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1.
Ecotoxicol Environ Saf ; 276: 116313, 2024 May.
Article En | MEDLINE | ID: mdl-38626602

Wheat (Triticum aestivum L.) is a major foodstuff for over 40% of the world's population. However, hexavalent chromium [Cr(VI)] in contaminated soil significantly affects wheat production and its ecological environment. Streptomyces sp. HU2014 was first used to investigate the effects of Cr (VI) stress on wheat growth. We analyzed the Cr(VI) concentration, physicochemical properties of wheat and soil, total Cr content, and microbial community structures during their interactions. HU2014 reduced the toxicity of Cr(VI) and promoted wheat growth by increasing total nitrogen, nitrate nitrogen, total phosphorus, and Olsen-phosphorus in Cr(VI)-contaminated soil. These four soil variables had strong positive effects on two bacterial taxa, Proteobacteria and Bacteroidota, in the HU2014 treatments. In addition, the level of the dominant Proteobacteria positively correlated with the total Cr content in the soil. Among the fungal communities, which had weaker correlations with soil variables compared with bacterial communities, Ascomycota was the most abundant. Our findings suggest that HU2014 can promote the phytoremediation of Cr(VI)-contaminated soil.


Biodegradation, Environmental , Chromium , Rhizosphere , Soil Microbiology , Soil Pollutants , Streptomyces , Triticum , Chromium/toxicity , Streptomyces/drug effects , Triticum/growth & development , Triticum/microbiology , Triticum/drug effects , Soil Pollutants/toxicity , Soil/chemistry , Proteobacteria/drug effects , Nitrogen/metabolism , Phosphorus
2.
Nutrients ; 14(2)2022 Jan 06.
Article En | MEDLINE | ID: mdl-35057422

Integrated data from molecular and improved culturomics studies might offer holistic insights on gut microbiome dysbiosis triggered by xenobiotics, such as obesity and metabolic disorders. Bisphenol A (BPA), a dietary xenobiotic obesogen, was chosen for a directed culturing approach using microbiota specimens from 46 children with obesity and normal-weight profiles. In parallel, a complementary molecular analysis was carried out to estimate the BPA metabolising capacities. Firstly, catalogues of 237 BPA directed-cultured microorganisms were isolated using five selected media and several BPA treatments and conditions. Taxa from Firmicutes, Proteobacteria, and Actinobacteria were the most abundant in normal-weight and overweight/obese children, with species belonging to the genera Enterococcus, Escherichia, Staphylococcus, Bacillus, and Clostridium. Secondly, the representative isolated taxa from normal-weight vs. overweight/obese were grouped as BPA biodegrader, tolerant, or resistant bacteria, according to the presence of genes encoding BPA enzymes in their whole genome sequences. Remarkably, the presence of sporobiota and concretely Bacillus spp. showed the higher BPA biodegradation potential in overweight/obese group compared to normal-weight, which could drive a relevant role in obesity and metabolic dysbiosis triggered by these xenobiotics.


Benzhydryl Compounds/adverse effects , Dietary Exposure/adverse effects , Gastrointestinal Microbiome/genetics , Pediatric Obesity/microbiology , Phenols/adverse effects , Xenobiotics/adverse effects , Actinobacillus/drug effects , Case-Control Studies , Child , Dysbiosis/microbiology , Female , Firmicutes/drug effects , Humans , Male , Phenotype , Proteobacteria/drug effects
3.
PLoS One ; 16(11): e0259671, 2021.
Article En | MEDLINE | ID: mdl-34780518

The effects of TiO2 nanoparticles (nano-TiO2) together with antibiotics leaking into wastewater treatment plants (WWTPs), especially the partial nitrification (PN) process remain unclear. To evaluate the combined impact and mechanisms of nano-TiO2 and antibiotics on PN systems, batch experiments were carried out with six bench-scale sequencing batch reactors. Nano-TiO2 at a low level had minimal effects on the PN system. In combination with tetracycline and erythromycin, the acute impact of antibiotics was enhanced. Both steps of nitrification were retarded due to the decrease of bacterial activity and abundance, while nitrite-oxidizing bacteria were more sensitive to the inhibition than ammonia-oxidizing bacteria. Proteobacteria at the phylum level and Nitrosospira at the genus level remained predominant under single and combined impacts. The flow cytometry analysis showed that nano-TiO2 enhanced the toxicity of antibiotics through increasing cell permeability. Our results can help clarify the risks of nano-TiO2 combined with antibiotics to PN systems and explaining the behavior of nanoparticles in WWTPs.


Anti-Bacterial Agents/pharmacology , Metal Nanoparticles/chemistry , Titanium/chemistry , Titanium/pharmacology , Erythromycin/pharmacology , Nitrites/chemistry , Nitrosomonadaceae/drug effects , Proteobacteria/drug effects , Tetracycline/pharmacology , Water Purification
4.
Gut Microbes ; 13(1): 1946369, 2021.
Article En | MEDLINE | ID: mdl-34275417

Gasdermin D (GSDMD) functions as a key pyroptotic executor through its secreted N-terminal domain (GSDMD-N). However, the functional relevance and mechanistic basis of the precise roles of host colonic GSDMD in high-fat diet (HFD)-induced gut dysbiosis and systemic endotoxemia remain elusive. In this study, we demonstrate that HFD feeding triggers GSDMD-N secretion of both T-lymphocytes and enterocytes in mouse colons. GSDMD deficiency aggravates HFD-induced systemic endotoxemia, gut barrier impairment, and colonic inflammation. More importantly, active GSDMD-N kills the Proteobacteria phylum via directly interacting with Cardiolipin. Mechanistically, we identify that the Glu236 (a known residue for GSDMD protein cleavage) is a bona fide important site for the bacterial recognition of GSDMD. Collectively, our findings explain the mechanism by which colonic GSDMD-N maintains low levels of HFD-induced metabolic endotoxemia. A GSDMD-N mimetic containing an exposed Glu236 site could be an attractive strategy for the treatment of HFD-induced metabolic endotoxemia.


Colon/microbiology , Dysbiosis/chemically induced , Dysbiosis/drug therapy , Endotoxemia/chemically induced , Endotoxemia/drug therapy , Neoplasm Proteins/pharmacokinetics , Neoplasm Proteins/therapeutic use , Proteobacteria/drug effects , Animals , Cardiolipins/analysis , Diet, High-Fat/adverse effects , Disease Models, Animal , Gastrointestinal Microbiome/drug effects , Humans , Mice
5.
Cell Host Microbe ; 29(6): 975-987.e4, 2021 06 09.
Article En | MEDLINE | ID: mdl-33887206

Antimicrobial resistance (AMR) is an accelerating global threat, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts of diverse environmental exposures on ARG load. Our study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli. ARG profiles were significantly affected by various environmental factors. Among these factors, the importance of antibiotics diminished with time since treatment. Finally, ARG load and ARG clusters were also associated with the maturity of the gut microbiome and a bacterial composition associated with increased risk of asthma. These findings broaden our understanding of AMR in early life and have critical implications for efforts to mitigate its spread.


Anti-Bacterial Agents/pharmacology , Asthma/microbiology , Drug Resistance, Microbial/genetics , Environmental Exposure/statistics & numerical data , Escherichia coli/genetics , Gastrointestinal Microbiome/drug effects , Child , Child, Preschool , Cohort Studies , DNA, Bacterial , Escherichia coli/drug effects , Feces/microbiology , Female , Genes, Bacterial , Humans , Infant , Infant, Newborn , Male , Metagenomics , Pregnancy , Proteobacteria/drug effects , Risk Assessment
6.
Article En | MEDLINE | ID: mdl-32998606

Given the toxicity and widespread occurrence of hexavalent chromium [Cr(VI)] in aquatic environments, we investigated the feasibility of a down-flow hanging sponge (DHS) biofilm reactor for the enrichment of microbial communities capable of Cr(VI) removal. In the present study, a laboratory-scale DHS reactor fed with a molasses-based medium containing Cr(VI) was operated for 112 days for the investigation. The enrichment of Cr(VI)-removing microbial communities was evaluated based on water quality and prokaryotic community analyses. Once the DHS reactor began to operate, high average volumetric Cr(VI) removal rates of 1.21-1.45 mg L-sponge-1 h-1 were confirmed under varying influent Cr(VI) concentrations (approximately 20-40 mg L-1). 16S rRNA gene amplicon sequencing analysis suggested the presence of phylogenetically diverse prokaryotic lineages, including phyla that contain well-known Cr(VI)-reducing bacteria (e.g., Bacteroidetes, Firmicutes, and Proteobacteria) in the polyurethane sponge media of the DHS reactor. Therefore, our findings indicate that DHS reactors have great potential for the enrichment of Cr(VI)-removing microbial communities.


Biofilms/growth & development , Bioreactors/microbiology , Chromium/analysis , Microbiota/drug effects , Water Pollutants, Chemical/analysis , Water Purification/methods , Bacteroidetes/drug effects , Firmicutes/drug effects , Polyurethanes/chemistry , Proteobacteria/drug effects , RNA, Ribosomal, 16S/genetics
7.
Ecotoxicol Environ Saf ; 205: 111267, 2020 Dec 01.
Article En | MEDLINE | ID: mdl-32992213

Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.


Actinobacteria/drug effects , Arsenic/toxicity , Firmicutes/drug effects , Metagenomics/methods , Proteobacteria/drug effects , Soil Pollutants/toxicity , Actinobacteria/cytology , Actinobacteria/genetics , Arsenic/analysis , Biodegradation, Environmental , Culture Media/chemistry , Drug Resistance, Bacterial/drug effects , Firmicutes/cytology , Firmicutes/genetics , Gold , Microbial Sensitivity Tests , Microbiota/drug effects , Microbiota/genetics , Mining , Proteobacteria/cytology , Proteobacteria/genetics , RNA, Ribosomal, 16S/genetics , Soil/chemistry , Soil Microbiology , Soil Pollutants/analysis
8.
Aquat Toxicol ; 227: 105591, 2020 Oct.
Article En | MEDLINE | ID: mdl-32853898

The effects of allelopathy and the potential harm of several isolated allelochemicals have been studied in detail. Microorganisms in the phycosphere play an important role in algal growth, decay and nutrient cycling. However, it is unknown and often neglected whether allelochemicals affect the phycosphere. The present study selected a phenolic acid protocatechuic acid (PA) - previously shown to be an allelochemical. We studied PA at a half maximal effective concentration of 0.20 mM (30 mg L-1) against Scrippsiella trochoidea to assess the effect of PA on its phycosphere in an acute time period (48 h). The results showed that: 1) OTUs (operational taxonomic units) in the treatment groups (31.4 ± 0.55) exceeded those of the control groups (28.2 ± 1.30) and the Shannon and Simpson indices were lower than the control groups (3.31 ± 0.08 and 0.84 ± 0.02, 3.45 ± 0.09 and 0.88 ± 0.01); 2) Gammaproteobacteria predominated in the treatment groups (44.71 ± 2.13 %) while Alphaproteobacteria dominated in the controls (67.17 ± 3.87 %); 3) Gammaproteobacteria and Alphaproteobacteria were important biomarkers in the treatment and control groups respectively (LDA > 4.0). PA improved the relative abundance of Alteromonas significantly and decreased the one of Rhodobacteraceae. PICRUSt analysis showed that the decrease of Rhodobacterceae was closely related with the decline of most functional genes in metabolism such as amino acid, carbohydrate, xenobiotics, cofactors and vitamins metabolism after PA-treated.


Allelopathy/drug effects , Dinoflagellida/drug effects , Harmful Algal Bloom/drug effects , Hydroxybenzoates/pharmacology , Microbiota/drug effects , Pheromones/pharmacology , Allelopathy/genetics , Bacteroidetes/drug effects , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , Dinoflagellida/genetics , Dinoflagellida/growth & development , Microbiota/genetics , Proteobacteria/drug effects , Proteobacteria/genetics , Proteobacteria/isolation & purification
9.
Ecotoxicol Environ Saf ; 204: 111083, 2020 Nov.
Article En | MEDLINE | ID: mdl-32791359

Due to the accumulation of heavy metals in soil ecosystems, the response of soil microorganisms to the disturbance of heavy metals were widely studied. However, little was known about the interactions among microorganisms in heavy metals and total petroleum hydrocarbons (TPH) co-contaminated soils. In the present study, the microbiota shifts of 2 different contamination types of heavy metal-TPH polluted soils were investigated. NGS sequencing approach was adopted to illustrate the microbial community structure and to predict community function. Networks were established to reveal the interactions between microbes and environmental pollutants. Results showed that the alpha diversity and OTUs number of soil microbiota were reduced under heavy metals and TPH pollutants. TPH was the major pollutant in HT1 group, in which Proteobacteria phylum increased significantly, including Arenimonas genus, Sphingomonadaceae family and Burkholderiaceae family. Moreover, the function structures based on the KEGG database of HT1 group was enriched in the benzene matter metabolism and bacterial motoricity in microbiota. In contrast, severe Cr-Pb-TPH co-pollutants in HT2 increased the abundance of Firmicutes. In details, the relative abundance of Streptococcus genus and Bacilli class raised sharply. The DNA replication functions in microbiota were enriched under severely contaminated soil as a result of high concentrations of heavy metals and TPH pollutants' damage to bacteria. Furthermore, according to the correlation analysis between microbes and the pollutants, Streptococcus, Neisseria, Aeromonas, Porphyromonas and Acinetobacter were suggested as the bioremediation bacteria for Cr and Pb polluted soils, while Syntrophaceae spp. and Immundisolibacter were suggested as the bioremediation bacteria for TPH polluted soil. The study took a survey on the microbiota shifts of the heavy metals and TPH polluted soils, and the microbe's biomarkers provided new insights for the candidate strains of biodegradation, while further researches are required to verify the biodegradation mechanism of these biomarkers.


Hydrocarbons/toxicity , Metals, Heavy/toxicity , Microbiota/drug effects , Petroleum/toxicity , Soil Microbiology , Soil Pollutants/toxicity , Soil/chemistry , Biodegradation, Environmental , Firmicutes/drug effects , Firmicutes/metabolism , Hydrocarbons/analysis , Metals, Heavy/analysis , Petroleum/analysis , Petroleum Pollution/analysis , Proteobacteria/drug effects , Proteobacteria/metabolism , Soil Pollutants/analysis
10.
Carbohydr Polym ; 246: 116637, 2020 Oct 15.
Article En | MEDLINE | ID: mdl-32747272

In this study, rice starch-oleic acid complex with well-controlled digestibility was chosen as a supplementary diet for rats fed with high fat diet. Our results demonstrated that rice starch-oleic acid complex supplementation significantly decreased body weight, improved serum lipid profiles, hepatic metabolism and altered the composition of gut microbiota of rats, which might be related to the higher resistant starch (RS) level. Interestingly, rice starch-oleic acid complex supplementation contributed to the proliferation and growth of butyrate-producing bacteria. The Spearman's correlation analysis revealed that the genus Turicibacter and Romboutsia genus were positively correlated to HDL-c and SOD level. Meanwhile, based on the metagenomic data, Bifidobacteria genus might be a main primary degrader after rice starch-oleic acid complex intake, which was associated with the changes of key starch-degradation enzymes. Overall, our results provided basic data for the rational design of rice starch-based foods with nutritional functions and physiological benefits.


DNA, Bacterial/genetics , Gastrointestinal Microbiome/drug effects , Obesity/prevention & control , Oleic Acid/administration & dosage , Resistant Starch/administration & dosage , Actinobacteria/classification , Actinobacteria/drug effects , Actinobacteria/genetics , Actinobacteria/isolation & purification , Animals , Bacteroidetes/classification , Bacteroidetes/drug effects , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , Butyrates/metabolism , Cholesterol, LDL/metabolism , Diet, High-Fat/adverse effects , Firmicutes/classification , Firmicutes/drug effects , Firmicutes/genetics , Firmicutes/isolation & purification , Gastrointestinal Microbiome/genetics , Gene Expression , Glutathione Peroxidase/genetics , Glutathione Peroxidase/metabolism , Lipid Metabolism/drug effects , Lipid Metabolism/genetics , Liver/drug effects , Liver/metabolism , Male , Obesity/etiology , Obesity/genetics , Obesity/microbiology , Phylogeny , Proteobacteria/classification , Proteobacteria/drug effects , Proteobacteria/genetics , Proteobacteria/isolation & purification , Rats , Rats, Sprague-Dawley , Superoxide Dismutase/genetics , Superoxide Dismutase/metabolism
11.
Int J Biol Macromol ; 162: 414-424, 2020 Nov 01.
Article En | MEDLINE | ID: mdl-32569687

Artemisia sphaerocephala Krasch polysaccharide (ASKP) and its two fractions-60P (branched xylan) and 60S (branched glucomannan), were subjected to simulated gastrointestinal digestion and in vitro fermentation by human fecal microbiota. The results showed that all polysaccharide fractions could transit through gastrointestinal tract without dramatic degradation and be utilized by gut microbiota. ASKP exhibited the highest depletion rate and highest capability to decrease the pH than its fractions. Meanwhile, 60S showed the stronger capability to increase the production of propionic acid and reduce the ratio of acetic acid to propionic acid. At the phylum level, all polysaccharides efficiently reduced the Firmicutes/Bacteroidetes ratio and relative abundance of Proteobacteria, with ASKP being the most capable to suppress the proliferation of Proteobacteria. At the genus level, ASKP and 60P markedly promoted the growth of Bacteroidetes, and 60S promoted the growth of Parabacteroides and Collinsella. Prediction on metabolic function revealed that polysaccharide administration could dramatically change the metabolic profile of bacteria compared with fructooligosaccharides. Besides, all the polysaccharides dramatically promoted the bile acid metabolism. Compared with 60S, ASKP and 60P showed stronger ability to suppress the metabolisms on carbohydrate and amino acid. In summary, both ASKP and its two fractions showed the prebiotic potentials.


Artemisia/chemistry , Dietary Carbohydrates/administration & dosage , Feces/microbiology , Gastrointestinal Microbiome/drug effects , Polysaccharides/administration & dosage , Prebiotics/administration & dosage , Seeds/chemistry , Acetic Acid/metabolism , Actinobacteria/drug effects , Amino Acids/drug effects , Amino Acids/metabolism , Bacteroidetes/drug effects , Bile Acids and Salts/metabolism , Carbohydrate Metabolism/drug effects , Dietary Carbohydrates/analysis , Dietary Carbohydrates/metabolism , Digestion , Fermentation/drug effects , Firmicutes/drug effects , Humans , In Vitro Techniques , Polysaccharides/analysis , Polysaccharides/chemistry , Polysaccharides/metabolism , Propionates/metabolism , Proteobacteria/drug effects
12.
FEMS Microbiol Lett ; 367(12)2020 06 01.
Article En | MEDLINE | ID: mdl-32556312

Wetlands have been proposed as a sink for pollutants such as heavy metals. Wetland plants play a significant role in the phytoremediation of heavy metals. Here, we isolated and characterized three novel nickel (Ni)-resistant endophytic bacteria (NiEB) from the wetland plant Tamarix chinensis. The NiEB were identified as Stenotrophomonas sp. S20, Pseudomonas sp. P21 and Sphingobium sp. S42. All isolates tolerated 50 mg L-1 Ni, with isolates S20 and P21 being more tolerant to Ni at up to 400 mg L-1. Moreover, isolate S42 removed 33.7% of nickel sulfate from the water by forming white precipitates. The three isolates exhibited different plant growth-promoting (PGP) traits related to the production of indole acetic acid (IAA), siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Phytotoxicity studies revealed that the growth of the wetland plants in a high Ni concentration (200 mg L-1) recovered after co-incubation with isolate S42. Overall, this study presents the first report of NiEB isolation from wetland plants and provides novel insights into the diverse functions of endophytic bacteria in a plant host with the potential to improve Ni phytoremediation.


Biodegradation, Environmental , Drug Resistance, Bacterial , Nickel , Proteobacteria/drug effects , Proteobacteria/metabolism , Tamaricaceae/microbiology , Endophytes/drug effects , Endophytes/isolation & purification , Endophytes/metabolism , Nickel/toxicity , Proteobacteria/isolation & purification
13.
J Microbiol ; 58(8): 703-710, 2020 Aug.
Article En | MEDLINE | ID: mdl-32583287

The gut microbiome, which is symbiotic within the human body, assists in human digestion. It plays significant roles in identifying intestinal disease as well as in maintaining a healthy body with functional immune and metabolic activities. To confirm the consistency of fecal intestinal microbial research, it is necessary to study the changes in intestinal microbial flora according to the fecal collection solution and storage period. We collected fecal samples from three healthy Korean adults. To examine the efficacy of fecal collection solution, we used NBgene-Gut, OMNIgene-Gut, 70% ethanol (Ethanol-70%), and RNAlater. The samples were stored for up to two months at room temperature using three different methods, and we observed changes in microbial communities over time. We analyzed clusters of changes in the microbial flora by observing fecal stock solutions and metagenome sequencing performed over time. In particular, we confirmed the profiling of alpha and beta diversity and microbial classification according to the differences in intestinal environment among individuals. We also confirmed that the microbial profile remained stable for two months and that the microbial profile did not change significantly over time. In addition, our results suggest the possibility of verifying microbial profiling even for long-term storage of a single sample. In conclusion, collecting fecal samples using a stock solution rather than freezing feces seems to be relatively reproducible and stable for GUT metagenome analysis. Therefore, stock solution tubes in intestinal microbial research can be used without problems.


Bacteria/classification , Bacteria/drug effects , Ethanol/pharmacology , Gastrointestinal Microbiome/drug effects , Specimen Handling/methods , Adult , Bacteria/genetics , Bacteroidetes/drug effects , Feces/microbiology , Female , Firmicutes/drug effects , Humans , Male , Proteobacteria/drug effects , RNA, Ribosomal, 16S/genetics , Republic of Korea , Young Adult
14.
Cell Rep ; 31(12): 107813, 2020 06 23.
Article En | MEDLINE | ID: mdl-32579939

Type VI secretion systems (T6SSs) are nanomachines used by bacteria to inject toxic effectors into competitors. The identity and mechanism of many effectors remain unknown. We characterized a Salmonella T6SS antibacterial effector called Tlde1 that is toxic in target-cell periplasm and is neutralized by its cognate immunity protein (Tldi1). Microscopy analysis reveals that cells expressing Tlde1 stop dividing and lose cell envelope integrity. Bioinformatic analysis uncovers similarities between Tlde1 and the catalytic domain of l,d-transpeptidases. Point mutations on conserved catalytic residues abrogate toxicity. Biochemical assays reveal that Tlde1 displays both l,d-carboxypeptidase activity by cleaving peptidoglycan tetrapeptides between meso-diaminopimelic acid3 and d-alanine4 and l,d-transpeptidase exchange activity by replacing d-alanine4 by a non-canonical d-amino acid. Phylogenetic analysis shows that Tlde1 homologs constitute a family of T6SS-associated effectors broadly distributed among Proteobacteria. This work expands our current knowledge about bacterial effectors used in interbacterial competition and reveals a different mechanism of bacterial antagonism.


Anti-Bacterial Agents/pharmacology , Peptidoglycan/metabolism , Peptidyl Transferases/metabolism , Type VI Secretion Systems/metabolism , Bacterial Proteins/metabolism , Cell Division/drug effects , Escherichia coli/drug effects , Escherichia coli/metabolism , Evolution, Molecular , Periplasm/drug effects , Periplasm/metabolism , Proteobacteria/drug effects , Proteobacteria/metabolism , Salmonella typhimurium/drug effects , Salmonella typhimurium/metabolism
15.
Toxicol Appl Pharmacol ; 398: 115031, 2020 07 01.
Article En | MEDLINE | ID: mdl-32389661

Mildronate is a cardiac and neuroprotective drug that is widely used in some countries. By inhibiting carnitine biosynthesis, mildronate impairs the fatty acids transport into mitochondria, thereby decreasing the ß-oxidation intensity. Since 2016, it has been prohibited by the World Anti-Doping Agency (WADA). However, the information on its safety and its influence on the athletes' health is scarce. There are no published studies on whether mildronate-induced long-term metabolism "rearrangement" may cause negative effects on high-metabolic-rate organs and on the whole organism. Here, we demonstrate that long-term mildronate treatment of healthy mice induced global metabolism change at the transcriptome level in liver, heart, and brain. Mildronate treatment also induced some behavioral changes such as anxiety-related behavior and diminished explorative behavior. We also found that mildronate induced a dysbiosis, as manifested by an increase in Proteobacteria level in gut microbiome. At the same time, the absence of a statistically significant increase in mouse strength and endurance procedures suggests that mildronate effect on productivity is negligible. The sum of our data suggests that long-term treatment of healthy mice with mildronate induces dysbiosis and behavioral deviations despite the effectiveness of mildronate for cardiac and neurological diseases. Thus, we suggest that long-term mildronate treatment is undesirable or at the very least should be accompanied by prebiotics treatments, but this issue should be studied further.


Behavior, Animal/drug effects , Brain/drug effects , Gastrointestinal Microbiome/drug effects , Heart/drug effects , Liver/drug effects , Methylhydrazines/adverse effects , Proteobacteria/drug effects , Transcriptome/drug effects , Animals , Brain/metabolism , Carnitine/metabolism , Methylhydrazines/administration & dosage , Mice
16.
Gut Microbes ; 11(5): 1348-1361, 2020 09 02.
Article En | MEDLINE | ID: mdl-32372706

The understanding of the effects of compounds on the gut microbiome is limited. In particular, it is unclear whether structurally similar compounds would have similar or distinct effects on the gut microbiome. Here, we selected berberine (BBR), an isoquinoline quaternary alkaloid, and 16 structural analogs and evaluated their effects on seven individual gut microbiomes cultured in vitro. The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. We show that both interindividual differences and compound treatments significantly contributed to the variance of metaproteomic profiles. BBR and eight analogs led to changes in proteins involved in microbial defense and stress responses and enrichment of proteins from Verrucomicrobia, Proteobacteria, and Bacteroidetes phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, sanguinarine, chelerythrine, and ethoxysanguinarine, activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins, and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the Akkermansia genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that ex vivo microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogs can have distinct effects on the microbiome.


Bacteroidetes/drug effects , Berberine/analogs & derivatives , Berberine/pharmacology , Firmicutes/drug effects , Gastrointestinal Microbiome/drug effects , Proteobacteria/drug effects , Verrucomicrobia/drug effects , Bacterial Proteins/metabolism , Bacteroidetes/growth & development , Bacteroidetes/metabolism , Berberine/chemistry , Biological Variation, Population , Butyrates/metabolism , Firmicutes/growth & development , Firmicutes/metabolism , Gastrointestinal Microbiome/physiology , Humans , Metabolic Networks and Pathways , Molecular Structure , Proteobacteria/growth & development , Proteobacteria/metabolism , Proteomics , Verrucomicrobia/growth & development , Verrucomicrobia/metabolism
17.
Sci Rep ; 10(1): 5190, 2020 03 23.
Article En | MEDLINE | ID: mdl-32251347

Recent studies have used ethanol stool disinfection as a mean of promoting valuable species' cultivation in bacteriotherapy trials for Clostridium difficile infections (CDI) treatment with a particular focus on sporulating bacteria. Moreover, the culturomic approach has considerably enriched the repertoire of cultivable organisms in the human gut in recent years. This study aimed to apply this culturomic approach on fecal donor samples treated with ethanol disinfection to evidence potential beneficial microbes that could be used in bacteriotherapy trials for the treatment of CDI. Thereby, a total of 254 bacterial species were identified, 9 of which were novel. Of these, 242 have never been included in clinical trials for the treatment of CDIs, representing potential new candidates for bacteriotherapy trials. While non-sporulating species were nevertheless more affected by the ethanol pretreatment than sporulating species, the ethanol disinfection technique did not specifically select bacteria able to sporulate, as suggested by previous studies. Furthermore, some bacteria previously considered as potential candidates for bacteriotherapy have been lost after ethanol treatment. This study, while enriching the bacterial repertoire of the human intestine, would nevertheless require determining the exact contribution of each of species composing the bacterial consortia intended to be administered for CDI treatment.


Bacteria/isolation & purification , Bacteriological Techniques , Clostridioides difficile/drug effects , Clostridium Infections/therapy , Ethanol/pharmacology , Feces/microbiology , Gastrointestinal Microbiome , Specimen Handling/methods , Actinobacteria/drug effects , Actinobacteria/isolation & purification , Adult , Aged , Bacteria/drug effects , Bacteroidetes/drug effects , Bacteroidetes/isolation & purification , Clostridioides difficile/isolation & purification , Clostridioides difficile/physiology , Disinfection , Fecal Microbiota Transplantation , Female , Firmicutes/drug effects , Firmicutes/isolation & purification , Humans , Male , Proteobacteria/drug effects , Proteobacteria/isolation & purification , Species Specificity , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Spores, Bacterial/drug effects , Succinates/metabolism
18.
Toxins (Basel) ; 12(3)2020 03 15.
Article En | MEDLINE | ID: mdl-32183408

Microcystins (MCs), which are produced by harmful cyanobacteria blooms, pose a serious threat to environmental health. However, the effect of MCs on the bacterial community under anaerobic conditions is still unclear. This study examined the dynamic changes of MC-degrading capacity, metabolic activity, and structure of the bacterial community in lake sediment repeatedly treated with 1 mg/L microcystin-LR (MC-LR) under anaerobic conditions. The results showed that the MC-degrading capacity of the bacterial community was increased nearly three-fold with increased treatment frequency. However, the metabolic profile behaved in exactly opposite trend, in which the overall carbon metabolic activity was inhibited by repeated toxin addition. Microbial diversity was suppressed by the first addition of MC-LR and then gradually recovered. The 16S amplicon sequencing showed that the dominant genera were changed from Exiguobacterium and Acinetobacter to Prosthecobacter, Dechloromonas, and Agrobacterium. Furthermore, the increase in the relative abundance of Dechloromonas, Pseudomonas, Hydrogenophaga, and Agrobacterium was positively correlated with the MC-LR treatment times. This indicates that they might be responsible for MC degradation under anaerobic conditions. Our findings reveal the relationship between MC-LR and the sediment bacterial community under anaerobic conditions and indicate that anaerobic biodegradation is an effective and promising method to remediate MCs pollution.


Geologic Sediments/microbiology , Lakes/microbiology , Marine Toxins/analysis , Metabolic Networks and Pathways/drug effects , Microbiota/drug effects , Microcystins/analysis , Water Microbiology , Actinobacteria/drug effects , Actinobacteria/metabolism , Anaerobiosis , Biodegradation, Environmental , Biodiversity , Firmicutes/drug effects , Firmicutes/metabolism , Geologic Sediments/chemistry , Lakes/chemistry , Marine Toxins/toxicity , Microbiota/physiology , Microcystins/toxicity , Proteobacteria/drug effects , Proteobacteria/metabolism , Time Factors
19.
Clin Transl Sci ; 13(4): 752-760, 2020 07.
Article En | MEDLINE | ID: mdl-32058642

The pharmacokinetic (PK) properties of drugs are affected in several ways by interactions with microbiota. The aim of this study was to investigate the effects of oral vancomycin on the gut microbiota and, consequently, on the PKs of simvastatin. An open-label, single arm, sequential crossover study was conducted in six healthy Korean male subjects. After 6 days on a control diet, simvastatin 40 mg was orally administered to the subjects before and after 1 week of oral vancomycin treatment. Blood samples for PK analysis and fecal samples for metagenomic and metabolomic analyses were collected. After vancomycin treatment, the richness of microbiota considerably decreased, and the composition was altered. In particular, the relative abundance of Bacteroidetes decreased, whereas that of proteobacteria increased. In addition, changes in fecal metabolites, including D-glucuronic acid, were observed. However, systemic exposure of simvastatin was not changed whereas that of hydroxysimvastatin showed a tendency to increase. The relationship between the change of PKs of simvastatin and the change of gut microbiota and fecal metabolites were not clearly observed.


Anti-Bacterial Agents/administration & dosage , Gastrointestinal Microbiome/drug effects , Simvastatin/pharmacokinetics , Vancomycin/administration & dosage , Administration, Oral , Adult , Bacteroidetes/drug effects , Bacteroidetes/isolation & purification , Bacteroidetes/metabolism , Cross-Over Studies , Drug Interactions , Feces/chemistry , Feces/microbiology , Gastrointestinal Microbiome/physiology , Glucuronic Acid/isolation & purification , Glucuronic Acid/metabolism , Healthy Volunteers , Humans , Hydroxymethylglutaryl-CoA Reductase Inhibitors , Male , Metabolomics , Middle Aged , Proteobacteria/drug effects , Proteobacteria/isolation & purification , Proteobacteria/metabolism , Simvastatin/administration & dosage , Young Adult
20.
Article En | MEDLINE | ID: mdl-32033408

Indiscriminate use of antibiotics has resulted in a catastrophic increase in the levels of antibiotic resistance in India. Hospitals treat critical bacterial infections and thus can serve as reservoirs of multidrug resistant (MDR) bacteria. Hence, this study was conducted to gauge the prevalence patterns of MDR bacteria in hospital wastewater. Water samples collected from 11 hospitals and 4 environmental sources belonging to 5 most-densely populated districts of West Bengal, India were grown on MacConkey and Eosin Methylene Blue agar. A total of 84 (hospital-associated = 70, environmental water sources = 14) isolates were characterized. The predominant species found in water from hospital-associated areas (HAA) were Acinetobacter baumannii (22.9%), Escherichia coli (28.6 %), and Klebsiella pneumoniae (25.7%). Greater than 75% of the HAA isolates were found to be mcr-1 gene negative and colistinresistant. Meropenem non-susceptibility was also high among the HAA isolates at 58.6%, with the presence of the carbapenemase gene and blaNDM in 67.1% of the non-susceptible isolates. Among the three predominant species, significantly higher numbers of E. coli isolates were found to be non-susceptible to meropenem ((80%), p-value = 0.00432) and amikacin (AK (90%), p-value = 0.00037). This study provides evidence for the presence of high numbers of colistin-resistant and carbapenem-hydrolyzing Proteobacteriain hospital wastewater.


Anti-Bacterial Agents/adverse effects , Carbapenems/toxicity , Colistin/adverse effects , Drug Resistance, Multiple, Bacterial/drug effects , Proteobacteria/drug effects , Proteobacteria/isolation & purification , Wastewater/toxicity , Humans , Microbial Sensitivity Tests , Prevalence , Wastewater/microbiology
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