A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer

The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and the functionality of microbial communities in medical, environmental, and biotechnological applications. We present an improved metaproteomics workflow using an updated sample preparation and a new version of the MetaProteomeAnalyzer software for data analysis. High resolution by multidimensional separation (GeLC, MudPIT) was sacrificed to aim at fast analysis of a broad range of different samples in less than 24 h. The improved workflow generated at least two times as many protein identifications than our previous workflow, and a drastic increase of taxonomic and functional annotations. Improvements of all aspects of the workflow, particularly the speed, are first steps toward potential routine clinical diagnostics (i.e., fecal samples) and analysis of technical and environmental samples. The MetaProteomeAnalyzer is provided to the scientific community as a central remote server solution at www.mpa.ovgu.de.Peer Reviewe

MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways

Taxonomic and functional characterization of microbial communities from diverse environments such as the human gut or biogas plants by multi-omics methods plays an ever more important role. Researchers assign all identified genes, transcripts, or proteins to biological pathways to better understand the function of single species and microbial communities. However, due to the versality of microbial metabolism and a still-increasing number of newly biological pathways, linkage to standard pathway maps such as the KEGG central carbon metabolism is often problematic. We successfully implemented and validated a new user-friendly, stand-alone web application, the MPA_Pathway_Tool. It consists of two parts, called ‘Pathway-Creator’ and ‘Pathway-Calculator’. The ‘Pathway-Creator’ enables an easy set-up of user-defined pathways with specific taxonomic constraints. The ‘Pathway-Calculator’ automatically maps microbial community data from multiple measurements on selected pathways and visualizes the results. The MPA_Pathway_Tool is implemented in Java and ReactJS

Atlantic Bluefin Tuna (Thunnus thynnus) Diet in the Gulf of St. Lawrence and on the Eastern Scotian Shelf

The stomach contents of 68 Atlantic bluefin tuna (Thunnus thynnus) landed in Port Hood and Canso, Nova Scotia, in 2010, were analyzed to characterize the diet of bluefin tuna at the two locations. Of the sampled fish, 54 stomachs had contents. Pelagic schooling fish such as herring (Clupea harengus) and mackerel (Scomber scombrus) dominated the diets in both regions. However, a number of rare species, including demersal species, were also observed. Despite the difference in location and the significantly larger size of the Atlantic bluefin tuna landed in Port Hood, the diets of the Atlantic bluefin tuna landed at both sites were similar

Prevention of mist formation in amine based carbon capture : field testing using a Wet ElectroStatic Precipitator (WESP) and a Gas-Gas Heater (GGH)

This study presents the results of two field tests that aimed at evaluating two countermeasures (WESP and GGH) to avoid acid mist formation. A WESP is shown to be very efficient for the removal of nuclei from the flue gas (100 % efficient) and thus can prevent aerosol formation inside an amine based absorber. This is however only valid in the absence of SO2 in the flue gas entering the WESP. A decreasing WESP efficiency is noted in the presence of SO2 with increasing voltages as a result of newly formed aerosols inside the WESP. This implies that no or very low levels of SO2 should be present in the flue gas entering the WESP. Since most of the amine carbon capture installations have a pre-scrubber (usually using NaOH to remove residual SO2 in the flue gas leaving the power plant's Flue Gas Desulphurisation) in front of their amine absorber, the WESP must be installed behind this pre-scrubber and not in front of it. Having a Gas-Gas Heater (or any type of flue gas cooling such as a Low Temperature Heat Exchanger) installed upstream of the wet scrubbing may prevent homogenous nucleation and thus prevent the conversion of H2SO4 into sulfuric acid aerosols and consequently mist formation issues in the amine based carbon capture installation. Which option to choose amongst the two countermeasures presented in this study will depend on whether a new built installation is being considered or whether a carbon capture is planned as a retrofit into an existing installation. (C) 2017 The Authors. Published by Elsevier Ltd

Prevention of Mist Formation in Amine Based Carbon Capture: Field Testing Using a Wet ElectroStatic Precipitator (WESP) and a Gas-Gas Heater (GGH)

This study presents the results of two field tests that aimed at evaluating two countermeasures (WESP and GGH) to avoid acid mist formation. A WESP is shown to be very efficient for the removal of nuclei from the flue gas (100 % efficient) and thus can prevent aerosol formation inside an amine based absorber. This is however only valid in the absence of SO2 in the flue gas entering the WESP. A decreasing WESP efficiency is noted in the presence of SO2 with increasing voltages as a result of newly formed aerosols inside the WESP. This implies that no or very low levels of SO2 should be present in the flue gas entering the WESP. Since most of the amine carbon capture installations have a pre-scrubber (usually using NaOH to remove residual SO2 in the flue gas leaving the power plant's Flue Gas Desulphurisation) in front of their amine absorber, the WESP must be installed behind this pre-scrubber and not in front of it. Having a Gas-Gas Heater (or any type of flue gas cooling such as a Low Temperature Heat Exchanger) installed upstream of the wet scrubbing may prevent homogenous nucleation and thus prevent the conversion of H2SO4 into sulfuric acid aerosols and consequently mist formation issues in the amine based carbon capture installation. Which option to choose amongst the two countermeasures presented in this study will depend on whether a new built installation is being considered or whether a carbon capture is planned as a retrofit into an existing installation. (C) 2017 The Authors. Published by Elsevier Ltd

Fecal Metaproteomics Reveals Reduced Gut Inflammation and Changed Microbial Metabolism Following Lifestyle-Induced Weight Loss

Gut microbiota-mediated inflammation promotes obesity-associated low-grade inflammation, which represents a hallmark of metabolic syndrome. To investigate if lifestyle-induced weight loss (WL) may modulate the gut microbiome composition and its interaction with the host on a functional level, we analyzed the fecal metaproteome of 33 individuals with metabolic syndrome in a longitudinal study before and after lifestyle-induced WL in a well-defined cohort. The 6-month WL intervention resulted in reduced BMI (−13.7%), improved insulin sensitivity (HOMA-IR, −46.1%), and reduced levels of circulating hsCRP (−39.9%), indicating metabolic syndrome reversal. The metaprotein spectra revealed a decrease of human proteins associated with gut inflammation. Taxonomic analysis revealed only minor changes in the bacterial composition with an increase of the families Desulfovibrionaceae, Leptospiraceae, Syntrophomonadaceae, Thermotogaceae and Verrucomicrobiaceae. Yet we detected an increased abundance of microbial metaprotein spectra that suggest an enhanced hydrolysis of complex carbohydrates. Hence, lifestyle-induced WL was associated with reduced gut inflammation and functional changes of human and microbial enzymes for carbohydrate hydrolysis while the taxonomic composition of the gut microbiome remained almost stable. The metaproteomics workflow has proven to be a suitable method for monitoring inflammatory changes in the fecal metaproteome

Pop-up archival tags reveal environmental influences on the vertical movements of silvertip sharks (Carcharhinus albimarginatus)

Vertical space use informs the ecology and management of marine species, but studies of reef-associated sharks often focus on horizontal movements. We analysed the vertical movements of silvertip sharks (Carcharhinus albimarginatus) using pop-up archival tags deployed on seven individuals in the Chagos Archipelago, central Indian Ocean. The sharks changed depth predictably with water column thermal structure, moving deeper with seasonal increases in mixed layer depth while occupying a narrow ambient water temperature range around ~27°C. At shorter timescales, higher resolution data from five tags showed that silvertip shark depth varied cyclically with surface light levels, increasing during daylight and on nights around full moon. This matches the diel vertical migrations of many fish species, suggesting the sharks’ light-driven depth changes might relate to foraging. While most vertical movements (>98%) were within the mixed layer, deeper dives to 200-800 m occurred approximately every three days. High-resolution data from one recovered tag showed the shark ascending deep (>200 m) dives in two sharply defined phases, initially fast then slow. Analysis of dive profiles against dissolved oxygen (DO) data suggested that the shark may have ascended rapidly to escape low DO levels at depth, then reduced its ascent rate 50-80% once DO levels increased. While a small sample, the electronic tags deployed in this study revealed the silvertip sharks’ predictable use of mixed layer waters, narrow thermal range and apparent intolerance of hypoxic conditions. These characteristics may exacerbate the species’ vulnerability as oceanic warming and shoaling oxygen minimum zones modify vertical habitat availability

Detecting Mediterranean White Sharks with Environmental DNA

The white shark (Carcharodon carcharias) is a globally distributed, ecologically important top predator whose biology and population dynamics are challenging to study. Basic biological parameters remain virtually unknown in the Mediterranean Sea due to its historically low population density, dwindling population size, and lack of substantial sightings. White sharks are considered Critically Endangered in the Mediterranean Sea, and recent analyses suggest that the population has declined by 52% to 96% from historical levels in different Mediterranean sectors (Moro et al., 2020). Thus, white shark sightings dating back to 1860 are being used to estimate population trajectories throughout the entire region. Though the population size is unknown, remaining individuals are thought to be primarily restricted to a handful of hotspots deemed important for their reproduction and foraging. One of these hypothesized hotspots is the Sicilian Channel, which accounts for 19% of total historical sightings

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants

Background: In biogas plants, complex microbial communities produce methane and carbon dioxide by anaerobic digestion of biomass. For the characterization of the microbial functional networks, samples of 11 reactors were analyzed using a high-resolution metaproteomics pipeline. Results: Examined methanogenesis archaeal communities were either mixotrophic or strictly hydrogenotrophic in syntrophy with bacterial acetate oxidizers. Mapping of identified metaproteins with process steps described by the Anaerobic Digestion Model 1 confirmed its main assumptions and also proposed some extensions such as syntrophic acetate oxidation or fermentation of alcohols. Results indicate that the microbial communities were shaped by syntrophy as well as competition and phage-host interactions causing cell lysis. For the families Bacillaceae, Enterobacteriaceae, and Clostridiaceae, the number of phages exceeded up to 20-fold the number of host cells. Conclusion: Phage-induced cell lysis might slow down the conversion of substrates to biogas, though, it could support the growth of auxotrophic microbes by cycling of nutrients. © 2019 The Author(s)