-
Applied and Environmental Microbiology Jun 2024In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on... (Review)
Review
In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of , spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the phylum, specific members exemplify the diverse capabilities of these microorganisms: showcases adaptability through its thermophilic and phototrophic growth, whereas members of the class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of in such environments with the potential application of their metabolisms in biotechnological approaches.
Topics: Biotechnology; Chloroflexi; Anaerobiosis
PubMed: 38709098
DOI: 10.1128/aem.01756-23 -
Current Opinion in Microbiology Jun 2024This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like... (Review)
Review
This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.
Topics: Alkanes; Archaea; Oxidation-Reduction; Oxidoreductases; Phylogeny; Electron Transport; Archaeal Proteins; Gene Transfer, Horizontal; Bacteria
PubMed: 38733792
DOI: 10.1016/j.mib.2024.102486 -
EBioMedicine Dec 2023The human microbiome is linked to multiple metabolic disorders such as obesity and diabetes. Obstructive sleep apnoea (OSA) is a common sleep disorder with several...
BACKGROUND
The human microbiome is linked to multiple metabolic disorders such as obesity and diabetes. Obstructive sleep apnoea (OSA) is a common sleep disorder with several metabolic risk factors. We investigated the associations between the gut microbiome composition and function, and measures of OSA severity in participants from a prospective community-based cohort study: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).
METHODS
Bacterial-Wide Association Analysis (BWAS) of gut microbiome measured via metagenomics with OSA measures was performed adjusting for clinical, lifestyle and co-morbidities. This was followed by functional analysis of the OSA-enriched bacteria. We utilized additional metabolomic and transcriptomic associations to suggest possible mechanisms explaining the microbiome effects on OSA.
FINDINGS
Several uncommon anaerobic human pathogens were associated with OSA severity. These belong to the Lachnospira, Actinomyces, Kingella and Eubacterium genera. Functional analysis revealed enrichment in 49 processes including many anaerobic-related ones. Severe OSA was associated with the depletion of the amino acids glycine and glutamine in the blood, yet neither diet nor gene expression revealed any changes in the production or consumption of these amino acids.
INTERPRETATION
We show anaerobic bacterial communities to be a novel component of OSA pathophysiology. These are established in the oxygen-poor environments characteristic of OSA. We hypothesize that these bacteria deplete certain amino acids required for normal human homeostasis and muscle tone, contributing to OSA phenotypes. Future work should test this hypothesis as well as consider diagnostics via anaerobic bacteria detection and possible interventions via antibiotics and amino-acid supplementation.
FUNDING
Described in methods.
Topics: Humans; Amino Acids; Anaerobiosis; Cohort Studies; Prospective Studies; Sleep Apnea, Obstructive
PubMed: 38006744
DOI: 10.1016/j.ebiom.2023.104891 -
Life (Basel, Switzerland) May 2024Microorganisms are key players in the global biogeochemical sulfur cycle. Among them, some have garnered particular attention due to their electrical activity and... (Review)
Review
Microorganisms are key players in the global biogeochemical sulfur cycle. Among them, some have garnered particular attention due to their electrical activity and ability to perform extracellular electron transfer. A growing body of research has highlighted their extensive phylogenetic and metabolic diversity, revealing their crucial roles in ecological processes. In this review, we delve into the electron transfer process between sulfate-reducing bacteria and anaerobic alkane-oxidizing archaea, which facilitates growth within syntrophic communities. Furthermore, we review the phenomenon of long-distance electron transfer and potential extracellular electron transfer in multicellular filamentous sulfur-oxidizing bacteria. These bacteria, with their vast application prospects and ecological significance, play a pivotal role in various ecological processes. Subsequently, we discuss the important role of the pili/cytochrome for electron transfer and presented cutting-edge approaches for exploring and studying electroactive microorganisms. This review provides a comprehensive overview of electroactive microorganisms participating in the biogeochemical sulfur cycle. By examining their electron transfer mechanisms, and the potential ecological and applied implications, we offer novel insights into microbial sulfur metabolism, thereby advancing applications in the development of sustainable bioelectronics materials and bioremediation technologies.
PubMed: 38792612
DOI: 10.3390/life14050591 -
Microbial Physiology 2024The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied... (Review)
Review
The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied best on the proteogenomic level. This review summarizes the current state of knowledge about the anaerobic and aerobic degradation (to CO2) of 47 organic growth substrates (23 aromatic, 21 aliphatic, and 3 amino acids) as well as the modes of respiratory energy conservation (denitrification vs. O2-respiration). The constructed catabolic network is comprised of 256 genes, which occupy ∼7.5% of the coding regions of the genome. In total, 219 encoded proteins have been identified by differential proteomics, yielding a proteome coverage of ∼74% of the network. Its degradation section is composed of 31 peripheral and 4 central pathways, with several peripheral modules (e.g., for 4-ethylphenol, 2-phenylethylamine, indoleacetate, and phenylpropanoids) discovered only after the complete genome [Arch Microbiol. 2005 Jan;183(1):27-36] and a first proteomic survey [Proteomics. 2007 Jun;7(13):2222-39] of A. aromaticum EbN1T were reported. The activation of recalcitrant aromatic compounds involves a suite of biochemically intriguing reactions ranging from C-H-bond activation (e.g., ethylbenzene dehydrogenase) via carboxylation (e.g., acetophenone carboxylase) to oxidative deamination (e.g., benzylamine), reductive dearomatization (benzoyl-CoA), and epoxide-forming oxygenases (e.g., phenylacetyl-CoA). The peripheral reaction sequences are substrate-specifically induced, mediated by specific transcriptional regulators with in vivo response thresholds in the nanomolar range. While lipophilic substrates (e.g., phenolics) enter the cells via passive diffusion, polar ones require active uptake that is driven by specific transporters. Next to the protein repertoire for canonical complexes I-III, denitrification, and O2-respiration (low- and high-affinity oxidases), the genome encodes an Ndh-II, a tetrathionate reductase, two ETF:quinone oxidoreductases, and two Rnf-type complexes, broadening the electron transfer flexibility of the strain. Taken together, the detailed catabolic network presented here forms a solid basis for future systems biology-level studies with A. aromaticum EbN1T.
Topics: Bacterial Proteins; Anaerobiosis; Metabolic Networks and Pathways; Aerobiosis; Proteome; Proteomics; Denitrification; Rhodocyclaceae
PubMed: 37816339
DOI: 10.1159/000534425 -
Cancer Immunology, Immunotherapy : CII Dec 2023Even in present-day times, cancer is one of the most fatal diseases. People are overwhelmed by pricey chemotherapy, immunotherapy, and other costly cancer therapies in... (Review)
Review
INTRODUCTION
Even in present-day times, cancer is one of the most fatal diseases. People are overwhelmed by pricey chemotherapy, immunotherapy, and other costly cancer therapies in poor and middle-income countries. Cancer cells grow under anaerobic and hypoxic conditions. Pyruvate is the final product of the anaerobic glycolysis pathway, and many cancer cells utilize pyruvate for their growth and development. The anaerobic microbiome produces many anti-cancer substances that can act as anti-tumor agents and are both feasible and of low cost. There are different mechanisms of action of the anaerobic microbiome, such as the production of short-chain fatty acids (SCFAs), and competition for the anaerobic environment includes the metabolic product pyruvate to form lactic acid for energy.
KEY FINDINGS
In this review, we have summarized the role of the metabolic approach of the anaerobic human microbiome in cancer prevention and treatment by interfering with cancer metabolite pyruvate. SCFAs possess decisive outcomes in condoning almost all the hallmarks of cancer and helping the spread of cancer to other body parts. Studies have demonstrated the impact and significance of using SCFA, which results from anaerobic bacteria, as an anti-cancer agent. Anaerobic bacteria-based cancer therapy has become a promising approach to treat cancer using obligate and facultative anaerobic bacteria because of their ability to penetrate and increase in an acidic hypoxic environment.
SIGNIFICANCE
This review attempts to provide the interconnection of cancer metabolism and anaerobic microbiome metabolism with a focus on pyruvate metabolism to understand and design unique anaerobic microbiota-based therapy for cancer patients.
Topics: Humans; Anaerobiosis; Microbiota; Neoplasms; Pyruvates; Bacteria, Anaerobic
PubMed: 37882845
DOI: 10.1007/s00262-023-03551-y -
Applied and Environmental Microbiology Dec 2023Many parameters affect phage-bacteria interaction. Some of these parameters depend on the environment in which the bacteria are present. Anaerobiosis effect on phage...
Many parameters affect phage-bacteria interaction. Some of these parameters depend on the environment in which the bacteria are present. Anaerobiosis effect on phage infection in facultative anaerobic bacteria has not yet been studied. The absence of oxygen triggers metabolic changes in facultative bacteria and this affects phage infection and viral life cycle. Understanding how an anaerobic environment can alter the behavior of phages during infection is relevant for the phage therapy success.
Topics: Bacteriophages; Anaerobiosis; Bacteria
PubMed: 37966212
DOI: 10.1128/aem.01491-23 -
Foods (Basel, Switzerland) Sep 2023On the basis of routine microbiological tests and selected physicochemical parameters, the quality and food safety of Polish varietal honeys were evaluated. The study...
On the basis of routine microbiological tests and selected physicochemical parameters, the quality and food safety of Polish varietal honeys were evaluated. The study included 21 honey samples from 5 varieties (multifloral, honeydew, rapeseed, buckwheat and linden), in which the moisture and extract content, water activity, pH and free acids were determined, and the colony count, the presumptive spp., the total fungal count and the presence of anaerobic spore-forming bacilli were examined. More than half (52%, 11/21) of the analyzed honeys contained fewer microorganisms than 10 cfu/g, and in the remaining samples, their numbers ranged from 5 × 10 cfu/g to 4.5 × 10 cfu/g. In all the honeys, the number of presumptive spp. in 1 g was less than 10 cfu. In 81% (17/21) of the samples, the total count of fungi in 1 g of honey was less than 10 cfu, and the most contaminated was buckwheat honey (3 samples). The anaerobic spore-forming bacteria was detected in 0.1 g only in one sample of buckwheat honey. The values of the physicochemical parameters did not exceed the accepted limits, which indicated that the honey environment was unfavourable for the development of the tested microbial profile.
PubMed: 37761060
DOI: 10.3390/foods12183349 -
Frontiers in Bioengineering and... 2023The is a family of anaerobic bacteria in the class Clostridia with potential to advance the bio-economy and intestinal therapeutics. Some species of metabolize... (Review)
Review
The is a family of anaerobic bacteria in the class Clostridia with potential to advance the bio-economy and intestinal therapeutics. Some species of metabolize abundant, low-cost feedstocks such as lignocellulose and carbon dioxide into value-added chemicals. Others are among the dominant species of the human colon and animal rumen, where they ferment dietary fiber to promote healthy gut and immune function. Here, we summarize recent studies of the physiology, cultivation, and genetics of , highlighting their wide substrate utilization and metabolic products with industrial applications. We examine studies of these bacteria as Live Biotherapeutic Products (LBPs), focusing on disease models and clinical studies using them to treat infection, inflammation, metabolic syndrome, and cancer. We discuss key research areas including elucidation of intra-specific diversity and genetic modification of candidate strains that will facilitate the exploitation of in industry and medicine.
PubMed: 38239921
DOI: 10.3389/fbioe.2023.1324396 -
Food and Waterborne Parasitology Dec 2023The protozoan parasites , , and are major causes of waterborne and foodborne diseases worldwide. The assessment of their removal or inactivation during water treatment... (Review)
Review
The protozoan parasites , , and are major causes of waterborne and foodborne diseases worldwide. The assessment of their removal or inactivation during water treatment and food processing remains challenging, partly because research on these parasites is hindered by various economical, ethical, methodological, and biological constraints. To address public health concerns and gain new knowledge, researchers are increasingly seeking alternatives to the use of such pathogenic parasites. Over the past few decades, several non-pathogenic microorganisms and manufactured microparticles have been evaluated as potential surrogates of waterborne and foodborne protozoan parasites. Here, we review the surrogates that have been reported for , , and oocysts, and discuss their use and relevance to assess the transport, removal, and inactivation of these parasites in food and water matrices. Biological surrogates including non-human pathogenic parasites, microorganisms found in water sources (anaerobic and aerobic spore-forming bacteria, algae), and non-biological surrogates (i.e. manufactured microparticles) have been identified. We emphasize that such surrogates have to be carefully selected and implemented depending on the parasite and the targeted application. oocysts appear as promising surrogates to investigate in the future the pathogenic coccidian parasites and that are the most challenging to work with.
PubMed: 38028241
DOI: 10.1016/j.fawpar.2023.e00212