Is mechanical bowel preparation mandatory for elective colon surgery? A systematic review and meta-analysis.

BACKGROUND: Growing evidence demonstrates minimal impact of mechanical bowel preparation (MBP) on reducing postoperative complications following elective colectomy. This study investigated the necessity of MBP prior to elective colonic resection. METHOD: A systematic literature review was conducted across PubMed, Ovid, and the Cochrane Library to identify studies comparing the effects of MBP with no preparation before elective colectomy, up until May 26, 2023. Surgical-related outcomes were compiled and subsequently analyzed. The primary outcomes included the incidence of anastomosis leakage (AL) and surgical site infection (SSI), analyzed using Review Manager Software (v 5.3). RESULTS: The analysis included 14 studies, comprising seven RCTs with 5146 participants. Demographic information was consistent across groups. No significant differences were found between the groups in terms of AL ((P = 0.43, OR = 1.16, 95% CI (0.80, 1.68), I2 = 0%) or SSI (P = 0.47, OR = 1.20, 95% CI (0.73, 1.96), I2 = 0%), nor were there significant differences in other outcomes. Subgroup analysis on oral antibiotic use showed no significant changes in results. However, in cases of right colectomy, the group without preparation showed a significantly lower incidence of SSI (P = 0.01, OR = 0.52, 95% CI (0.31, 0.86), I2 = 1%). No significant differences were found in other subgroup analyses. CONCLUSION: The current evidence robustly indicates that MBP before elective colectomy does not confer significant benefits in reducing postoperative complications. Therefore, it is justified to forego MBP prior to elective colectomy, irrespective of tumor location.

Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China.

A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3T grew optimally at 35 °C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C16:0, 11-methyl C18:1ω7c and Summed Feature 8 (including C18:1ω7c/C18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3T showed identities of 98.50% with Devosia beringensis S02T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935T. The genome size of strain CJK-A8-3T was 3.81 Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4-63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3T (= MCCC 1K06953T = KCTC 92162T).

Rheinheimera oceanensis sp. nov., a novel member of the genus Rheinheimera, isolated from the West Pacific Ocean.

Two Gram-stain-negative, aerobic, non-motile and short-rod-shaped bacteria, designated as strains GL-53T and GL-15-2-5, were isolated from the seamount area of the West Pacific Ocean and identified using a polyphasic taxonomic approach. The growth of strains GL-53ᵀ and GL-15-2-5 occurred at pH 5.5-10.0, 4-40 °C (optimum at 28 °C) and 0-10.0 % NaCl concentrations (optimum at 0-5.0 %). On the basis of 16S rRNA gene sequence analysis, strains GL-53ᵀ and GL-15-2-5 exhibited the highest similarity to Rheinheimera lutimaris YQF-2T (98.4 %), followed by Rheinheimera pacifica KMM 1406T (98.1 %), Rheinheimera nanhaiensis E407-8T (97.4 %), Rheinheimera aestuarii H29T (97.4 %), Rheinheimera hassiensis E48T (97.2 %) and Rheinheimera aquimaris SW-353T (97.2 %). Phylogenetic analysis revealed that the isolates were affiliated with the genus Rheinheimera and represented an independent lineage. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The sole isoprenoid quinone was ubiquinone 8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid (and one unidentified glycolipid. The DNA G+C content was 48.5 mol%. The average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization values among the genomes of strain GL-53ᵀ and the related strains in the genus Rheinheimera were 75.5-90.1 %, 67.5-93.9 % and 21.4-41.4 %, respectively. Based on their phenotypic, chemotaxonomic and genotypic properties, the two strains were identified as representing a novel species of the genus Rheinheimera, for which the name Rheinheimera oceanensis sp. nov. is proposed. The type strain is GL-53T (=KCTC 82651T=MCCC M20598T).

Reproductive outcomes after pregnancy-induced displacement of preexisting microchimeric cells.

Pregnancy confers partner-specific protection against complications in future pregnancy that parallel persistence of fetal microchimeric cells (FMcs) in mothers after parturition. We show that preexisting FMcs become displaced by new FMcs during pregnancy and that FMc tonic stimulation is essential for expansion of protective fetal-specific forkhead box P3 (FOXP3)-positive regulatory T cells (Treg cells). Maternal microchimeric cells and accumulation of Treg cells with noninherited maternal antigen (NIMA) specificity are similarly overturned in daughters after pregnancy, highlighting a fixed microchimeric cell niche. Whereas NIMA-specific tolerance is functionally erased by pregnancy, partner-specific resiliency against pregnancy complications persists in mothers despite paternity changes in intervening pregnancy. Persistent fetal tolerance reflects FOXP3 expression plasticity, which allows mothers to more durably remember their babies, whereas daughters forget their mothers with new pregnancy-imprinted immunological memories.

Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields.

BACKGROUND: Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats. RESULTS: Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments. CONCLUSIONS: This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.

Microbulbifer zhoushanensis sp. nov., Microbulbifer sediminum sp. nov. and Microbulbifer guangxiensis sp. nov., three marine bacteria isolated from a tidal flat.

Three strains, TT30T, TT37T and L3T, were isolated from tidal flat samples. Cells were Gram-stain-negative, non-motile and rod shaped. Cells of strains TT30T and TT37T were able to grow in a medium containing 1.0-15.0 % (w/v) NaCl (optimum, 3.0 and 4.0 %, respectively), and cells of strain L3T was able to grow in a medium containing 1.0-10.0 % (w/v) NaCl (optimum, 1.0 %). Growth of the three strains was observed at pH 6.0-10.0 and at 10-40 °C. Strains TT30T, TT37T and L3T showed the highest similarity to Microbulbifer hydrolyticus DSM 11525T (97.7 %), M. yueqingensis CGMCC 1.10658T (98.0 %) and M. elongatus DSM 6810T (97.9 %), respectively. Results of phylogenetic analyses indicated that the three isolates represented two distinct lineages within the genus Microbulbifer. The DNA G+C contents of strains TT30T, TT37T and L3T were 61.3, 60.9 and 60.2%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among strains TT30T, TT37T and L3T and the reference strains were 84.4-87.4 and 19.6-28.9 %, respectively. Differential phenotypic properties, chemotaxonomic differences, phylogenetic distinctiveness, together with the genomic data, demonstrated that strains TT30T, TT37 T and L3T represent novel species of the genus Microbulbifer, which are named Microbulbifer zhoushanensis sp. nov. (TT30T=KCTC 92167T=MCCC 1K07276T), Microbulbifer sediminum sp. nov. (TT37T=KCTC 92168T=MCCC 1K07277T) and Microbulbifer guangxiensis sp. nov. (L3T=KCTC 92165T=MCCC 1K07278T).

Effects of cancer-associated point mutations on the structure, function, and stability of isocitrate dehydrogenase 2.

Mutations in isocitrate dehydrogenase (IDH) are frequently found in low-grade gliomas, secondary glioblastoma, chondrosarcoma, acute myeloid leukemias, and intrahepatic cholangiocarcinoma. However, the molecular mechanisms of how IDH2 mutations induce carcinogenesis remain unclear. Using overlapping PCR, transfection, immunoblotting, immunoprecipitation, measurements of enzyme activity, glucose, lactic acid, ATP, and reactive oxygen species (ROS), cell viability, protein degradation assays post-inhibition of the 26S proteasome (bortezomib) or HSP90 (17-AAG), and a homology model, we demonstrated that the properties of ten cancer-associated IDH2 variants (R140G/Q/W and R172S/K/M/W/G/C/P) arising from point mutations are closely related to their structure and stability. Compared with wild-type IDH2, the R172 and R140 point mutations resulted in a decrease in IDH2 activity, ROS, and lactate levels and an increase in glucose and ATP levels under normal and hypoxic conditions, indicating that mutant IDH2 increases cell dependency on mitochondrial oxidative phosphorylation, and reduces glycolysis under hypoxia. Overexpression of most of IDH2 point mutants showed anti-proliferative effects in the 293T and BV2 cell lines by inhibition of PI3K/AKT signaling and cyclin D1 expression and/or induced the expression of TNF-α and IL-6. Furthermore, bortezomib treatment resulted in dramatic degradation of IDH2 mutants, including R140G, R140Q, R140W, R172S and R172K, whereas it had little impact on the expression of WT and other mutants (R172M, R172W, R172G, R172C and R172P). In addition, targeting HSP90 minimally affected the expression of mutated IDH2 due to a lack of interaction between HSP90 and IDH2. The homology model further revealed that changes in conformation and IDH2 protein stability appeared to be associated with these point mutations. Taken together, our findings provide information important for understanding the molecular mechanisms of IDH2 mutations in tumors.

Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge.

The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.

Genomic characterization of multidrug-resistance gene cfr in Escherichia coli recovered from food animals in Eastern China.

The plasmid-borne cfr gene, mediating multiple drug resistance (MDR), has been observed in many Gram-positive bacteria. The prevalence of cfr and its co-occurrence with additional antimicrobial resistance (AMR) determinants in Escherichia coli is an ongoing issue. Additionally, the prevalence and transfer mechanism of the cfr gene remain partially investigated. Here, eight cfr-positive E. coli strains were screened using PCR from an extensive collection of E. coli (n = 2,165) strains isolated from pigs and chickens in 2021 in China, with a prevalence rate of 0.37%. All of them were MDR and resistant to florfenicol and tetracycline. These strains can transfer the cfr gene to E. coli J53 by conjugation (1.05 × 10-1 - 1.01 × 10-6). Moreover, the IncX4 plasmid p727A3-62 K-cfr (62,717 bp) harboring cfr in strain EC727A3 was confirmed using Oxford Nanopore Technology. The unknown type plasmid p737A1-27K-cfr (27,742 bp) harboring cfr in strain EC737A1 was also identified. Notably, it was verified by PCR that three of the eight E. coli strains were able to form the cfr-IS26 circular intermediate. It was 2,365 bp in length in strains EC727A3 and ECJHZ21-173, and 2,022 bp in length in EC737A1. Collectively, this study demonstrated that IS26 plays a vital role in transmitting the MDR gene cfr in E. coli via conjugation and provided updated knowledge regarding cfr in E. coli in Eastern China.

Pregnancy enables antibody protection against intracellular infection.

Adaptive immune components are thought to exert non-overlapping roles in antimicrobial host defence, with antibodies targeting pathogens in the extracellular environment and T cells eliminating infection inside cells1,2. Reliance on antibodies for vertically transferred immunity from mothers to babies may explain neonatal susceptibility to intracellular infections3,4. Here we show that pregnancy-induced post-translational antibody modification enables protection against the prototypical intracellular pathogen Listeria monocytogenes. Infection susceptibility was reversed in neonatal mice born to preconceptually primed mothers possessing L. monocytogenes-specific IgG or after passive transfer of antibodies from primed pregnant, but not virgin, mice. Although maternal B cells were essential for producing IgGs that mediate vertically transferred protection, they were dispensable for antibody acquisition of protective function, which instead required sialic acid acetyl esterase5 to deacetylate terminal sialic acid residues on IgG variable-region N-linked glycans. Deacetylated L. monocytogenes-specific IgG protected neonates through the sialic acid receptor CD226,7, which suppressed IL-10 production by B cells leading to antibody-mediated protection. Consideration of the maternal-fetal dyad as a joined immunological unit reveals protective roles for antibodies against intracellular infection and fine-tuned adaptations to enhance host defence during pregnancy and early life.

Genome sequence of five Zetaproteobacteria metagenome-assembled genomes recovered from hydrothermal vent Longqi, Southwest Indian Ridge.

Southwest Indian Ridge (SWIR) increasingly becomes the hot spot of deep-sea mining and extreme life research. Strategies for future environmental conservation are undoubtedly required which makes investigation of microbial iron metabolisms imperative. Through deep metagenome sequencing, five iron-oxidizing Zetaproteoabacteria metagenome-assembled genomes were recovered from Longqi hydrothermal vent in the SWIR. Phylogenetic analysis revealed that two of the MAGs might represent novel genus in Zetaproteobacteria while other MAGs were related to Mariprofundus. Functional profile suggested that they might be aerobic chemolithoautotrophic species with genes encoding cytochrome c oxidase, iron oxidase cyc2 homologs and carbon fixation CBB pathway. Versatile capabilities of synthesizing diverse amino acids and cofactors were indicated while possession of various metal ion transporters could be vital to heavy metal resistance. Our work has provided more understanding about phylogenetic and functional features of iron-oxidizing Zetaproteobacteria, which might be important to investigate iron biogeochemistry and mineral oxidation in SWIR.

Adenine Base Editing System for Pseudomonas and Prediction Workflow for Protein Dysfunction via ABE.

Pseudomonas is a large genus that inhabits diverse environments due to its distinct metabolic versatility. Its applications range from environmental to industrial biotechnology. Molecular tools that allow precise and efficient genetic manipulation are required to understand and harness its full potential. Here, we report the development of a highly efficient adenine base editing system, i.e., dxABE-PS, for Pseudomonas species. The system allows A:T → G:C transition with up to 100% efficiency along a broad target spectrum because we use xCas9 3.7, which recognizes NG PAM. To enhance the dxABE-PS utility, we develop a prediction workflow for protein dysfunction using ABE, namely, DABE-CSP (dysfunction via ABE through CRISPOR-SIFT prediction). We applied DABE-CSP to inactivate several genes in Pseudomonas putida KT2440 to accumulate a nylon precursor, i.e., muconic acid from catechol with 100% yield. Moreover, we expanded the ABE to non-model Pseudomonas species by developing an nxABE system for P. chengduensisDY56-96, isolated from sediment samples from the seamount area in the West Pacific Ocean. Taken together, the establishment of the ABE systems along with DABE-CSP will fast-track research on Pseudomonas species.

Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean.

Two strains (GL-11-2T and ZH2-Y79) were isolated from the seawater collected from the West Pacific Ocean and the East China Sea, respectively. Cells were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Cells grew in the medium containing 0.5-7.5 % NaCl (w/v, optimum, 1.0-3.0 %), at pH 6.0-8.0 (optimum, pH 6.5-7.0) and at 4-40 °C (optimum, 30 °C). H2S production occurred in marine broth supplemented with sodium thiosulphate. The almost-complete 16S rRNA gene sequences of the two isolates were identical, and exhibited the highest similarity to Pseudoruegeria aquimaris JCM 13603T (97.5 %), followed by Ruegeria conchae TW15T (97.2%), Shimia aestuarii DSM 15283T (97.1 %) and Ruegeria lacuscaerulensis ITI-1157T (97.0 %). Phylogenetic analysis revealed that the isolates were affiliated with the family Roseobacteraceae and represented an independent lineage. The sole isoprenoid quinone was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and cyclo-C19 : 0 ω8c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content was 62.3 mol%. The orthologous average nucleotide identity, in silico DNA-DNA hybridization and average amino acid identity values among the genomes of strain GL-11-2T and the reference strains were 73.2-79.0, 20.3-22.5 and 66.0-80.8 %, respectively. Strains GL-11-2ᵀ and ZH2-Y79 possessed complete metabolic pathways for thiosulphate oxidation, dissimilatory nitrate reduction and denitrification. Phylogenetic distinctiveness, chemotaxonomic differences and phenotypic properties revealed that the isolates represent a novel genus and species of the family Roseobacteraceae, belonging to the class Alphaproteobacteria, for which the name Thiosulfatihalobacter marinus gen. nov., sp. nov. (type strain, GL-11-2T=KCTC 82723T=MCCC M20691T) is proposed.

Mesobacterium pallidum gen. nov., sp. nov., Heliomarina baculiformis gen. nov., sp. nov. and Oricola indica sp. nov., three novel Alphaproteobacteria members isolated from deep-sea water in the southwest Indian ridge.

Three Gram-staining-negative, aerobic and rod-shaped strains, designated as T40-1T, T40-3T and JL-62T, were isolated from the deep-sea water in the southwest Indian ridge. For strain T40-1T, growth occurred at 15-37 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0.5-5.0 % NaCl (w/v; optimum, 2.0 %). Strain T40-3T could grow at 15-40 °C (optimum, 28 °C), with 0.5-11.0 % NaCl (optimum, 2.0 %, w/v) at pH 6.0-9.5 (optimum, 8.0). The temperature, pH and salinity ranges for growth of strain JL-62T were 15-40 °C (optimum, 30 °C), pH 5.5-9.0 (optimum, pH 7.5-8.0) and 0.5-9.0 % NaCl (w/v; optimum, 4.0 %). Ubiquinone-10 was the sole ubiquinone in all strains, the major fatty acids (>20 %) were summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c). The major polar lipids of strains T40-1T and T40-3T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain JL-62T contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sulfoquinovosyldiacylglycerol as major polar lipids. Phylogenetic trees based on 16S rRNA gene and core-genomic sequences revealed affiliation of strains T40-1Tand T40-3T to the family Roseobacteraceae and formed two independent clades from other Roseobacteraceae genera, and those two strains had average nucleotide identities of 62.0-72.0 % to their phylogenetically related species which fell into to the genus boundary range, indicating that they represent two novel genera. While strain JL-62T represents a novel species in the genus Oricola belonging to the family Phyllobacteriaceae, which was supported by overall genomic relatedness index calculations. The DNA G+C contents of strains T40-1T, T40-3T and JL-62T were 66.5, 60.1 and 62.1 mol %, respectively. Based on the polyphasic taxonomic data, strains T40-1T (=MCCC M24557T=KCTC 82975T) and T40-3T (=MCCC 1K05135T=KCTC 82976T) are classified as representing two novel genera belonging to the family Roseobacteraceae with the names Mesobacterium pallidum gen. nov., sp. nov. and Heliomarina baculiformis gen. nov., sp. nov. are proposed, and strain JL-62T (=MCCC M24579T=KCTC 82974T) is proposed to represent a novel species within the genus Oricola with the name Oricola indica sp. nov. is proposed.

Emergence of Incl2 plasmid-mediated colistin resistance in avian Escherichia fergusonii.

Escherichia fergusonii, an opportunistic zoonotic pathogen, has a greatly increased importance in public health with the discovery of cephalosporin- and colistin-resistant strains. The IncHI2 plasmid carrying mcr-1 has been reported in E. fergusonii, but the other types of plasmids carrying mcr-1 have never been reported. In this study, 268 samples of cecal contents or anal swabs were collected from slaughterhouses and farms in two cities in Zhejiang, China, where 54 E. fergusonii strains (18.88%) were isolated between 2020 and 2021. To our knowledge, this is the first report of the isolation of E. fergusonii in meat ducks (slaughterhouse). The minimum inhibitory concentration (MIC) of isolates was determined by the broth microdilution method, in which it was determined that the tetracycline resistance rate was the highest (83.33%) and the multidrug-resistance (MDR) rate was 75.93%. A total of four strains of colistin-resistant E. fergusonii were found and identified as mcr-1-positive by PCR. Importantly, these strains could transfer the mcr-1 gene to strain E. coli J53 by conjugation. Genome sequencing revealed that the mcr-1 genes of the above four strains were all located on the Incl2 plasmid, and the mobile element ISApl1 upstream of mcr-1 was missing. Moreover, the plasmid pEF45-4 (61 140 bp) harboring mcr-1 in strain EF20JDJ4045 was revealed by Oxford Nanopore Technology, showing high homology with the previously reported in E. coli. Taken together, the high antimicrobial resistance (AMR) rate of E. fergusonii may herald a novel reservoir of AMR genes and IncI2 plasmid may be an important factor affecting mcr-1 transfer in poultry.

Endosomal Sequestration of TLR4 Antibody Induces Myeloid-Derived Suppressor Cells and Reverses Acute Type 1 Diabetes.

We previously showed that treating NOD mice with an agonistic monoclonal anti-TLR4/MD2 antibody (TLR4-Ab) reversed acute type 1 diabetes (T1D). Here, we show that TLR4-Ab reverses T1D by induction of myeloid-derived suppressor cells (MDSCs). Unbiased gene expression analysis after TLR4-Ab treatment demonstrated upregulation of genes associated with CD11b+Ly6G+ myeloid cells and downregulation of T-cell genes. Further RNA sequencing of purified, TLR4-Ab-treated CD11b+ cells showed significant upregulation of genes associated with bone marrow-derived CD11b+ cells and innate immune system genes. TLR4-Ab significantly increased percentages and numbers of CD11b+ cells. TLR4-Ab-induced CD11b+ cells, derived ex vivo from TLR4-Ab-treated mice, suppress T cells, and TLR4-Ab-conditioned bone marrow cells suppress acute T1D when transferred into acutely diabetic mice. Thus, the TLR4-Ab-induced CD11b+ cells, by the currently accepted definition, are MDSCs able to reverse T1D. To understand the TLR4-Ab mechanism, we compared TLR4-Ab with TLR4 agonist lipopolysaccharide (LPS), which cannot reverse T1D. TLR4-Ab remains sequestered at least 48 times longer than LPS within early endosomes, alters TLR4 signaling, and downregulates inflammatory genes and proteins, including nuclear factor-κB. TLR4-Ab in the endosome, therefore, induces a sustained, attenuated inflammatory response, providing an ideal "second signal" for the activation/maturation of MDSCs that can reverse acute T1D.

Luteirhabdus pelagi gen. nov., sp. nov., a novel member of the family Flavobacteriaceae, isolated from the West Pacific Ocean.

A Gram-stain-negative, aerobic, and yellow-pigmented bacterium, designated A3-108T, was isolated from seawater of the West Pacific Ocean. Cells were non-motile and rod-shaped, with carotenoid-type pigments. Strain A3-108T grew at pH 6.0-8.5 (optimum 6.5) and 15-40 °C (optimum 28 °C), in the presence of 0.5-10% (w/v) NaCl (optimum 1.0%). It possessed the ability to produce H2S. Based on the 16S rRNA gene analysis, strain A3-108T exhibited highest similarity with Aureisphaera salina A6D-50T (90.6%). Phylogenetic analysis shown that strain A3-108T affiliated with members of the family Flavobacteriaceae and represented an independent lineage. The principal fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:1 G, and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The sole isoprenoid quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid and one unidentified lipid. The ANIb, in silico DDH and AAI values among the genomes of strain A3-108T and three reference strains were 67.3-71.1%, 18.7-22.1%, and 58.8-71.4%, respectively. The G + C content was 41.0%. Distinctness of the phylogenetic position as well as differentiating chemotaxonomic and other phenotypic traits revealed that strain A3-108T represented a novel genus and species of the family Flavobacteriaceae, for which the name Luteirhabdus pelagi gen. nov., sp. nov. is proposed (type strain, A3-108T = CGMCC 1.18821T = KCTC 82563T).

Enhancing Antigen Presentation and Inducing Antigen-Specific Immune Tolerance with Amphiphilic Peptides.

Ag-specific immunotherapy to restore immune tolerance to self-antigens, without global immune suppression, is a long-standing goal in the treatment of autoimmune disorders such as type 1 diabetes (T1D). However, vaccination with autoantigens such as insulin or glutamic acid decarboxylase have largely failed in human T1D trials. Induction and maintenance of peripheral tolerance by vaccination requires efficient autoantigen presentation by APCs. In this study, we show that a lipophilic modification at the N-terminal end of CD4+ epitopes (lipo-peptides) dramatically improves peptide Ag presentation. We designed amphiphilic lipo-peptides to efficiently target APCs in the lymph nodes by binding and trafficking with endogenous albumin. Additionally, we show that lipophilic modification anchors the peptide into the membranes of APCs, enabling a bivalent cell-surface Ag presentation. The s.c. injected lipo-peptide accumulates in the APCs in the lymph node, enhances the potency and duration of peptide Ag presentation by APCs, and induces Ag-specific immune tolerance that controls both T cell- and B cell-mediated immunity. Immunization with an amphiphilic insulin B chain 9-23 peptide, an immunodominant CD4+ T cell epitope in NOD mice, significantly suppresses the activation of T cells, increases inhibitory cytokine production, induces regulatory T cells, and delays the onset and lowers the incidence of T1D. Importantly, treatment with a lipophilic ß-cell peptide mixture delays progression to end-stage diabetes in acutely diabetic NOD mice, whereas the same doses of standard soluble peptides were not effective. Amphiphilic modification effectively enhances Ag presentation for peptide-based immune regulation of autoimmune diseases.