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Background: Qin-Yu-Qing-Chang decoction (QYQC), an herbal formula from China, is extensively employed to manage ulcerative colitis (UC) and exhibits potential benefits for colonic function. Nevertheless, the fundamental molecular mechanisms of QYQC remain largely uncharted. Methods: The primary constituents of QYQC were determined utilizing UHPLC-MS/MS analysis and the effectiveness of QYQC was assessed in a mouse model of colitis induced by dextran sulfate sodium. Evaluations of colon inflammatory responses and mucosal barrier function were thoroughly assessed. RNA sequencing, molecular docking, colonic energy metabolism, and 16S rRNA sequencing analysis were applied to uncover the complex mechanisms of QYQC in treating UC. Detect the signal transduction of the peroxisome proliferator-activated receptor-γ (PPAR-γ) both in the nucleus and cytoplasm. Furthermore, a PPAR-γ antagonist was strategically utilized to confirm the functional targets that QYQC exerts. Results: Utilizing UHPLC-MS/MS, the principal constituents of the nine traditional Chinese medicinal herbs comprising QYQC were systematically identified. QYQC treatment substantially ameliorated colitis in mice, as evidenced by the improvement in symptoms and the reduction in colonic pathological injuries. Besides, QYQC treatment mitigated the inflammatory response and improved mucosal barrier function. Furthermore, QYQC enhanced the mitochondria citrate cycle (TCA cycle) by triggering PPAR-γ signaling and increasing the proportion of PPAR-γ entering the nucleus. This prevented the unconstrained expansion of facultative anaerobes, particularly pathogenic Escherichia coli (E. coli, family Enterobacteriaceae) and thus improved colitis. Results of molecular docking indicated that the representative chemical components of QYQC including Baicalin, Paeoniflorin, Mollugin, and Imperatorin bound well with PPAR-γ. The impact of QYQC on colitis was diminished in the presence of a PPAR-γ antagonist. Conclusions: In summary, QYQC ameliorates UC by activating PPAR-γ signaling and increasing the proportion of PPAR-γ entering the nucleus, which enhances the energy metabolism of intestinal epithelial cells and thereby preventing the uncontrolled proliferation of facultative anaerobes. [ABSTRACT FROM AUTHOR]

Abstract Background Qin-Yu-Qing-Chang decoction (QYQC), an herbal formula from China, is extensively employed to manage ulcerative colitis (UC) and exhibits potential benefits for colonic function. Nevertheless, the fundamental molecular mechanisms of QYQC remain largely uncharted. Methods The primary constituents of QYQC were determined utilizing UHPLC-MS/MS analysis and the effectiveness of QYQC was assessed in a mouse model of colitis induced by dextran sulfate sodium. Evaluations of colon inflammatory responses and mucosal barrier function were thoroughly assessed. RNA sequencing, molecular docking, colonic energy metabolism, and 16S rRNA sequencing analysis were applied to uncover the complex mechanisms of QYQC in treating UC. Detect the signal transduction of the peroxisome proliferator-activated receptor-γ (PPAR-γ) both in the nucleus and cytoplasm. Furthermore, a PPAR-γ antagonist was strategically utilized to confirm the functional targets that QYQC exerts. Results Utilizing UHPLC-MS/MS, the principal constituents of the nine traditional Chinese medicinal herbs comprising QYQC were systematically identified. QYQC treatment substantially ameliorated colitis in mice, as evidenced by the improvement in symptoms and the reduction in colonic pathological injuries. Besides, QYQC treatment mitigated the inflammatory response and improved mucosal barrier function. Furthermore, QYQC enhanced the mitochondria citrate cycle (TCA cycle) by triggering PPAR-γ signaling and increasing the proportion of PPAR-γ entering the nucleus. This prevented the unconstrained expansion of facultative anaerobes, particularly pathogenic Escherichia coli (E. coli, family Enterobacteriaceae) and thus improved colitis. Results of molecular docking indicated that the representative chemical components of QYQC including Baicalin, Paeoniflorin, Mollugin, and Imperatorin bound well with PPAR-γ. The impact of QYQC on colitis was diminished in the presence of a PPAR-γ antagonist. Conclusions In summary, QYQC ameliorates UC by activating PPAR-γ signaling and increasing the proportion of PPAR-γ entering the nucleus, which enhances the energy metabolism of intestinal epithelial cells and thereby preventing the uncontrolled proliferation of facultative anaerobes.

The Yessentuki mineral water deposit (YMWD) is a well-known source of balneologically valuable drinking mineral water, but it has rarely been investigated in terms of the microbes inhabiting it. In this work, we have studied the microbial communities of the continuously operating production well 9, penetrating the Lower Cretaceous aquifer of the YMWD, and characterized, in detail, two novel representatives of class Ignavibacteria (Bacteroidota). One representative of the so-called XYB12-FULL-38-5 group within the family Melioribacteraceae has been isolated in pure culture, designated strain 09-Me, and physiologically characterized. It is a facultatively anaerobic thermotolerant microorganism capable of fermentation and respiration on simple and complex sugars (lichenan, xanthan gum, glucomannan, curdlan, pachyman). In addition to oxygen, ferric iron, arsenate, and elemental sulfur were also used as electron acceptors. Phylogenomic and physiological analyses reveal this novel isolate to represent a novel genus and species for which the name Stygiobacter electus gen. nov., sp. nov. is proposed. The second representative of the family Melioribacteraceae described here belonged to the so-called DSXH01 group, which comprises the dominant group (up to 28%) of the microbial community of well 9 water. The organism was characterized through the analysis of its genome, assembled from metagenome of well 9 (Ess09-04 MAG). Genes encoding enzymes of carbohydrate utilization and genes responsible for aerobic and anaerobic respiration have been identified in the genomes of both bacteria. The investigation of the environmental distribution of Stygiobacter genus-related bacteria and representatives of the lineage DSXH01 has shown that they all are typical inhabitants of the subsurface biosphere, and are often found in bioreactors. These data significantly expand our knowledge on the microbes of subsurface water basins and pave the way for future studies of the novel members of Ignavibacteria class. [ABSTRACT FROM AUTHOR]

This study examines the possibility of directly producing and utilizing useful substances in the intestines of animals using anaerobic bacteria that can grow in the intestines of animals. A facultative anaerobe producing a large amount of α-glucosidase inhibitor was isolated from hay and identified and named Bacillus coagulans CC. The main compound of α-glucosidase inhibitor produced by Bacillus coagulans CC was identified as 1-deoxynojirimycin. α-glucosidase inhibitor activity was confirmed in the intestinal contents and feces of mice orally administered with spores of this strain, and it was confirmed that this strain could efficiently reach the intestines, proliferate, and produce α-glucosidase inhibitors. As a result of administering Bacillus coagulans CC to mice at 109 cells per 1 kg body weight of spores for 8 weeks, the high-carbohydrate diet and the high-fat diet showed a 5% lower weight gain compared to the non-administrated group. At this point, in the spore-administered group, a decrease was observed in both the visceral and subcutaneous fat layers of the abdomen and thorax in both high-carbohydrate and high-fat diet groups compared to the non-administered group on computed tomography. The results of this study show that α-glucosidase inhibitors produced in the intestine by specific strains can work efficiently. [ABSTRACT FROM AUTHOR]

The mounting disquiets about the usage of precarious chemicals in the textile industry have steered to the development of eco-friendly and biological methods of fiber processing in the ever-escalating horizon of textile fibers. The current study targets the isolation, identification, and screening of lignin-degrading bacteria from termite gut microflora which could be employed in the textile trade, especially in coir industries for developing a biological method for softening coir fibers. Based on the morphology and taxonomic keys, termites used in the study were identified as Odontotermes obesus. The bacteria isolated from the termite gut having lignolytic activity were picked by using the methylene blue dye decolorizing method. The same was confirmed by using tannic acid. The isolates were then identified as Kosakonia oryzendophytica and Pseudomonas chengduensis by 16s rRNA sequencing. The isolates were further checked for their ability to produce extracellular lignolytic enzymes. The enzyme concentration was found to be significantly higher in the medium containing the microbial consortium than in those with the individual cultures. The consortium filtrate has MnP activity of 41.6 U/mL, LiP activity of 114.3 U/mL, and laccase activity of 61.85 U/mL at 72 hours of incubation. It was found that the enzyme activities were increased considerably until 72 hours of incubation but showed an insignificant increase at 96 hours.

The advent of sensitive enhanced culture (metaculturomic) and culture-independent DNA-based (metagenomic) methods has revealed a rich collection of microbial species that inhabit the human urinary tract. Known as the urinary microbiome, this community of microbes consists of hundreds of distinct species that range across the entire phylogenetic spectrum. This new knowledge clashes with standard clinical microbiology laboratory methods, established more than 60 years ago, that focus attention on a relatively small subset of universally acknowledged uropathogens. Increasing reports support the hypothesis that this focus is too narrow. Single uropathogen reports are common in women with recurrent urinary tract infection (UTI), although wider disruption of their urinary microbiome is likely. Typical “UTI” symptoms occur in patients with “no growth” reported from standard culture and sometimes antibiotics improve these symptoms. Metaculturomic and metagenomic methods have repeatedly detected fastidious, slow growing, and/or anaerobic microbes that are not detected by the standard test in urine samples of patients with lower urinary tract symptoms. Many of these microbes are also detected in serious non-urinary tract infections, providing evidence that they can be opportunistic pathogens. In this review, we present a set of poorly understood, emerging, and suspected uropathogens. The goal is to stimulate research into the biology of these microbes with a focus on their life as commensals and their transition into pathogens

Antimicrobial resistance is rising as a major global public health threat and antibiotic resistance genes are widely spread among species, including human oral pathogens, e.g., Aggregatibacter actinomycetemcomitans. This Gram-negative, capnophilic, facultative anaerobe is well recognized as a causative agent leading to periodontal diseases, as well as seriously systemic infections including endocarditis. A. actinomycetemcomitans has also evolved mechanisms against complement-mediated phagocytosis and resiliently survives in serum-rich in vivo environments, i.e., inflamed periodontal pockets and blood circulations. This bacterium, however, demonstrated increasing sensitivity to human serum, when being infected by a pseudolysogenic bacteriophage S1249, which switched to the lytic state as a response to human serum. Concomitantly, the pyruvate dehydrogenase complex (PDHc), which is composed of multiple copies of three enzymes (E1, E2, and E3) and oxidatively decarboxylates pyruvate to acetyl-CoA available for tricarboxylic acid (TCA) cycle, was found up-regulated 10-fold in the bacterial lysogen after human serum exposure. The data clearly indicated that certain human serum components induced phage virion replication and egress, resulting in bacterial lysis. Phage manipulation of bacterial ATP production through regulation of PDHc, a gatekeeper linking glycolysis to TCA cycle through aerobic respiration, suggests that a more efficient energy production and delivery system is required for phage progeny replication and release in this in vivo environment. Insights into bacteriophage regulation of bacterial fitness in a mimic in vivo condition will provide alternative strategies to control bacterial infection, in addition to antibiotics. [ABSTRACT FROM AUTHOR]

A novel facultatively anaerobic moderately thermophilic bacteria, strains 4137-MeT and 4148-MeT, were isolated from hot springs of Karmadon and Ursdon, respectively (North Ossetia, Russian Federation). Gram-negative, motile rods were present singly, in pairs, rosettes, and aggregates, or formed biofilms. Both strains grew optimally at 50–55 °C, pH 7.0 and did not require sodium chloride or yeast extract for growth. They were chemoorganoheterotrophs, growing on mono-, di- and polysaccharides (cellulose, starch, xylan, lichenan, galactan, xyloglucan, mannan, xanthan gum, guar gum) as well as proteinaceous substrates (gelatin, peptone, beef and yeast extract). Growth under anaerobic conditions was observed in presence and absence of external electron acceptors. Sulfur, thiosulfate, arsenate, Fe-citrate, and ferrihydrite were reduced with acetate, starch, or yeast extract as electron donors. The respiratory quinone was MK-7. Major cellular fatty acids of both strains were iso -C 15:0 , anteiso -C 17:0 , C 15:0 , iso -C 16:0 and additionally iso -C 17:0 for strain 4137-MeT. The size of the genome and genomic DNA G + C content of strain 4137-MeT were 3.24 Mb. and 29.9 %, respectively; for strain 4148-MeT – 3.33 Mb and 30.7 %. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strains 4137-MeT and 4148-MeT represented a distinct lineage of the family Melioribacteraceae within the class Ignavibacteria. Based on phylogenetic analysis and phenotypic features, the novel isolates were assigned to a novel genus, for which the name Rosettibacter gen. nov. is proposed. Strain 4148-MeT represents its type species Rosettibacter primus sp. nov., while strain 4137-MeT represents a new species Rosettibacter firmus sp. nov. [ABSTRACT FROM AUTHOR]

The Yessentuki mineral water deposit (YMWD) is a well-known source of balneologically valuable drinking mineral water, but it has rarely been investigated in terms of the microbes inhabiting it. In this work, we have studied the microbial communities of the continuously operating production well 9, penetrating the Lower Cretaceous aquifer of the YMWD, and characterized, in detail, two novel representatives of class Ignavibacteria (Bacteroidota). One representative of the so-called XYB12-FULL-38-5 group within the family Melioribacteraceae has been isolated in pure culture, designated strain 09-Me, and physiologically characterized. It is a facultatively anaerobic thermotolerant microorganism capable of fermentation and respiration on simple and complex sugars (lichenan, xanthan gum, glucomannan, curdlan, pachyman). In addition to oxygen, ferric iron, arsenate, and elemental sulfur were also used as electron acceptors. Phylogenomic and physiological analyses reveal this novel isolate to represent a novel genus and species for which the name Stygiobacter electus gen. nov., sp. nov. is proposed. The second representative of the family Melioribacteraceae described here belonged to the so-called DSXH01 group, which comprises the dominant group (up to 28%) of the microbial community of well 9 water. The organism was characterized through the analysis of its genome, assembled from metagenome of well 9 (Ess09-04 MAG). Genes encoding enzymes of carbohydrate utilization and genes responsible for aerobic and anaerobic respiration have been identified in the genomes of both bacteria. The investigation of the environmental distribution of Stygiobacter genus-related bacteria and representatives of the lineage DSXH01 has shown that they all are typical inhabitants of the subsurface biosphere, and are often found in bioreactors. These data significantly expand our knowledge on the microbes of subsurface water basins and pave the way for future studies of the novel members of Ignavibacteria class.

The mounting disquiets about the usage of precarious chemicals in the textile industry have steered to the development of eco-friendly and biological methods of fiber processing in the ever-escalating horizon of textile fibers. The current study targets the isolation, identification, and screening of lignin-degrading bacteria from termite gut microflora which could be employed in the textile trade, especially in coir industries for developing a biological method for softening coir fibers. Based on the morphology and taxonomic keys, termites used in the study were identified as Odontotermes obesus. The bacteria isolated from the termite gut having lignolytic activity were picked by using the methylene blue dye decolorizing method. The same was confirmed by using tannic acid. The isolates were then identified as Kosakonia oryzendophytica and Pseudomonas chengduensis by 16s rRNA sequencing. The isolates were further checked for their ability to produce extracellular lignolytic enzymes. The enzyme concentration was found to be significantly higher in the medium containing the microbial consortium than in those with the individual cultures. The consortium filtrate has MnP activity of 41.6 U/mL, LiP activity of 114.3 U/mL, and laccase activity of 61.85 U/mL at 72 hours of incubation. It was found that the enzyme activities were increased considerably until 72 hours of incubation but showed an insignificant increase at 96 hours. [ABSTRACT FROM AUTHOR]

This study examines the possibility of directly producing and utilizing useful substances in the intestines of animals using anaerobic bacteria that can grow in the intestines of animals. A facultative anaerobe producing a large amount of α-glucosidase inhibitor was isolated from hay and identified and named Bacillus coagulans CC. The main compound of α-glucosidase inhibitor produced by Bacillus coagulans CC was identified as 1-deoxynojirimycin. α-glucosidase inhibitor activity was confirmed in the intestinal contents and feces of mice orally administered with spores of this strain, and it was confirmed that this strain could efficiently reach the intestines, proliferate, and produce α-glucosidase inhibitors. As a result of administering Bacillus coagulans CC to mice at 109 cells per 1 kg body weight of spores for 8 weeks, the high-carbohydrate diet and the high-fat diet showed a 5% lower weight gain compared to the non-administrated group. At this point, in the spore-administered group, a decrease was observed in both the visceral and subcutaneous fat layers of the abdomen and thorax in both high-carbohydrate and high-fat diet groups compared to the non-administered group on computed tomography. The results of this study show that α-glucosidase inhibitors produced in the intestine by specific strains can work efficiently.

Antimicrobial resistance is rising as a major global public health threat and antibiotic resistance genes are widely spread among species, including human oral pathogens, e.g., Aggregatibacter actinomycetemcomitans. This Gram-negative, capnophilic, facultative anaerobe is well recognized as a causative agent leading to periodontal diseases, as well as seriously systemic infections including endocarditis. A. actinomycetemcomitans has also evolved mechanisms against complement-mediated phagocytosis and resiliently survives in serum-rich in vivo environments, i.e., inflamed periodontal pockets and blood circulations. This bacterium, however, demonstrated increasing sensitivity to human serum, when being infected by a pseudolysogenic bacteriophage S1249, which switched to the lytic state as a response to human serum. Concomitantly, the pyruvate dehydrogenase complex (PDHc), which is composed of multiple copies of three enzymes (E1, E2, and E3) and oxidatively decarboxylates pyruvate to acetyl-CoA available for tricarboxylic acid (TCA) cycle, was found up-regulated 10-fold in the bacterial lysogen after human serum exposure. The data clearly indicated that certain human serum components induced phage virion replication and egress, resulting in bacterial lysis. Phage manipulation of bacterial ATP production through regulation of PDHc, a gatekeeper linking glycolysis to TCA cycle through aerobic respiration, suggests that a more efficient energy production and delivery system is required for phage progeny replication and release in this in vivo environment. Insights into bacteriophage regulation of bacterial fitness in a mimic in vivo condition will provide alternative strategies to control bacterial infection, in addition to antibiotics.

Leisingera nanhaiensis DSM 24252(T) is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252(T) possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M.

Enterobacter sp. IIT-BT 08 belongs to Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae. The organism was isolated from the leaves of a local plant near the Kharagpur railway station, Kharagpur, West Bengal, India. It has been extensively studied for fermentative hydrogen production because of its high hydrogen yield. For further enhancement of hydrogen production by strain development, complete genome sequence analysis was carried out. Sequence analysis revealed that the genome was linear, 4.67 Mbp long and had a GC content of 56.01%. The genome properties encode 4,393 protein-coding and 179 RNA genes. Additionally, a putative pathway of hydrogen production was suggested based on the presence of formate hydrogen lyase complex and other related genes identified in the genome. Thus, in the present study we describe the specific properties of the organism and the generation, annotation and analysis of its genome sequence as well as discuss the putative pathway of hydrogen production by this organism.

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Enterobacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of "E. lignolyticus" SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster.

Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the type species of the genus Arcanobacterium, which belongs to the family Actinomycetaceae. The strain is of interest because it is an obligate parasite of the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The strain described in this study was isolated from infections amongst American soldiers of certain islands of the North and West Pacific. This is the first completed sequence of a member of the genus Arcanobacterium and the ninth type strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Microbial antimonate (Sb(V)) reduction is a promising approach to remove Sb(V) from wastewater. However, current knowledge regarding microbial Sb(V) reduction is limited to strictly anaerobic conditions. This study was the first to isolate three facultative-anaerobic Sb(V)-reducing bacterial strains from the sludge collected from a wastewater treatment facility in an antimony products plant. Two of the isolated strains, designated Dechloromonas sp. AR-2 and Propionivibrio sp. AR-3, were characterized based on their Sb(V)-reducing abilities. When cultivated under anaerobic conditions with Sb(V) and acetate as the electron acceptor and donor, respectively, both strains could efficiently reduce 5.0 mM Sb(V), removing most of it from the water phase within 7 d. Along with Sb(V) reduction by the strains, white precipitates, which were likely amorphous Sb(OH)3 solids, were formed with a minor generation of soluble antimonite. Additionally, respiratory Sb(V) reduction by both strains occurred not only under anaerobic but also microaerobic conditions. It was suggested that Sb(V) reduction and the growth abilities of the strains under microaerobic conditions presented a substantial advantage of the use of strains AR-2 and AR-3 for practical applications to Sb(V)-containing wastewater treatment.

Abstract The potential for bioremoval of copper ions was investigated by a novel strain of bacterium Citrobacter freundii JPG1, which was newly isolated from gold mining tailing in China and grew either aerobically or anaerobically. The strain cross-tolerated heavy metals of Ag+, Cd2+, Co2+, Cr6+, Cu2+ and Ni2+ and removed copper under both aerobic and anaerobic conditions with the stress of copper. Under aerobic conditions, the cells grew rapidly and exhibited higher biomass at low copper concentrations (<1 mmol L−1), while the growth of cells was almost completely inhibited at high copper concentrations (2 mmol L−1). However, the cell growths were less affected by copper under anaerobic conditions. Similarly, the copper-removal efficiency was affected by oxygen and the capability of copper removal by anaerobic cells was significantly higher than that of aerobic cells (P < 0.05). The quantitative measurement of extracellular biosorption and intercellular bioaccumulation of copper indicated that biosorption efficiencies for aerobic cells (37%) and anaerobic cells (38%) were similar but the bioaccumulation by anaerobic cells was almost ten-fold higher than that by aerobic cells, indicating bioaccumulation contributed most in copper reduction under anaerobic conditions. Overall, the results suggested the facultative strain C. freundii JPG1 had great potential in the treatment of copper-laden industrial wastewater under both aerobic and anaerobic conditions. Graphical abstract Image 1 Highlights • Bacterium of Citrobacter freundii JPG1 was newly isolated from a gold mining tailing in China. • The strain JPG1 was heavy metal resistant and was flexible to aerobic/anaerobic conditions. • The strain JPG1 was able to remove copper under either aerobic or anaerobic conditions. • The copper-removal efficiency by anaerobic cells was significantly better than those of aerobic cells (P < 0.05). [ABSTRACT FROM AUTHOR]

The terrestrial serpentinite-hosted ecosystem known as "The Cedars" is home to a diverse microbial community persisting under highly alkaline (pH ~ 12) and reducing (Eh < -550 mV) conditions. This extreme environment presents particular difficulties for microbial life, and efforts to isolate microorganisms from The Cedars over the past decade have remained challenging. Herein, we report the initial physiological assessment and/or full genomic characterization of three isolates: Paenibacillus sp. Cedars ('Paeni-Cedars'), Alishewanella sp. BS5-314 ('Ali-BS5-314'), and Anaerobacillus sp. CMMVII ('Anaero-CMMVII'). Paeni-Cedars is a Gram-positive, rod-shaped, mesophilic facultative anaerobe that grows between pH 7-10 (minimum pH tested was 7), temperatures 20-40°C, and 0-3% NaCl concentration. The addition of 10-20 mM CaCl 2 enhanced growth, and iron reduction was observed in the following order, 2-line ferrihydrite > magnetite > serpentinite ~ chromite ~ hematite. Genome analysis identified genes for flavin-mediated iron reduction and synthesis of a bacillibactin-like, catechol-type siderophore. Ali-BS5-314 is a Gram-negative, rod-shaped, mesophilic, facultative anaerobic alkaliphile that grows between pH 10-12 and temperatures 10-40°C, with limited growth observed 1-5% NaCl. Nitrate is used as a terminal electron acceptor under anaerobic conditions, which was corroborated by genome analysis. The Ali-BS5-314 genome also includes genes for benzoate-like compound metabolism. Anaero-CMMVII remained difficult to cultivate for physiological studies; however, growth was observed between pH 9-12, with the addition of 0.01-1% yeast extract. Anaero-CMMVII is a probable oxygen-tolerant anaerobic alkaliphile with hydrogenotrophic respiration coupled with nitrate reduction, as determined by genome analysis. Based on single-copy genes, ANI, AAI and dDDH analyses, Paeni-Cedars and Ali-BS5-314 are related to other species ( P. glucanolyticus and A. aestuarii, respectively), and Anaero-CMMVII represents a new species. The characterization of these three isolates demonstrate the range of ecophysiological adaptations and metabolisms present in serpentinite-hosted ecosystems, including mineral reduction, alkaliphily, and siderophore production., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Thompson, Barr, Babcock-Adams, Bird, La Cava, Garber, Hongoh, Liu, Nealson, Okamoto, Repeta, Suzuki, Tacto, Tashjian and Merino.)

Cellulomonas uda (DSM 20108/ATCC 21399) is one of the few described cellulolytic facultative anaerobes. Based on these characteristics, we initiated a physiological study of C. uda with the aim to exploit it for cellulase production in simple bioreactors with no or sporadic aeration. Growth, cellulase activity and fermentation product formation were evaluated in different media under both aerobic and anaerobic conditions and in experiments where C. uda was exposed to alternating aerobic/anaerobic growth conditions. Here we show that C. uda behaves as a true facultative anaerobe when cultivated on soluble substrates such as glucose and cellobiose, but for reasons unknown cellulase activity is only induced under aerobic conditions on insoluble cellulosic substrates and not under anaerobic conditions. These findings enhance knowledge on the limited number of described facultative cellulolytic anaerobes, and in addition it greatly limits the utility of C. uda as an 'easy to handle' cellulase producer with low aeration demands. [ABSTRACT FROM AUTHOR]

Shigellosis is a global human health problem caused by Shigella species spreading through highly contaminated food and water. Four species of Shigella i.e. S. dysenteriae, S. flexneri, S. boydii and S. sonnei are able to cause the disease. Worldwide, 90 million cases of shigellosis have been reported according to the World Health Organization. In order to control fatality of shigellosis different strategies have been used to develop broadspectrum antibiotics and multivalent vaccines which may reduce mortality rate. [ABSTRACT FROM AUTHOR]

Salmonella arizonae (also called Salmonella subgroup IIIa) is a Gram-negative, non-spore-forming, motile, rod-shaped, facultatively anaerobic bacterium. S. arizonae strain RKS2983 was isolated from a human in California, USA. S. arizonae lies somewhere between Salmonella subgroups I (human pathogens) and V (also called S. bongori; usually non-pathogenic to humans) and so is an ideal model organism for studies of bacterial evolution from non-human pathogen to human pathogens. We hence sequenced the genome of RKS2983 for clues of genomic events that might have led to the divergence and speciation of Salmonella into distinct lineages with diverse host ranges and pathogenic features. The 4,574,836 bp complete genome contains 4,203 protein-coding genes, 82 tRNA genes and 7 rRNA operons. This genome contains several characteristics not reported to date in Salmonella subgroup I or V and may provide information about the genetic divergence of Salmonella pathogens. [ABSTRACT FROM AUTHOR]

Members of the genus Aromatoleum thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O 2 respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1 T , we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied. Their substrate-dependent regulation showed differing degrees of specificity, ranging from high with 3-(4-hydroxyphenyl)propanoate to mostly relaxed with benzoate. For benzoate, the transcript and protein formation were essentially constitutive, contrasted by that of anoxia-specific versus oxia-specific metabolite profiles. The matrix factorization of transcriptomic data revealed that the anaerobic modules accounted for most of the variance across the degradation network. The respiration network appeared to be constitutive, both on the transcript and protein levels, except for nitrate reductase (with narGHI expression occurring only under nitrate-reducing conditions). The anoxia/nitrate-dependent transcription of denitrification genes is apparently controlled by three FNR-type regulators as well as by NarXL (all constitutively formed). The resequencing and functional reannotation of the genome fostered a genome-scale metabolic model, which is comprised of 655 enzyme-catalyzed reactions and 731 distinct metabolites. The model predictions for growth rates and biomass yields agreed well with experimental stoichiometric data, except for 3-(4-hydroxyphenyl)propanoate, with which 4-hydroxybenzoate was exported. Taken together, the combination of multi-omics, growth physiology, and a metabolic model advanced our knowledge of an environmentally relevant microorganism that differs significantly from other bacterial model strains. IMPORTANCE Aromatic compounds are abundant constituents not only of natural organic matter but also of bulk industrial chemicals and fuel components of environmental concern. Considering the widespread occurrence of redox gradients in the biosphere, facultative anaerobic degradation specialists can be assumed to play a prominent role in the natural mineralization of organic matter and in bioremediation at contaminated sites. Surprisingly, differential multi-omics profiling of the A. aromaticum EbN1 T studied here revealed relaxed regulatory stringency across its four main physiological modi operandi (i.e., O 2 -independent and O 2 -dependent degradation reactions versus denitrification and O 2 respiration). Combining multi-omics analyses with a genome-scale metabolic model aligned with measured growth performances establishes A. aromaticum EbN1 T as a systems-biology model organism and provides unprecedented insights into how this bacterium functions on a holistic level. Moreover, this experimental platform invites future studies on eco-systems and synthetic biology of the environmentally relevant betaproteobacterial Aromatoleum / Azoarcus / Thauera cluster.

Polycyclic aromatic hydrocarbons (PAHs) are harmful persistent organic pollutants, while the high-molecular-weight (HMW) PAHs are even more detrimental to the environment and human health. However, microbial anaerobic degradation of HMW PAHs has rarely been reported. One facultative anaerobe Pseudomonas sp. JP1 was isolated from Shantou Bay, Shantou, China, which could degrade a variety of HMW PAHs. After 40 days cultivation with strain JP1, anaerobic biodegradation rate of benzo[a]pyrene (BaP), fluoranthene, and phenanthrene was 30, 47, and 5 %, respectively. Consumption of nitrate as the electron acceptor was confirmed by N-(1-naphthyl) ethylenediamine spectrophotometry. Supplementation of sodium sulfite, maltose, or glycine, and in a salinity of 0-20 ‰ significantly stimulated anaerobic degradation of BaP. Lastly, the anaerobic degradation metabolites of BaP by strain JP1 were investigated using GC/MS, and the degradation pathway was proposed. This study is helpful for further studies on the mechanism of anaerobic biodegradation of PAHs. [ABSTRACT FROM AUTHOR]

Decreased oxygen availability impairs cellular energy production and, without a coordinated and matched decrease in energy consumption, cellular and whole organism death rapidly ensues. Of particular interest are mechanisms that protect brain from low oxygen injury, as this organ is not only the most sensitive to hypoxia, but must also remain active and functional during low oxygen stress. As a result of natural selective pressures, some species have evolved molecular and physiological mechanisms to tolerate prolonged hypoxia with no apparent detriment. Among these mechanisms are a handful of responses that are essential for hypoxia tolerance, including ( i) sensors that detect changes in oxygen availability and initiate protective responses; ( ii) mechanisms of energy conservation; ( iii) maintenance of basic brain function; and ( iv) avoidance of catastrophic cell death cascades. As the study of hypoxia-tolerant brain progresses, it is becoming increasingly apparent that mitochondria play a central role in regulating all of these critical mechanisms. Furthermore, modulation of mitochondrial function to mimic endogenous neuroprotective mechanisms found in hypoxia-tolerant species confers protection against otherwise lethal hypoxic stresses in hypoxia-intolerant organs and organisms. Therefore, lessons gleaned from the investigation of endogenous mechanisms of hypoxia tolerance in hypoxia-tolerant organisms may provide insight into clinical pathologies related to low oxygen stress. [ABSTRACT FROM AUTHOR]

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The genus Amphibacillus was established in 1990, and seven additional species were described in the past two decades. Amphibacillus jilinensis Y1 is a facultatively anaerobic and alkaliphilic bacterium isolated from a soda lake in China. Here we describe the structural and genetic features of the draft genome about the type strain Y1 (3,831,075 bp, with a G+C content of 37.27%). This is the first genome report of the Amphibacillus genus. [ABSTRACT FROM AUTHOR]

Abstract: In this study, the toxicity effects of benzene (B), toluene (T), ethylbenzene (E), xylene (X) alone and substrate interactions in binary mixtures of BT, BE and BX mixed with equal mass concentrations on facultative anaerobic Rhodococcus sp. ustb-1 in LB medium were examined by a microcalorimetric method. The results showed that T, E and X alone aren''t severely toxic to strain ustb-1 when the concentrations reach 800 μg mg−1, but B alone and these binary mixtures exhibit obvious inhibitory effects on the growth of ustb-1 at the dose of 100 μg mg−1. The toxicity of B in the presence of T and X is not significantly different from B alone, but E increased the toxicity of B. In mineral salt medium, all T and X were removed within 72 h, while complete degradation of B and E did not occur during biodegradation of these binary mixtures. The degradation of B was stimulated in the presence of T and X, but it was inhibited by E. The decreased degradation of B in BE, compared with the degradation of B alone, was attributed to an increase in the toxicity of B in the presence of E. [Copyright &y& Elsevier]