Bacterial Species Research Articles

The Role of the Intestinal Flora and Its Derivatives in Neurocognitive Disorders: A Narrative Review from Surgical Perspective.

Perioperative neurocognitive dysfunction is a significant concern for population health, impacting postoperative recovery and increasing the financial burden on patients. With an increasing number of surgical procedures being performed, the prevention and management of perioperative neurocognitive dysfunction have garnered significant attention. While factors such as age, lifestyle, genetics, and education are known to influence the development of cognitive dysfunction, recent research has highlighted the role of the gut microbiota in neurological health. An increased abundance of pro-inflammatory gut microbiota can trigger and worsen neuroinflammation, neuronal cell damage, and impaired cellular autophagy. Moreover, the inflammation-promoting gut microbiota can disrupt immune function, impair neuroautophagy, and affect the production and circulation of extracellular vesicles and neurotransmitters. These factors collectively play a role in the onset and advancement of cognitive impairment. This narrative review delves into the molecular mechanisms through which gut microbiota and their derivatives contribute to cognitive impairment, focusing on the impact of anesthesia surgery, changes in gut microbial populations, and perioperative cognitive impairment associations. The study suggests that alterations in the abundance of various bacterial species and their metabolites pre- and post-surgery may be linked to postoperative cognitive impairment. Furthermore, the potential of probiotics or prebiotics in addressing cognitive impairment is discussed, offering a promising avenue for investigating the treatment of perioperative neurocognitive disorders.

Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment.

Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.

Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.

T-box riboswitches are widespread bacterial regulatory noncoding RNAs that directly interact with tRNAs and switch conformations to regulate the transcription or translation of genes related to amino acid metabolism. Recent studies in Bacilli have revealed the core mechanisms of T-boxes that enable multivalent, specific recognition of both the identity and aminoacylation status of the tRNA substrates. However, in-depth knowledge of a vast number of T-boxes in other bacterial species remains scarce, although a remarkable structural diversity particularly among pathogens, is apparent. In the present study, analysis of T-boxes that control the transcription of glycyl-tRNA synthetases from four prominent human pathogens revealed significant structural idiosyncrasies. Nonetheless, these diverse T-boxes maintain functional T-box:tRNAGly interactions both in vitro and in vivo. Probing analysis not only validated recent structural observations but also expanded our knowledge on the substantial diversities among T-boxes and suggest interesting distinctions from the canonical Bacilli T-boxes. Surprisingly, some glycyl T-boxes seem to redirect the T-box trajectory in the absence of recognizable K-turns or contain Stem II modules that are generally absent in glycyl T-boxes. These results consolidate the notion of lineage-specific diversification and elaboration of the T-box mechanism and corroborate the potential of T-boxes as promising species-specific RNA targets for next-generation antibacterial compounds.

Thiosemicarbazones and derived tin complexes: Synthesis, structural analysis and in vitro evaluation against bacterial and cancer cells

Two complexes of Sn (IV), Sn (IV)‐TSC 1 and Sn (IV)‐TSC 2, with the ligands 4‐(2,4‐dimethylphenyl)‐1‐([pyridin‐2‐yl]methylene)thiosemicarbazide (TSC 1) and 4‐(2,5‐dimethoxyphenyl)‐1‐([pyridin‐2‐yl]methylene)thiosemicarbazide (TSC 2) were synthesized. X‐ray crystallographic investigation of Sn (IV)‐TSC 2 afforded valuable information on its octahedral geometry, monoclinic lattice and C 1 2/c 1 space group. The ligands are monoanionic tridentate via a deprotonated thiol sulfur atom and two nitrogen atoms of pyridine and azomethine moieties. These atoms coordinate tin alongside three independent chlorine atoms making the tin atoms in the complexes tetravalent, despite of incorporating tin (II) chloride in the reactions. Solutions of the ligands TSC 1 and TSC 2 (20 mg/ml in dimethyl sulfoxide) induced growth inhibitions only to Staphylococcus aureus (14 and 10 mm) and Escherichia coli (15 and 10 mm) bacteria. But the complexes displayed activities against four bacterial species, that is, S. aureus, E. coli, Bacillus subtilis and Pseudomonas aeruginosa (complex Sn (IV)‐TSC 1, complex Sn (IV)‐TSC 2 and ampicillin showed inhibition diameters with 12–14, 13–14 and 21–26 mm). All TSC ligands and coordination compounds induced cytotoxicity in MCF‐7 cancer and BHK normal cells. The compounds TSC 1, TSC 2, Sn (IV)‐TSC 1, Sn (IV)‐TSC 2 and doxorubicin inhibited the MCF‐7 (BHK) cells with IC50 values of 68.9 (126.6), 145.4 (110.6), 22.6 (16.7), 34.2 (16.1) and 9.66 (36.42) μM, respectively.

Neoadjuvant Immunotherapy and Intestinal Microbiota: Unraveling their roles in Anastomotic Leakage and Fistula after Colorectal Cancer Surgery

This comprehensive review explores the multifaceted relationship between neoadjuvant immunotherapy, intestinal microbiota alterations, and anastomotic leakage risk in patients undergoing colectomy for colon neoplasia. With the advent of immunotherapy, remarkably immune checkpoint inhibitors, there has been a significant shift in the treatment paradigms for various cancers, including colon neoplasia. These treatments, while effective, have been associated with changes in the intestinal microbiome, which, in turn, may influence wound healing and the integrity of anastomotic sites. The review delves into the complex interactions between the immune system and the gut microbiota, examining how immunotherapy-induced dysbiosis could disrupt the delicate balance necessary for optimal anastomotic healing. It discusses the role of specific bacterial species in modulating the immune response to cancer and their impact on the efficacy of immunotherapeutic agents. Moreover, the review highlights the potential mechanisms through which the microbiota-immune system interaction could affect surgical outcomes, focusing on the development of anastomotic leaks. The implications of these findings for clinical practice are discussed, including the need for targeted strategies to modulate the gut microbiota in patients undergoing immunotherapy and colectomy. Through this discussion, the review aims to provide insights into improving patient outcomes by integrating microbiome management into colon neoplasia patients' treatment and perioperative care.

Mycobacteriophage Alexphander Gene 94 Encodes an Essential dsDNA-Binding Protein during Lytic Infection

Mycobacteriophages are viruses that specifically infect bacterial species within the genera Mycobacterium and Mycolicibacterium. Over 2400 mycobacteriophages have been isolated on the host Mycolicibacterium smegmatis and sequenced. This wealth of genomic data indicates that mycobacteriophage genomes are diverse, mosaic, and contain numerous (35–60%) genes for which there is no predicted function based on sequence similarity to characterized orthologs, many of which are essential to lytic growth. To fully understand the molecular aspects of mycobacteriophage–host interactions, it is paramount to investigate the function of these genes and gene products. Here we show that the temperate mycobacteriophage, Alexphander, makes stable lysogens with a frequency of 2.8%. Alexphander gene 94 is essential for lytic infection and encodes a protein predicted to contain a C-terminal MerR family helix–turn–helix DNA-binding motif (HTH) and an N-terminal DinB/YfiT motif, a putative metal-binding motif found in stress-inducible gene products. Full-length and C-terminal gp94 constructs form high-order nucleoprotein complexes on 100–500 base pair double-stranded DNA fragments and full-length phage genomic DNA with little sequence discrimination for the DNA fragments tested. Maximum gene 94 mRNA levels are observed late in the lytic growth cycle, and gene 94 is transcribed in a message with neighboring genes 92 through 96. We hypothesize that gp94 is an essential DNA-binding protein for Alexphander during lytic growth. We proposed that gp94 forms multiprotein complexes on DNA through cooperative interactions involving its HTH DNA-binding motif at sites throughout the phage chromosome, facilitating essential DNA transactions required for lytic propagation.

Isolation, Characterisation and Identification of Bacteria from Three Different Unpasteurized Fruit Juices Sold at a Local Market in Guyana

Fruit juices are widely consumed for their nutritional value. However, fruit juices that are unpasteurised may be unsafe to drink because they are not subject to heat processing and much of their human handling results in contamination. The fruits used to make these juices have resident microflora, transient bacteria from handling and equipment, and bacteria from water used to wash fruits and in some cases make the juice. The objective of this research was to determine the bacteria present in unpasteurised passionfruit, cherry, and tamarind juices respectively. Through the use of a survey, and standard methods for isolation, identification and characterisation of bacteria, the results showed that temperature and pH did not significantly affect the diversity of bacteria. Cherry juice had the highest number of Colony Forming Units while passion fruit juice had the lowest. In total seven (7) species of bacteria were found including E.coli, S. aureus, Lactobacillus sp, Acetobacter sp, Bacillus subtilis, Bacillus cereus, and Micrococcus. The results for the Colony Forming Units were found to be above maximum acceptable levels for fruit juices. The results of this study demonstrate that unpasteurised juices may be a threat to public health and hazardous to humans if not processed in a sanitary manner.

Genomic Characterization of Piscicolin CM22 Produced by Carnobacterium maltaromaticum CM22 Strain Isolated from Salmon (Salmo salar).

Carnobacterium maltaromaticum is a species of lactic acid bacteria (LAB) that has been isolated from various natural environments. It is well-known for producing a diverse spectrum of bacteriocins with potential biotechnological applications. In the present study, a new psychrotolerant strain of C. maltaromaticum CM22 is reported, isolated from a salmon gut sample and producing a variant of the bacteriocin piscicolin 126that has been named piscicolin CM22. After identification by 16S rRNA gene, this strain has been genomically characterized by sequencing and assembling its complete genome. Moreover, its bacteriocin was purified and characterized. In vitro tests demonstrated that both the strain and its bacteriocin possess antimicrobial activity against several Gram-positive bacteria of interest in human and animal health, such as Listeria monocytogenes, Clostridium perfringens, or Enterococcus faecalis. However, this bacteriocin did not produce any antimicrobial effect on Gram-negative species. The study of its genome showed the genetic structure of the gene cluster that encodes the bacteriocin, showing a high degree of homology to the gene cluster of piscicolin 126described in other C. maltaromaticum. Although more studies are necessary concerning its functional properties, this new psychrotolerant strain C. maltaromaticum CM22 and its bacteriocin could be considered an interesting candidate with potential application in agri-food industry.

Effects of the combined compost of grape branches and sheep manure on a soil-microorganism-chardonnay (Vitis vinifera L.) plant ecosystem

A low-cost and sustainable composting strategy of grape branches and sheep manure is needed for vineyards. This study investigated the response of soil and grape plant characteristics to the compost, detected the changes in soil microbial community by high-throughput sequencing, and analyzed the relationship between soil microorganisms and soil characteristics and grape plant characteristics. The BM55 (1:1 grapevine branch to sheep manure by volume) group was the most effective treatment for increasing soil nutrients and enzyme activities. The BM3711Abbreviations: CK, Control check; GB, 100 % Grape branches; BM73, 70 % grape branches and 30 % sheep manure; BM55, 50 % grape branches and 50 % sheep manure; BM37, 30 % grape branches and 70 % sheep manure; SM, 100 % Sheep manure; Bd, Bulk density; Fc, Field capacity; EC, Electric conductivity; OM, Organic carbon; TC, Total C; TN, Total N; NO3, NO3--N; NH4, NH4+-N; OP, Olsen-P; AK, Available K, S-AKP/ALP, Soil alkaline phosphatase; S-CAT, Soil catalase; S-UE, Soil urease; S-SC, Soil sucrase. SS, Soluble solids; TA, Titratable acid; Ci, Intercellular CO2 concentration; Tr, Transpiration rate; Gs, Stomatal conductance; Pn, Net photosynthetic rate; SPAD, Chlorophyll content. (3:7 vol ratio of grapevine branches to sheep manure) treatment was the most effective in increasing fruit yield and quality. The dominant species of bacteria (Proteobacteria, Actinobacteria, Bacteroidetes, Ascomycota, and Basidiomycota) did not change but their relative abundance changed. Redundancy analysis showed that the soil biotic factors, abiotic factors, and microorganisms interact to form a complex relationship, in which biotic factors were the key factors influencing the composition and abundance of microbial communities, and the bacterial community was more sensitive than the fungal community. The combined composting stimulated microorganisms to participate in the synthesis and circulation of soil nutrients, which was not achieved by returning to the field respectively. Therefore, the combined composting is an effective way to enhance soil fertility, promote microbial metabolism, and improve fruit quality in vineyards, promote microbial metabolism, and improve fruit quality. Our results also provide a valuable scientific basis for understanding the interaction between soil microorganisms and soil properties as well as grape plant characteristics.

Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation

BackgroundThe gut microbiota controls broad aspects of human metabolism and feeding behavior, but the basis for this control remains largely unclear. Given the key role of human dipeptidyl peptidase 4 (DPP4) in host metabolism, we investigate whether microbiota DPP4-like counterparts perform the same function.ResultsWe identify novel functional homologs of human DPP4 in several bacterial species inhabiting the human gut, and specific associations between Parabacteroides and Porphyromonas DPP4-like genes and type 2 diabetes (T2D). We also find that the DPP4-like enzyme from the gut symbiont Parabacteroides merdae mimics the proteolytic activity of the human enzyme on peptide YY, neuropeptide Y, gastric inhibitory polypeptide (GIP), and glucagon-like peptide 1 (GLP-1) hormones in vitro. Importantly, administration of E. coli overexpressing the P. merdae DPP4-like enzyme to lipopolysaccharide-treated mice with impaired gut barrier function reduces active GIP and GLP-1 levels, which is attributed to increased DPP4 activity in the portal circulation and the cecal content. Finally, we observe that linagliptin, saxagliptin, sitagliptin, and vildagliptin, antidiabetic drugs with DPP4 inhibitory activity, differentially inhibit the activity of the DPP4-like enzyme from P. merdae.ConclusionsOur findings confirm that proteolytic enzymes produced by the gut microbiota are likely to contribute to the glucose metabolic dysfunction that underlies T2D by inactivating incretins, which might inspire the development of improved antidiabetic therapies.

Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery.

The application of dyes to understanding the aetiology of infection inspired antimicrobial chemotherapy and the first wave of antibacterial drugs. The second wave of antibacterial drug discovery was driven by rapid discovery of natural products, now making up 69% of current antibacterial drugs. But now with the most prevalent natural products already discovered, ∼107 new soil-dwelling bacterial species must be screened to discover one new class of natural product. Therefore, instead of a third wave of antibacterial drug discovery, there is now a discovery bottleneck. Unlike natural products which are curated by billions of years of microbial antagonism, the vast synthetic chemical space still requires artificial curation through the therapeutics science of antibacterial drugs - a systematic understanding of how small molecules interact with bacterial physiology, effect desired phenotypes, and benefit the host. Bacterial molecular genetics can elucidate pathogen biology relevant to therapeutics development, but it can also be applied directly to understanding mechanisms and liabilities of new chemical agents with new mechanisms of action. Therefore, the next phase of antibacterial drug discovery could be enabled by integrating chemical expertise with systematic dissection of bacterial infection biology. Facing the ambitious endeavour to find new molecules from nature or new-to-nature which cure bacterial infections, the capabilities furnished by modern chemical biology and molecular genetics can be applied to prospecting for chemical modulators of new targets which circumvent prevalent resistance mechanisms.

Identification of commensal gut microbiota signatures as predictors of clinical severity and disease progression in multiple sclerosis

Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system and a leading cause of neurological disability in young adults. Clinical presentation and disease course are highly heterogeneous. Typically, disease progression occurs over time and is characterized by the gradual accumulation of disability. The risk of developing MS is driven by complex interactions between genetic and environmental factors, including the gut microbiome. How the commensal gut microbiota impacts disease severity and progression over time remains unknown. In a longitudinal study, disability status and associated clinical features in 58 MS patients were tracked over 4.2 ± 0.98 years, and the baseline fecal gut microbiome was characterized via 16S amplicon sequencing. Progressor status, defined as patients with an increase in Expanded Disability Status Scale (EDSS), were correlated with features of the gut microbiome to determine candidate microbiota associated with risk of MS disease progression. We found no overt differences in microbial community diversity and overall structure between MS patients exhibiting disease progression and non-progressors. However, a total of 41 bacterial species were associated with worsening disease, including a marked depletion in Akkermansia, Lachnospiraceae, and Oscillospiraceae, with an expansion of Alloprevotella, Prevotella-9, and Rhodospirillales. Analysis of the metabolic potential of the inferred metagenome from taxa associated with progression revealed enrichment in oxidative stress-inducing aerobic respiration at the expense of microbial vitamin K2 production (linked to Akkermansia), and a depletion in SCFA metabolism (linked to Oscillospiraceae). Further, as a proof of principle, statistical modeling demonstrated that microbiota composition and clinical features were sufficient to predict disease progression. Additionally, we found that constipation, a frequent gastrointestinal comorbidity among MS patients, exhibited a divergent microbial signature compared with progressor status. These results demonstrate a proof of principle for the utility of the gut microbiome for predicting disease progression in MS in a small well-defined cohort. Further, analysis of the inferred metagenome suggested that oxidative stress, vitamin K2, and SCFAs are associated with progression, warranting future functional validation and mechanistic study.

Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. & Cham.

Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. & Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.

Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria.

Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here we exploited publicly available and new freshwater metagenomes in combination with genomes of abundant freshwater bacteria to reveal geographic and temporal population structure. We focused on species that were detected across broad geographic ranges at high enough sequence coverage for meaningful population genomic analyses, associated to the predominant freshwater taxa acI, LD12, Polynucleobacter and Ca. Methylopumilus. Despite the broad geographic ranges, each species appeared as sequence-discrete cluster, in contrast to abundant marine taxa, for which continuous diversity structures were reported on global scale. Population differentiation increased significantly with spatial distance in all species, but notable dispersal barriers (e.g. oceanic) were not apparent. Yet, the different species showed contrasting rates of geographic divergence and strikingly different intra-population dynamics in time series within individual habitats. Change of an LD12 population over seven years was minor (FST= 0.04) compared to differentiation between lakes, whereas a Polynucleobacter population displayed strong changes within merely two months (FST up to 0.54), similar in scale to differentiation between populations separated by thousands of kilometers. The slowly and steadily evolving LD12 population showed high strain diversity, whereas the dynamic Polynucleobacter population exhibited alternating clonal expansions of mostly two strains only. Based on the contrasting population structures we propose distinct models of speciation.

The complete genomic sequence of the type strain Brochothrix thermosphacta DSM 20171 highlights a diversity of prophages in this species.

The bacterium Brochothrix thermosphacta is a known muscle food spoiler. Here, the complete genome sequence of the B. thermosphacta type strain, DSM 20171, is reported. Prediction of prophages and genomic islands reveals an unsuspected diversity in this bacterial species that deserves further investigation.

Oral Microbiota Alterations in Subjects with SARS-CoV-2 Displaying Prevalence of the Opportunistic Fungal Pathogen Candida albicans

The oral cavity remains an underappreciated site for SARS-CoV-2 infection despite the myriad of oral conditions in COVID-19 patients. Recently, SARS-CoV-2 was shown to replicate in the salivary gland cells causing tissue inflammation. Given the established association between inflammation and microbiome disruption, we comparatively profiled oral microbial differences at a metagenomic level in a cohort of hospitalized COVID-19 patients and matched healthy controls. Specifically, we aimed to evaluate colonization by the opportunistic fungal pathogen Candida albicans, the etiologic agent of oral candidiasis. Comprehensive shotgun metagenomic analysis indicated that, overall, COVID-19 patients exhibited significantly reduced bacterial and viral diversity/richness; we identified 12 differentially abundant bacterial species to be negatively associated with COVID-19, and the functional pathways of certain bacteria to be highly associated with COVID-19 status. Strikingly, C. albicans was recovered from approximately half of the COVID-19 subjects but not from any of the healthy controls. The prevalence of Candida is likely linked to immune hypo-dysregulation caused by COVID-19 favoring Candida proliferation, warranting investigations into the interplay between Candida and SARS-CoV2 and potential therapeutic approaches directed toward oral candidiasis. Collectively, our findings prompt a reassessment of oral opportunistic infection risks during COVID-19 disease and their potential long-term impacts on oral health.

A Comparative Study of Human Leptospirosis between Mayotte and Reunion Islands Highlights Distinct Clinical and Microbial Features Arising from Distinct Inter-Island Bacterial Ecology.

Leptospirosis is a neglected zoonosis for which investigations assessing host-pathogen interaction are scarce. The aim of this study was to compare the severity and bacterial species involved in human cases of leptospirosis on Reunion and Mayotte islands, territories located in the southwest Indian Ocean that have recorded high human leptospirosis incidence but display fairly distinct epidemiological situations. A retrospective multicentric study including all patients over 18 years of age from Mayotte or Reunion with proven leptospirosis was conducted from January 2018 to April 2020. This study collected demographic, geographical, clinical, and biological data. Overall, 490 patients were included, 222 on Mayotte and 268 on Reunion. More patients were hospitalized on Reunion (n = 215, 80%) compared with Mayotte (n = 102, 46%). Severe disease was more common on Reunion (n = 75, 28%) than on Mayotte (n = 22, 10%). The dominant Leptospira species on Reunion was Leptospira interrogans (79%) followed by Leptospira borgpetersenii (21%), contrasting with the epidemiological situation on Mayotte where L. interrogans was found in only a minority of patients (10%). The high frequency of severe cases on Reunion could be explained not only by higher comorbidities but also by the higher occurrence of L. interrogans infections compared with Mayotte. Finally, the distribution of cases linked to L. borgpetersenii was found almost exclusively on the west coast of Reunion, raising the potential role of a ruminant reservoir.

Granular sludge characterization and microbial response in a hydroxyapatite (HAP)- anammox coupled process at different nitrogen loading rates

To enhance the treatment capacity and operational stability of the anammox process for nutrient-rich wastewater disposal, a hydroxyapatite (HAP)-anammox coupled process was developed in a granular sludge-based upflow bioreactor. The impact of nitrogen loading rate (NLR) on process performance was investigated by gradually increasing the NLR from 1 to 1.5, 3, and 5 kgN/m3/d for 264 days continuous operation. TN and TP removal rates of 82.51 ± 3.58 % and 60.49 ± 2.82 % were achieved at the NLR of 5 kgN/m3/d. The precipitation of Ca and phosphorus resulted in HAP crystals formation evidenced by sludge morphology and component analysis, which enhanced sludge settling properties and facilitated biomass enrichment. The HAP-anammox granular sludge was characterized by the outer layer HAP crystals formed on inner anammox granules, while highly mineralized granular sludge with higher density distributed at the bottom of the reactor is conducive to HAP-based phosphorus recovery. After a long-term accumulation, the abundance of Planctomycetota phylum gradually increased (from 7.7 % to 14.1 %), consisting of three species of anammox bacteria, namely Candidatus_Brocadia_sapporoensis, Candidatus_Brocadia_sinica and Candidatus_Kuenenia_stuttgartiensis. Nitrogen metabolic pathway analysis illustrated that denitrification was also present except the anammox reaction, synergistically contributing to superior nitrogen removal in the HAP-anammox process.

Multikingdom characterization of gut microbiota in patients with rheumatoid arthritis and rheumatoid arthritis-associated interstitial lung disease.

Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a serious and common extra-articular disease manifestation. Patients with RA-ILD experience reduced bacterial diversity and gut bacteriome alterations. However, the gut mycobiome and virome in these patients have been largely neglected. In this study, we performed whole-metagenome shotgun sequencing on fecal samples from 30 patients with RA-ILD, and 30 with RA-non-ILD, and 40 matched healthy controls. The gut bacteriome and mycobiome were explored using a reference-based approach, while the gut virome was profiled based on a nonredundant viral operational taxonomic unit (vOTU) catalog. The results revealed significant alterations in the gut microbiomes of both RA-ILD and RA-non-ILD groups compared with healthy controls. These alterations encompassed changes in the relative abundances of 351 bacterial species, 65 fungal species, and 4,367 vOTUs. Bacteria such as Bifidobacterium longum, Dorea formicigenerans, and Collinsella aerofaciens were enriched in both patient groups. Ruminococcus gnavus (RA-ILD), Gemmiger formicilis, and Ruminococcus bromii (RA-non-ILD) were uniquely enriched. Conversely, Faecalibacterium prausnitzii, Bacteroides spp., and Roseburia inulinivorans showed depletion in both patient groups. Mycobiome analysis revealed depletion of certain fungi, including Saccharomyces cerevisiae and Candida albicans, in patients with RA compared with healthy subjects. Notably, gut virome alterations were characterized by an increase in Siphoviridae and a decrease in Myoviridae, Microviridae, and Autographiviridae in both patient groups. Hence, multikingdom gut microbial signatures showed promise as diagnostic indicators for both RA-ILD and RA-non-ILD. Overall, this study provides comprehensive insights into the fecal virome, bacteriome, and mycobiome landscapes of RA-ILD and RA-non-ILD gut microbiota, thereby offering potential biomarkers for further mechanistic and clinical research.

Effect of fermented Rosa roxburghii tratt fruit juice on gut microbiota in a dextran sulfate sodium (DSS)-induced colitis mouse model

This study mainly investigated the regulatory effect of Rosa roxburghii Tratt fruit juice fermented by Lacticaseibacillus paracasei SR10-1 (LAB-RRTJ) on modulating gut microbiota in dextran sulfate sodium (DSS)-induced ulcerative colitis in mice. Compared to control group, DSS induction decreased body weight of mice, indexes of Shannon, Simpson, Chao 1 and Faith_pd, and increased disease activity index (DAI) and levels of interleukin 1β (IL-1β), IL-6, tumor necrosis factor α (TNF-α) and interferon-γ (IFN-γ); And this induction also led to an increase in Proteobacteria, Verrucomicrobia and Actinobacteria at phylum level, harmful bacterial species richness at genus level, and relative richness of S. sciuri, desulfovibrio C21_c20, R. gnavus and Akkermansia muciniphila at species level, and a decrease in Firmicutes at phylum level and relative richness of B. acidifaciens in mice. LAB-RRTJ increased body weight of mice with DSS induced ulcerative colitis (UC) and indexes of Shannon, Simpson, Chao 1 and Faith_pd, reduced DAI and the content of four inflammatory factors and improved gut microbiota imbalance in DSS induced UC mice. Besides, the number of OTUs increased, alpha diversity and beta diversity were restored and similar to those in mice in the Control group after LAB-RRTJ treatment. Compared with the positive drug treatment group, LAB-RRTJ has a better effect on regulating gut microbiota diversity in colitis mice. Correlation analysis showed that inflammatory factors were positively correlated with harmful bacteria and negatively correlated with beneficial bacteria which commonly found in some colitis mice. Taken together, our study demonstrated that LAB-RRTJ could alleviate DSS-induced colitis in mice through the modulation of inflammatory cytokines and gut microbiota composition.