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Anaerobe Feb 2015
Topics: Anti-Bacterial Agents; Bacteria, Anaerobic; Bacterial Infections; Drug Resistance, Bacterial; Microbial Sensitivity Tests
PubMed: 25464139
DOI: 10.1016/j.anaerobe.2014.11.002 -
Microbiology Spectrum Aug 2016Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to... (Review)
Review
Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.
Topics: Bacteria, Anaerobic; Bacterial Infections; Bacteriological Techniques; Disease Susceptibility; Humans; Immunocompromised Host
PubMed: 27726792
DOI: 10.1128/microbiolspec.DMIH2-0015-2015 -
Applied Microbiology and Biotechnology Jun 2020Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its... (Review)
Review
Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its recalcitrant nature is a major hurdle that must be overcome to enable economic conversion processes. Deconstruction of lignocellulose is part of the global carbon cycle, and efficient microbial degradation systems have evolved that might serve as models to improve commercial conversion processes. Biofilms-matrix encased, spatially organized clusters of microbial cells and the predominating lifestyle in nature-have been recognized for their essential role in the degradation of cellulose in nature, e.g., in soils or in the digestive tracts of ruminant animals. Cellulolytic biofilms allow for a high concentration of enzymes at the boundary layer between the solid substrate and the liquid phase and the more complete capture of hydrolysis products directly at the hydrolysis site, which is energetically favorable. Furthermore, enhanced expression of genes for carbohydrate active enzymes as a response to the attachment on solid substrate has been demonstrated for cellulolytic aerobic fungi and anerobic bacteria. In natural multispecies biofilms, the vicinity of different microbial species allows the creation of efficient food webs and synergistic interactions thereby, e.g., avoiding the accumulation of inhibiting metabolites. In this review, these topics are discussed and attempts to realize the benefits of biofilms in targeted applications such as the consolidated bioprocessing of lignocellulose are highlighted. KEY POINTS: Multispecies biofilms enable efficient lignocellulose destruction in the biosphere. Cellulose degradation by anaerobic bacteria often occurs by monolayered biofilms. Fungal biofilms immobilize enzymes and substrates in an external digestion system. Surface attached cultures typically show higher expression of cellulolytic enzymes.
Topics: Aerobiosis; Anaerobiosis; Bacteria, Anaerobic; Biofilms; Cellulose; Fungi; Hydrolysis; Lignin
PubMed: 32337627
DOI: 10.1007/s00253-020-10595-y -
Journal of Industrial Microbiology &... Mar 2019Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode... (Review)
Review
Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode unexpected biosynthetic potential for natural products, however, chemical data on natural products from the anaerobic world are extremely limited. Here, we review the current body of work on natural products isolated from strictly anaerobic microbes, including recent genome mining efforts to discover polyketides and non-ribosomal peptides from anaerobes. These known natural products of anaerobes have demonstrated interesting molecular scaffolds, biosynthetic logic, and/or biological activities, making anaerobes a promising reservoir for future natural product discovery.
Topics: Bacteria, Anaerobic; Biological Products; Biosynthetic Pathways; Chromans; Multigene Family; Naphthols; Peptides; Phenazines; Polycyclic Aromatic Hydrocarbons; Polyketides; Thioamides
PubMed: 30284140
DOI: 10.1007/s10295-018-2086-5 -
Journal of Inorganic Biochemistry Sep 2021Selenium (Se) respiration in bacteria was revealed for the first time at the end of 1980s. Although thermodynamically-favorable, energy-dense and documented in... (Review)
Review
Selenium (Se) respiration in bacteria was revealed for the first time at the end of 1980s. Although thermodynamically-favorable, energy-dense and documented in phylogenetically-diverse bacteria, this metabolic process appears to be accompanied by a number of challenges and numerous unanswered questions. Selenium oxyanions, SeO and SeO, are reduced to elemental Se (Se) through anaerobic respiration, the end product being solid and displaying a considerable size (up to 500 nm) at the bacterial scale. Compared to other electron acceptors used in anaerobic respiration (e.g. N, S, Fe, Mn, and As), Se is one of the few elements whose end product is solid. Furthermore, unlike other known bacterial intracellular accumulations such as volutin (inorganic polyphosphate), S, glycogen or magnetite, Se has not been shown to play a nutritional or ecological role for its host. In the context of anaerobic respiration of Se oxyanions, biogenic Se appears to be a by-product, a waste that needs proper handling, and this raises the question of the evolutionary implications of this process. Why would bacteria use a respiratory substrate that is useful, in the first place, and then highly detrimental? Interestingly, in certain artificial ecosystems (e.g. upflow bioreactors) Se might help bacterial cells to increase their density and buoyancy and thus avoid biomass wash-out, ensuring survival. This review article provides an in-depth analysis of selenium respiration (model selenium respiring bacteria, thermodynamics, respiratory enzymes, and genetic determinants), complemented by an extensive discussion about the evolutionary implications and the properties of biogenic Se using published and original/unpublished results.
Topics: Bacteria, Anaerobic; Bacterial Proteins; Cell Respiration; Oxidoreductases; Selenium; Thermodynamics
PubMed: 34118782
DOI: 10.1016/j.jinorgbio.2021.111509 -
MBio Apr 2021Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed...
Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising " Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated " Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An ()-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota. Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.
Topics: Anaerobiosis; Bacteria, Anaerobic; Base Composition; Dichloroacetic Acid; Fermentation; Humans; Peptococcaceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 33906923
DOI: 10.1128/mBio.00537-21 -
Journal of Molecular Microbiology and... 2016The anaerobic degradation of 4-alkylbenzoates and 4-alkyltoluenes is to date a rarely reported microbial capacity. The newly isolated Alphaproteobacterium... (Review)
Review
The anaerobic degradation of 4-alkylbenzoates and 4-alkyltoluenes is to date a rarely reported microbial capacity. The newly isolated Alphaproteobacterium Magnetospirillum sp. strain pMbN1 represents the first pure culture demonstrated to degrade 4-methylbenzoate completely to CO2 in a process coupled to denitrification. Differential proteogenomic studies in conjunction with targeted metabolite analyses and enzyme activity measurements elucidated a specific 4-methylbenzoyl-coenzyme A (CoA) pathway in this bacterium alongside the classical central benzoyl-CoA pathway. Whilst these two pathways are analogous, in the former the p-methyl group is retained and its 4-methylbenzoyl-CoA reductase (MbrCBAD) is phylogenetically distinct from the archetypical class I benzoyl-CoA reductase (BcrCBAD). Subsequent global regulatory studies on strain pMbN1 grown with binary or ternary substrate mixtures revealed benzoate to repress the anaerobic utilization of 4-methylbenzoate and succinate. The shared nutritional property of betaproteobacterial 'Aromatoleum aromaticum' pCyN1 and Thauera sp. strain pCyN2 is the anaerobic degradation of the plant-derived hydrocarbon p-cymene (4-isopropyltoluene) coupled to denitrification. Notably, the two strains employ two different peripheral pathways for the conversion of p-cymene to 4-isopropylbenzoyl-CoA as the possible first common intermediate. In 'A. aromaticum' pCyN1 a putative p-cymene dehydrogenase (CmdABC) is proposed to hydroxylate the benzylic methyl group, which is subsequently further oxidized to the CoA-thioester. In contrast, Thauera sp. strain pCyN2 employs a reaction sequence analogous to the known anaerobic toluene pathway, involving a distinct branching (4-isopropylbenzyl)succinate synthase (IbsABCDEF).
Topics: Anaerobiosis; Bacteria, Anaerobic; Benzoates; Biodegradation, Environmental; Magnetospirillum; Phylogeny; Toluene
PubMed: 26960059
DOI: 10.1159/000441144 -
Folia Microbiologica May 2019Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies... (Review)
Review
Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.
Topics: Anaerobiosis; Bacteria, Anaerobic; Biomass; Bioreactors; Fermentation; Industrial Microbiology; Metabolic Engineering
PubMed: 30446943
DOI: 10.1007/s12223-018-0658-4 -
Environment International Mar 2019The technology of integrating nanoscale zero-valent iron (nZVI) and functional anaerobic bacteria has broad prospects for groundwater remediation. This review focuses on... (Review)
Review
The technology of integrating nanoscale zero-valent iron (nZVI) and functional anaerobic bacteria has broad prospects for groundwater remediation. This review focuses on the interactions between nZVI and three kinds of functional anaerobic bacteria: organohalide-respiring bacteria (OHRB), sulfate reducing bacteria (SRB) and iron reducing bacteria (IRB), which are commonly used in the anaerobic bioremediation. The coupling effects of nZVI and the functional bacteria on the contaminant removal in the integrated system are summarized. Generally, nZVI could create a suitable living condition for the growth and activity of anaerobic bacteria. OHRB and SRB could synergistically degrade organic halides and remove heavy metals with nZVI, and IRB could reactive the passivated nZVI by reducing the iron (hydr)oxides on the surface of nZVI. Moreover, the roles of these anaerobic bacteria in contaminant removal coupling with nZVI and the degradation mechanisms are illustrated. In addition, this review also discusses the main factors influencing the removal efficiency of contaminants in the integrated treatment system, including nZVI species and dosage, inorganic ions, organic matters, pH, type of pollutants, temperature, and carbon/energy sources, etc. Among these factors, the nZVI species and dosage play a fundamental role due to the potential cytotoxicity of nZVI, which might exert a negative impact on the performance of this integrated system. Lastly, the future research needs are proposed to better understand this integrated technology and effectively apply it in groundwater remediation.
Topics: Bacteria, Anaerobic; Biodegradation, Environmental; Environmental Restoration and Remediation; Groundwater; Iron; Nanotechnology; Water Pollutants, Chemical; Water Purification
PubMed: 30660027
DOI: 10.1016/j.envint.2019.01.030 -
Biotechnology Advances 2016Trace metals are essential for the growth of anaerobic microorganisms, however, in practice they are often added to anaerobic digesters in excessive amounts, which can... (Review)
Review
Trace metals are essential for the growth of anaerobic microorganisms, however, in practice they are often added to anaerobic digesters in excessive amounts, which can lead to inhibition. The concept of bioavailability of metals in anaerobic digestion has been poorly understood in the past, and a lack of deep understanding of the relationship between trace metal speciation and bioavailability can result in ineffective metal dosing strategies for anaerobic digesters. Sequential extraction schemes are useful for fractionating trace metals into their different forms, and metal sulfides can serve as a store and source for trace metals during anaerobic digestion, while natural/synthetic chelating agents (soluble microbial products-SMPs, extracellular polysaccharides-EPS, and EDTA/NTA) are capable of controlling trace metal bioavailability. Nevertheless, more work is needed to: investigate the speciation and bioavailability of Ca, Mg, Mn, W, and Se; compare the bioavailability of different forms of trace metals e.g. carbonates, sulfides, phosphates to different anaerobic trophic groups; determine what factors influence metal sulfide dissolution; investigate whether chelating agents can increase trace metal bioavailability; develop and adapt specialized analytical techniques, and; determine how trace metal dynamics change in an anaerobic membrane bioreactor (AnMBR).
Topics: Anaerobiosis; Bacteria, Anaerobic; Bioreactors; Metals
PubMed: 26707985
DOI: 10.1016/j.biotechadv.2015.12.006