Akkermansia Muciniphila induces chronic extramedullary hematopoiesis through cooperative IL-1R and TLR signals

Bacterial infections can activate and mobilize hematopoietic stem and progenitor cells (HSPCs) from the bone marrow (BM) to spleen, which is termed as extramedullary hematopoiesis (EMH). Recent studies suggest that commensal bacteria, particularly the microbiota, regulates not only the host immune system but also hematopoietic homeostasis. However, the impact of gut microbial species on hematopoietic pathology remains largely unknown. Here we found that systemic injection of Akkermansia muciniphila (A. m.), a mucin-degrading bacterium abundantly existing in the human gut rapidly activates BM myelopoiesis, and induces a slow but long-lasting hepato-splenomegaly, characterized by the expansion and differentiation of functional HSPCs, which we termed chronic EMH. Genetic deletion of Toll-like receptor-2 and -4 (TLR2/4) partially diminished A. m.-induced chronic EMH, while additional pharmacological inhibition of the interleukin-1 receptor (IL-1R) completely alleviated splenomegaly and EMH. Our results demonstrate that cooperative IL-1R- and TLR-mediated innate immune signals regulate commensal bacteria-driven EMH, which might be relevant for certain autoimmune disorders.

Screening And Genome Sequencing of a di-n-butyl Phthalate Degrading Bacterium J2 Isolated From Peanut Field Soil

Di-n-butyl phthalate (DBP) is commonly used plasticizers in agricultural plastic films, and is a priority pollutant due to its toxicity to human health. A newly isolated strain J2, which used DBP as its sole carbon source, was screened from peanut filed soil by continuous enrichment cultivation. Based on morphological, physiological characteristics and 16S rRNA gene sequence analysis (GenBank accession No. OK598965), it was identified as Priestia sp. J2. The research results revealed the optimal conditions for DBP degradation as 35 oC and pH 8.0. The strain could effectively degrade 97.6% DBP within 5 days. Substrate tests showed that strain J2 could utilize shorter side-chained PAEs, but could not utilize long-chained PAEs. The whole genome comprises a complete chromosome of 5,067,299 bp and four plasmids of 147,924 bp, 75,940 bp, 11,604 bp, 11,333 bp (GenBank accession No. CP086208-CP086212). This genome harbors 5,585 predicted protein-encoding genes, 130 tRNA genes, and 42 rRNA genes. Gene annotation analyses showed a DBP-degrading gene contained an open reading frame of 930 bp, and the enzyme was named Est-J2-1. The amino acid sequence of the Est-J2-1 exhibited no significant homology with those of reported DBP-degrading enzymes, suggesting the enzyme is a novel enzyme. The gene of Est-J2-1 was found to be located on the chromosome. This study provided strain resource for DBP removal from farmland and other environments.

Isolation and Molecular Identification of Phenol Degrading Bacterium from Industrial Wastes, Collected from Jeddah Saudi Arabia

In the past two decades, phenolic compounds have had different applications, however their use in densification has increased considerably due to Covid 19. Discharge of these dangerous materials is highly toxic and causes risk and severe problems to the environment and health of human and animals, in addition to it being harmful to the aquatic life. Phenol degradation is very important due to high toxicity and stability. The aim of this study is to isolate phenol-degrading aerobic bacteria from hydrocarbon contaminated soil or wastewater, collected from the industrial area of Jeddah. Minimal medium containing phenol as carbon source was used to isolate different bacteria. About 30 actinomycete isolates were obtained, purified and preserved on Starch nitrate. Out of 30 isolates, eight isolates (27%) grow well in medium containing 0.1% phenol. After growing in broth medium, isolate BA4 and isolate BA8 were very active in phenol degradation. Growth and phenol degradation was measured in liquid medium for the two isolates. Morphological and physiological characters of these isolates were detected using different methods. Using molecular methods, they were belonging to a genus of actinomycetes. They were identified as Streptomyces flavabus BA4 and Streptomyces sp. BA8.The effects of some growth factors on growth and phenol degradation were determined. Growth was measured by dry weight (mg/l) while phenol degradation was detected by assaying the residual phenol concentration. The presence of electron donors such as glucose, starch, glycine, peptone, and Na acetate affect both growth and phenol degradation. It was clear that addition of 1 g/l peptone enhanced both growth and phenol degradation. The isolate use phenol and its derivatives m-cresol and o-cresol as carbon sources and addition of vitamin B complex increased the bacterial growth. In conclusion, phenol degradation was detected by actinobacteria and was affected by some physical and biochemical factors. It was noticed that optimization of growth conditions enhanced both growth and phenol degradation by the two selected Streptomyces isolate. Degradation process by isolate BA4 could be a promising solution for removal of phenol from wastewater.

Xanthobacter dioxanivorans sp. nov., a 1,4-dioxane-degrading bacterium

A Gram-stain-negative bacterium, designated as YN2T, that is capable of degrading 1,4-dioxane, was isolated from active sludge collected from a wastewater treatment plant in Harbin, PR China. Cells of strain YN2T were aerobic, motile, pleomorphic rods, mostly twisted, and contained the water-insoluble yellow zeaxanthin dirhamnoside. Strain YN2T grew at 10–40 °C (optimum, 30 °C), pH 5.0–8.0 (pH 7.0) and with 0–1 % (w/v) NaCl (0.1 %). It also could grow chemolithoautotrophically and fix N2 when no ammonium or nitrate was supplied. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2T belongs to the genus Xanthobacter and shares the highest pairwise identity with Xanthobacter autotrophicus 7cT (98.6 %) and Xanthobacter flavus 301T (98.4 %). The major respiratory quinone was ubiquinone-10. Chemotaxonomic analysis revealed that the strain possesses C16 : 0, C19 : 0 cyclo ω8c and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 67.95 mol%. Based on genome sequences, the DNA–DNA hybridization estimate values between strain YN2T and X. autotrophicus 7cT, X. flavus 301T and X. tagetidis TagT2CT (the only three species of Xanthobacter with currently available genomes) were 31.70, 31.30 and 28.50 %; average nucleotide identity values were 85.23, 84.84 and 83.59 %; average amino acid identity values were 81.24, 80.23 and 73.57 %. Based on its phylogenetic, phenotypic, and physiological characteristics, strain YN2T is considered to represent a novel species of the genus Xanthobacter , for which the name Xanthobacter dioxanivorans sp. nov. is proposed. The type strain is YN2T (=CGMCC 1.19031T=JCM 34666T).

Ottowia caeni sp. nov., a novel phenylacetic acid degrading bacterium isolated from sludge

A novel bacterium, designated BD-1T, was isolated from a sludge sample. Cells of the novel Gram-stain-negative strain were identified to be facultative anaerobic, non-motile and short rod-shaped. Growth occurred at 15–37 °C (optimum, 30 °C), pH 5.0–10.0 (pH 7.0) and in 0–4.0 % NaCl (2.0 %, w/v). The 16S rRNA gene sequence of strain BD-1T showed the highest sequence similarity to Ottowia thiooxydans DSM 14619T (97.0 %), followed by Ottowia pentelensis DSM 21699T (96.3 %) and less than 96 % to other related strains. The phylogenetic trees revealed that strain BD-1T clustered within the genus Ottowia . Summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 48.2 %), C16 : 0 (23.2 %) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c, 8.6 %) were the major fatty acids (>5 %), and ubiquinone-8 was the respiratory quinone. Phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylglycerol were identified as the major polar lipids. Meanwhile, the G+C content of the DNA was 63.6 mol% based on the draft genome analysis. The average nucleotide identity and digital DNA–DNA hybridization values between strain BD-1T and DSM 14619T were 74.5 and 21.4 %, respectively. In addition, the novel strain completely degraded 500 mg l−1 phenylacetic acid within 72 h under the condition of 3 % NaCl. Given the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain BD-1T was considered to represent a novel species of the genus Ottowia , for which the name Ottowia caeni sp. nov. is proposed. The strain is a potential resource for the bioremediation of phenylacetic acid contaminated water. The type strain is BD-1T (=CGMCC 1.18541T=KCTC 82183T).

Draft Whole-Genome Sequence of Sphingobium sp. Strain PNB, a Versatile Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

Sphingobium sp. strain PNB can completely degrade phenanthrene, naphthalene, and biphenyl as the sole carbon and energy source. The strain is also capable of cometabolizing benzo[a]pyrene, pyrene, acenaphthene, fluoranthene, etc. Here, we report the 5.69-Mb assembly and annotation of the genome sequence of strain PNB, obtained using Illumina sequencing.

In vitro co-metabolism of epigallocatechin-3-gallate (EGCG) by the mucin-degrading bacterium Akkermansia muciniphila

Akkermansia muciniphila is a Gram-negative bacterium that resides within the gut mucus layer, and plays an important role in promoting gut barrier integrity, modulating the immune response and inhibiting gut inflammation. Growth stimulation of A. muciniphila by polyphenols including epigallocatechin-3-gallate (EGCG) from difference sources is well-documented. However, no published in vitro culture data on utilization of polyphenols by A. muciniphila are available, and the mechanism of growth-stimulating prebiotic effect of polyphenols on it remains unclear. Here in vitro culture studies have been carried out on the metabolism of EGCG by A. muciniphila in the presence of either mucin or glucose. We found that A. muciniphila did not metabolize EGCG alone but could co-metabolize it together with both these substrates in the presence of mineral salts and amino acids for mucin and protein sources for glucose. Our metabolomic data show that A. muciniphila converts EGCG to gallic acid, epigallocatechin, and (-)-epicatechin through ester hydrolysis. The (-)-epicatechin formed is then further converted to hydroxyhydroquinone. Co-metabolism of A. muciniphila of EGCG together with either mucin or glucose promoted substantially its growth, which serves as a further demonstration of the growth-promoting effect of polyphenols on A. muciniphila and provides an important addition to the currently available proposed mechanisms of polyphenolic prebiotic effects on A. muciniphila.