More Like this

1. Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome

   https://doi.org/10.1038/s41598-018-29092-4  

   Afiuni-Zadeh, Somaieh ; Boylan, Kristin L. M. ; Jagtap, Pratik D. ; Griffin, Timothy J. ; Rudney, Joel D. ; Peterson, Marnie L. ; Skubitz, Amy P. N. ( July 2018 , Scientific Reports)

   The human cervical-vaginal area contains proteins derived from microorganisms that may prevent or predispose women to gynecological conditions. The liquid Pap test fixative is an unexplored resource for analysis of microbial communities and the microbe-host interaction. Previously, we showed that the residual cell-free fixative from discarded Pap tests of healthy women could be used for mass spectrometry (MS) based proteomic identification of cervical-vaginal proteins. In this study, we reprocessed these MS raw data files for metaproteomic analysis to characterize the microbial community composition and function of microbial proteins in the cervical-vaginal region. This was accomplished by developing a customized protein sequence database encompassing microbes likely present in the vagina. High-mass accuracy data were searched against the protein FASTA database using a two-step search method within the Galaxy for proteomics platform. Data was analyzed by MEGAN6 (MetaGenomeAnalyzer) for phylogenetic and functional characterization. We identified over 300 unique peptides from a variety of bacterial phyla andCandida. Peptides corresponding to proteins involved in carbohydrate metabolism, oxidation-reduction, and transport were identified. By identifying microbial peptides in Pap test supernatants it may be possible to acquire a functional signature of these microbes, as well as detect specific proteins associated with cervical health and disease.

    

   more » « less
2. SpecEncoder: deep metric learning for accurate peptide identification in proteomics

   https://doi.org/10.1093/bioinformatics/btae220  

   Liu, Kaiyuan ; Tao, Chenghua ; Ye, Yuzhen ; Tang, Haixu ( June 2024 , Bioinformatics)

   Tandem mass spectrometry (MS/MS) is a crucial technology for large-scale proteomic analysis. The protein database search or the spectral library search are commonly used for peptide identification from MS/MS spectra, which, however, may face challenges due to experimental variations between replicated spectra and similar fragmentation patterns among distinct peptides. To address this challenge, we present SpecEncoder, a deep metric learning approach to address these challenges by transforming MS/MS spectra into robust and sensitive embedding vectors in a latent space. The SpecEncoder model can also embed predicted MS/MS spectra of peptides, enabling a hybrid search approach that combines spectral library and protein database searches for peptide identification.

   We evaluated SpecEncoder on three large human proteomics datasets, and the results showed a consistent improvement in peptide identification. For spectral library search, SpecEncoder identifies 1%–2% more unique peptides (and PSMs) than SpectraST. For protein database search, it identifies 6%–15% more unique peptides than MSGF+ enhanced by Percolator, Furthermore, SpecEncoder identified 6%–12% additional unique peptides when utilizing a combined library of experimental and predicted spectra. SpecEncoder can also identify more peptides when compared to deep-learning enhanced methods (MSFragger boosted by MSBooster). These results demonstrate SpecEncoder’s potential to enhance peptide identification for proteomic data analyses.

   The source code and scripts for SpecEncoder and peptide identification are available on GitHub at https://github.com/lkytal/SpecEncoder. Contact: hatang@iu.edu.

    

   more » « less
3. Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs

   https://doi.org/10.1038/s41396-023-01452-7  

   Pherribo, Gordon J. ; Taga, Michiko E. ( June 2023 , The ISME Journal)

   Microbial communities host many auxotrophs—organisms unable to synthesize one or more metabolites required for their growth. Auxotrophy is thought to confer an evolutionary advantage, yet auxotrophs must rely on other organisms that produce the metabolites they require. The mechanisms of metabolite provisioning by “producers” remain unknown. In particular, it is unclear how metabolites such as amino acids and cofactors, which are found inside the cell, are released by producers to become available to auxotrophs. Here, we explore metabolite secretion and cell lysis as two distinct possible mechanisms that result in the release of intracellular metabolites from producer cells. We measured the extent to which secretion or lysis of Escherichia coli and Bacteroides thetaiotaomicron amino acid producers can support the growth of engineered Escherichia coli amino acid auxotrophs. We found that cell-free supernatants and mechanically lysed cells provide minimal levels of amino acids to auxotrophs. In contrast, bacteriophage lysates of the same producer bacteria can support as many as 47 auxotroph cells per lysed producer cell. Each phage lysate released distinct levels of different amino acids, suggesting that in a microbial community the collective lysis of many different hosts by multiple phages could contribute to the availability of an array of intracellular metabolites for use by auxotrophs. Based on these results, we speculate that viral lysis could be a dominant mechanism of provisioning of intracellular metabolites that shapes microbial community structure.

    

   more » « less
4. The role of differential DMSP production and community composition in predicting variability of global surface DMSP concentrations

   https://doi.org/10.1002/lno.11076  

   McParland, Erin L. ; Levine, Naomi M. ( November 2018 , Limnology and Oceanography)

   Dimethylsulfoniopropionate (DMSP) is an important labile component of the marine dissolved organic matter pool that is produced by the majority of eukaryotic marine phytoplankton and by many prokaryotes. Despite decades of research, the contribution of different environmental drivers of DMSP production to regional and seasonal variability remains unknown. A synthesis of the current state‐of‐knowledge suggested that approximately half of confirmed DMSP producers are low producers (intracellular DMSP < 50 mM). Low DMSP producers (LoDPs; e.g., diatoms) were shown to strongly regulate intracellular DMSP concentrations (~ 16‐fold change) as a predictable function of nutrient stress. By comparison, high DMSP producers (HiDPs; e.g., coccolithophores) showed very little response (~ 1.5‐fold change). To assess the importance of differential DMSP production by low and high producers, DMSP concentrations were predicted for two time‐series sites (a high‐ and low‐productivity site) and for the global ocean by explicitly incorporating both community composition and mechanistic nutrient stress. Despite large, predictable intracellular DMSP changes, low producers contributed less than 5% to global DMSP. This indicates that, while variations in DMSP production by low producers could be important for predicting microbial interactions and low producer physiology, it is not necessary for predicting global DMSP concentrations. Our analysis suggests that community composition, particularly HiDP biomass, is the dominant driver of variability in in situ DMSP concentrations, even in low‐productivity regions where high producers are typically the subdominant group. Accurate predictions of in situ DMSP concentrations require improved representation of subdominant community dynamics in ecosystem models and remote‐sensing algorithms.

    

   more » « less
5. Global biogeography and ecological implications of cobamide-producing prokaryotes

   https://doi.org/10.1093/ismejo/wrae009  

   Wang, Jichen ; Zhu, Yong-Guan ; Tiedje, James M. ; Ge, Yuan ( January 2024 , The ISME Journal)

   Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.

    

   more » « less