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Nature Medicine Apr 2020Mucosal immunity develops in the human fetal intestine by 11-14 weeks of gestation, yet whether viable microbes exist in utero and interact with the intestinal immune...
Mucosal immunity develops in the human fetal intestine by 11-14 weeks of gestation, yet whether viable microbes exist in utero and interact with the intestinal immune system is unknown. Bacteria-like morphology was identified in pockets of human fetal meconium at mid-gestation by scanning electron microscopy (n = 4), and a sparse bacterial signal was detected by 16S rRNA sequencing (n = 40 of 50) compared to environmental controls (n = 87). Eighteen taxa were enriched in fetal meconium, with Micrococcaceae (n = 9) and Lactobacillus (n = 6) the most abundant. Fetal intestines dominated by Micrococcaceae exhibited distinct patterns of T cell composition and epithelial transcription. Fetal Micrococcus luteus, isolated only in the presence of monocytes, grew on placental hormones, remained viable within antigen presenting cells, limited inflammation ex vivo and possessed genomic features linked with survival in the fetus. Thus, viable bacteria are highly limited in the fetal intestine at mid-gestation, although strains with immunomodulatory capacity are detected in subsets of specimens.
Topics: Autopsy; Bacteria; Bacterial Typing Techniques; Female; Fetus; Gastrointestinal Microbiome; Gestational Age; Humans; Infant, Newborn; Intestinal Mucosa; Intestines; Lactobacillus; Meconium; Microbial Viability; Micrococcaceae; Pregnancy; Pregnancy Trimester, Second; RNA, Ribosomal, 16S
PubMed: 32094926
DOI: 10.1038/s41591-020-0761-3 -
Genes Jul 2020Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as...
Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. Microscopic observation of Nile Red stained cells proved to be the most reliable screening method as it allowed to confirm the characteristic bright orange glow of the Nile Red-PHA complex as well as the typical morphology of the PHA inclusions. Psychrophilic PHA-producers belonged mostly to the family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, and also featured prominently. Glacial and postglacial habitats as well as developed polar region soils, were evaluated as promising for PHA-producer bioprospection. This study highlights the importance of psychrophiles as biodiverse and potent polyhydroxyalkanoate sources for scientific and application-aimed research.
Topics: Arctic Regions; Comamonadaceae; Microbiota; Micrococcaceae; Phylogeny; Polyhydroxyalkanoates; Polymorphism, Genetic; Seawater; Soil Microbiology
PubMed: 32752049
DOI: 10.3390/genes11080873 -
Clinical Microbiology Reviews Apr 1998The contribution of enzyme tests to the accurate and rapid routine identification of gram-positive cocci is introduced. The current taxonomy of the genera of aerobic and... (Review)
Review
The contribution of enzyme tests to the accurate and rapid routine identification of gram-positive cocci is introduced. The current taxonomy of the genera of aerobic and facultatively anaerobic cocci based on genotypic and phenotypic characterization is reviewed. The clinical and economic importance of members of these taxa is briefly summarized. Tables summarizing test schemes and kits available for the identification of staphylococci, enterococci, and streptococci on the basis of general requirements, number of tests, number of taxa, test classes, and completion times are discussed. Enzyme tests included in each scheme are compared on the basis of their synthetic moiety. The current understanding of the activity of enzymes important for classification and identification of the major groups, methods of testing, and relevance to the ease and speed of identification are reviewed. Publications describing the use of different identification kits are listed, and overall identification successes and problems are discussed. The relationships between the results of conventional biochemical and rapid enzyme tests are described and considered. The use of synthetic substrates for the detection of glycosidases and peptidases is reviewed, and the advantages of fluorogenic synthetic moieties are discussed. The relevance of enzyme tests to accurate and meaningful rapid routine identification is discussed.
Topics: Animals; Bacteria, Anaerobic; Bacteriological Techniques; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans; Micrococcaceae; Reagent Kits, Diagnostic; Streptococcaceae
PubMed: 9564566
DOI: 10.1128/CMR.11.2.318 -
Scientific Reports Oct 2022Marine pigmented bacteria are a promising natural source of carotenoids. Kocuria sp. RAM1 was isolated from the Red Sea Bohadschia graeffei collected from Marsa Alam,...
Marine pigmented bacteria are a promising natural source of carotenoids. Kocuria sp. RAM1 was isolated from the Red Sea Bohadschia graeffei collected from Marsa Alam, Egypt, and used for carotenoids production. The extracted carotenoids were purified by thin-layer chromatography (TLC). The characteristic UV absorbance of the three purified fractions gave us an inkling of what the purified pigments were. The chemical structures were confirmed by nuclear magnetic resonance spectroscopy (NMR) and LC-ESI-QTOF-MS/MS. The three different red pigments were identified as two C-carotenoids, namely bisanhydrobacterioruberin and trisanhydrobacterioruberin, in addition to 3,4,3',4'-Tetrahydrospirilloxanthin (C-carotenoids). Kocuria sp. RAM1 carotenoids were investigated for multiple activities, including antimicrobial, anti-inflammatory, antioxidant, anti-HSV-1, anticancer, antidiabetic and wound healing. These new observations suggest that Kocuria sp. RAM1 carotenoids can be used as a distinctive natural pigment with potent properties.
Topics: Carotenoids; Tandem Mass Spectrometry; Micrococcaceae; Bacteria; Chromatography, Thin Layer
PubMed: 36307503
DOI: 10.1038/s41598-022-22897-4 -
NPJ Biofilms and Microbiomes Aug 2021Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we...
Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources-particularly oxygen-and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.
Topics: Bacillus thuringiensis; Bacteria; Bacterial Physiological Phenomena; Biofilms; Biomass; Kinetics; Microbial Interactions; Microbiota; Micrococcaceae; Pseudomonas fluorescens; Rhodocyclaceae; Species Specificity
PubMed: 34354076
DOI: 10.1038/s41522-021-00233-4 -
CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection.Microbiome Jun 2023Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a...
BACKGROUND
Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a household study, we determined whether metagenomic-type analyses of the microbiome provide the resolution necessary to track transmission of airway bacteria. Microbiome studies have shown that the microbial community across various body sites tends to be more similar between individuals who cohabit in the same household than between individuals from different households. We tested whether there was increased sharing of bacteria from the airways within households with influenza infections as compared to control households with no influenza.
RESULTS
We obtained 221 respiratory samples that were collected from 54 individuals at 4 to 5 time points across 10 households, with and without influenza infection, in Managua, Nicaragua. From these samples, we generated metagenomic (whole genome shotgun sequencing) datasets to profile microbial taxonomy. Overall, specific bacteria and phages were differentially abundant between influenza positive households and control (no influenza infection) households, with bacteria like Rothia, and phages like Staphylococcus P68virus that were significantly enriched in the influenza-positive households. We identified CRISPR spacers detected in the metagenomic sequence reads and used these to track bacteria transmission within and across households. We observed a clear sharing of bacterial commensals and pathobionts, such as Rothia, Neisseria, and Prevotella, within and between households. However, due to the relatively small number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection.
CONCLUSION
We observed that airway microbial composition differences across households were associated with what appeared to be different susceptibility to influenza infection. We also demonstrate that CRISPR spacers from the whole microbial community can be used as markers to study bacterial transmission between individuals. Although additional evidence is needed to study transmission of specific bacterial strains, we observed sharing of respiratory commensals and pathobionts within and across households. Video Abstract.
Topics: Humans; Clustered Regularly Interspaced Short Palindromic Repeats; Influenza, Human; Bacteria; Metagenome; Microbiota; Micrococcaceae
PubMed: 37330554
DOI: 10.1186/s40168-023-01568-0 -
Journal of Dairy Science Oct 2020The objective of this work was to determine the effect of milk bactofugation on the counts and microbial diversity of mesophilic (MT), psychrotrophic (PT), and...
The objective of this work was to determine the effect of milk bactofugation on the counts and microbial diversity of mesophilic (MT), psychrotrophic (PT), and thermophilic (TT) thermoduric bacteria and its potential as a technological method to remove spoilage microorganisms resistant to pasteurization. Different batches of raw milk from 69 dairy farms divided into sets in 3 bulk tanks (A, B, C) were evaluated at different times during the technological process. As the raw milk was preheated (∼55°C) immediately before bactofugation (10,000 × g), the effect of bactofugation was estimated by comparing the counts in raw, preheated, and bactofuged milk. This centrifugation was sufficient to reduce the isolation of 88% of the MT in preheated milk. For PT, it was possible to verify a reduction of 72.5% in batch C. The TT were not recovered at higher detection limits (<5 cfu/mL). For diversity, 310 isolates were identified using a molecular approach; 15 species of contaminating thermoduric bacteria were identified from raw and preheated milk, and only 6 species were recovered in bactofuged milk. Only MT were recovered from the bactofuged milk, mainly the species Lysinibacillus fusiformis (61.7%) and Bacillus licheniformis (12.3%). Both species are known to be endospore-forming psychrotrophs and have proteolytic or lipolytic activity. The bactofugation of raw milk reduced the number of isolates of B. licheniformis, Bacillus toyonensis, Micrococcus aloeverae, and Aestuariimicrobium kwangyangense by 33, 43, 86, and 92%, respectively, and reduced the isolates of Macrococcus caseolyticus, Lysinibacillus varians, Carnobacterium divergens, Microbacterium hominis, Kocuria indica, Micrococcus yunnanensis, Gordonia paraffinivorans, Bacillus invictae, and Kocuria kristinae to undetectable levels. The results of this study indicate that bactofugation can be applied by the dairy industry to reduce pasteurization-resistant microorganisms in combination with prophylactic measures to prevent the contamination of raw milk by spores and vegetative forms of bacteria.
Topics: Actinobacteria; Animals; Bacillaceae; Bacillus; Bacteria, Thermoduric; Carnobacterium; Centrifugation; Micrococcaceae; Micrococcus; Milk; Propionibacteriaceae; Staphylococcaceae
PubMed: 32828509
DOI: 10.3168/jds.2020-18591 -
BMJ Case Reports Jan 2021is a Gram-positive aerobic coccus usually found in the oral and respiratory tract. Septic arthritis is an uncommon condition, but is an orthopaedic emergency. A rare... (Review)
Review
is a Gram-positive aerobic coccus usually found in the oral and respiratory tract. Septic arthritis is an uncommon condition, but is an orthopaedic emergency. A rare case of knee septic arthritis due to is presented. Patient management and outcomes are discussed, and learning points from this case are outlined to help manage any further cases that may arise.
Topics: Arthritis, Infectious; Female; Gram-Positive Bacterial Infections; Humans; Knee Joint; Micrococcaceae; Middle Aged
PubMed: 33462004
DOI: 10.1136/bcr-2020-237015 -
Microbial Genomics Sep 2022species are understudied members of the phylum Actinobacteria and prevalent colonizers of the human and animal upper respiratory tract and oral cavity. The oral cavity,...
species are understudied members of the phylum Actinobacteria and prevalent colonizers of the human and animal upper respiratory tract and oral cavity. The oral cavity, including the palatine tonsils, is colonized by a complex microbial community, which compete for resources, actively suppress competitors and influence host physiology. We analysed genomic data from 43 new porcine isolates, together with 112 publicly available draft genome sequences of isolates from humans, animals and the environment. In all genomes, we identified biosynthetic gene clusters predicted to produce antibiotic non-ribosomal peptides, iron scavenging siderophores and other secondary metabolites that modulate microbe-microbe and potentially microbe-host interactions. overlay inhibition assays corroborated the hypothesis that specific strains produce natural antibiotics. genomes encode a large number of carbohydrate-active enzymes (CAZy), with varying CAZy activities among the species found in different hosts, host niches and environments. These findings reveal competition mechanisms and metabolic specializations linked to ecological adaptation of species in different hosts.
Topics: Animals; Anti-Bacterial Agents; Carbohydrates; Eukaryota; Genomics; Humans; Iron; Micrococcaceae; Multigene Family; Peptides; Siderophores; Swine
PubMed: 36165601
DOI: 10.1099/mgen.0.000854 -
Molecules (Basel, Switzerland) Jul 2021decomposes nicotine through the pyridine pathway. 6-hydroxypseudooxynicotine 2-oxidoreductase (also named ketone dehydrogenase, Kdh) is an important enzyme in nicotine...
decomposes nicotine through the pyridine pathway. 6-hydroxypseudooxynicotine 2-oxidoreductase (also named ketone dehydrogenase, Kdh) is an important enzyme in nicotine degradation pathway of , and is responsible for the second hydroxylation of nicotine. Kdh belongs to the molybdenum hydroxylase family, and catalyzes the oxidation of 6-hydroxy-pseudooxynicotine (6-HPON) to 2,6-dihydroxy-pseudooxynicotine (2,6-DHPON). We determined the crystal structure of the Kdh holoenzyme from , with its three subunits KdhL, KdhM, and KdhS, and their associated cofactors molybdopterin cytosine dinucleotide (MCD), two iron-sulfur clusters (FeS), and flavin adenine dinucleotide (FAD), respectively. In addition, we obtained a structural model of the substrate 6-HPON-bound Kdh through molecular docking, and performed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations to unveil the catalytic mechanism of Kdh. The residues Glu345, Try551, and Glu748 of KdhL were found to participate in substrate binding, and Phe269 and Arg383 of KdhL were found to contribute to stabilize the MCD conformation. Furthermore, site-directed mutagenesis and enzymatic activity assays were performed to support our structural and computational results, which also revealed a trend of increasing catalytic efficiency with the increase in the buffer pH. Lastly, our electrochemical results demonstrated electron transfer among the various cofactors of Kdh. Therefore, our work provides a comprehensive structural, mechanistic, and functional study on the molybdenum hydroxylase Kdh in the nicotine degradation pathway of
Topics: Bacterial Proteins; Cloning, Molecular; Cytosine Nucleotides; Micrococcaceae; Mixed Function Oxygenases; Molecular Docking Simulation; Molybdenum; Nicotine; Pterins; Structure-Activity Relationship
PubMed: 34299660
DOI: 10.3390/molecules26144387