Human Gut Microbial Taxa Metabolizing Dietary Obesogens: A BPA 1 directed-culturing and Bioinformatics Combined Approach

Abstract Background Integrated data from culturomics and functional omics may depict holistic understanding on gut microbiome eubiosis or dysbiosis, and microbial isolates can become a source of differential enzymes and useful bioactive compounds. Culturing methods developed during last decade swift increases the importance of gut microbial isolates, focusing on media, modifications and conditions that propitiate cultured taxa that previously were considered fastidious or unculturable. In this context and focusing on gut microbiota dysbiosis triggered by obesogens and microbiota disrupting chemicals (MDC), we have conducted a directed-culturing and bioinformatics combined approach, adding bisphenol A (BPA) and specific treatments to find resistant spore-forming bacteria, to obtain isolated strains for further explore their molecular BPA metabolizing or neutralizing capacities. Results Overall microbiota culturing media and conditions have been retrieved and organized according to main gut taxa isolated during last decade. Furthermore, a catalogue of BPA directed-cultured microorganisms has been obtained from 46 fecal samples from two populations, children with obesity and normo-weight. A total of 235 BPA tolerating and potentially BPA biodegrading microorganisms were mainly grouped to strictly anaerobic sporuled/non-sporuled, anaerobic facultative sporuled/non-sporuled. Firmicutes, Enterobacteria and Actinobacteria species showed the major representation in both groups. However, differential BPA tolerant microbiota composition from the populations was detected. Bioinformatics analysis disclosed and predicted the variability of harboring genes encoding specific enzyme for BPA biodegradation pathways that corroborated from directed-culturing microbiota consortia obtained. Conclusions Strains from Staphylococcus , Bacillus and Enterococcus genera represented the majority of the successfully cultured bacteria in both population specimens. From them, the bioinformatics prediction assigned to Bacillus spp. the higher potential for BPA biodegradation. Therefore, extensive directed-culturomics approaches could be designed for different MDC with common biodegradation pathways, such as parabens, phthalates, and benzophenones.

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Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco

Agronomy ◽

10.3390/agronomy11071344 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1344

Author(s):

Naima Lemjiber ◽

Khalid Naamani ◽

Annabelle Merieau ◽

Abdelhi Dihazi ◽

Nawal Zhar ◽

...

Keyword(s):

16S Rrna Gene Sequencing ◽

Genomic Islands ◽

Rrna Gene ◽

In Planta ◽

Bacterial Strains ◽

Bacillus Altitudinis ◽

Genes Encoding ◽

Bacillus Spp ◽

Pear Trees ◽

Rrna Gene Sequencing

Bacterial burn is one of the major diseases affecting pear trees worldwide, with serious impacts on producers and economy. In Morocco, several pear trees (Pyrus communis) have shown leaf burns since 2015. To characterize the causal agent of this disease, we isolated fourteen bacterial strains from different parts of symptomatic pear trees (leaves, shoots, fruits and flowers) that were tested in planta for their pathogenicity on Louise bonne and Williams cultivars. The results showed necrotic lesions with a significant severity range from 47.63 to 57.77% on leaves of the Louise bonne cultivar inoculated with isolate B10, while the other bacterial isolates did not induce any disease symptom. 16S rRNA gene sequencing did not allow robust taxonomic discrimination of the incriminated isolate. Thus, we conducted whole-genome sequencing (WGS) and phylogenetic analyzes based on gyrA, gyrB and cdaA gene sequences, indicating that this isolate belongs to the Bacillus altitudinis species. This taxonomic classification was further confirmed by the Average Nucleotide Identity (ANI) and the in silico DNA-DNA hybridization (isDDH) analyzes compared to sixty-five Bacillus spp. type strains. The genome was mined for genes encoding carbohydrate-active enzymes (CAZymes) known to play a role in the vegetal tissue degradation. 177 candidates with functions that may support the in planta phytopathogenicity results were identified. To the best of our knowledge, this is the first data reporting B. altitudinis as agent of leaf burn in P. communis in Morocco. Our dataset will improve our knowledge on spread and pathogenicity of B. altitudinis genotypes that appears as emergent phytopathogenic agent, unveiling virulence factors and their genomic location (i.e., within genomic islands or the accessory genome) to induce trees disease.

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Oxygen reduction in the strict anaerobe Desulfovibrio vulgaris Hildenborough: characterization of two membrane-bound oxygen reductases

Microbiology ◽

10.1099/mic.0.049171-0 ◽

2011 ◽

Vol 157 (9) ◽

pp. 2720-2732 ◽

Cited By ~ 22

Author(s):

O. Lamrabet ◽

L. Pieulle ◽

C. Aubert ◽

F. Mouhamar ◽

P. Stocker ◽

...

Keyword(s):

Electron Donor ◽

Desulfovibrio Vulgaris ◽

Strictly Anaerobic ◽

Quinol Oxidase ◽

Genes Encoding ◽

Oxygen Reductase ◽

Membrane Bound ◽

Carbon Monoxide Binding ◽

Cellular Compartments ◽

Encoding Genes

Although Desulfovibrio vulgaris Hildenborough (DvH) is a strictly anaerobic bacterium, it is able to consume oxygen in different cellular compartments, including extensive periplasmic O2 reduction with hydrogen as electron donor. The genome of DvH revealed the presence of cydAB and cox genes, encoding a quinol oxidase bd and a cytochrome c oxidase, respectively. In the membranes of DvH, we detected both quinol oxygen reductase [inhibited by heptyl-hydroxyquinoline-N-oxide (HQNO)] and cytochrome c oxidase activities. Spectral and HPLC data for the membrane fraction revealed the presence of o-, b- and d-type haems, in addition to a majority of c-type haems, but no a-type haem, in agreement with carbon monoxide-binding analysis. The cytochrome c oxidase is thus of the cc(o/b)o 3 type, a type not previously described. The monohaem cytochrome c 553 is an electron donor to the cytochrome c oxidase; its encoding gene is located upstream of the cox operon and is 50-fold more transcribed than coxI encoding the cytochrome c oxidase subunit I. Even when DvH is grown under anaerobic conditions in lactate/sulfate medium, the two terminal oxidase-encoding genes are expressed. Furthermore, the quinol oxidase bd-encoding genes are more highly expressed than the cox genes. The cox operon exhibits an atypical genomic organization, with the gene coxII located downstream of coxIV. The occurrence of these membrane-bound oxygen reductases in other strictly anaerobic Deltaproteobacteria is discussed.

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Evaluation of three commercial assays for rapid detection of genes encoding clinically relevant carbapenemases in cultured bacteria

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dku571 ◽

2015 ◽

Vol 70 (5) ◽

pp. 1338-1342 ◽

Cited By ~ 78

Author(s):

Jacqueline Findlay ◽

Katie L. Hopkins ◽

Daniele Meunier ◽

Neil Woodford

Keyword(s):

Rapid Detection ◽

Genes Encoding ◽

Cultured Bacteria

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Cytochrome bd Oxidase, Oxidative Stress, and Dioxygen Tolerance of the Strictly Anaerobic Bacterium Moorella thermoacetica

Journal of Bacteriology ◽

10.1128/jb.187.6.2020-2029.2005 ◽

2005 ◽

Vol 187 (6) ◽

pp. 2020-2029 ◽

Cited By ~ 64

Author(s):

Amaresh Das ◽

Radu Silaghi-Dumitrescu ◽

Lars G. Ljungdahl ◽

Donald M. Kurtz

Keyword(s):

Oxidative Stress ◽

Growth Conditions ◽

Strictly Anaerobic ◽

Paramagnetic Resonance ◽

Cysteine Synthase ◽

Moorella Thermoacetica ◽

Genes Encoding ◽

Uptake Activity ◽

Acetogenic Bacterium ◽

Cytochrome Bd Oxidase

ABSTRACT The gram-positive, thermophilic, acetogenic bacterium Moorella thermoacetica can reduce CO2 to acetate via the Wood-Ljungdahl (acetyl coenzyme A synthesis) pathway. This report demonstrates that, despite its classification as a strict anaerobe, M. thermoacetica contains a membrane-bound cytochrome bd oxidase that can catalyze reduction of low levels of dioxygen. Whole-cell suspensions of M. thermoacetica had significant endogenous O2 uptake activity, and this activity was increased in the presence of methanol or CO, which are substrates in the Wood-Ljungdahl pathway. Cyanide and azide strongly (∼70%) inhibited both the endogenous and CO/methanol-dependent O2 uptake. UV-visible light absorption and electron paramagnetic resonance spectra of n-dodecyl-β-maltoside extracts of M. thermoacetica membranes showed the presence of a cytochrome bd oxidase complex containing cytochrome b 561, cytochrome b 595, and cytochrome d (chlorin). Subunits I and II of the bd oxidase were identified by N-terminal amino acid sequencing. The M. thermoacetica cytochrome bd oxidase exhibited cyanide-sensitive quinol oxidase activity. The M. thermoacetica cytochrome bd (cyd) operon consists of four genes, encoding subunits I and II along with two ABC-type transporter proteins, homologs of which in other bacteria are required for assembly of the bd complex. The level of this cyd operon transcript was significantly increased when M. thermoacetica was grown in the absence of added reducing agent (cysteine + H2S). Expression of a 35-kDa cytosolic protein, identified as a cysteine synthase (CysK), was also induced by the nonreducing growth conditions. The combined evidence indicates that cytochrome bd oxidase and cysteine synthase protect against oxidative stress and contribute to the limited dioxygen tolerance of M. thermoacetica.

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Metagenome Sequences of a Wastewater Treatment Plant Digester Sludge-Derived Enrichment Culture

Microbiology Resource Announcements ◽

10.1128/mra.00712-20 ◽

2020 ◽

Vol 9 (32) ◽

Author(s):

Heiko Nacke ◽

Laura L. Kirck ◽

Sophia Schwarz ◽

Dominik Schneider ◽

Anja Poehlein ◽

...

Keyword(s):

Wastewater Treatment ◽

Microbial Community ◽

Wastewater Treatment Plant ◽

Enrichment Culture ◽

Treatment Plant ◽

Methanogenic Archaea ◽

Metagenomic Analysis ◽

Strictly Anaerobic ◽

Anaerobic Conditions ◽

Genes Encoding

ABSTRACT We sequenced the metagenome of a microbial community enriched under strictly anaerobic conditions from wastewater treatment plant-derived digester sludge. The metagenomic analysis of the enrichment revealed that Acetobacterium and methanogenic archaea belonged to the dominant prokaryotes, and genes encoding components of the Wood-Ljungdahl pathway were identified.

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Spore-forming bacteria that carboxylate phenol to benzoic acid under anaerobic conditions

Canadian Journal of Microbiology ◽

10.1139/m95-036 ◽

1995 ◽

Vol 41 (3) ◽

pp. 266-272 ◽

Cited By ~ 11

Author(s):

L. Létouraeau ◽

J.-G. Bisaillon ◽

F. Lépine ◽

R. Beaudet

Keyword(s):

Benzoic Acid ◽

Solid Medium ◽

Hydroxybenzoic Acid ◽

Strictly Anaerobic ◽

Anaerobic Conditions ◽

Electron Microscopic ◽

Untreated Culture ◽

Spore Forming Bacteria ◽

Hydroxybenzyl Alcohol ◽

Methanogenic Consortium

A methanogenic consortium transforming phenol to benzoic acid was submitted to different treatments to characterize the carboxylating microorganisms and eventually to facilitate their isolation. Under aerobic conditions, phenol was not transformed by the consortium and no growth was observed on solid medium. The consortium from an inoculum that was treated with heat, or heat and ethanol, retained the ability to carboxylate phenol under strictly anaerobic conditions. Electron microscopic observations of the consortium from an inoculum that was heated for 15 min at 80 °C revealed only Gram-positive bacilli. In this culture, methane production was not detected and benzoic acid accumulated. Five colonies with distinct morphologies were isolated from this culture on solid medium. Four of these strains were identified as Clostridium spp. In contrast to the untreated culture, none of the strains isolated were able to carboxylate phenol in pure culture or in coculture, nor could they decarboxylate or dehydroxylate 4-hydroxybenzoic acid, or oxidize 2-hydroxybenzyl alcohol, or O-demethylate anisole or 2-methoxyphenol. Also, the consortium from a treated inoculum retained its ability to decarboxylate and dehydroxylate 4-hydroxybenzoic acid forming phenol and benzoic acid, respectively, but could not accomplish the other reactions. These results suggest that spore-forming microorganisms are involved in the carboxylation of phenol and in the decarboxylation and dehydroxylation of 4-hydroxybenzoic acid.Key words: spore-forming bacteria, phenol, benzoic acid, methanogenic conditions, carboxylation.

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Characterization of (R)-2-Hydroxyisocaproate Dehydrogenase and a Family III Coenzyme A Transferase Involved in Reduction of l-Leucine to Isocaproate by Clostridium difficile

Applied and Environmental Microbiology ◽

10.1128/aem.00772-06 ◽

2006 ◽

Vol 72 (9) ◽

pp. 6062-6069 ◽

Cited By ~ 39

Author(s):

Jihoe Kim ◽

Daniel Darley ◽

Thorsten Selmer ◽

Wolfgang Buckel

Keyword(s):

Amino Acid ◽

Clostridium Difficile ◽

Coenzyme A ◽

Amino Acid Sequences ◽

Site Directed Mutagenesis ◽

Transferase Activity ◽

Strictly Anaerobic ◽

Radical Intermediates ◽

Coa Transferase ◽

Genes Encoding

ABSTRACT The strictly anaerobic pathogenic bacterium Clostridium difficile occurs in the human gut and is able to thrive from fermentation of leucine. Thereby the amino acid is both oxidized to isovalerate plus CO2 and reduced to isocaproate. In the reductive branch of this pathway, the dehydration of (R)-2-hydroxyisocaproyl-coenzyme A (CoA) to (E)-2-isocaprenoyl-CoA is probably catalyzed via radical intermediates. The dehydratase requires activation by an ATP-dependent one-electron transfer (J. Kim, D. Darley, and W. Buckel, FEBS J. 272:550-561, 2005). Prior to the dehydration, a dehydrogenase and a CoA transferase are supposed to be involved in the formation of (R)-2-hydroxyisocaproyl-CoA. Deduced amino acid sequences of ldhA and hadA from the genome of C. difficile showed high identities to d-lactate dehydrogenase and family III CoA transferase, respectively. Both putative genes encoding the dehydrogenase and CoA transferase were cloned and overexpressed in Escherichia coli; the recombinant Strep tag II fusion proteins were purified to homogeneity and characterized. The substrate specificity of the monomeric LdhA (36.5 kDa) indicated that 2-oxoisocaproate (Km = 68 μM, k cat = 31 s−1) and NADH were the native substrates. For the reverse reaction, the enzyme accepted (R)- but not (S)-2-hydroxyisocaproate and therefore was named (R)-2-hydroxyisocaproate dehydrogenase. HadA showed CoA transferase activity with (R)-2-hydroxyisocaproyl-CoA as a donor and isocaproate or (E)-2-isocaprenoate as an acceptor. By site-directed mutagenesis, the conserved D171 was identified as an essential catalytic residue probably involved in the formation of a mixed anhydride with the acyl group of the thioester substrate. However, neither hydroxylamine nor sodium borohydride, both of which are inactivators of the CoA transferase, modified this residue. The dehydrogenase and the CoA transferase fit well into the proposed pathway of leucine reduction to isocaproate.

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Multicentre evaluation of a real-time PCR assay to detect genes encoding clinically relevant carbapenemases in cultured bacteria

International Journal of Antimicrobial Agents ◽

10.1016/j.ijantimicag.2015.11.013 ◽

2016 ◽

Vol 47 (2) ◽

pp. 151-154 ◽

Cited By ~ 28

Author(s):

Matthew J. Ellington ◽

Jacqueline Findlay ◽

Katie L. Hopkins ◽

Danièle Meunier ◽

Adela Alvarez-Buylla ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Pcr Assay ◽

Genes Encoding ◽

Cultured Bacteria

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Detection of toxin genes and RAPD analysis of bacillus cereus isolates from different soil types

Genetika ◽

10.2298/gensr1502627s ◽

2015 ◽

Vol 47 (2) ◽

pp. 627-638 ◽

Cited By ~ 4

Author(s):

Dejana Savic ◽

Dragana Josic ◽

Elizabeta Ristanovic ◽

Radmila Pivic ◽

Aleksandra Stanojkovic-Sebic ◽

...

Keyword(s):

Antibiotic Resistance ◽

Genetic Heterogeneity ◽

Soil Type ◽

Rapd Analysis ◽

Soil Types ◽

Toxin Genes ◽

Microbiological Methods ◽

Genes Encoding ◽

Bacillus Spp ◽

Intraspecies Diversity

The aim of this study was to detect genes for enterotoxins (hbla, entFM and bceT) and for emetic toxin (cer), to determine antibiotic resistance, and to estimate intraspecies diversity in B. cereus isolates by RAPD analysis. B. cereus was identified in 12 out of 117 indigenous Bacillus spp. using the classical microbiological methods and PCR. All isolates were resistant to penicillin and ampicillin, two to tetracyclin and four to trimethoprim-sulphamethoxazole. Also, all isolates produced inducible penicillinases and ?-lactamase. Toxin genes were detected with PCR. EntFM and cer genes were present in all isolates, hbla in all, but two, and bceT in none. RAPD analysis was performed with four different primers, two of them designed for this study. The intraspecies diversity revealed 10 different patterns at the 90% similarity level. Two separate clusters were formed regardless of a soil type or utilization. The detection of genes encoding toxins in all B. cereus isolates indicated these bacteria as potentially pathogenic and seriously for human health. Regardless of a soil type or utilization, the RAPD analysis showed high intraspecies heterogeneity in B. cereus isolates. To the best of our knowledge, this is the first study to analyse the presence of entero- and emetic toxin genes and genetic heterogeneity in B. cereus isolates from different soil types and different soil utilization in Serbia.

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Differences in the Bacteriome of Smokeless Tobacco Products with Different Oral Carcinogenicity: Compositional and Predicted Functional Analysis

10.20944/preprints201703.0030.v1 ◽

2017 ◽

Cited By ~ 1

Author(s):

Nezar Noor Al-hebshi ◽

Fahd Ali Alharbi ◽

Mohammed Mahri ◽

Tsute Chen

Keyword(s):

16S Rrna ◽

Smokeless Tobacco ◽

Bacterial Load ◽

Transport Systems ◽

Genes Encoding ◽

Bacillus Spp ◽

And Function ◽

Generation Sequencing ◽

Swedish Snus ◽

Bacterial Constituents

Smokeless tobacco (ST) products vary significantly in their oral carcinogenicity. Much is known about the differences in chemical, but not bacterial, constituents of these products. In this study, we explore the composition and function of the bacteriome in ST products from 4 countries using q-PCR and 16S rRNA-based next generation sequencing. The bacterial load (16S rRNA copies/gram) was lowest in Swedish snus (3.4E+6) and highest in Yemeni shammah (6.6E+11). A total of 491 species-level taxa, many of which are potentially novel, belonging to 178 genera and 11 phyla were identified. Species richness and diversity were highest for Swedish snus and lowest for Yemeni shammah. Bacillus, Paenibacillus, and Oceanobacillus spp. were the most abundant in American snuff; species of Pseudomonas, Massilia, Propionibacterium, Puniceispirillum and Gloeothece predominated in Swedish snus. In Sudanese toombak, Facklamia, Desemzia, Atopostipes and Lysinibacillus spp. accounted for the majority of the bacteriome. Yemeni shammah exclusively contained Bacillus spp. PICRUSt functional prediction showed that genes encoding cadmium/zinc and nickel transport systems were enriched in the presumptively “high carcinogenicity” products. The bacteriome of ST products thus differed qualitatively, quantitatively and functionally. The relevance of these differences, particularly with respect to nickel and cadmium, to oral carcinogenesis warrants further investigation.

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