-
Advances in Biochemical... 2016Human gastrointestinal microbiota (HGIM) incorporate a large number of microbes from different species. Anaerobic bacteria are the dominant organisms in this microbial... (Review)
Review
Human gastrointestinal microbiota (HGIM) incorporate a large number of microbes from different species. Anaerobic bacteria are the dominant organisms in this microbial consortium and play a crucial role in human health. In addition to their functional role as the main source of many essential metabolites for human health, they are considered as biotherapeutic agents in the regulation of different human metabolites. They are also important in the prevention and in the treatment of different physical and mental diseases. Bifidobacteria are the dominant anaerobic bacteria in HGIM and are widely used in the development of probiotic products for infants, children and adults. To develop bifidobacteria-based bioproducts, therefore, it is necessary to develop a large-scale biomass production platform based on a good understanding of the ideal medium and bioprocessing parameters for their growth and viability. In addition, high cell viability should be maintained during downstream processing and storage of probiotic cell powder or the final formulated product. In this work we review the latest information about the biology, therapeutic activities, cultivation and industrial production of bifidobacteria.
Topics: Anaerobiosis; Bacteria, Anaerobic; Batch Cell Culture Techniques; Bifidobacterium; Bioreactors; Probiotics; Species Specificity
PubMed: 26907552
DOI: 10.1007/10_2015_5008 -
Journal of Microbiology and... Jul 2017Composting is widely used to transform waste into valuable agricultural organic fertilizer. Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the...
Composting is widely used to transform waste into valuable agricultural organic fertilizer. Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the global nitrogen cycle, but their role in composting remains poorly understood. In the present study, the community structure, diversity, and abundance of anammox bacteria were analyzed using cloning and sequencing methods by targeting the 16S rRNA gene and the hydrazine oxidase gene () in samples isolated from compost produced from cow manure and rice straw. A total of 25 operational taxonomic units were classified based on 16S rRNA gene clone libraries, and 14 operational taxonomic units were classified based on gene clone libraries. The phylogenetic tree analysis of the 16S rRNA gene and deduced HZO protein sequences from the corresponding encoding genes indicated that the majority of the obtained clones were related to the known anammox bacteria "Brocadia," "Kuenenia," and "Scalindua." The abundances of anammox bacteria were determined by quantitative PCR, and between 2.13 × 10 and 1.15 × 10 16S rRNA gene copies per gram of compost were found. This study provides the first demonstration of the existence of anammox bacteria with limited diversity in cow manure composting.
Topics: Ammonium Compounds; Anaerobiosis; Animals; Bacteria, Anaerobic; Biodiversity; Cattle; Composting; DNA, Bacterial; DNA, Ribosomal; Female; Manure; Microbial Consortia; Nitrogen Cycle; Oxidation-Reduction; Phylogeny; RNA, Ribosomal, 16S
PubMed: 28511295
DOI: 10.4014/jmb.1702.02065 -
Correlation between antibiotic resistance and clinical outcome of anaerobic infections; mini-review.Anaerobe Dec 2021In anaerobic infections, the relationship between clinical failure and antibiotic resistance is difficult to demonstrate, especially in mixed anaerobic-aerobic... (Review)
Review
In anaerobic infections, the relationship between clinical failure and antibiotic resistance is difficult to demonstrate, especially in mixed anaerobic-aerobic infections. Single isolates of anaerobes in cases of bacteraemia revealed that treatment failures were due to inappropriate therapy. We review here cases, where the empiric treatment was unsuccessful due to resistance of anaerobic bacteria to the administered agents and where the change of the antibiotic allowed the patients to be cured. Many therapeutic failures could be linked to the lack of timely detection of resistance, including heteroresistance of the anaerobes. Disk diffusion or Etest methodology may be suitable, at least for rapidly growing anaerobes, to detect both resistance and heteroresistance to antibiotics widely used for empirical therapy.
Topics: Anti-Bacterial Agents; Bacteremia; Bacteria, Anaerobic; Bacterial Infections; Clinical Decision-Making; Disease Management; Drug Resistance, Bacterial; Humans; Microbial Sensitivity Tests; Prognosis; Treatment Outcome
PubMed: 34597797
DOI: 10.1016/j.anaerobe.2021.102463 -
Bioresource Technology Jun 2015Dark fermentation is a bioprocess driven by anaerobic bacteria that can produce hydrogen (H2) from organic waste and wastewater. This review analyses a relevant number... (Review)
Review
Dark fermentation is a bioprocess driven by anaerobic bacteria that can produce hydrogen (H2) from organic waste and wastewater. This review analyses a relevant number of recent studies that have investigated dark fermentative H2 production from wastewater using two different types of anaerobic biofilm reactors: anaerobic packed bed reactor (APBR) and anaerobic fluidized bed reactor (AFBR). The effect of various parameters, including temperature, pH, carrier material, inoculum pretreatment, hydraulic retention time, substrate type and concentration, on reactor performances was investigated by a critical discussion of the results published in the literature. Also, this review presents an in-depth study on the influence of the main operating parameters on the metabolic pathways. The aim of this review is to provide to researchers and practitioners in the field of H2 production key elements for the best operation of the reactors. Finally, some perspectives and technical challenges to improve H2 production were proposed.
Topics: Anaerobiosis; Bacteria, Anaerobic; Biofilms; Bioreactors; Carbohydrates; Fermentation; Gases; Hydrogen; Hydrogen-Ion Concentration; Hydrolysis; Surface Properties; Temperature; Waste Disposal, Fluid; Wastewater
PubMed: 25746594
DOI: 10.1016/j.biortech.2015.02.063 -
Journal of Biotechnology Dec 2019The development of a bio-refinery industry based on liquid fuels is presumably key to successful replacement of fossil fuels and a reduction of carbon dioxide (CO)... (Review)
Review
The development of a bio-refinery industry based on liquid fuels is presumably key to successful replacement of fossil fuels and a reduction of carbon dioxide (CO) emissions. Ethanol and longer-chain alcohols are supposed to play a key role since they are relatively easy to produce, using microorganisms as whole-cell biocatalysts. Alcohols may be produced from lignocellulose-derived biomass or from synthesis gas (hydrogen, H; CO, carbon monoxide, CO). In anaerobes, common pathways involve the reduction of the intermediate acetyl-CoA with NAD(P)H by aldehyde (ALDH) and alcohol dehydrogenases (ADH). Alternatively, alcohols may be produced by the direct reduction of externally added or intermediately produced organic acids with reduced ferredoxin (Fd). The key enzyme catalyzing this thermodynamically difficult reaction is aldehyde:ferredoxin oxidoreductase (AOR), an oxygen sensitive protein present in some anaerobic bacteria and archaea. Here, we present increasing evidence for the importance of the AOR-ADH pathway in alcohol producing anaerobes. AOR heavily depends on compounds with a low redox potential, and reactions potentially coupled to the pathway are discussed. The putative ancient AOR-ADH pathway may be relatively widespread among anaerobes, and it may play an important role in a sustainable bioenergy concept via the reduction of organic acids to their corresponding alcohols.
Topics: Alcohols; Aldehyde Oxidoreductases; Aldehydes; Bacteria, Anaerobic; Biocatalysis; Biofuels; Carboxylic Acids; Ferredoxins; Gases; Oxidation-Reduction
PubMed: 31541665
DOI: 10.1016/j.jbiotec.2019.09.005 -
Applied and Environmental Microbiology Apr 2021The isolation of bacteria that represent the diversity of autochthonous taxa in the gastrointestinal tract is necessary to fully ascertain their function, but the...
The isolation of bacteria that represent the diversity of autochthonous taxa in the gastrointestinal tract is necessary to fully ascertain their function, but the majority of bacterial species inhabiting the intestines of mammals are fastidious and thus challenging to isolate. The goal of the current study was to isolate a diverse assemblage of anaerobic bacteria from the intestine of pigs as a model animal and to comparatively examine various novel and traditional isolation strategies. Methods used included long-term enrichments, direct plating, a modified ichip method, as well as ethanol and tyndallization treatments of samples to select for endospore-forming taxa. A total of 234 taxa (91 previously uncultured) comprising 80 genera and 7 phyla were isolated from mucosal and luminal samples from the ileum, cecum, ascending colon, and spiral colon removed from animals under anesthesia. The diversity of bacteria isolated from the large intestine was less than that detected by next-generation sequence analysis. Long-term enrichments yielded the greatest diversity of recovered bacteria (Shannon's index [SI] = 4.7). Methods designed to isolate endospore-forming bacteria produced the lowest diversity (SI ≤ 2.7), with tyndallization yielding lower diversity than the ethanol method. However, the isolation frequency of previously uncultured bacteria was highest for ethanol-treated samples (41.9%) and the ichip method (32.5%). The goal of recovering a diverse collection of enteric bacteria was achieved. Importantly, the study findings demonstrate that it is necessary to use a combination of methods in concert to isolate bacteria that are representative of the diversity within the intestines of mammals. This work determined that using a combination of anaerobic isolation methods is necessary to increase the diversity of bacteria recovered from the intestines of monogastric mammals. Direct plating methods have traditionally been used to isolate enteric bacteria, and recent methods (e.g., diffusion methods [i.e., ichip] or differential isolation of endospore-forming bacteria) have been suggested to be superior at increasing diversity, including the recovery of previously uncultured taxa. We showed that long-term enrichment of samples using a variety of media isolated the most diverse and novel bacteria. Application of the ichip method delivered a diversity of bacteria similar to those of enrichment and direct plating methods. Methods that selected for endospore-forming bacteria generated collections that differed in composition from those of other methods with reduced diversity. However, the ethanol treatment frequently isolated novel bacteria. By using a combination of methods in concert, a diverse collection of enteric bacteria was generated for ancillary experimentation.
Topics: Animals; Bacteria, Anaerobic; Bacteriological Techniques; Endospore-Forming Bacteria; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; Intestines; Male; Swine
PubMed: 33608289
DOI: 10.1128/AEM.00088-21 -
Applied Microbiology and Biotechnology Aug 2018Biological soil disinfestation (BSD) or reductive soil disinfestation (RSD) is an environmental biotechnology to eliminate soil-borne plant pathogens based on functions... (Review)
Review
Biological soil disinfestation (BSD) or reductive soil disinfestation (RSD) is an environmental biotechnology to eliminate soil-borne plant pathogens based on functions of indigenous microbes. BSD treatments using different types of organic materials have been reported to effectively control a wide range of plant pathogens. Various studies have shown that development of reducing or anoxic conditions in soil is the most important aspect for effective BSD treatments. Substances such as organic acids, FeS, or phenolic compounds generated in the treated soil have been suggested to contribute to inactivation of pathogens. Additionally, anaerobic bacteria grown in the BSD-treated soil may produce and release enzymes with anti-pathogenic activities in soil. Clone library analyses as well as a next-generation sequence analysis based on 16S rRNA genes have revealed prosperity of obligate anaerobic bacteria from the class Clostridia in differently treated BSD soils. Two anaerobic bacterial strains isolated from BSD-treated soil samples and identified as Clostridium beijerinckii were found to decompose major cell wall polysaccharides of ascomycetous fungi, chitosan and β-1,3-glucan. C. beijerinckii is a species most frequently detected in the clone library analyses for various BSD-treated soils as a closely related species. The two anaerobic isolates severely degraded mycelial cells of the Fusarium pathogen of spinach wilt disease during anaerobic co-incubation of each isolate and the Fusarium pathogen. These reports suggest that antifungal enzymes produced by predominant anaerobic bacteria grown in the BSD-treated soil play important roles to control soil-borne fungal pathogens. Further studies using different bacterial isolates from BSD-treated soils are expected to know their anti-pathogenic abilities.
Topics: Agriculture; Bacteria, Anaerobic; Disinfection; Plant Diseases; RNA, Ribosomal, 16S; Soil; Soil Microbiology
PubMed: 29858952
DOI: 10.1007/s00253-018-9119-x -
Reviews of Environmental Contamination... 2020Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to... (Review)
Review
Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.
Topics: Bacteria, Anaerobic; Biodegradation, Environmental; Environmental Pollutants; Nitrates; Polycyclic Aromatic Hydrocarbons
PubMed: 31011832
DOI: 10.1007/398_2019_29 -
Ortopedia, Traumatologia, Rehabilitacja Jun 2020This article presents a detailed review of the 49 reported cases of emphysematous osteomyelitis. Infection of the bones and joints usually developed in various locations... (Review)
Review
This article presents a detailed review of the 49 reported cases of emphysematous osteomyelitis. Infection of the bones and joints usually developed in various locations of patients with concomitant diseases. The treatment includes antibiotic therapy and minor surgery, usually drainage.
Topics: Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Bacteria, Anaerobic; Bacterial Infections; Female; Humans; Male; Middle Aged; Osteomyelitis; Treatment Outcome
PubMed: 32732448
DOI: 10.5604/01.3001.0014.3231 -
Anaerobe Dec 2015The etiology of veterinary infectious diseases has been the focus of considerable research, yet relatively little is known about the causative agents of anaerobic...
The etiology of veterinary infectious diseases has been the focus of considerable research, yet relatively little is known about the causative agents of anaerobic infections. Susceptibility studies have documented the emergence of antimicrobial resistance and indicate distinct differences in resistance patterns related to veterinary hospitals, geographic regions, and antibiotic-prescribing regimens. The aim of the present study was to identify the obligate anaerobic bacteria from veterinary clinical samples and to determinate the in vitro susceptibility to eight antimicrobials and their resistance-associated genes. 81 clinical specimens obtained from food-producing animals, pets and wild animals were examined to determine the relative prevalence of obligate anaerobic bacteria, and the species represented. Bacteroides spp, Prevotella spp and Clostridium spp represented approximately 80% of all anaerobic isolates. Resistance to metronidazole, clindamycin, tetracycline and fluoroquinolones was found in strains isolated from food-producing animals. Ciprofloxacin, enrofloxacin and cephalotin showed the highest resistance in all isolates. In 17%, 4% and 14% of tetracycline-resistant isolates, the resistance genes tetL, tetM and tetW were respectively amplified by PCR whereas in 4% of clindamycin-resistant strains the ermG gene was detected. 26% of the isolates were positive for cepA, while only 6% harbored the cfxA (resistance-conferring genes to beta-lactams). In this study, the obligate anaerobic bacteria from Costa Rica showed a high degree of resistance to most antimicrobials tested. Nevertheless, in the majority of cases this resistance was not related to the resistance acquired genes usually described in anaerobes. It is important to address and regulate the use of antimicrobials in the agricultural industry and the empirical therapy in anaerobic bacterial infections in veterinary medicine, especially since antibiotics and resistant bacteria can persist in the environment.
Topics: Animals; Animals, Wild; Anti-Bacterial Agents; Bacteria, Anaerobic; Bacterial Infections; Cattle; Dogs; Ducks; Horses; Livestock; Microbial Sensitivity Tests; Pets; Rabbits; Sheep; Snakes; Swine
PubMed: 26385434
DOI: 10.1016/j.anaerobe.2015.09.003