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Nature Aug 2023The human gut microbiota has gained interest as an environmental factor that may contribute to health or disease. The development of next-generation probiotics is a...
The human gut microbiota has gained interest as an environmental factor that may contribute to health or disease. The development of next-generation probiotics is a promising strategy to modulate the gut microbiota and improve human health; however, several key candidate next-generation probiotics are strictly anaerobic and may require synergy with other bacteria for optimal growth. Faecalibacterium prausnitzii is a highly prevalent and abundant human gut bacterium associated with human health, but it has not yet been developed into probiotic formulations. Here we describe the co-isolation of F. prausnitzii and Desulfovibrio piger, a sulfate-reducing bacterium, and their cross-feeding for growth and butyrate production. To produce a next-generation probiotic formulation, we adapted F. prausnitzii to tolerate oxygen exposure, and, in proof-of-concept studies, we demonstrate that the symbiotic product is tolerated by mice and humans (ClinicalTrials.gov identifier: NCT03728868 ) and is detected in the human gut in a subset of study participants. Our study describes a technology for the production of next-generation probiotics based on the adaptation of strictly anaerobic bacteria to tolerate oxygen exposures without a reduction in potential beneficial properties. Our technology may be used for the development of other strictly anaerobic strains as next-generation probiotics.
Topics: Animals; Humans; Mice; Butyrates; Gastrointestinal Microbiome; Oxygen; Probiotics; Aerobiosis; Faecalibacterium prausnitzii; Symbiosis; Biotechnology
PubMed: 37532933
DOI: 10.1038/s41586-023-06378-w -
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 -
Applied Microbiology and Biotechnology May 2024Aerobic granular sludge (AGS) and conventional activated sludge (CAS) are two different biological wastewater treatment processes. AGS consists of self-immobilised...
Aerobic granular sludge (AGS) and conventional activated sludge (CAS) are two different biological wastewater treatment processes. AGS consists of self-immobilised microorganisms that are transformed into spherical biofilms, whereas CAS has floccular sludge of lower density. In this study, we investigated the treatment performance and microbiome dynamics of two full-scale AGS reactors and a parallel CAS system at a municipal WWTP in Sweden. Both systems produced low effluent concentrations, with some fluctuations in phosphate and nitrate mainly due to variations in organic substrate availability. The microbial diversity was slightly higher in the AGS, with different dynamics in the microbiome over time. Seasonal periodicity was observed in both sludge types, with a larger shift in the CAS microbiome compared to the AGS. Groups important for reactor function, such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), followed similar trends in both systems, with higher relative abundances of PAOs and GAOs in the AGS. However, microbial composition and dynamics differed between the two systems at the genus level. For instance, among PAOs, Tetrasphaera was more prevalent in the AGS, while Dechloromonas was more common in the CAS. Among NOB, Ca. Nitrotoga had a higher relative abundance in the AGS, while Nitrospira was the main nitrifier in the CAS. Furthermore, network analysis revealed the clustering of the various genera within the guilds to modules with different temporal patterns, suggesting functional redundancy in both AGS and CAS. KEY POINTS: • Microbial community succession in parallel full-scale aerobic granular sludge (AGS) and conventional activated sludge (CAS) processes. • Higher periodicity in microbial community structure in CAS compared to in AGS. • Similar functional groups between AGS and CAS but different composition and dynamics at genus level.
Topics: Sewage; Microbiota; Bacteria; Bioreactors; Aerobiosis; Sweden; Glycogen; Ammonia; Nitrites; Nitrates; Phosphates; Water Purification
PubMed: 38739161
DOI: 10.1007/s00253-024-13165-8 -
Foods (Basel, Switzerland) Sep 2023The aim of this study was to assess the antimicrobial effects of myrtle ( L.) essential oil (EO) on pathogenic ( O157:H7 NCTC 12900; Listeria monocytogenes ATCC BAA-679)...
The aim of this study was to assess the antimicrobial effects of myrtle ( L.) essential oil (EO) on pathogenic ( O157:H7 NCTC 12900; Listeria monocytogenes ATCC BAA-679) and spoilage microbiota in beef and determine its minimum inhibitory concentration (MIC) and antioxidant activity. The behavior of LAB, Enterobacteriaceae, spp., and fungi, as well as total mesophilic (TM) and total psychotropic (TP) counts, in beef samples, was analyzed during storage at 2 and 8 °C in two different packaging systems (aerobiosis and vacuum). Leaves of myrtle were dried, its EO was extracted by hydrodistillation using a Clevenger-type apparatus, and the chemical composition was determined using chromatographical techniques. The major compounds obtained were myrtenyl acetate (15.5%), β-linalool (12.3%), 1,8-cineole (eucalyptol; 9.9%), geranyl acetate (7.4%), limonene (6.2%), α-pinene (4.4%), linalyl o-aminobenzoate (5.8%), α-terpineol (2.7%), and myrtenol (1.2%). Myrtle EO presented a MIC of 25 µL/mL for O157:H7 NCTC 12900, , ATCC BAA-679, Enterobacteriaceae, and O157:H7 ATCC 35150 and 50µL/mL for spp. The samples packed in aerobiosis had higher counts of deteriorative microorganisms than samples packed under vacuum, and samples with myrtle EO presented the lowest microbial contents, indicating good antimicrobial activity in beef samples. Myrtle EO is a viable natural alternative to eliminate or reduce the pathogenic and deteriorative microorganisms of meat, preventing their growth and enhancing meat safety.
PubMed: 37761099
DOI: 10.3390/foods12183390 -
Foods (Basel, Switzerland) Feb 2024The primary goal of this scoping review is to collect, analyze, and critically describe information regarding the role of the main compounds (reuterin, phenyllactic... (Review)
Review
The primary goal of this scoping review is to collect, analyze, and critically describe information regarding the role of the main compounds (reuterin, phenyllactic acid, and exopolysaccharides) produced by LAB that possess antifungal properties and provide some suggestions for further research. The use of lactic acid bacteria (LAB) to mitigate spoilage and extend the shelf life of foodstuffs has a long history. Recently, there has been a growing interest in the unique properties of these additions to the foodstuffs in which they are applied. In recent studies regarding biopreservation, significant attention has been given to the role of these microorganisms and their metabolites. This fascinating recent discipline aims not only to replace traditional preservation systems, but also to improve the overall quality of the final product. The biologically active by-products produced by lactic acid bacteria are synthesized under certain conditions (time, temperature, aerobiosis, acidity, water activity, etc.), which can be enacted through one of the oldest approaches to food processing: fermentation (commonly used in the dairy and bakery sectors). This study also delves into the biosynthetic pathways through which they are synthesized, with a particular emphasis on what is known about the mechanisms of action against molds in relation to the type of food.
PubMed: 38472865
DOI: 10.3390/foods13050752 -
Role of the ubiquinone-synthesizing UbiUVT pathway in adaptation to changing respiratory conditions.MBio Aug 2023Isoprenoid quinones are essential for cellular physiology. They act as electron and proton shuttles in respiratory chains and various biological processes. and many...
Isoprenoid quinones are essential for cellular physiology. They act as electron and proton shuttles in respiratory chains and various biological processes. and many α-, β-, and γ-proteobacteria possess two types of isoprenoid quinones: ubiquinone (UQ) is mainly used under aerobiosis, while demethylmenaquinones (DMK) are mostly used under anaerobiosis. Yet, we recently established the existence of an anaerobic O-independent UQ biosynthesis pathway controlled by , , and genes. Here, we characterize the regulation of genes in . We show that the three genes are transcribed as two divergent operons that are both under the control of the O-sensing Fnr transcriptional regulator. Phenotypic analyses using a mutant devoid of DMK revealed that UbiUV-dependent UQ synthesis is essential for nitrate respiration and uracil biosynthesis under anaerobiosis, while it contributes, though modestly, to bacterial multiplication in the mouse gut. Moreover, we showed by genetic study and O labeling that UbiUV contributes to the hydroxylation of ubiquinone precursors through a unique O-independent process. Last, we report the crucial role of in allowing to shift efficiently from anaerobic to aerobic conditions. Overall, this study uncovers a new facet of the strategy used by to adjust its metabolism on changing O levels and respiratory conditions. This work links respiratory mechanisms to phenotypic adaptation, a major driver in the capacity of to multiply in gut microbiota and of facultative anaerobic pathogens to multiply in their host. IMPORTANCE Enterobacteria multiplication in the gastrointestinal tract is linked to microaerobic respiration and associated with various inflammatory bowel diseases. Our study focuses on the biosynthesis of ubiquinone, a key player in respiratory chains, under anaerobiosis. The importance of this study stems from the fact that UQ usage was for long considered to be restricted to aerobic conditions. Here we investigated the molecular mechanism allowing UQ synthesis in the absence of O and searched for the anaerobic processes that UQ is fueling in such conditions. We found that UQ biosynthesis involves anaerobic hydroxylases, that is, enzymes able to insert an O atom in the absence of O. We also found that anaerobically synthesized UQ can be used for respiration on nitrate and the synthesis of pyrimidine. Our findings are likely to be applicable to most facultative anaerobes, which count many pathogens (, , and ) and will help in unraveling microbiota dynamics.
Topics: Animals; Mice; Escherichia coli; Ubiquinone; Nitrates; Quinones; Terpenes
PubMed: 37283518
DOI: 10.1128/mbio.03298-22 -
Nature Communications Apr 2024Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH) under anoxic and hypoxic...
Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and CH-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH oxidation in supporting denitrification. Our results reveal positive relationships between CH oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, CH-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of C-metagenome-assembled genomes and C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH oxidation, for the coupling of CH oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.
Topics: Methane; Oryza; Denitrification; Soil Microbiology; Oxidation-Reduction; China; Soil; Aerobiosis; Bacteria; Nitrous Oxide; Phylogeny; Carbon Isotopes; Metagenome
PubMed: 38658559
DOI: 10.1038/s41467-024-47827-y -
The Science of the Total Environment May 2024In situ aerobic cometabolism of groundwater contaminants has been demonstrated to be a valuable bioremediation technology to treat many legacy and emerging contaminants... (Review)
Review
In situ aerobic cometabolism of groundwater contaminants has been demonstrated to be a valuable bioremediation technology to treat many legacy and emerging contaminants in dilute plumes. Several well-designed and documented field studies have shown that this technology can concurrently treat multiple contaminants and reach very low cleanup goals. Fundamentally different from metabolism-based biodegradation of contaminants, microorganisms that cometabolically degrade contaminants do not obtain sufficient carbon and energy from the degradation process to support their growth and require an exogenous growth supporting primary substrate. Successful applications of aerobic cometabolic treatment therefore require special considerations beyond conventional in situ bioremediation, such as competitive inhibition between growth-supporting primary substrate(s) and contaminant non-growth substrates, toxic effects resulting from contaminant degradation, and differences in microbial population dynamics exhibited by biostimulated indigenous consortia versus bioaugmentation cultures. This article first provides a general review of microbiological factors that are likely to affect the rate of aerobic cometabolic biodegradation. We subsequently review fourteen well documented field-scale aerobic cometabolic bioremediation studies and summarize the underlying microbiological factors that may affect the performance observed in these field studies. The combination of microbiological and engineering principles gained from field testing leads to insights and recommendations on planning, design, and operation of an in situ aerobic cometabolic treatment system. With a vision of more aerobic cometabolic treatments being considered to tackle large, dilute plumes, we present several novel topics and future research directions that can potentially enhance technology development and foster success in implementing this technology for environmental restoration.
Topics: Biodegradation, Environmental; Aerobiosis; Groundwater; Water Pollutants, Chemical
PubMed: 38485017
DOI: 10.1016/j.scitotenv.2024.171667 -
PloS One 2024Bacteria are exposed to reactive oxygen and nitrogen species that provoke oxidative and nitrosative stress which can lead to macromolecule damage. Coping with stress...
Bacteria are exposed to reactive oxygen and nitrogen species that provoke oxidative and nitrosative stress which can lead to macromolecule damage. Coping with stress conditions involves the adjustment of cellular responses, which helps to address metabolic challenges. In this study, we performed a global transcriptomic analysis of the response of Pseudomonas extremaustralis to nitrosative stress, induced by S-nitrosoglutathione (GSNO), a nitric oxide donor, under microaerobic conditions. The analysis revealed the upregulation of genes associated with inositol catabolism; a compound widely distributed in nature whose metabolism in bacteria has aroused interest. The RNAseq data also showed heightened expression of genes involved in essential cellular processes like transcription, translation, amino acid transport and biosynthesis, as well as in stress resistance including iron-dependent superoxide dismutase, alkyl hydroperoxide reductase, thioredoxin, and glutathione S-transferase in response to GSNO. Furthermore, GSNO exposure differentially affected the expression of genes encoding nitrosylation target proteins, encompassing metalloproteins and proteins with free cysteine and /or tyrosine residues. Notably, genes associated with iron metabolism, such as pyoverdine synthesis and iron transporter genes, showed activation in the presence of GSNO, likely as response to enhanced protein turnover. Physiological assays demonstrated that P. extremaustralis can utilize inositol proficiently under both aerobic and microaerobic conditions, achieving growth comparable to glucose-supplemented cultures. Moreover, supplementing the culture medium with inositol enhances the stress tolerance of P. extremaustralis against combined oxidative-nitrosative stress. Concordant with the heightened expression of pyoverdine genes under nitrosative stress, elevated pyoverdine production was observed when myo-inositol was added to the culture medium. These findings highlight the influence of nitrosative stress on proteins susceptible to nitrosylation and iron metabolism. Furthermore, the activation of myo-inositol catabolism emerges as a protective mechanism against nitrosative stress, shedding light on this pathway in bacterial systems, and holding significance in the adaptation to unfavorable conditions.
Topics: Inositol; Pseudomonas; Nitrosative Stress; Gene Expression Regulation, Bacterial; S-Nitrosoglutathione; Aerobiosis; Bacterial Proteins; Gene Expression Profiling; Oxidative Stress
PubMed: 38696454
DOI: 10.1371/journal.pone.0301252 -
Microbiology Spectrum Sep 2023Quaternary ammonium compounds (QACs) have been extensively used in the community, healthcare facilities, and food chain, in concentrations between 20 and 30,000 mg/L....
Quaternary ammonium compounds (QACs) have been extensively used in the community, healthcare facilities, and food chain, in concentrations between 20 and 30,000 mg/L. and are ubiquitous in these settings and are recognized as nosocomial pathogens worldwide, but QACs' activity against strains from diverse epidemiological and genomic backgrounds remained largely unexplored. We evaluated the role of isolates from different sources, years, and clonal lineages as hosts of QACs tolerance genes and their susceptibility to QACs in optimal, single-stress and cross-stress growth conditions. Only 1% of the isolates included in this study and 0.5% of publicly available genomes carried or genes, shared with >60 species of Bacillota, Pseudomonadota, Actinomycetota, or Spirochaetota. These genes were generally found within close proximity of antibiotics and/or metals resistance genes. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) of benzalkonium chloride (BC) and didecyldimethylammonium chloride ranged between 0.5 and 4 mg/L (microdilution: 37°C/20 h/pH = 7/aerobiosis) for 210 and isolates (two isolates carrying ). Modified growth conditions (e.g., 22°C/pH = 5) increased MIC/MBC (maximum of eightfold and MBC = 16 mg/L) and changed bacterial growth kinetics under BC toward later stationary phases in both species, including in isolates without QACs tolerance genes. In conclusion, are susceptible to in-use QACs concentrations and rarely carry QACs tolerance genes. However, their potential gene exchange with different microbiota, the decreased susceptibility to QACs under specific environmental conditions, and the presence of subinhibitory QACs concentrations in various settings may contribute to the selection of particular strains and, thus, require a One Health strategy to maintain QACs effectiveness. IMPORTANCE Despite the increasing use of quaternary ammonium compounds (QACs), the susceptibility of pathogens to these antimicrobials remains largely unknown. and are susceptible to in-use QACs concentrations and are not main hosts of QACs tolerance genes but participate in gene transfer pathways with diverse bacterial taxa exposed to these biocides. Moreover, QACs tolerance genes often share the same genetic contexts with antibiotics and/or metals resistance genes, raising concerns about potential co-selection events. and showed increased tolerance to benzalkonium chloride under specific environmental conditions (22°C, pH = 5), suggesting that strains might be selected in settings where they occur along with subinhibitory QACs concentrations. Transcriptomic studies investigating the cellular mechanisms of adaptation to QACs tolerance, along with longitudinal metadata analysis of tolerant populations dynamics under the influence of diverse environmental factors, are essential and should be prioritized within a One Health strategy.
PubMed: 37737589
DOI: 10.1128/spectrum.02324-23