substrates, such as the needle subunits, it has little effect on secretion of late T3SS substrates, including the virulence effectors. We found that pilotins transiently interact with other injectisome components such as the secretin in the outer membrane, but mostly form transient mobile clusters in the bacterial membrane, which do not colocalize with assembled injectisomes. Together, these findings provide a new view on the role of pilotins during and after assembly of type III secretion injectisomes.

microbiology↗

bioRxiv2020

Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types

Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with 5-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater--critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here. ImportanceViruses in diverse habitats numerically dominate microbial community members and are consequential for host fate and responsible for disease outbreaks. Metagenomics has provided novel insights into their presence, diversity, and ecosystem impacts. Yet the approach is hindered by the challenge that, despite their numbers, viral genomes comprise a minor portion of total community DNA in a sample. To comprehensively describe a viral community with metagenomics, viral genomes must be effectively concentrated and purified to capture low abundance and rare viruses amidst the overwhelming presence of cellular genomic DNA. We evaluated two commonly applied methods for concentrating and purifying viral DNA, ultrafiltration and iron chloride flocculation, across four aquatic sample types that differ in their solids content and salinity. Our findings demonstrated the importance of sample characteristics for method effectivity and provided performance measures for a variety of matrices. These findings contribute a more comprehensive understanding of the impacts of virome sample preparation across diverse matrices and are thus important for guiding future virome studies, given the wide range of habitats in which viruses are studied.

microbiology↗

bioRxiv2020

Dissection of the Fgf8 regulatory landscape by in vivo CRISPR-editing reveals extensive inter- and intra-enhancer redundancy

Developmental genes are often regulated by multiple elements with overlapping activity. Yet, in most cases, the relative function of those elements and their contribution to endogenous gene expression remain uncharacterized. Illustrating this situation, distinct sets of enhancers have been proposed to direct Fgf8 in the limb apical ectodermal ridge (AER) and the midbrain-hindbrain boundary (MHB). Using in vivo CRISPR/Cas9 genome engineering, we functionally dissect this complex regulatory ensemble and demonstrate two distinct regulatory logics. In the AER, the control of Fgf8 expression appears extremely distributed between different enhancers. In contrast, in the MHB, one of the three active enhancers is essential while the other two are dispensable. Further dissection of the essential MHB enhancer revealed another layer of redundancy and identified two sub-parts required independently for Fgf8 expression and formation of midbrain and cerebellar structures. Interestingly, cross-species transgenic analysis of this enhancer suggests changes of the organisation of this essential regulatory node in the vertebrate lineage.

developmental biology↗

bioRxiv2019

LITESEC-T3SS - Light-controlled protein delivery into eukaryotic cells with high spatial and temporal resolution

Many bacteria employ a type III secretion system (T3SS), also called injectisome, to translocate proteins into eukaryotic host cells through a hollow extracellular needle. The system can efficiently transport heterologous cargo, which makes it a uniquely suited tool for the translocation of proteins into eukaryotic cells. However, the injectisome indiscriminately injects proteins into any adjoining eukaryotic cell, and this lack of target specificity currently limits its application in biotechnology and healthcare. In this study, we exploit the dynamic nature of the T3SS to control protein secretion and translocation into eukaryotic cells by light. By combining optogenetic interaction switches with the dynamic cytosolic T3SS component SctQ, the cytosolic availability of SctQ and in consequence T3SS-dependent effector secretion can be regulated by external light. The resulting system, which we call LITESEC-T3SS (Light-induced translocation of effectors through sequestration of endogenous components of the T3SS), allows rapid, specific, and reversible activation or deactivation of the T3SS upon illumination. We demonstrate the application of the system for light-regulated translocation of a heterologous reporter protein into cultured eukaryotic cells. LITESEC-T3SS represents a new method to achieve unparalleled spatial and temporal resolution for the controlled protein translocation into eukaryotic host cells.

microbiology↗