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1.
Front Fungal Biol ; 4: 1285531, 2023.
Article in English | MEDLINE | ID: mdl-38155707

ABSTRACT

Members of the fungal genus Morchella are widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained from Morchella isolates grown in vitro. These investigations included diverse representatives from both Elata and Esculenta Morchella clades. Unique bacterial community compositions were observed across the various structures examined, both within and across individual Morchella isolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genus Pseudomonas and Ralstonia constituted the core bacterial associates of Morchella mycelia and sclerotia, while other genera (e.g., Pedobacter spp., Deviosa spp., and Bradyrhizobium spp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance of Pseudomonas as a key member of the bacteriome was supported by the isolation of several Pseudomonas strains from mycelia during in vitro cultivation. Four of the six mycelial-derived Pseudomonas isolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and various Morchella isolates. Genome sequences obtained from these Pseudomonas isolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence that Pseudomonas spp. are frequently associated with Morchella and these associations may greatly impact fungal physiology.

2.
Nat Commun ; 14(1): 5533, 2023 09 18.
Article in English | MEDLINE | ID: mdl-37723166

ABSTRACT

Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.


Subject(s)
Affect , Salmonella enterica , Humans , Animals , Mice , Bile Acids and Salts , Taurine , Sulfur
3.
Microbiome ; 11(1): 192, 2023 08 26.
Article in English | MEDLINE | ID: mdl-37626434

ABSTRACT

As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.


Subject(s)
Microbiota , Multiomics , Data Analysis , Eukaryota , Microbiota/genetics , Prokaryotic Cells
4.
JBJS Rev ; 9(7)2021 07 02.
Article in English | MEDLINE | ID: mdl-34223828

ABSTRACT

BACKGROUND: The literature on osteochondral lesions of the tibial plafond (OLTPs) is sparse. The aim of this study was therefore to provide an overview of clinical and radiological outcomes following treatment of OLTPs. METHODS: We performed a systematic search of the MEDLINE, Embase, and Cochrane library databases. The review was performed in accordance with the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines and included all original articles on treatment outcomes for OLTPs. The methodological quality of the articles was assessed using the Methodological Index for Non-Randomized Studies (MINORS). Baseline patient and lesion characteristics were pooled and weighted according to the number of lesions per study. The primary outcome was any clinical or patient-reported outcome measure pooled by treatment method when separable data were available. Secondary outcomes were complications, reoperation rates, radiological outcomes, and sport outcomes. RESULTS: The search yielded 2,079 articles, of which 10 studies (1 prospective case series, 1 retrospective comparative study, and 8 retrospective case series) with a total of 175 patients were included. The overall methodological quality of the studies was low. All patients were treated surgically; 96% of the lesions were primary cases (i.e., first-time surgery) and 58% were solitary tibial lesions (i.e., no opposing talar lesion). Arthroscopic bone marrow stimulation was the most frequently used treatment strategy (51%), followed by cartilage transplantation (17%), chondrogenesis-inducing techniques (11%), osteochondral transplantation (3%), retrograde drilling (3%), and mixed (i.e., inseparable) treatments (15%). The clinical outcomes of the different surgical therapies were considered to be moderate to good. The pooled postoperative AOFAS (American Orthopaedic Foot & Ankle Society) score for bone marrow stimulation and osteochondral transplantation was 54.8 (95% confidence interval [CI], 49.5 to 85.0) (n = 14) and 85.3 (95% CI, 56 to 100) (n = 3), respectively. Overall, complications and reoperations were rarely reported. The pooled complication and reoperation rates could only be calculated for bone marrow stimulation and were 5% and 7%, respectively. CONCLUSIONS: Surgical interventions for OLTPs appear to yield moderate to good clinical outcomes. Bone marrow stimulation resulted in a moderate AOFAS score. Complications and reintervention rates were found to be low. The current evidence in the literature is limited because of the underreporting of clinical, radiological, and sport data and the heterogenous outcome scores reported. LEVEL OF EVIDENCE: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.


Subject(s)
Intra-Articular Fractures , Magnetic Resonance Imaging , Bone Transplantation , Humans , Retrospective Studies , Tibia/surgery
5.
Int J Food Microbiol ; 349: 109232, 2021 Jul 02.
Article in English | MEDLINE | ID: mdl-34022615

ABSTRACT

Biofilms are formed by microorganisms protected by a self-produced matrix, most often attached to a surface. In the food processing environments biofilms endanger the product safety by the transmission of spoilage and pathogenic bacteria. In this study, we characterised the biofilm formation of the following eleven strains isolated from biofilms in a meat-processing environment: Acinetobacter harbinensis BF1, Arthrobacter sp. BF1, Brochothrix thermosphacta BF1, Carnobacterium maltaromaticum BF1, Kocuria salsicia BF1, Lactococcus piscium BF1, Microbacterium sp. BF1, Pseudomonas fragi BF1, Psychrobacter sp. BF1, Rhodococcus erythropolis BF1, Stenotrophomonas sp. BF1. We applied whole- genome sequencing and subsequent genome analysis to elucidate genetic features associated with the biofilm lifestyle. We furthermore determined the motility and studied biofilm formation on stainless steel using a static mono-species biofilm model mimicking the meat processing environment. The biomass and the EPS components carbohydrates, proteins and extracellular DNA (eDNA) of the biofilms were investigated after seven days at 10 °C. Whole-genome analysis of the isolates revealed that all strains except the Kocuria salsicia BF1 isolate, harboured biofilm associated genes, including genes for matrix production and motility. Genes involved in cellulose metabolism (present in 82% of the eleven strains) and twitching motility (present in 45%) were most frequently found. The capacity for twitching was confirmed using plate assays for all strains except Lactococcus piscium BF1, which showed the lowest motility behaviour. Differences in biofilm forming abilities could be demonstrated. The bacterial load ranged from 5.4 log CFU/cm2 (Psychrobacter sp. isolate) to 8.7 log CFU/cm2 (Microbacterium sp. isolate). The amount of the matrix components varied between isolates. In the biofilm of six strains we detected all three matrix components at different levels (carbohydrates, proteins and eDNA), in two only carbohydrates and eDNA, and in three only carbohydrates. Carbohydrates were detected in biofilms of all strains ranging from 0.5 to 4.3 µg glucose equivalents/cm2. Overall, the Microbacterium sp. strain showed the highest biofilm forming ability with high bacterial load (8.7 log CFU/cm2) and high amounts of carbohydrates (2.2 µg glucose equivalents/cm2), proteins (present in all experiments) and eDNA (549 ng/cm2). In contrast, Brochothrix thermosphacta was a weak biofilm former, showing low bacterial load and low levels of carbohydrates in the matrix (6.2 log CFU/cm2 and 0.5 µg glucose equivalents/cm2). This study contributes to our understanding of the biofilm forming ability of bacteria highly abundant in the meat processing environment, which is crucial to develop strategies to prevent and reduce biofilm formation in the food producing environment.


Subject(s)
Bacteria/isolation & purification , Biofilms/growth & development , Meat/microbiology , Bacteria/classification , Bacteria/genetics , Bacteria/growth & development , Colony Count, Microbial , Extracellular Polymeric Substance Matrix/chemistry , Extracellular Polymeric Substance Matrix/genetics , Food Microbiology , Food-Processing Industry , Genome, Bacterial/genetics , Locomotion/genetics , Species Specificity
6.
ISME J ; 15(9): 2779-2791, 2021 09.
Article in English | MEDLINE | ID: mdl-33790426

ABSTRACT

Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (H2S), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H2S production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of H2S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.


Subject(s)
Hydrogen Sulfide , Bacteria/genetics , Feces , Humans , Methylglucosides , Nutrients
7.
IMA Fungus ; 11: 20, 2020.
Article in English | MEDLINE | ID: mdl-33062585

ABSTRACT

We formed the Collection of Zoosporic Eufungi at the University of Michigan (CZEUM) in 2018 as a cryopreserved fungal collection consolidating the University of Maine Culture Collection (UMCC, or JEL), the University of Alabama Chytrid Culture Collection (UACCC), and additional zoosporic eufungal accessions. The CZEUM is established as a community resource containing 1045 cryopreserved cultures of Chytridiomycota, Monoblepharidomycota, and Blastocladiomycota, with 52 cultures being ex-type strains. We molecularly characterized 431 cultures by amplifying the majority of the rDNA operon in a single reaction, yielding an average fragment length of 4739 bp. We sequenced multiplexed samples with an Oxford Nanopore Technology MinION device and software, and demonstrate the method is accurate by producing sequences identical to published Sanger sequences. With these data, we generated a phylogeny of 882 zoosporic eufungi strains to produce the most comprehensive phylogeny of these taxa to date. The CZEUM is thus largely characterized by molecular data, which can guide instructors and researchers on future studies of these organisms. Cultures from the CZEUM can be purchased through an online portal.

8.
iScience ; 23(9): 101510, 2020 Sep 25.
Article in English | MEDLINE | ID: mdl-32919372

ABSTRACT

Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae, and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattai strain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum, and Eubacterium rectale strains also express transaldolase pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic lifestyle of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.

9.
Front Microbiol ; 10: 979, 2019.
Article in English | MEDLINE | ID: mdl-31143163

ABSTRACT

Few studies have investigated bacterial community succession and the role of bacterial decomposition over a continuum of wood decay. Here, we identified how (i) the diversity and abundance of bacteria changed along a chronosequence of decay in Populus grandidentata (bigtooth aspen); (ii) bacterial community succession was dependent on the physical and chemical characteristics of the wood; (iii) interspecific bacterial interactions may mediate community structure. Four hundred and fifty-nine taxa were identified through Illumina sequencing of 16S rRNA amplicons from samples taken along a continuum of decay, representing standing dead trees, downed wood, and soil. Community diversity increased as decomposition progressed, peaking in the most decomposed trees. While a small proportion of taxa displayed a significant pattern in regards to decay status of the host log, many bacterial taxa followed a stochastic distribution. Changes in the water availability and chemical composition of standing dead and downed trees and soil were strongly coupled with shifts in bacterial communities. Nitrogen was a major driver of succession and nitrogen-fixing taxa of the order Rhizobiales were abundant early in decomposition. Recently downed logs shared 65% of their bacterial abundance with the microbiomes of standing dead trees while only sharing 16% with soil. As decay proceeds, bacterial communities appear to respond less to shifting resource availability and more to interspecific bacterial interactions - we report an increase in both the proportion (+9.3%) and the intensity (+62.3%) of interspecific interactions in later stages of decomposition, suggesting the emergence of a more complex community structure as wood decay progresses.

10.
Environ Microbiol ; 20(10): 3543-3559, 2018 10.
Article in English | MEDLINE | ID: mdl-30051558

ABSTRACT

Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from 13 C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.


Subject(s)
Bacteria/metabolism , Groundwater/microbiology , Naphthalenes/metabolism , Soil Microbiology , Soil Pollutants/metabolism , Water Microbiology , Water Pollutants, Chemical/metabolism , Bacteria/genetics , Biodegradation, Environmental , Metagenome , Metagenomics
11.
Herz ; 42(3): 241-254, 2017 May.
Article in German | MEDLINE | ID: mdl-28229203

ABSTRACT

Besides providing spatial anatomic information on heart valves, real-time three-dimensional echocardiography (3DE) combined with color Doppler has the potential to overcome the limitations of flow quantification inherent to conventional 2D color Doppler methods. Recent studies validated the application of color Doppler 3DE (cD-3DE) for the quantification of regurgitation flow based on the vena contracta area (VCA) and the proximal isovelocity surface area (PISA) methods. Particularly the assessment of VCA by cD-3DE led to a change of paradigm by understanding of the VCA as being strongly asymmetric in the majority of patients and etiologies. This review provides a comprehensive description of the different concepts of cD-3DE-based flow quantification in the setting of different valvular heart diseases and their presentation in recent guidelines.


Subject(s)
Cardiology/standards , Echocardiography, Three-Dimensional/standards , Evidence-Based Medicine/standards , Heart Valve Diseases/diagnostic imaging , Practice Guidelines as Topic , Radiology/standards , Severity of Illness Index , Computer Systems , Germany
12.
J Chem Phys ; 145(18): 181102, 2016 Nov 14.
Article in English | MEDLINE | ID: mdl-27846697

ABSTRACT

Chemisorption of muonium onto the surface of gold nanoparticles has been observed. Muonium (µ+e-), a light hydrogen-like atom, reacts chemically with uncapped 7 nm gold nanoparticles embedded in mesoporous silica (SBA-15) with a strong temperature-dependent rate. The addition rate is fast enough to allow coherent spin transfer into a diamagnetic muon state on the nanoparticle surface. The muon is well established as a sensitive probe of static or slowly fluctuating magnetic fields in bulk matter. These results represent the first muon spin rotation signal on a nanoparticle surface or any metallic surface. Only weak magnetic effects are seen on the surface of these Au nanoparticles consistent with Pauli paramagnetism.

13.
J Ovarian Res ; 9(1): 62, 2016 Sep 29.
Article in English | MEDLINE | ID: mdl-27686972

ABSTRACT

BACKGROUND: A previous study showed that dopamine (DA), which is contained in follicular fluid (FF) from IVF patients, strongly increased the production of reactive oxygen species (ROS) by cultured human granulosa cells (GCs). ROS, including H2O2, are assumed to play roles in ovarian physiology and pathology. Ovarian DA could be derived from the circulation, ovarian innervation and/or unknown ovarian sources. L-DOPA is the direct precursor of DA in its synthetic pathway. It was not yet described in FF. We examined L-DOPA levels in FF from IVF patients. As it may exert anti-oxidative and ROS-scavenging functions, we studied whether it exerts such actions in human GCs and whether DOPA-decarboxylase (DDC), the enzyme converting L-DOPA to DA, is expressed in the human ovary. RESULTS: ELISA measurements revealed that human IVF-derived FF contains L-DOPA. In cultured human GCs automated confluence analyses showed that L-DOPA enhanced their survival. This is in contrast to the actions of DA, which reduced cell survival. A dose-dependent mode of action of L-DOPA was identified using a fluorescent ROS indicator. The results showed that it antagonized intracellular ROS accumulation induced by exogenous H2O2. DDC was absent in follicular GCs, but immunohistochemistry identified it in theca cells (TCs) of large follicles in the human ovary. Laser micro-dissection followed by RT-PCR corroborated the expression. DDC was also identified in the steroidogenic cells of the corpus luteum. CONCLUSIONS: L-DOPA in FF is an antioxidant factor and exerts positive influences on GCs. Ovarian DA is derived from L-DOPA and has opposite actions. Exogenous L-DOPA is a standard therapy for Parkinson's disease, and the results raise the possibility that it may be able to exert positive actions as an antioxidant in ovarian conditions, as well.

14.
Phys Rev Lett ; 116(10): 106103, 2016 Mar 11.
Article in English | MEDLINE | ID: mdl-27015494

ABSTRACT

By measuring the prototypical antiferromagnet α-Fe_{2}O_{3}, we show that it is possible to determine the static spin orientation and dynamic spin correlations within nanometers from an antiferromagnetic surface using the nuclear spin polarization of implanted ^{8}Li^{+} ions detected with ß-NMR. Remarkably, the first-order Morin spin reorientation in single crystal α-Fe_{2}O_{3} occurs at the same temperature at all depths between 1 and 100 nm from the (110) surface; however, the implanted nuclear spin experiences an increased 1/T_{1} relaxation rate at shallow depths revealing soft-surface magnons. The surface-localized dynamics decay towards the bulk with a characteristic length of ε=11±1 nm, closely matching the finite-size thresholds of hematite nanostructures.

15.
Proc Natl Acad Sci U S A ; 112(2): E194-203, 2015 Jan 13.
Article in English | MEDLINE | ID: mdl-25550518

ABSTRACT

Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.


Subject(s)
Deuterium Oxide/metabolism , Microbial Consortia , Animals , Archaea/genetics , Archaea/isolation & purification , Archaea/metabolism , Bacteria/genetics , Bacteria/isolation & purification , Bacteria/metabolism , Base Sequence , Biomass , Cecum/microbiology , DNA, Archaeal/genetics , DNA, Bacterial/genetics , Escherichia coli/genetics , Escherichia coli/growth & development , Escherichia coli/metabolism , Humans , In Situ Hybridization, Fluorescence , Mice , Mice, Inbred C57BL , Microbial Consortia/genetics , Microbiological Techniques , Molecular Sequence Data , Optical Tweezers , Phylogeny , Spectrum Analysis, Raman
16.
Environ Microbiol Rep ; 7(2): 252-64, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25403415

ABSTRACT

Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here, we used environmental metaproteomics to obtain information about the identity of subsurface microbial populations in coal tar-contaminated groundwater and the metabolic processes they catalyze. Metaproteomic libraries (two shotgun and seven slices from one SDS-PAGE gel) were generated from replicate samples of microbial biomass. Peptide fragment analysis using nano-liquid chromatography (LC)-mass spectrometry (MS)/MS of the three protein pools generated a total of 95,725 mass spectra. When analyzed using mascot v.2.3.02 and searched against the NCBInr bacterial database [confidence interval 99% (P < 0.01)], a total of 1,270 proteins had at least two peptide matches. Replication of identified proteins across the three libraries was low (3.3%); however, in each library, the most frequently identified protein host was Candidatus Methylomirabilis oxyfera (15, 12 and 62 proteins for each shotgun and the gel-slice library respectively). Remarkably, eight of the nine proteins in the nitrite-dependent anaerobic methane oxidation pathway were found. Additionally, 39 proteins were matched to known anammox bacteria including hydroxylamine and hydrazine oxidase. Metaproteomics thus revealed a microbial population, closely related to Ca. Methylomirabilis oxyfera, actively engaged in nitrite-dependent anaerobic methane oxidation and likely competing for nitrite with anammox bacteria.


Subject(s)
Bacteria/chemistry , Bacteria/metabolism , Bacterial Proteins/analysis , Groundwater/microbiology , Methane/metabolism , Nitrites/metabolism , Proteome/analysis , Anaerobiosis , Chromatography, Liquid , Metabolic Networks and Pathways , Oxidation-Reduction , Tandem Mass Spectrometry
17.
Microb Ecol ; 67(3): 520-39, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24425229

ABSTRACT

Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.


Subject(s)
Bacterial Proteins/genetics , Cyanobacteria/physiology , Proteobacteria/physiology , Proteomics , Bacterial Proteins/metabolism , Biodiversity , Chromatography, Liquid , Cyanobacteria/classification , Cyanobacteria/genetics , Fresh Water/microbiology , Molecular Sequence Data , Pacific Ocean , Phylogeny , Phylogeography , Proteobacteria/classification , Proteobacteria/genetics , Seawater/microbiology , Sequence Analysis, DNA , Tandem Mass Spectrometry , United States
18.
Dtsch Med Wochenschr ; 138(9): 423-36, 2013 Mar.
Article in German | MEDLINE | ID: mdl-23423939

ABSTRACT

The incidence of first stroke in Germany is about 200.000, most of which are ischemic. The benefit of stroke unit treatment and systemic thrombolysis has been shown in large randomized trials. Diagnostic work-up besides neurologic examination includes cerebral imaging by CT or MR imaging including angiography, ultrasound of brain supplying arteries, ECG and Holter ECG and - if indicated - transesophageal echocardiography. Aspirin is the cornerstone of early secondary prevention in the acute phase, thereafter secondary prevention is determined by stroke etiology. Carotid endarterectomy or stent-assisted angioplasty are indicated in patients with hemodynamic or arterio-arterial stroke etiologies due to high-grade carotid stenosis. For cardioembolism due to atrial fibrillation, oral anticoagulation with vitamin K-antagonists or new oral anticoagulants should be started after the acute phase. In patients with non-cardioembolic stroke etiologies, platelet inhibitors are used for secondary prevention.


Subject(s)
Anticoagulants/therapeutic use , Brain Ischemia/diagnosis , Brain Ischemia/therapy , Cerebral Angiography/methods , Stroke/diagnosis , Stroke/therapy , Thrombolytic Therapy/methods , Brain Ischemia/complications , Electrocardiography/methods , Endarterectomy/methods , Humans , Stroke/complications
19.
Herz ; 38(1): 33-41, 2013 Feb.
Article in German | MEDLINE | ID: mdl-23344389

ABSTRACT

Real-time 3D echocardiography is one of the most important developments in the field of non-invasive cardiac imaging within the last years. To investigate whether this new technology can be considered as a standard method the current guidelines and recommendations were reviewed. In the field of left ventricular function assessment, evaluation of mitral valve pathologies and peri-interventional monitoring of percutaneous valve repair procedures 3D echocardiography plays a major role. For other clinical applications, such as right heart assessment, congenital heart disease and stress echocardiography, a high potential is seen but evidence is currently too weak for general recommendations. However, in the near future no echo laboratory will be working without 3D modalities.


Subject(s)
Cardiology/standards , Echocardiography, Three-Dimensional/standards , Practice Guidelines as Topic , Radiology/standards , Cardiology/trends , Echocardiography, Three-Dimensional/trends , Germany , Internationality , Radiology/trends
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