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PLoS Neglected Tropical Diseases Aug 2017Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes...
BACKGROUND
Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies.
METHODOLOGY
Seventy participants from Eggua, southwestern Nigeria provided morning urine samples and were screened for urogenital schistosomiasis infection and bladder pathologies in a cross-sectional study. Highthroughput NGS sequencing was carried out, targeting the 16S V3 region. Filtered reads were processed and analyzed in a bioinformatics pipeline.
PRINCIPAL FINDINGS
The study participants (36 males and 34 females, between ages 15 and 65) were categorized into four groups according to status of schistosomiasis infection and bladder pathology. Data analytics of the next-generation sequencing reads revealed that Proteobacteria and Firmicutes dominated and had influence on microbiome structure of both non-infected persons and persons with urogenital schistosomiasis. Furthermore, gender and age influenced taxa abundance independent of infection or bladder pathology. Several taxa distinguished urogenital schistosomiasis induced bladder pathologies from urogenital schistosomiasis infection alone and from healthy persons, including known immune-stimulatory taxa such as Fusobacterium, Sphingobacterium and Enterococcus. Some of these significant taxa, especially Sphingobacterium were projected as markers of infection, while several genera including potentially beneficial taxa such as Trabulsiella and Weissella, were markers of the non-infected. Finally, expected changes in protein functional categories were observed to relate to cellular maintenance and lipid metabolism.
CONCLUSION
The urinary microbiome is a factor to be considered in developing biomarkers, diagnostic tools, and new treatment for urogenital schistosomiasis and induced bladder pathologies.
Topics: Adolescent; Adult; Bacteria; Cluster Analysis; Cross-Sectional Studies; DNA, Bacterial; DNA, Ribosomal; Female; High-Throughput Nucleotide Sequencing; Humans; Male; Microbiota; Middle Aged; Nigeria; Phylogeny; RNA, Ribosomal, 16S; Schistosomiasis haematobia; Sequence Analysis, DNA; Urinary Bladder; Urine; Young Adult
PubMed: 28793309
DOI: 10.1371/journal.pntd.0005826 -
Frontiers in Microbiology 2020Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as...
Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as so4 and w15 based on 16S rRNA gene sequencing and comparison to the respective and type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of so4, but absent from that of w15. In the genome of w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with w15 primarily attacking the WS hemicellulose and so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, so4 may secrete secondary metabolites that w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.
PubMed: 32194522
DOI: 10.3389/fmicb.2020.00248 -
Frontiers in Microbiology 2021The safe and effective storage of forage are very important. As an important storage method, ensiling can keep fresh forage for a long time with less nutritional loss....
The safe and effective storage of forage are very important. As an important storage method, ensiling can keep fresh forage for a long time with less nutritional loss. Melatonin has antioxidant and bacteriostasis, usually used as a natural preservative. The influence of melatonin on silage microbial or fermentation quality has not been clarified. In the present study, we aimed to clarify whether melatonin affected stylo () silage quality via microbiota and metabolites. Melatonin addition significantly improved the silage fermentation quality, including the increased contents of lactic acid and total acid (244.18-255.81% and 63.95-78.97%, respectively), as well as the decreased in pH and butyric acid content compare with control group. Moreover, 16S rRNA sequencing indicated that melatonin addition enhanced the silage microbial diversity indices (such as increase in Shannon indices but decrease in Simpson indices), and significantly shaped the composition of silage microbiota (such as increased abundances of , , , and , and decreased abundance of ). Melatonin addition also dramatically affected the metabolites of sylo silage, such as raised malonic acid and some amino acid metabolism(glycine, threonine, methionine and ornithine), while reduced nucleic acid metabolism(2-deoxyuridine and thymine) and carbon metabolism(allose and 2-deoxy-D-glucose). Collectively, our results confirmed that the lowest melatonin addition (5 mg/kg) could improve the fermentation quality, and the potential mechanisms might be associated with the microbiota and metabolites in stylo.
PubMed: 34122385
DOI: 10.3389/fmicb.2021.670764 -
Revista Paulista de Pediatria : Orgao... Sep 2016To report a case septic arthritis with a rare pathogen in a immunosuppressed child.
OBJECTIVE
To report a case septic arthritis with a rare pathogen in a immunosuppressed child.
CASE DESCRIPTION
Male patient, 6 years old, had liver transplant 5 and half years ago due to biliary atresia. Patient was using tacrolimus 1mg q.12hours. This patient started to have pain in left foot and ankle and had one episode of fever 3 days before hospital admission. Physical Examination showed weight 17kg, height 109cm, temperature 36,4°C, with pain, swelling and heat in the left ankle, without other clinical signs. Initial tests: hemoglobin 11,7g/dL hematocrit 36.4%, leukocyte count 17600/uL (7% banded neutrophils, 70% segmented neutrophils, 2% eosinophils, basophils 1%, 13% lymphocytes, 7% monocytes) C-reactive protein 170,88mg/L. Joint ultrasound showed moderate effusion in the site. Patient was submitted to surgical procedure and S. multivorum was isolated from the effusion. The germ was susceptible to broad spectrum cephalosporins (ceftriaxone and cefepime) and fluoroquinolones (ciprofloxacin and levofloxacin), and it was resistant to carbapenemic antibiotics and aminoglycosides. He was treated intravenously with oxacillin for 15 days and ceftriaxone for 13 days, and orally with ciprofloxacin for 15 days, with good outcome.
COMMENTS
The Sphingobacterium multivorum is a gram negative bacillus that belongs to Flavobacteriaceae family and it is considered non-pathogenic. It has rarely been described as a cause of infections in humans, especially in hospital environment and in immunosuppressed patients. This case report is relevant for its unusual etiology and for the site affected, which may be the first case of septic arthritis described.
Topics: Arthritis, Infectious; Child; Gram-Negative Bacterial Infections; Humans; Immunocompromised Host; Male; Sphingobacterium
PubMed: 26915918
DOI: 10.1016/j.rpped.2015.12.001 -
Animal Bioscience Dec 2022The observation that temperate C3 and tropical C4 forage silages easily produce large amounts of ethanol or acetic acid has puzzled researchers for many years. Hence,...
OBJECTIVE
The observation that temperate C3 and tropical C4 forage silages easily produce large amounts of ethanol or acetic acid has puzzled researchers for many years. Hence, this study aimed to assess the effects of epiphytic microbiota from C3 forages (Italian ryegrass and oat) on fermentative products and bacterial community structure in C4 forage (sorghum) silage.
METHODS
Through microbiota transplantation and γ-ray irradiation sterilization, the irradiated sorghum was treated: i) sterile distilled water (STSG); ii) epiphytic microbiota from sorghum (SGSG); iii) epiphytic microbiota from Italian ryegrass (SGIR); iv) epiphytic microbiota from oat (SGOT).
RESULTS
After 60 days, all the treated groups had high lactic acid (>63.0 g/kg dry matter [DM]) contents and low pH values (<3.70), acetic acid (<14.0 g/kg DM) and ammonia nitrogen (<80.0 g/kg total nitrogen) contents. Notably, SGIR (59.8 g/kg DM) and SGOT (77.6 g/kg DM) had significantly (p<0.05) higher ethanol concentrations than SGSG (14.2 g/kg DM) on day 60. After 60 days, Lactobacillus were predominant genus in three treated groups. Higher proportions of Chishuiella (12.9%) and Chryseobacterium (7.33%) were first found in silages. The ethanol contents had a positive correlation (p<0.05) with the abundances of Chishuiella, Acinetobacter, Stenotrophomonas, Chryseobacterium, and Sphingobacterium.
CONCLUSION
The epiphytic bacteria on raw materials played important roles in influencing the silage fermentation products between temperate C3 and tropical C4 forages. The quantity and activity of hetero-fermentative Lactobacillus, Chishuiella, Acinetobacter, Stenotrophomonas, Chryseobacterium, and Sphingobacterium may be the key factors for the higher ethanol contents and DM loss in silages.
PubMed: 35507862
DOI: 10.5713/ab.21.0543 -
The Journal of Biological Chemistry May 2023Serine palmitoyltransferase (SPT) is a key enzyme of sphingolipid biosynthesis, which catalyzes the pyridoxal-5'-phosphate-dependent decarboxylative condensation...
Serine palmitoyltransferase (SPT) is a key enzyme of sphingolipid biosynthesis, which catalyzes the pyridoxal-5'-phosphate-dependent decarboxylative condensation reaction of l-serine (l-Ser) and palmitoyl-CoA (PalCoA) to form 3-ketodihydrosphingosine called long chain base (LCB). SPT is also able to metabolize l-alanine (l-Ala) and glycine (Gly), albeit with much lower efficiency. Human SPT is a membrane-bound large protein complex containing SPTLC1/SPTLC2 heterodimer as the core subunits, and it is known that mutations of the SPTLC1/SPTLC2 genes increase the formation of deoxy-type of LCBs derived from l-Ala and Gly to cause some neurodegenerative diseases. In order to study the substrate recognition of SPT, we examined the reactivity of Sphingobacterium multivorum SPT on various amino acids in the presence of PalCoA. The S. multivorum SPT could convert not only l-Ala and Gly but also l-homoserine, in addition to l-Ser, into the corresponding LCBs. Furthermore, we obtained high-quality crystals of the ligand-free form and the binary complexes with a series of amino acids, including a nonproductive amino acid, l-threonine, and determined the structures at 1.40 to 1.55 Å resolutions. The S. multivorum SPT accommodated various amino acid substrates through subtle rearrangements of the active-site amino acid residues and water molecules. It was also suggested that non-active-site residues mutated in the human SPT genes might indirectly influence the substrate specificity by affecting the hydrogen-bonding networks involving the bound substrate, water molecules, and amino acid residues in the active site of this enzyme. Collectively, our results highlight SPT structural features affecting substrate specificity for this stage of sphingolipid biosynthesis.
Topics: Humans; Palmitoyl Coenzyme A; Serine; Serine C-Palmitoyltransferase; Sphingobacterium; Sphingolipids; Substrate Specificity
PubMed: 37030501
DOI: 10.1016/j.jbc.2023.104684 -
Microbial Biotechnology Oct 2022Black soldier fly (BSF) larvae are considered a promising biological reactor to convert organic waste and reduce the impact of zoonotic pathogens on the environment. We...
Black soldier fly (BSF) larvae are considered a promising biological reactor to convert organic waste and reduce the impact of zoonotic pathogens on the environment. We analysed the effects of BSF larvae on Staphylococcus aureus and Salmonella spp. populations in pig manure (PM), which showed that BSF larvae can significantly reduce the counts of the associated S. aureus and Salmonella spp. Then, using a sterile BSF larval system, we validated the function of BSF larval intestinal microbiota in vivo to suppress pathogens, and lastly, we isolated eight bacterial strains from the BSF larval gut that inhibit S. aureus. Results indicated that functional microbes are essential for BSF larvae to antagonise S. aureus. Moreover, the analysis results of the relationship between the intestinal microbiota and S. aureus and Salmonella spp. showed that Myroides, Tissierella, Oblitimonas, Paenalcalignes, Terrisporobacter, Clostridium, Fastidiosipila, Pseudomonas, Ignatzschineria, Savagea, Moheibacter and Sphingobacterium were negatively correlated with S. aureus and Salmonella. Overall, these results suggested that the potential ability of BSF larvae to inhibit S. aureus and Salmonella spp. present in PM is accomplished primarily by gut-associated microorganisms.
Topics: Animals; Diptera; Gastrointestinal Microbiome; Larva; Manure; Staphylococcus aureus; Swine
PubMed: 35881487
DOI: 10.1111/1751-7915.14113 -
Frontiers in Microbiology 2022Caves are extreme, often oligotrophic, environments that house diverse groups of microorganisms. Many of these microbes can perform microbiologically induced carbonate...
Caves are extreme, often oligotrophic, environments that house diverse groups of microorganisms. Many of these microbes can perform microbiologically induced carbonate precipitation (MICP) to form crystalline secondary cave deposits known as speleothems. The urease family is a group of enzymes involved in MICP that catalyze the breakdown of urea, which is a source of energy, into ammonia and carbonate. Carbonate anions are effluxed to the extracellular surface of the bacterium where it then binds to environmental calcium to form calcium carbonate which then continues to grow in crystal form. Here, we studied bacterial communities from speleothems collected from the Iron Curtain Cave (ICC) in Chilliwack, B.C., Canada, to characterize these organisms and determine whether urease-positive (U+) bacteria were present in the cave and their potential impact on speleothem formation. The ICC is a carbonate cave located on the northside of Chipmunk Ridge, presenting a unique environment with high iron content sediment and limestone structures throughout. With six pools of water throughout the cave, the environment is highly humid, with temperatures ranging between 4 and 12°C depending on the time of year. Ninety-nine bacterial strains were isolated from popcorn (PCS) and soda straw (SSS) speleothems. These isolates were screened for urease enzymatic activity, with 11 candidates found to be urease-positive. After incubation, species-specific crystal morphologies were observed. Popcorn speleothem provided more bacterial diversity overall when compared to soda straw speleothem when examined under a culture-based method. Nearly twice as many U+ isolates were isolated from popcorn speleothems compared to soda straw speleothems. The U+ candidates were identified to the genus level by 16S rRNA analysis, and two isolates underwent whole-genome sequencing. Two novel species were identified as sp. PCS056 and sp. SSS035. Both isolates demonstrated the most crystal production as well as the most morphologically dissimilar crystal shapes in broth culture and were found to produce crystals as previously observed in both agar and broth media. The results from this study are consistent with the involvement of urease-positive bacteria isolated from the ICC in the formation of cave speleothems. 16S rRNA sequencing revealed a diverse set of microbes inhabiting the speleothems that have urease activity. Whole-genome sequencing of the two chosen isolates confirmed the presence of urease pathways, while revealing differences in urease pathway structure and number. This research contributes to understanding microbial-associated cave formation and degradation, with applications to cave conservation, microbiota composition, and their role in shaping the cave environment.
PubMed: 35847116
DOI: 10.3389/fmicb.2022.933388 -
Frontiers in Microbiology 2021Unlike for vertebrates, the impact of starvation on the gut microbiome of invertebrates is poorly studied. Deciphering shifts in metabolically active associated...
Unlike for vertebrates, the impact of starvation on the gut microbiome of invertebrates is poorly studied. Deciphering shifts in metabolically active associated bacterial communities in vertebrates has led to determining the role of the associated microbiome in the sensation of hunger and discoveries of associated regulatory mechanisms. From an invertebrate perspective, such as the black soldier fly, such information could lead to enhanced processes for optimized biomass production and waste conversion. Bacteria associated with food substrates of black soldier fly are known to impact corresponding larval life-history traits (e.g., larval development); however, whether black soldier fly larval host state (i.e., starved) impacts the gut microbiome is not known. In this study, we measured microbial community structural and functional shifts due to black soldier fly larvae starvation. Data generated demonstrate such a physiological state (i.e., starvation) does in fact impact both aspects of the microbiome. At the phylum level, community diversity decreased significantly during black soldier fly larval starvation ( = 0.0025). Genus level DESeq2 analysis identified five genera with significantly different relative abundance ( < 0.05) across the 24 and 48 H post initiation of starvation: , , , , and . Finally, we inferred potential gene function and significantly predicted functional KEGG Orthology (KO) abundance. We demonstrated the metabolically active microbial community structure and function could be influenced by host-feeding status. Such perturbations, even when short in duration (e.g., 24 H) could stunt larval growth and waste conversion due to lacking a full complement of bacteria and associated functions.
PubMed: 33664713
DOI: 10.3389/fmicb.2021.601253 -
FEMS Microbiology Ecology Feb 2021Bacteria-fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the...
Bacteria-fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments.
Topics: Agaricales; Bacteria; Ecosystem; Fungi; Soil; Soil Microbiology
PubMed: 33440006
DOI: 10.1093/femsec/fiab003