Key Bacteria Research Articles

Identification of key yeast species and microbe-microbe interactions impacting larval growth of Drosophila in the wild.

Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. However, it is unclear which species are essential to this impact and how they affect the host. This study analyzed and isolated microbes from natural food sources of Drosophila larvae, and investigated their functions. Hanseniaspora uvarum is the predominant yeast responsible for larval growth in the earlier stage of fermentation. As fermentation progresses, Acetobacter orientalis emerges as the key bacterium responsible for larval growth, although yeasts and lactic acid bacteria must coexist along with the bacterium to stabilize this host-bacterial association. By providing nutrients to the larvae in an accessible form, the microbiota contributes to the upregulation of various genes that function in larval cell growth and metabolism. Thus, this study elucidates the key microbial species that support animal growth under microbial transition.

Identification of key yeast species and microbe–microbe interactions impacting larval growth of Drosophila in the wild

Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. However, it is unclear which species are essential to this impact and how they affect the host. This study analyzed and isolated microbes from natural food sources of Drosophila larvae, and investigated their functions. Hanseniaspora uvarum is the predominant yeast responsible for larval growth in the earlier stage of fermentation. As fermentation progresses, Acetobacter orientalis emerges as the key bacterium responsible for larval growth, although yeasts and lactic acid bacteria must coexist along with the bacterium to stabilize this host–bacterial association. By providing nutrients to the larvae in an accessible form, the microbiota contributes to the upregulation of various genes that function in larval cell growth and metabolism. Thus, this study elucidates the key microbial species that support animal growth under microbial transition.

Metabarcoding analysis reveals a differential bacterial community profile associated with ‘Torta del Casar’ and ‘Queso de la Serena’ PDO cheeses

A detailed understanding of the microbial ecology of artisanal cheeses is a crucial factor for implementation practices that can help to update their quality. In this study, the bacterial communities of Protected Designation of Origin (PDO) ‘Queso de la Serena’ and ‘Torta del Casar’ cheeses were characterised by 16S rRNA gene metabarcoding sequencing over 60 days of ripening at three dairies for each cheese variety. Both PDO cheeses presented a distinctive and unique bacterial community, suggesting that the manufacturing practices of each PDO shaped the microbiota. Lactococcus lactis and, to a lesser extent, Leuconostoc mesenteroides were the key lactic acid bacteria (LAB) species that drove the ripening process of PDO ‘Torta del Casar’, whereas in PDO ‘Queso de la Serena’, Leu. mesenteroides was the main LAB species, followed by Lactococcus raffinolactis and Lc. lactis, depending on the dairy. Furthermore, a wide range of non-starter LAB, Gram-negative bacteria and Gram-positive catalase-positive cocci were found, with a variable presence and abundance between dairies. In this regard, the dairy was a strong contributing factor to the variability in the composition of the bacterial community in each cheese type. In contrast, the impact of the ripening process was limited. Overall, this study enhances the understanding of the bacterial dynamics that occur during the ripening of these traditional PDO cheeses, highlighting the need to improve the standardisation of the raw materials and manufacturing practices to minimise inter-dairy variability, ensuring final quality and their unique sensory traits.

Contrasting fertilization response of soil phosphorus forms and functional bacteria in two newly reclaimed vegetable soils

Fertilization is a pervasive approach to agricultural production enhancing vegetable nutrients such as phosphorus (P) absorption. However, unreasonable fertilization strategies result in high levels of residual P in vegetable planting systems. To better understand the mechanisms of soil phosphorus dynamics responding to inorganic/organic fertilization, we conducted a 3-year field experiment in two newly reclaimed vegetable fields in southern China. The results revealed that soil Olsen-P in CF (mineral fertilization) and OF (Combined application of organic and inorganic fertilizers) increased by approximately 210.6 % and 183.6 %, respectively, while stable P proportion decreased by approximately 9.2 % and 18.1 %, respectively, compared with CK. Combined application of organic and inorganic fertilizer increased the proportion of moderately labile P (NaOH-P) by 1–6 % in comparison with chemical fertilizer and facilitated the conversion from diester-P to monoester-P, indicating that applying pig manure enhanced the potential soil P bioavailability. Besides, organic-inorganic fertilization shaped a bacterial community with more connectivity and stability and changed keystone taxa related to the P transformation of the network. Phenylobacterium, Solirubrobacter, and Modestobacter were regarded as core genera for mobilizing soil phosphorus. However, residual P content in newly reclaimed soils under fertilization, especially for chemical fertilizer, remained non-negligible and may cause potential environmental risks. The partial least squares path modeling results demonstrated that fertilization management had both direct and indirect positive effects on P fraction through the improvement of soil nutrients e.g. total N and soil organic carbon, and bacterial community, while soil properties mainly determined the variation of soil P species. Our results provide comprehensive insights into the current status of legacy P forms and the vital role of fertilizer, key soil properties and bacteria in P dynamics in newly reclaimed vegetable field.

Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.

Reshaping the plastisphere upon deposition: Promote N2O production through affecting sediment microbial communities in aquaculture pond

Microplastics (MPs) could provide vector for microorganisms to form biofilm (plastisphere), but the shaping process of MPs biofilm and its effects on the structure and function of sedimentary microbial communities especially in aquaculture environments are not reported. For this, we incubated MPs biofilm in situ in an aquaculture pond and established a sediment microcosm with plastisphere. We found that the formation of MPs biofilm in surface water was basically stable after 30 d incubation, but the biofilm communities were reshaped after deposition for another 30 d, because they were more similar to plastisphere communities incubated directly within sediment but not surface water. Moreover, microbial communities of MPs-contaminated sediment were altered, which was mainly driven by the biofilm communities present on MPs, because they but not sediment communities in proximity to MPs had a more pronounced separation from the control sediment communities. In the presence of MPs, increased sediment nitrification, denitrification and N2O production rates were observed. The K00371 (NO2-⇋NO3-) pathway and elevated abundance of nxrB and narH genes were screened by metagenomic analysis. Based on structural equation model, two key bacteria (Alphaproteobacteria bacterium and Rhodobacteraceae bacterium) associated with N2O production were further identified. Overall, the settling of MPs could reshape the original biofilm and promote N2O production by selectively elevating sedimental microorganisms and functional genes in aquaculture pond.

Soil nutrient conditions alter viral lifestyle strategy and potential function in phosphorous and nitrogen metabolisms

As one of the most abundant members of microbial communities, viruses are considered to influence prokaryotic mortality and biogeochemical cycles. While extensive research has been conducted to explore viral diversity and community dynamics in marine ecosystems, our understanding of soil viruses, particularly within agroecosystems, remains limited. Here, we conducted metagenomics and viromics analyses in a paddy ecosystem subjected to four different levels of soil nutrient modification by pig manure applications (PM0: 0 kg ha−1, PM1: 1930 kg ha−1, PM2: 3860 kg ha−1 and PM3: 5790 kg ha−1) over a period of 9 years. We aimed to investigate viral community adaptation and virus-host interactions in response to varying soil nutrient conditions. Our findings revealed that the viral communities are more adaptable to changes in soil nutrient contents compared to prokaryotic communities. Specifically, the relative abundance of Caudoviricetes decreased significantly with increasing levels of soil available phosphorus and total nitrogen. The ratio of lytic-lysogenic cycles increased with higher manure application rates, accompanied by an elevated prevalence of functional genes related to cell processes and viral protein structure. Moreover, we identified several putative auxiliary metabolic genes (AMGs) associated with phosphorus and nitrogen cycles, including phoA, phoH, phoB, and gdh, with the first discovery of phoB and gdh as soil viral-encoded AMG. Notably, the association between viruses and phoB-encoding bacteria displayed greater similarity within nutrient-deficient environments compared to nutrient-enriched environments, while the converse interaction pattern emerged between viruses and gdh-encoding bacteria. Collectively, our study highlights the importance of soil nutrient conditions in driving the transition between lytic-lysogenic cycles, as well as the interaction patterns between viruses and key bacteria. The insights gleaned from our findings significantly enrich our understanding of viral ecology within agricultural ecosystems.

Novel ferrous disulfide loaded palygorskite composites as additives in lignocellulosic waste composting for improving humification

Improving the composting efficiency of lignocellulose wastes has been the focus in the field of aerobic fermentation. In this study, FeS2 was modified on the surface of palygorskite to regulate the straw composting. Material characterizations showed that FeS2/Pal composite exhibited glutathione oxidase and catalase activities, attributing to the fact that nano FeS2 filled the aggregation space of the original palygorskite, exposing more active sulfur vacancy defects. During the composting process, the addition of FeS2/Pal could adjust pH value and increase electrical conductivity, which was conducive to improving the efficiency of biological redox process. The total degradation ratio of cellulose was 52.54% with FeS2/Pal added. The repolymerization of small molecule intermediates was strengthened, and the final polymerization degree and maturity of composting products was improved. Since the sequence abundance of aromatic amino acids biosynthesis and carbon fixation pathways was higher revealed by PICRUSt. High-throughput sequencing results showed that bacterial community was more dominant than fungi, with community richness index increased by 2.3–3.7 times. The pathogenic bacteria such as Atopostipes and Corynebacterium were disappeared, and heat-resistant bacteria were dominant. The key bacteria and fungi in the group added with FeS2/Pal were Limnochordaceae and Melanocarpus genus, which were related to the cellulose enzymatic hydrolysis and humification degree.

Optimization of the Antibacterial Spectrum and the Developability Profile of the Novel-Class Natural Product Corramycin.

Corramycin 1 is a novel zwitterionic antibacterial peptide isolated from a culture of the myxobacterium Corallococcus coralloides. Though Corramycin displayed a narrow spectrum and modest MICs against sensitive bacteria, its ADMET and physchem profile as well as its high tolerability in mice along with an outstanding in vivo efficacy in an Escherichia coli septicemia mouse model were promising and prompted us to embark on an optimization program aiming at enlarging the spectrum and at increasing the antibacterial activities by modulating membrane permeability. Scanning the peptidic moiety by the Ala-scan strategy followed by key stabilization and introduction of groups such as a primary amine or siderophore allowed us to enlarge the spectrum and increase the overall developability profile. The optimized Corramycin 28 showed an improved mouse IV PK and a broader spectrum with high potency against key Gram-negative bacteria that translated into excellent efficacy in several in vivo mouse infection models.

Host microbiome associated low intestinal acetate correlates with progressive NLRP3-dependent hepatic-immunotoxicity in early life microcystin-LR exposure

BackgroundMicrocystins (MCs), potent hepatotoxins pose a significant health risk to humans, particularly children, who are more vulnerable due to higher water intake and increased exposure during recreational activities.MethodsHere, we investigated the role of host microbiome-linked acetate in modulating inflammation caused by early-life exposure to the cyanotoxin Microcystin-LR (MC-LR) in a juvenile mice model.ResultsOur study revealed that early-life MC-LR exposure disrupted the gut microbiome, leading to a depletion of key acetate-producing bacteria and decreased luminal acetate concentration. Consequently, the dysbiosis hindered the establishment of a gut homeostatic microenvironment and disrupted gut barrier function. The NOD-like receptor family pyrin domain – containing 3 (NLRP3) inflammasome, a key player in MC-induced hepatoxicity emerged as a central player in this process, with acetate supplementation effectively preventing NLRP3 inflammasome activation, attenuating hepatic inflammation, and decreasing pro-inflammatory cytokine production. To elucidate the mechanism underlying the association between early-life MC-LR exposure and the progression of metabolic dysfunction associated steatotic liver disease (MASLD), we investigated the role of acetate binding to its receptor -G-protein coupled receptor 43 (GPR43) on NLRP3 inflammasome activation. Our results demonstrated that acetate-GPR43 signaling was crucial for decreasing NLRP3 protein levels and inhibiting NLRP3 inflammasome assembly. Further, acetate-induced decrease in NLRP3 protein levels was likely mediated through proteasomal degradation rather than autophagy. Overall, our findings underscore the significance of a healthy gut microbiome and its metabolites, particularly acetate, in the progression of hepatotoxicity induced by early life toxin exposure, crucial for MASLD progression.ConclusionsThis study highlights potential therapeutic targets in gut dysbiosis and NLRP3 inflammasome activation for mitigating toxin-associated inflammatory liver diseases.

Process conditions affect microbial diversity and activity in a haloalkaline biodesulfurization system.

Biodesulfurization (BD) systems that treat sour gas employ mixtures of haloalkaliphilic sulfur-oxidizing bacteria to convert sulfide to elemental sulfur. In the past years, these systems have seen major technical innovations that have led to changes in microbial community composition. Different studies have identified and discussed the microbial communities in both traditional and improved systems. However, these studies do not identify metabolically active community members and merely focus on members' presence/absence. Therefore, their results cannot confirm the activity and role of certain bacteria in the BD system. To investigate the active community members, we determined the microbial communities of six different runs of a pilot-scale BD system. 16S rRNA gene-based amplicon sequencing was performed using both DNA and RNA. A comparison of the DNA- and RNA-based sequencing results identified the active microbes in the BD system. Statistical analyses indicated that not all the existing microbes were actively involved in the system and that microbial communities continuously evolved during the operation. At the end of the run, strains affiliated with Alkalilimnicola ehrlichii and Thioalkalivibrio sulfidiphilus were confirmed as the most active key bacteria in the BD system. This study determined that microbial communities were shaped predominantly by the combination of hydraulic retention time (HRT) and sulfide concentration in the anoxic reactor and, to a lesser extent, by other operational parameters.IMPORTANCEHaloalkaliphilic sulfur-oxidizing bacteria are integral to biodesulfurization (BD) systems and are responsible for converting sulfide to sulfur. To understand the cause of conversions occurring in the BD systems, knowing which bacteria are present and active in the systems is essential. So far, only a few studies have investigated the BD system's microbial composition, but none have identified the active microbial community. Here, we reveal the metabolically active community, their succession, and their influence on product formation.

Dysbiosis of gut microbiota and metabolites during AIDS: implications for CD4 + T cell reduction and immune activation.

Identifying the gut microbiota associated with host immunity in the AIDS stage. We performed a cross-sectional study. We recruited people with HIV (PWH) in the AIDS or non-AIDS stage and evaluated their gut microbiota and metabolites by using 16S ribosomal RNA (rRNA) sequencing and liquid chromatography-mass spectrometry (LC-MS). Machine learning models were used to analyze the correlations between key bacteria and CD4 + T cell count, CD4 + T cell activation, bacterial translocation, gut metabolites, and KEGG functional pathways. We recruited 114 PWH in the AIDS stage and 203 PWH in the non-AIDS stage. The α-diversity of gut microbiota was downregulated in the AIDS stage ( P < 0.05). Several machine learning models could be used to identify key gut microbiota associated with AIDS, including the logistic regression model with area under the curve (AUC), sensitivity, specificity, and Brier scores of 0.854, 0.813, 0.813, and 0.160, respectively. The decreased key bacteria ASV1 ( Bacteroides sp.), ASV8 ( Fusobacterium sp.), ASV30 ( Roseburia sp.), ASV37 ( Bacteroides sp.), and ASV41 ( Lactobacillus sp.) in the AIDS stage were positively correlated with the CD4 + T cell count, the EndoCAb IgM level, 4-hydroxyphenylpyruvic acid abundance, and the predicted cell growth pathway, and negatively correlated with the CD3 + CD4 + CD38 + HLA-DR + T cell count and the sCD14 level. Machine learning has the potential to recognize key gut microbiota related to AIDS. The key five bacteria in the AIDS stage and their metabolites might be related to CD4 + T cell reduction and immune activation.

Berberine-microbiota interplay: orchestrating gut health through modulation of the gut microbiota and metabolic transformation into bioactive metabolites.

Berberine is an isoquinoline alkaloid found in plants. It presents a wide range of pharmacological activities, including anti-inflammatory and antioxidant properties, despite a low oral bioavailability. Growing evidence suggests that the gut microbiota is the target of berberine, and that the microbiota metabolizes berberine to active metabolites, although little evidence exists in the specific species involved in its therapeutic effects. This study was performed to detail the bidirectional interactions of berberine with the broiler chicken gut microbiota, including the regulation of gut microbiota composition and metabolism by berberine and metabolization of berberine by the gut microbiota, and how they contribute to berberine-mediated effects on gut health. As previous evidence showed that high concentrations of berberine may induce dysbiosis, low (0.1g/kg feed), middle (0.5g/kg feed) and high (1g/kg feed) doses were here investigated. Low and middle doses of in-feed berberine stimulated potent beneficial bacteria from the Lachnospiraceae family in the large intestine of chickens, while middle and high doses tended to increase villus length in the small intestine. Plasma levels of the berberine-derived metabolites berberrubine, thalifendine and demethyleneberberine were positively correlated with the villus length of chickens. Berberrubine and thalifendine were the main metabolites of berberine in the caecum, and they were produced in vitro by the caecal microbiota, confirming their microbial origin. We show that members of the genus Blautia could demethylate berberine into mainly thalifendine, and that this reaction may stimulate the production of short-chain fatty acids (SCFAs) acetate and butyrate, via acetogenesis and cross-feeding respectively. We hypothesize that acetogens such as Blautia spp. are key bacteria in the metabolization of berberine, and that berberrubine, thalifendine and SCFAs play a significant role in the biological effect of berberine.

Differential Nitrous oxide emission and microbiota succession in constructed wetlands induced by nitrogen forms

Nitrous oxide (N2O) emission during the sewage treatment process is a serious environmental issue that requires attention. However, the N2O emission in constructed wetlands (CWs) as affected by different nitrogen forms in influents remain largely unknown. This study investigated the N2O emission profiles driven by microorganisms in CWs when exposed to two typical nitrogen sources (NH4+-N or NO3–-N) along with different carbon source supply (COD/N ratios: 3, 6, and 9). The results showed that CWs receiving NO3–-N caused a slight increase in total nitrogen removal (by up to 11.8 %). This increase was accomplished by an enrichment of key bacteria groups, including denitrifiers, dissimilatory nitrate reducers, and assimilatory nitrate reducers, which enhanced the stability of microbial interaction. Additionally, it led to a greater abundance of denitrification genes (e.g., nirK, norB, norC, and nosZ) as inferred from the database. Consequently, this led to a gradual increase in N2O emission from 66.51 to 486.77 ug-N/(m2·h) as the COD/N ratio increased in CWs. Conversely, in CWs receiving NH4+-N, an increasing influent COD/N ratio had a negative impact on nitrogen biotransformation. This resulted in fluctuating trend of N2O emissions, which decreased initially, followed by an increase at later stage (with values of 122.87, 44.00, and 148.59 ug-N/(m2·h)). Furthermore, NH4+-N in the aquatic improved the nitrogen uptake by plants and promoted the production of more root exudates. As a result, it adjusted the nitrogen-transforming function, ultimately reducing N2O emissions in CWs. This study highlights the divergence in microbiota succession and nitrogen transformation in CWs induced by nitrogen form and COD/N ratio, contributing to a better understanding of the microbial mechanisms of N2O emission in CWs with NH4+-N or NO3–-N at different COD/N ratios.

Abstract C091: Newly identified Fannyhessea species contributions in HPV infection, cervical dysplasia, and cancer in two Arizonan cohorts

Abstract The vaginal microbiome can impact gynecologic health and disease. It is still unclear the extent to which the microbiome plays in the progression and development of gynecologic cancers. Fannyhessea vaginae is a key vaginal bacterium linked to bacterial vaginosis, HPV acquisition, and cervical cancer. F. vaginae was recently proposed for reclassification as three species: F.vaginae, Fannyhessea massiliense, and Fannyhessea species type 2. We hypothesize that these Fannyhessea species vary in terms of their host-microbe interactions which contribute to cancer progression/severity. We investigated the prevalence of Fannyhessea species in two of our Arizona-based HPV and cervical cancer cohorts recruited in Phoenix or Flagstaff area. The Phoenix (Phx) cohort included: women diagnosed with invasive cervical cancer (ICC=9), high-grade squamous intraepithelial lesion (HSIL=27), and low-grade squamous intraepithelial lesion (LSIL=11), as well as controls who were either HPV-positive=20 or HPV-negative without dysplasia=31. While the Flagstaff cohort (Flg) consisted of 31 women that were HPV-positive=7 or HPV-negative=24. The 16S rDNA sequencing information was analyzed with DADA2 and QIIME2 to identify the microbial composition of the cervicovaginal profiles of these patients. Statistical analyses are ongoing, utilizing survey data on these species to decipher their clinical associations with factors such as HPV status and genotype. The cohorts had a prevalence of 59.2% of Atopobiaceae bacteria in Phx and 38.7% prevalence in Flg cohort. We observed F. vaginae (50% and 38.7%, respectively), Fannyhessea species type 2 (16.4% and 25.0%, respectively), F. massiliense (21.0% and 18.8%, respectively) in these cohorts. Interestingly, in both dysplasia groups of the Phx cohort these species had an increased abundance, but it did not reach significance. Other clinical and demographic factors in both cohorts, vaginal pH (p = 0.0005 and 0.47, respectively), Native American race (p=0.002) and Hispanic ethnicity (p= 0.013 and 0.63, respectively), indicated significant species-specific differences in the prevalence of Atopobiaceae. Additionally, genital inflammation scores were higher in profiles that contained Atopobiaceae species (p= 0.05) in Phoenix cohort. In addition, microbial co-occurrence analysis identified that Fannyhessea species highly co-occurred with one another. Sneathia amnii, Sneathia sanguinegens, and other BV-associated bacteria also co-occurred with Fannyhessea species, indicating an association between multiple Fannyhessea species and a potential link to cancer that requires further investigation. This research highlights potential associations of BV-associated bacteria and their role in HPV infection and cervical cancer and investigates the relationship of underexplored Fannyhessea species in historically understudied populations that have the highest disease burden. The overall data from our study provide foundational knowledge on putative oncogenic bacteria that could be exploited to modulate the microbiome and improve cancer outcomes. Citation Format: Nicole R. Jimenez, Paweł Łaniewski, Naomi R. Lee, J. Gregory Caporaso, Melissa M. Herbst-Kralovetz. Newly identified Fannyhessea species contributions in HPV infection, cervical dysplasia, and cancer in two Arizonan cohorts [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C091.

Gut Microbial Dysbiosis in Myeloid Neoplasms: Correlations with Clinical and Genomic Features

Background Deeper insights into somatic mutations have advanced our understanding of myeloid malignancies like Myelodysplastic Neoplasms (MDS), Myeloproliferative Neoplasms (MPN), and Acute Myeloid Leukemia (AML), particularly in terms of malignant clone interactions and immune dysregulation. However, the role of diverse extrinsic factors, such as gut microbial dysbiosis, in interacting with and modifying the microenvironment is still being studied. Here we analyzed gut microbial species and function in AML, MDS, and MPN patients, investigating correlation of disease metagenomic signatures with blood indices, somatic mutations, and disease subtype. Methods Fecal samples were collected from 337 Caucasian adult patients with MDS, MPN, and AML at Humanitas Research Hospital, Milan, Italy. Extracted DNA samples were sequenced (Illumina Novaseq 6000) and quality-trimmed data mapped against Integrated Gut Catalog (IGC2) using METEOR pipeline (Plaza Oñate et al., 2019). Human contaminant sequences were removed, and gene count tables were normalized according to the FPKM strategy using MOMR normFreqRPKM function. Results Overall 138 AML patients (63 females, 75 males, average age 62.3 ± 13.64); 93 MPN patients (29 females, 77 males, average age 66.3 ± 10.61) and 106 MDS patients (29 females, 77 males, average age 71.7 ± 10.87) were included. Concerning microbial richness we observed significantly lower richness and diversity in AML patients vs MDS or MPN. Principal Coordinates Analysis (PCoA) at the species level revealed significant differences in gut microbiomes among disease groups (PERMANOVA R2=7.38, p&amp;lt;0.001)(Figure 1A). AML and MDS shared seven depleted species, including three MetaGenomic Species (MGS) for Faecalibacterium prausnitzii, a key beneficial gut bacterium. Random Forest classification modelling to accurately identified AML, MDS, and MPN patients (AUCROC=0.91, 0.89, 0.85,MDS, AML, MPN respectively), with primary distinguishing features tied to increased levels of inflammation-inducing species. We further investigated mutation-specific microbiome signatures using Shannon Diversity:, JAK2 V617F mutated MPN had significantly greater diversity than MDS or AML (log2(MPN/AML)=0.28,p=7.7e-12, log2(MPN/MDS)=0.12,p=1.3e-9)). Additionally, within MDS, patients with SF3B1 mutation were significantly different from those with TP53 mutation (log2(SF3B1/TP53)=0.23,p=0.03)). We conducted a correlation analysis with blood indices. Two depleted signatures in AML and MDS, butyrate producing species such as Faecalibacterium prausnitzii , positively correlated with platelets (rho=0.17,q=0.001) and hemoglobin (rho=0.23, q=1.7e-5). Conversely, enriched species like Erysipiclostridium ramosum showed a negative correlation with hemoglobin (rho=-0.23,q=1.26e-5), and platelet count (rho=-0.17,q=0.002) in AML and MDS. Notably, in MPN, the pattern was reversed; depleted species like Flavonifractor plautii were negatively correlated with hemoglobin (rho=-0.15,p=0.004) and platelet count (rho=-0.19,q=0.4e-3)). (Figure 1B). We compared microbiome signatures at diagnosis and disease relapse in 94 patients with MDS/AML treated with hypomethylating-based therapies. A significant reduced taxonomical abundances was found in samples collected at disease relapse with respect to those from the same subject at diagnosis (p&amp;lt;0.001). Finally, in 133 MDS/AML patients who underwent disease modifying treatment at diagnosis, we evaluate the incidence of severe infections and the possible associations with specific microbiome signatures. We noticed that patients who developed a severe infection (G3-G4) showed a significantly reduced taxonomical abundances in gut microbiome (as evaluated at disease diagnosis before treatment) with respect to those subject who didn't experience relevant infectious complications (P&amp;lt;.001) Conclusion Our study reveals striking correlations between gut microbiome and clinical/genetic features of AML, MDS, and MPN, suggesting gut microbiome as potential disease markers and therapeutic targets. This enhances our grasp of myeloid malignancies' pathophysiology, setting the stage for further investigations into the intricate interaction between the gut microbiome, genetic mutations, and clinical traits in these conditions, potentially leading to the development of microbiome-focused therapies.

A dynamics association study of gut barrier and microbiota in hyperuricemia.

The intricate interplay between gut microbiota and hyperuricemia remains a subject of growing interest. However, existing studies only provided snapshots of the gut microbiome at single time points, the temporal dynamics of gut microbiota alterations during hyperuricemia progression and the intricate interplay between the gut barrier and microbiota remain underexplored. Our investigation revealed compelling insights into the dynamic changes in both gut microbiota and intestinal barrier function throughout the course of hyperuricemia. The hyperuricemia mice (HY) were given intragastric administration of adenine and potassium oxalate. Gut microbiota was analyzed by 16S rRNA sequencing at 3, 7, 14, and 21 days after the start of the modeling process. Intestinal permeability as well as LPS, TNF-α, and IL-1β levels were measured at 3, 7, 14, and 21 days. We discovered that shifts in microbial community composition occur prior to the onset of hyperuricemia, key bacterial Bacteroidaceae, Bacteroides, and Blautia exhibited reduced levels, potentially fueling microbial dysbiosis as the disease progresses. During the course of hyperuricemia, the dynamic fluctuations in both uric acid levels and intestinal barrier function was accompanied with the depletion of key beneficial bacteria, including Prevotellaceae, Muribaculum, Parabacteroides, Akkermansia, and Bacteroides, and coincided with an increase in pathogenic bacteria such as Oscillibacter and Ruminiclostridium. This microbial community shift likely contributed to elevated lipopolysaccharide (LPS) and pro-inflammatory cytokine levels, ultimately promoting metabolic inflammation. The decline of Burkholderiaceae and Parasutterella was inversely related to uric acid levels, Conversely, key families Ruminococcaceae, Family_XIII, genera Anaeroplasma exhibited positive correlations with uric acid levels. Akkermansiaceae and Bacteroidaceae demonstrating negative correlations, while LPS-containing microbiota such as Desulfovibrio and Enterorhabdus exhibited positive correlations with intestinal permeability. In summary, this study offers a dynamic perspective on the complex interplay between gut microbiota, uric acid levels, and intestinal barrier function during hyperuricemia progression. Our study suggested that Ruminiclostridium, Bacteroides, Akkermansiaceae, Bilophila, Burkholderiaceae and Parasutterella were the key bacteria that play vital rols in the progress of hyperuricemia and compromised intestinal barrier, which provide a potential avenue for therapeutic interventions in hyperuricemia.

Developing a novel lightweight substrate for constructed treatment wetland: The idea and the reality

The cost-effective and environmentally friendly substrates play an important role in functioning constructed wetlands (CWs). This study innovatively composes aluminum sludge and polyurethane under the action of a catalyst to develop a novel lightweight substrate (Al-NLS), which is expected to be used as a main substrate in CWs. The driving force of it lies in reducing construction costs of CWs in practice, while offering a flexible and considerably efficient substrate in CW. The bulk density of the resultant Al-NLS was apparently reduced by about 80 % compared with common substrate of gravel. The static adsorption experiments showed that the adsorption behavior of Al-NLS on phosphorus (P) was in accordance with Langmuir isotherm (with maximum P adsorption capacity of 1.12 mg/g,) and quasi-second-order kinetic models. The use of Al-NLS as a single stage wetland substrate to treat real domestic wastewater has favorable removal efficiencies of COD (65.9–74.3 %), TP (86.9–98.6 %), NH4+-N (61.1–52.2 %) and TN (35.4–45.6 %). The mechanisms of P removal onto Al-NLS were examined by various physiochemical characterizations of Al-NLS and raw alum sludge, which revealed that P adsorption was via forming Hydroxy-Al by ion exchange. In addition, high throughput sequencing analysis revealed that Al-NLS had positive impact on the richness and diversity of microbial community for pollutants removal, while the abundance of key functional bacteria such as proteobacteria and bacteroidota was higher in the longer retention time of CW (HRT = 2 days). These results indicated that Al-NLS could be used as a new alternative substrate in CWs technology.

Exploring the interplay between Fusobacterium nucleatum with the expression of microRNA, and inflammatory mediators in colorectal cancer

BackgroundFusobacterium nucleatum has been recognized as an important key bacterium in the cause and spread of colorectal carcinogenesis. Nevertheless, the clinical relevance of F. nucleatum in colorectal cancer (CRC) and its effect on immune factors and the tumor microenvironment have not been fully elucidated.Materials and methodsThe frequency of F. nucleatum was measured in 100 paired tumor and normal tissue specimens by TaqMan quantification Real-Time Polymerase Chain Reaction (qPCR). The mRNA expression levels of cytokines (IL-6, IL-10, IL-12β, IL-17, TNF-α, TLR-2, and TLR-4), and miRNAs (miR-21, miR-31) were examined. Eventually, any potential correlations between the molecular and clinicopathological features of the neoplastic samples and the abundance of F. nucleatum were analyzed.ResultsThe relative frequency of F. nucleatum was significantly increased in cancerous tissue compared to adjacent non-tumor tissues. Furthermore, the high level of F. nucleatum was significantly associated with histological grade III and IV CRC tissues (P = 0.027 and P = 0.022, respectively) and perineural invasion-positive patients (P = 0.037). In addition, the expression levels of IL-6, IL-17, TNF-α,IL-12β, TLR-2, and TLR-4 as well as miR-21 and miR-31 showed a significant increase in the cancer group. A notable correlation was also observed between the high status of F. nucleatum and the expression of IL-6, TNF-α and miR-21.ConclusionOur results emphasize the importance of F. nucleatum and changes in the expression of genes involved in CRC. Studying the microbial profile and gene expression changes in CRC patients may be a promising approach to improve screening methods and provide therapeutic strategies.

Feasibility of anaerobic co-digestion of biodegradable plastics with food waste, investigation of microbial diversity and digestate phytotoxicity

The effects of biodegradable plastics of different thicknesses (30 and 40 μm) and sizes (20 × 20, 2 × 2, and 1 × 1 mm) on anaerobic digestion of food waste and digestate phytotoxicity were investigated. Methane productions (38 days) for the groups with 20 × 20, 2 × 2, and 1 × 1 mm of 30 μm plastics were 92.46, 138.27, and 259.95 mL/gVSremoval, respectively which are nearly 58 % higher than the control group (58.86 mL/gVSremoval). Methane production in 40 μm plastics groups was lower than in 30 μm groups of equal size. All sizes of 30 µm plastics promoted substrate hydrolysis, acidification, and relative abundance of key hydrolytic bacteria and methanogens. Phytotoxicity tests results showed that seed root elongation was inhibited in groups with 40 μm plastics. In conclusion, 30 μm biodegradable plastics were more suitable for anaerobic digestion with food waste than 40 μm.