Tight Cluster Research Articles

Optimizing IOL Calculators with Deep Learning Prediction of Total Corneal Astigmatism.

Background/Objectives: This study aims to identify the most accurate regression model for predicting total corneal astigmatism (TCA) from anterior corneal astigmatism (ACA) and to fine-tune the best model's architecture to further optimize predictive accuracy. Methods: A retrospective review of 19,468 eyes screened for refractive surgery was conducted using electronic medical records. Corneal topography data were acquired using the Pentacam HR. Various types (7) and subtypes (21) of regression learners were tested, with a deep neural network (DNN) emerging as the most suitable. The DNN was further refined, experimenting with 23 different architectures. Model performance was evaluated using root mean squared error (RMSE), R2, average residual error, and circular error. The final model only used age, ACA magnitude, and ACA axis to predict TCA magnitude and axis. Results were compared to predictions from one of the leading TCA prediction formulas. Results: Our model achieved higher performance for TCA magnitude prediction (R2 = 0.9740, RMSE = 0.0963 D, and average residual error = 0.0733 D) compared to the leading formula (R2 = 0.8590, RMSE = 0.2257 D, and average residual error = 0.1928 D). Axis prediction error also improved by an average of 8.1° (average axis prediction error = 4.74° versus 12.8°). The deep learning approach consistently demonstrated smaller errors and tighter clustering around actual values compared to the traditional formula. Conclusion: Deep learning techniques significantly outperformed traditional methods for TCA prediction accuracy using the Pentacam HR. This approach may lead to more precise TCA calculations and better IOL selection, potentially enhancing surgical outcomes.

A comparison of super-resolution microscopy techniques for imaging tightly packed microcolonies of an obligate intracellular bacterium.

Conventional optical microscopy imaging of obligate intracellular bacteria is hampered by the small size of bacterial cells, tight clustering exhibited by some bacterial species and challenges relating to labelling such as background from host cells, a lack of validated reagents, and a lack of tools for genetic manipulation. In this study we imaged intracellular bacteria from the species Orientia tsutsugamushi (Ot) using five different fluorescence microscopy techniques: standard confocal, Airyscan confocal, instant Structured Illumination Microscopy (iSIM), three-dimensional Structured Illumination Microscopy (3D-SIM) and Stimulated Emission Depletion Microscopy (STED). We compared the ability of each to resolve bacterial cells in intracellular clumps in the lateral (xy) axis, using full width half maximum (FWHM) measurements of a labelled outer membrane protein (ScaA) and the ability to detect small, outer membrane vesicles external to the cells. We next compared the ability of each technique to sufficiently resolve bacteria in the axial (z) direction and found 3D-STED to be the most successful method for this. We then combined this approach with a custom 3D cell segmentation and analysis pipeline using the open-source, deep learning software, Cellpose to segment the cells and subsequently the commercial software Imaris to analyze their 3D shape and size. Using this combination, we demonstrated differences in bacterial shape, but not their size, when grown in different mammalian cell lines. Overall, we compare the advantages and disadvantages of different super-resolution microscopy techniques for imaging this cytoplasmic obligate intracellular bacterium based on the specific research question being addressed.

Hidden rivals: the negative impacts of dolphinfish on seabird foraging behaviour.

Marine predators often aggregate at the air-sea boundary layer to pursue shared prey. In such scenarios, seabirds are likely to benefit from underwater predators herding fish schools into tight clusters thereby enhancing seabirds' prey detectability and capture potential. However, this coexistence can lead to competition, affecting not only immediate foraging strategies but also their distribution and interspecies dynamics. We investigated both the longitudinal relationships and instantaneous interactions between streaked shearwaters (Calonectris leucomelas) and common dolphinfish (Coryphaena hippurus), both preying on Japanese anchovy (Engraulis japonicus). Using GPS data from 2011 to 2021, we calculated behavioural parameters for streaked shearwaters as an index of time spent and distance travelled. Despite the abundance of Japanese anchovies, we found that streaked shearwaters might increase their foraging time in the presence of underwater predators. Moreover, video loggers provided direct evidence of streaked shearwaters and common dolphinfish attacking the same fish schools, potentially interfering with bird foraging by dolphinfish. Our results suggest that the presence of underwater predators in a given patch might increase the time spent by seabirds foraging without affecting the distance travelled. This highlights the need for future studies that consider the potential adverse effects of other top predators on seabird prey availability.

Genome-based reclassification of Sphingopyxis lutea Chhetri et al. 2023 as a later heterotypic synonym of Sphingopyxis jiangsuensis Gao et al. 2023.

Sphingopyxis lutea DHUNG17T was compared with Sphingopyxis jiangsuensis XHP0097T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of S. lutea DHUNG17T shared high similarity (99.9 %) to that of S. jiangsuensis XHP0097T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Sphingopyxis. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values between S. lutea DHUNG17T and S. jiangsuensis XHP0097T were below 99.0, 99.1 and 92.2±1.7 %, respectively, all of which were greater than the species delineation threshold for AAI (95.5 %), ANI (95-96 %) and dDDH (70 %), strongly indicating that the two strains represented a single species. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we propose Sphingopyxis lutea as a later heterotypic synonym of Sphingopyxis jiangsuensis.

Flow augmentation therapies preserve brain network integrity and hemodynamics in a canine permanent occlusion model

The acute phase of ischemic stroke presents a critical window for therapeutic intervention, where novel approaches such as hyper-acute cerebral flow augmentation offer promising avenues for neuroprotection. In this study, we investigated the effects of two such therapies, NEH (a combination of norepinephrine and hydralazine) and Sanguinate (pegylated bovine carboxyhemoglobin), on resting-state functional connectivity, global mean signal (GMS), and blood oxygen level-dependent (BOLD) time lag in a pre-clinical canine model of stroke via permanent occlusion of the middle cerebral artery (total of n = 40 IACUC-approved mongrel canines randomly split into control/natural history and two treatment groups). Utilizing group independent component analysis (ICA), we identified and examined the integrity of sensorimotor and visual networks both pre- and post-occlusion, across treatment and control groups. Our results demonstrated that while the control group exhibited significant disruptions in these networks following stroke, the treatment groups showed remarkable preservation of network integrity. Voxel-wise functional connectivity analysis revealed less pronounced alterations in the treatment groups, suggesting maintained neural connections. Notably, the treatments stabilized GMS, with only minimal reductions observed post-occlusion compared to significant decreases in the control group. Furthermore, BOLD time-lag unity plots indicated that NEH and Sanguinate maintained consistent hemodynamic response timing, as evidenced by tighter clustering around the line of unity, suggesting a potential neuroprotective effect. These findings were underscored by robust statistical analyses, including paired T-tests and Mann–Whitney U tests, which confirmed the significance of the connectivity changes observed. The correlation of BOLD time-lag variations with neuroimaging functional biomarkers highlighted the impact of stroke and the efficacy of early therapeutic interventions. Our study supports the further study of flow augmentation therapies such as NEH and Sanguinate in stroke treatment protocols and suggests flow augmentation therapies should be further explored in an effort to improve patient outcomes.

Distribution of the sand wasp Bicyrtes variegatus (Oliver, 1789) (Hymenoptera, Crabronidae) in the Galápagos Islands, with notes on its ecology

Very little is known about the sand wasp, Bicyrtes variegatus, in the Galápagos archipelago. In this study, we compiled information from surveys, museum collections and the literature to better understand its distribution and ecology. We found records of B. variegatus on seven islands with the earliest known record from 1964, from San Cristóbal Island. Wasps have been collected in the littoral, arid, transition and humid vegetation zones and have been reported visiting endemic, native, cryptogenic, and introduced plants. Sun dances and a tight cluster of wasps, similar in form to what others have called “mating balls”, were observed in the hot season.

XGBoost performance in predicting corrosion inhibition efficiency of Benzimidazole Compounds

In this study, we compare the performance of the XGBoost model with a Support Vector Machine (SVM) model from the literature in predicting a given task. Performance metrics such as the coefficient of determination (R2), root mean squared error (RMSE), and mean absolute error (MAE) were utilized to evaluate and compare the models. The XGBoost model achieved an R² of 0.99, an RMSE of 2.54, and an MAE of 1.96, significantly outperforming the SVM model, which recorded an R² of 0.96 and an RMSE of 6.79. The scatter plot for the XGBoost model further illustrated its superior performance, showing a tight clustering of points around the ideal line (y = x), indicating high accuracy and low prediction errors. These findings suggest that the XGBoost model is highly effective for the given prediction task, likely due to its ability to capture complex patterns and interactions within the data.

Comparison of the diversity of anaerobic-cultured gut bacterial communities on different culture media using 16S rDNA sequencing

The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.

Microbacterium algihabitans sp. nov., Microbacterium phycohabitans sp. nov., and Microbacterium galbum sp. nov., isolated from dried beach seaweeds.

Three actinobacterial strains, KSW2-21T, KSW2-29T and KSW4-17T, were isolated from dried seaweeds collected around Gwakji Beach in Jeju, Republic of Korea. Their taxonomic positions were determined based on genomic, physiological and morphological characteristics. The isolates were Gram-positive, aerobic, non-motile, rod-shaped bacteria characterized by the following chemotaxonomic features: ornithine as the cell wall diamino acid, the N-glycolyl type of murein, MK-11 as the predominant menaquinone, polar lipids including diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and four unidentified phospholipids, with anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the the major fatty acids. The 16S rRNA gene phylogeny showed that the novel strains formed three distinct sublines within the genus Microbacterium. Strain KSW4-17T formed a tight cluster with the type strain of Microbacterium hydrothermale, while strains KSW2-21T and KSW2-29T occupied distinct positions between the type strains of M. hydrothermale and Microbacterium testaceum. Strains KSW4-17T and KSW2-29T showed 99.9 % rRNA gene sequence similarity to M. hydrothermale CGMCC 1.12512T, while strain KSW2-21T revealed 99.4 % 16S rRNA gene sequence similarity to the type strains of M. hydrothermale and M. testaceum. The genome sizes and genomic G+C contents of the three isolates ranged from 3.44 to 3.74 Mbp and from 70.3 to 70.8 mol%, respectively. The phylogenomic tree based on 92 core gene sequences exhibited similar topologies to the 16S rRNA gene phylogeny. The comparison of overall genomic relatedness indices, such as average nucleotide indentity and digital DNA-DNA hybridization, supported that the isolates represent three new species of the genus Microbacterium. Based on the results obtained here, Microbacterium algihabitans sp. nov. (type strain, KSW2-21T=KACC 23322T=DSM 116381T), Microbacterium phycohabitans sp. nov. (type strain KSW2-29T=KACC 22350T=NBRC 115221T) and Microbacterium galbum sp. nov. (type strain, KSW4-17T=KACC 23323T=DSM 116383T) are proposed.

Size–shape–stable isotope (C and O) relationships of cryogenic cave carbonates formed in permafrost settings

Cryogenic cave carbonates (CCCs) genetically related to permafrost are of special interest in paleoclimate research. Their 230Th/U ages provide unique information about the former presence and depth of permafrost in presently permafrost-free areas. Details of CCC formation processes and their diagnostic features, however, remain incompletely understood. In this paper, we report the results of a study of CCCs from two northern Eurasian caves, currently located in permafrost-free rocks. CCCs in the caves occur in a wide range of grain sizes (micrometers to several centimeters). Stable isotope values of different CCC morphotypes (size range of 0.1 to 4 mm) plot within relatively tight clusters in δ18O-δ13C space, regardless of their grain size, indicating that CCCs of the same morphotype, but of different size, formed simultaneously at certain freezing stages. The clusters conform to an overall negative “freezing trend” in δ18O-δ13C space. The position on the trend indicates the relative age of individual morphotypes; scatter of the data in δ18O-δ13C space suggests multiple episodes of freezing (permafrost formation). The systematic characterization of CCC morphologies and the study of fine-size fractions of CCCs provide important insights into the processes involved in CCC formation in caves located in permafrost.

The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

Sepsis remains a major cause of mortality and morbidity in infants. In recent years, several gene marker strategies for the early identification of sepsis have been proposed but only a few have been independently validated for adult cohorts and applicability to infant sepsis remains unclear. Biomarkers to assess disease severity and risks of shock also represent an important unmet need. To elucidate characteristics driving sepsis in infants, we assembled a multi-transcriptomic dataset from public microarray datasets originating from five independent studies pertaining to bacterial sepsis in infant < 6-months of age (total n=335). We utilized a COmbat co-normalization strategy to enable comparative evaluation across multiple studies while preserving the relationship between cases and controls. We found good concordance with only two out of seven of the published adult sepsis gene signatures (accuracy > 80%), highlighting the narrow utility of adult-derived signatures for infant diagnosis. Pseudotime analysis of individual subjects' gene expression profiles showed a continuum of molecular changes forming tight clusters concurrent with disease progression between healthy controls and septic shock cases. In depth gene expression analyses between bacteremia, septic shock, and healthy controls characterized lymphocyte activity, hemostatic processes, and heightened innate immunity during the molecular transition toward a state of shock. Our analysis revealed the presence of multiple significant transcriptomic perturbations that occur during the progression to septic shock in infants that are characterized by late-stage induction of clotting factors, in parallel with a heightened innate immune response and a suppression of adaptive cell functionality.

Large hospital outbreak caused by OXA-244-producing Escherichia coli sequence type 38, Poland, 2023.

In February 2023, Escherichia coli sequence type (ST) 38 producing oxacillinase 244 (OXA-244-Ec ST38) was detected from three patients in a hospital in western Poland. Overall, OXA-244-Ec ST38 was detected from 38 colonised patients in 13 wards between February and June 2023. The outbreak was investigated on site by an infection control team, and the bacterial isolates were characterised microbiologically and by whole genome sequencing. We could not identify the primary source of the outbreak or reconstruct the transmission sequence. In some of the 13 affected wards or their groups linked by the patients' movement, local outbreaks occurred. The tested outbreak isolates were resistant to β-lactams (penicillins, cephalosporins, aztreonam and ertapenem) and to trimethoprim-sulfamethoxazole. Consistently, apart from bla OXA-244, all isolates contained also the bla CMY-2 and bla CTX-M-14 genes, coding for an AmpC-like cephalosporinase and extended-spectrum β-lactamase, respectively, and genes conferring resistance to trimethoprim-sulfamethoxazole, sul2 and dfrA1. Genomes of the isolates formed a tight cluster, not of the major recent European Cluster A but of the older Cluster B, with related isolates identified in Germany. This outbreak clearly demonstrates that OXA-244-Ec ST38 has a potential to cause hospital outbreaks which are difficult to detect, investigate and control.

Reclassification of Aestuariicella albida as Pseudomaricurvus albidus comb. nov. and Aestuariicella hydrocarbonica as Pseudomaricurvus hydrocarbonicus comb. nov. Based on Comparative Genomics and Molecular Synapomorphies.

The genus Aestuariicella has been recently reclassified as a member of the family Cellvibrionaceae. However, the taxonomic position of the genus as a distinct member of the family has not been clarified. In the present study, we performed multilayered analyses anchored on genome sequences to clarify the relationship between the genera Aestuariicella and Pseudomaricurvus within the family Cellvibrionaceae. Phylogenetic analyses based on 16S rRNA gene, RNA polymerase beta subunit (RpoB) protein, and core gene sequences showed a well-supported tight cluster formed by the members of the two genera. Moreover, the analysis of the average amino acid identity (AAI) revealed that the members of the two genera shared 68.16-79.48% AAI, values which were within the range of observed AAI (≥ 67.23%) among the members of the same genus within the family Cellvibrionaceae. Members of the two genera also shared several common characteristics. Furthermore, molecular synapomorphies in a form of conserved signature indels were identified in six protein sequences that were exclusively shared by the members of the two genera. Based on the phylogenetic and molecular evidence presented here, we propose the reclassification of the species Aestuariicella albida and Aestuariicella hydrocarbonica as Pseudomaricurvus albidus comb. nov. and Pseudomaricurvus hydrocarbonicus comb. nov., respectively.

A case report and literature review of IgA nephropathy presenting as nephrotic syndrome in polycythemia vera.

A 66-year-old non-smoker presented with a 2-week history of new-onset pedal oedema and gross haematuria. On evaluation, he was found to be hypertensive and oedematous with a haemoglobin of 19.1g/dl, platelet count of 546,000/mm3, and creatinine of 2.6mg/dl. Urine examination revealed abundant RBCs with 3+ albumin on three separate occasions. His 24-h urine protein level was 3830mg/day, with a serum cholesterol level of 303mg/dl. Secondary erythrocytosis and thrombocytosis tests were negative. Bone marrow examination revealed hypercellularity, erythroid hyperplasia, tight clusters of large megakaryocytes, and megakaryocytic hyperplasia suggestive of polycythemia vera. PCR analysis revealed a JAK2V617 F (exon 14) mutation. In view of nephrotic syndrome, azotemia, and microscopic haematuria, a renal biopsy was performed, which revealed features of IgA nephropathy with advanced interstitial fibrosis and tubular atrophy. He was started on angiotensin receptor blockers with hydroxy urea as a part of treatment. This case report highlights the association of glomerular disease with polycythaemia vera and the need of prompt renal biopsy for diagnosis and management.

A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco.

In Morocco, cutaneous leishmaniasis (CL) caused by Leishmania (L.) tropica is an important health problem. Despite the high incidence of CL in the country, the genomic heterogeneity of these parasites is still incompletely understood. In this study, we sequenced the genomes of 14 Moroccan isolates of L. tropica collected from confirmed cases of CL to investigate their genomic heterogeneity. Comparative genomics analyses were conducted by applying the recently established Genome Instability Pipeline (GIP), which allowed us to conduct phylogenomic and principal components analyses (PCA), and to assess genomic variations at the levels of the karyotype, gene copy number, single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs) variants. Read-depth analyses revealed a mostly disomic karyotype, with the exception of the stable tetrasomy of chromosome 31. In contrast, we identified important gene copy number variations across all isolates, which affect known virulence genes and thus were probably selected in the field. SNP-based cluster analysis of the 14 isolates revealed a core group of 12 strains that formed a tight cluster and shared 45.1 % (87 751) of SNPs, as well as two strains (M3015, Ltr_16) that clustered separately from each other and the core group, suggesting the circulation of genetically highly diverse strains in Morocco. Phylogenetic analysis, which compared our 14 L. tropica isolates against 40 published genomes of L. tropica from a diverse array of locations, confirmed the genetic difference of our Moroccan isolates from all other isolates examined. In conclusion, our results indicate potential regional variations in SNP profiles that may differentiate Moroccan L. tropica from other L. tropica strains circulating in endemic countries in the Middle East. Our report paves the way for future research with a larger number of strains that will allow correlation of diverse phenotypes (resistance to treatments, virulence) and origins (geography, host species, year of isolation) to defined genomic signals such as gene copy number variations or SNP profiles that may represent interesting biomarker candidates.

FaissMolLib: An efficient and easy deployable tool for ligand-based virtual screening

Virtual screening-based molecular similarity and fingerprint are crucial in drug design, target prediction, and ADMET prediction, aiding in identifying potential hits and optimizing lead compounds. However, challenges such as lack of comprehensive open-source molecular fingerprint databases and efficient search methods for virtual screening are prevalent. To address these issues, we introduce FaissMolLib, an open-source virtual screening tool that integrates 2.8 million compounds from ChEMBL and ZINC databases. Notably, FaissMolLib employs the highly efficient Faiss search algorithm, outperforming the Tanimoto algorithm in identifying similar molecules with its tighter clustering in scatter plots and lower mean, standard deviation, and variance in key molecular properties. This feature enables FaissMolLib to screen 2.8 million compounds in just 0.05 seconds, offering researchers an efficient, easily deployable solution for virtual screening on laptops and building unique compound databases. This significant advancement holds great potential for accelerating drug discovery efforts and enhancing chemical data analysis. FaissMolLib is freely available at http://liuhaihan.gnway.cc:80. The code and dataset of FaissMolLib are freely available at https://github.com/Superhaihan/FiassMolLib.

Loose–tight cluster regularization for unsupervised person re-identification

Loose–tight cluster regularization for unsupervised person re-identification

Microbacterium abyssi sp. nov. and Microbacterium limosum sp. nov., two new species of the genus Microbacterium, isolated from deep-sea sediment samples.

Two Gram-positive, non-motile, short rod-shaped actinomycete strains, designated as A18JL241T and Y20T, were isolated from deep-sea sediment samples collected from the Southwest Indian Ocean and Western Pacific Ocean, respectively. Both of the isolates were able to grow within the temperature range of 5-40 °C, NaCl concentration range of 0-7 % (w/v) and at pH 6.0-12.0. The two most abundant cellular fatty acids of both strains were anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipid contents of the two strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified glycolipid. These two strains shared common chemotaxonomic features comprising MK-10 and MK-12 as the respiratory quinones. The genomic DNA G+C contents of the two strains were 68.1 and 70.4 mol%, respectively. The 16S rRNA gene phylogeny showed that the novel strains formed two distinct sublines within the genus Microbacterium. Strain A18JL241T was most closely related to the type strain of Microbacterium tenebrionis KCTC 49593T (98.8 % sequence similarity), whereas strain Y20T formed a tight cluster with the type strain of Microbacterium schleiferi NBRC 15075T (99.0 %). The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the type strains of related Microbacterium species were in the range of 74.1-89.1 % and 19.4-36.9 %, respectively, which were below the recognized thresholds of 95-96 % ANI and 70 % dDDH for species definition. Based on the results obtained here, it can be concluded that strains A18JL241T and Y20T represent two novel species of the genus Microbacterium, for which the names Microbacterium abyssi sp. nov. (type strain A18JL241T=JCM 33956T=MCCC 1A16622T) and Microbacterium limosum sp. nov. (type strain Y20T=JCM 33960T=MCCC 1A16747T) are proposed.

Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat.

The current species of Halosegnis and Salella within the class Halobacteria are closely related based on phylogenetic, phylogenomic, and comparative genomic analyses. The Halosegnis species showed 99.8-100.0% 16S rRNA and 96.6-99.6% rpoB' gene similarities to the Salella species, respectively. Phylogenetic and phylogenomic analyses showed that Salella cibi CBA1133T, the sole species of Salella, formed a single tight cluster with Halosegnis longus F12-1T, then with Halosegnis rubeus F17-44T. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between Salella cibi CBA1133T and Halosegnis longus F12-1T were 99.2, 94.2, and 98.6%, respectively, much higher than the thresholds for species demarcation. This genome-based classification revealed that the genus Salella should be merged with Halosegnis, and Salella cibi should be a later heterotypic synonym of Halosegnis longus. Halophilic archaeal strains DT72T, DT80T, DT85T, and DT116T, isolated from the saline soil of a tidal flat in China, were subjected to polyphasic taxonomic characterization. The phenotypic, chemotaxonomic, phylogenetic, and phylogenomic features indicated that strains DT72T (= CGMCC 1.18925T = JCM 35418T), DT80T (= CGMCC 1.18926T = JCM 35419T), DT85T (= CGMCC 1.19049T = JCM 35605T), and DT116T (= CGMCC 1.19045T = JCM 35606T) represent four novel species of the genera Halorussus, Halosegnis and Haloglomus, respectively, for which the names, Halorussus caseinilyticus sp. nov., Halorussus lipolyticus sp. nov., Halosegnis marinus sp. nov., and Haloglomus litoreum sp. nov., are proposed.

Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus

Gut microbiota, or the collection of diverse microorganisms in a specific ecological niche, are known to significantly impact human health. Decreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome studies focus on ethnic majorities. This study aims to understand how the microbiome differs between an ethnic majority (the Dutch) and minority (the South-Asian Surinamese (SAS)) group with a lower and higher prevalence of T2DM, respectively. Microbiome data from the Healthy Life in an Urban Setting (HELIUS) cohort were used. Two age- and gender-matched groups were compared: the Dutch (n = 41) and SAS (n = 43). Microbial community compositions were generated via DADA2. Metrics of microbial diversity and similarity between groups were computed. Biomarker analyses were performed to determine discriminating taxa. Bacterial co-occurrence networks were constructed to examine ecological patterns. A tight microbiota cluster was observed in the Dutch women, which overlapped with some of the SAS microbiota. The Dutch gut contained a more interconnected microbial ecology, whereas the SAS network was dispersed, i.e., contained fewer inter-taxonomic correlational relationships. Bacteroides caccae, Butyricicoccus, Alistipes putredinis, Coprococcus comes, Odoribacter splanchnicus, and Lachnospira were enriched in the Dutch gut. Haemophilus, Bifidobacterium, and Anaerostipes hadrus discriminated the SAS gut. All but Lachnospira and certain strains of Haemophilus are known to produce SCFAs. The Dutch gut microbiome was distinguished from the SAS by diverse, differentially abundant SCFA-producing taxa with significant cooperation. The dynamic ecology observed in the Dutch was not detected in the SAS. Among several potential gut microbial biomarkers, Haemophilus parainfluenzae likely best characterizes the ethnic minority group, which is more predisposed to T2DM. The higher prevalence of T2DM in the SAS may be associated with the gut dysbiosis observed.