Higher Microbial Richness Research Articles

Comparative study on the effects of anionic, cationic, and nonionic polyacrylamide surface modified magnetic micro-particles (MMP) for anaerobic digestion treatment of vegetable waste water (VWW)

Anaerobic digestion provides a solution for the treatment of vegetable waste water (VWW), but there are currently limited targeted treatment methods available. Building upon previous studies, this research investigated the effects of polyacrylamide-modified magnetic micro-particles (MMP) on anaerobic digestion (AD) of VWW. Three variations of these particles were created by grafting anionic, cationic, and non-ionic polyacrylamide (PAM) onto the MMPs’ surfaces, resulting in aPAM-MMP, cPAM-MMP, and nPAM-MMP, respectively. In AD experiments, the addition of aPAM-MMP notably enhanced the degradation of chemical oxygen demand (COD) in VWW. COD decreased to 1290 mg/L in the reactor with aPAM-MMP by day 12 and remained low, while the other reactors had COD concentrations of 4137.5, 5510, and 3010 mg/L on the same day, decreasing thereafter. This modification also improved the production and utilization of hydrogen gas and volatile fatty acids (VFAs), along with the conversion of methane. When tested for bioaffinity using fluorescent GFP-E.coli bacteria, the aPAM-MMP, cPAM-MMP, and nPAM-MMP demonstrated increases in fluorescence intensity by 51.66%, 36.13%, and 37.02%, respectively, compared to unmodified MMP when attached with GFP-E.coli. Further analyses of microbial community revealed that the reactor with aPAM-MMP had the highest microbial richness and enriched bacteria capable of organic matter degradation, such as Bacteroidota, Synergistota, Chloroflexi, Halobacterota phyla, and Parabacteroides, Muribaculaceae, and Azotobacter genera. In conclusion, our experiment verifies that APAM-MMP promotes anaerobic treatment of VWW and provides a novel reference point for enhancing VWW degradation.

Gut resistome linked to sexual preference and HIV infection

BackgroundPeople living with HIV (PLWH) are at increased risk of acquisition of multidrug resistant organisms due to higher rates of predisposing factors. The gut microbiome is the main reservoir of the collection of antimicrobial resistance determinants known as the gut resistome. In PLWH, changes in gut microbiome have been linked to immune activation and HIV-1 associated complications. Specifically, gut dysbiosis defined by low microbial gene richness has been linked to low Nadir CD4 + T-cell counts. Additionally, sexual preference has been shown to strongly influence gut microbiome composition in PLWH resulting in different Prevotella or Bacteroides enriched enterotypes, in MSM (men-who-have–sex-with-men) or no-MSM, respectively. To date, little is known about gut resistome composition in PLWH due to the scarcity of studies using shotgun metagenomics. The present study aimed to detect associations between different microbiome features linked to HIV-1 infection and gut resistome composition.ResultsUsing shotgun metagenomics we characterized the gut resistome composition of 129 HIV-1 infected subjects showing different HIV clinical profiles and 27 HIV-1 negative controls from a cross-sectional observational study conducted in Barcelona, Spain. Most no-MSM showed a Bacteroides-enriched enterotype and low microbial gene richness microbiomes. We did not identify differences in resistome diversity and composition according to HIV-1 infection or immune status. However, gut resistome was more diverse in MSM group, Prevotella-enriched enterotype and gut micorbiomes with high microbial gene richness compared to no-MSM group, Bacteroides-enriched enterotype and gut microbiomes with low microbial gene richness. Additionally, gut resistome beta-diversity was different according to the defined groups and we identified a set of differentially abundant antimicrobial resistance determinants based on the established categories.ConclusionsOur findings reveal a significant correlation between gut resistome composition and various host variables commonly associated with gut microbiome, including microbiome enterotype, microbial gene richness, and sexual preference. These host variables have been previously linked to immune activation and lower Nadir CD4 + T-Cell counts, which are prognostic factors of HIV-related comorbidities. This study provides new insights into the relationship between antibiotic resistance and clinical characteristics of PLWH.

Abstract 750: Specific oral bacterial profile associated with oral HPV status in Puerto Rican People with HIV

Abstract Human papillomavirus (HPV) accounts for more than 70% of oropharyngeal cancers and people with HIV (PWH) are disproportionately affected by HPV infection even with successful antiretroviral therapy. Puerto Rico (PR) is in the top ten in terms of HIV prevalence in the US, and also has disparities in HPV-related malignancies. The oral microbiome can increase the risk of HPV infection and persistence; however, it has not been investigated in the context of HIV in PR. Therefore, we evaluated diversity and composition of the oral bacteriome of 48 virologically suppressed PWH (men and women ≥21 and <64 years old) living in PR in relation to HPV status (HPV+: n=18 vs. HPV-: n=30). We collected saliva (16S rDNA sequencing), oral rinse (HPV genotyping) as well as sociodemographic, lifestyle and behavioral characteristics. Short chain fatty acids (SCFA, acetate, butyrate and propionate) were quantified using gas chromatography and mass spectrometry. Periodontal disease was assessed by a clinical full-mouth periodontal assessment using the CDC/AAP guidelines. All analyses were performed using QIIME2 and R-statistical software. There were no significant differences in alpha diversity (Shannon, observed OTUs, and Faith) between HPV+ and HPV- groups. Absolute CD4 count was not significantly different between HPV+ and HPV- participants (794 cells/µL vs. 735 cells/µL), and did not correlate with either microbial richness or diversity. Higher microbial richness was associated with lower levels of acetate (r=-0.35, p<0.05) and propionate (r=-0.31, p<0.05,). Additionally, higher phylogenetic diversity was also associated with lower levels of acetate (r=-0.38, p<0.05) and propionate (r=-0.35, p<0.05) irrespective of the HPV status. On the other hand, higher levels of butyrate was significantly associated with higher microbial diversity (Shannon index; r=0.33, p< 0.05). Taxonomic analyses showed significantly higher abundance of Dialister and Nanosynbacter genera in HPV+ participants and higher abundance of Rothia genus and Capnocytophaga sputigena in HPV- participants. Overall, we found specific prokaryotic profile and associated metabolites associated with HPV infection, which may suggest that the oral microbiome could influence the natural history of HPV infection via SCFA signaling. Members of the Dialister genus have been found to be prevalent in Hispanic and Black women cervicovaginal microbiota, and as well as in HPV infection and oral cancer. Understanding the underpinning mechanisms of how the oral microbiome can facilitate HPV infection and persistence in PWH is essential to establish targets for early identification and personalized treatment approaches for oral HPV-related malignancies. Citation Format: Yakshi N. Ortiz-Maldonado, Gabriel Borges-Velez, Jurelis Torres-Reyes, Alvin A. Peralta-Betanncourt, Jeannette L. Salgado-Montilla, Jorge Viera-Vera, Maria M. Sanchez-Vazquez, Magaly Martinez-Ferrer, Ana P. Ortiz-Martinez, Ramon F. Gonzalez-Garcia, Josue Perez-Santiago. Specific oral bacterial profile associated with oral HPV status in Puerto Rican People with HIV [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 750.

Deciphering microbial communities and their unique metabolic repertoire across rock-soil-plant continuum in the Dayoukeng fumarolic geothermal field of the Tatun Volcano Group.

High temperature and sulfur concentrations in geothermal sulfur fumaroles host unique microbial ecosystems with niche-specific metabolic diversity and physiological functions. In this study, the microbial communities and their functionalities associated with the Dayoukeng geothermal field and the rock-soil-plant continuum were investigated to underpin the microbial modulation at different distances from the fumaroles source. At the phylum level, Bacteroidota, Planctomycetota, Armatimonadota, and Patescibacteria were abundant in plant samples; Elusimicrobiota and Desulfobacterota were in the rock samples while Nitrospirota, Micrarchaeota, and Deinococcota were dominant in the soil samples. Acidophilic thermophiles were enriched in samples within close proximity to the fumaroles, primarily at a distance of 1m. The sulfur and iron-oxidizing acidophilic bacterial genera such as Acidothiobacillus and Sulfobacillus were abundant in the rock samples. The thermoacidophilic archaeon Acidianus and acidophilic bacteria Acidiphilium were abundant in the soil samples. Additionally, Thermosporothrix and Acidothermus were found abundant in the plant samples. The results of the functional annotation indicated that dark sulfur oxidation, iron oxidation, and hydrogen oxidation pathways were abundant in the soil samples up to 1m from the fumaroles, while methanogenic and fermentation pathways were more prevalent in the soil samples located 10m from the fumaroles. Interestingly, the results of this study indicated a higher microbial richness and abundance of acidophilic communities in the soils and plants compared to the rocks of the DYK fumarolic geothermal field.

Soil multifunctionality predicted by bacterial network complexity explains differences in wheat productivity induced by fertilization management

Fertilization will cause changes in crop growth, soil microbial community and multiple ecosystem functions, but it is unclear whether and how the optimal productivity obtained by manure application and optimizing nitrogen is driven by microbial community and ecosystem multifunctionality. We explore this mechanism based on a field fertilization experiment using a split-plot design that began in 2014 with five N rates (N0, N75, N150, N225, N300) as main plots and two manure rates (M0, NPK group; M1, MNPK group) as subplots, respectively. In general, (1) grain yield was parabolically related to the N application rate. The N rates that obtained the highest yield were 150 kg ha−1 and 225 kg ha−1 for the MNPK and NPK groups, respectively. The average yield of the MNPK group was 10.5% higher than that of the NPK group. (2) Long-term fertilization management resulted in regular changes in soil multifunctionality (SMF) and the properties of various microbial communities. The richness, network complexity and soil multifunctionality of bacterial and fungal communities also increased initially and then decreased as the N rate. On average, the response ratio of soil multifunctionality to N75, N150, N225, N300 (control is N0) and M1 (control is M0) were 0.11, 0.41, 0.53, 0.44 and 1.19, respectively. The soil multifunctionality of MNPK was 260%, 722% and 101% higher than that of NPK at the tillering, jointing and harvest stages, respectively. (3) Soil multifunctionality not only always had a significant positive effect on aboveground biomass at all growth stages, but also had significant positive correlations with bacterial richness and network complexity. Based on the existing framework, we further demonstrated that high microbial richness supports multifunctionality by ensuring strong associative complexity among microorganisms. However, only bacterial network complexity always positively drove soil multifunctionality and indirectly influenced wheat growth at all growth stages in SEMs where multiple drivers were considered simultaneously (i.e., pH, SOC and biological factors). Random forest regression analysis showed that rare bacterial taxa had stronger predictive effects on soil multifunctionality than abundant taxa. Our results validate that M1N150 can ensure high yield in the study area while maintaining a high level of ecosystem function in the soil, which also contributes to the reduction of adverse environmental risks caused by fertilizer application. Importantly, the potential of microbial network complexity, especially bacterial network complexity, to influence crop growth by driving farmland ecosystem functions deserves to be explored under different crop types, cropping systems, and irrigation conditions, compared to previous microbial richness that has been simply quantified.

Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows

Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 ℃ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 ℃. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.

Effect of HRT on nitrogen removal from low carbon source wastewater enhanced by slurry and its mechanism

Insufficient carbon sources in low-carbon wastewater have consistently hindered nitrogen removal performance. This work utilized slurry after anaerobic digestion as an additional carbon source, and the optimal hydraulic retention time (HRT) parameters were obtained through adjustment. The findings revealed that, under HRT conditions of 24–12 h, the discharge standards of wastewater treatment plants (WWTPs) could be met. It had been proven that HRT 12 h was the more cost-effective parameter for application in WWTPs, and the removal efficiencies for COD, NH4+-N, NO3–-N, and TN reached impressive levels of 82.43%, 95.24%, 77.49%, and 86.70%, respectively. However, the HRT 6 h struggled to achieve efficient wastewater treatment. Mechanistic analysis demonstrated that shortening the HRT resulted in considerably higher microbial richness, diversity, and evenness, causing notable shifts in microbial community structure. Additionally, a shortened HRT reduced the enrichment abundance of key bacterial phyla (Proteobacteria, Bacteroidetes) and genera (Hydrogenophaga, Filimonas, Meganema) that played an important role in nitrogen and organic matter removal. Furthermore, a shortened HRT increased hydraulic shear forces, impeding the enrichment of carbon and nitrogen metabolism pathways, and reducing the abundance of essential genes associated with glycolysis (HK, pfkA, FBA, GAPDH) and nitrogen metabolism processes (narG, narH, narI, norB, nirS, nosZ). It was noteworthy that the microbial community under the HRT 6 h condition carried the highest risk of microbial pathogenicity. This work revealed the optimal parameters, and carbon and nitrogen metabolism mechanism of wastewater treatment systems with slurry as a carbon source for the first time, and provided novel ideas and insights for low-carbon wastewater treatment.

The heterogeneity of microbial diversity and its drivers in two types of sediments from tidal flats in Beibu Gulf, China

Mudflats and sandflats are two common types of coastal tidal flats, the structure and function differences of microbial communities between them are still underappreciated. Beibu Gulf is a diurnal tidal regime located in China, the differences between the two type of tidal flats could be more distinct. In this study, we collected a total of 6 samples from Beibu Gulf, consisting of 3 sandflats samples and 3 mudflats samples, classified based on clay and silt content. Generally, the mudflats samples exhibited higher levels of NH4+_N and TOC, but lower in ORP and pH. The microbial diversity of the two types of tidal flats was investigated, revealing great differences existed and sandflats had higher microbial richness and diversity than mudflats. Furthermore, we analyzed the association between microbial communities and environmental factors, finding NH4+_N to have the highest contribution to the total variation in microbial community structure, and microbial groups such as Desulfobacterota, Campilobacterota, Chloroflexota, Calditrichota, Spirochaetota, Zixibacteria, Latescibacterota and Sva0485 group in mudflats were positively associated with NH4+_N. The functions of microbial community were predicted using metagenomic sequences and metagenome assembled genome (MAG). Mudflats contained more genes for carbon fixation. Nitrate and nitrite reduction were widely existed in mudflats and sandflats, but nitrogen fixation was only existed in mudflats, and Campilobacterota, Desulfobacterota and Gammaproteobacteria MAGs were mainly responsible for it. Sandflats composed more genes for ammonium oxidation, but no MAG was found whether in sandflats or mudflats. Microbes in mudflats exhibited a greater abundance of genes related to sulfur cycling, especially in reduction process, unique MAGs in mudflats such as Calditrichota, Chloroflexota, Desulfobacterota and Zixibacteria MAGs are responsible for sulfate and sulfite reduction. Finally, we predicted functions of ammonium related microbes in mudflats based on MAGs and found Campilobacterota and Desulfobacterota MAGs were important for high accumulation of ammonium in mudflats. This study illuminated the structural and functional differences of microbial communities in mudflats and sandflats, providing new insights into the relationship of microbial communities and environment in the tidal flat.

Pooled allogeneic faecal microbiota MaaT013 for steroid-resistant gastrointestinal acute graft-versus-host disease: a single-arm, multicentre phase 2 trial

Failure of gastrointestinal acute graft-versus-host disease (GI-aGvHD) to respond to steroid therapy is associated with limited further therapeutic options. We aimed to assess the safety and efficacy of the first-in-human use of the pooled allogeneic faecal microbiota, MaaT013, for the treatment of steroid-refractory GI-aGvHD. This prospective, international, single-arm, phase 2a study reports clinical outcomes from a 24-patient cohort with grade III-IV, steroid refractory GI-aGvHD treated with the pooled allogeneic faecal microbiota MaaT013. MaaT013 involved pooling faecal matter from 3 to 8 screened donors then transplanting the pooled batches into patients to treat GI-aGVHD. The 24 patients were treated in the HERACLES study (Aug 2018 to Nov 2020) at 26 sites in Europe and an additional 52 patients were treated in a compassionate use/expanded access program (EAP) in France (July 2018 to April 2021). The primary endpoint was GI response at day 28, defined as the proportion of patients with GI-aGvHD who had a complete response (CR) or very good partial response (VGPR). GvHD grading and staging were assessed according to the revised Glucksberg criteria. Adverse events and severe adverse events were monitored for 6 months and 12 months, respectively. The HERACLES study was registered with ClinicalTrials.gov (NCT03359980). Compared with single donors, MaaT013 is characterised by higher microbial richness and reduced variability across batches. At day 28 (D28), the GI-overall response rate (ORR) was 38% in the prospective population, including 5 complete responses (CR), 2 very good partial responses (VGPR) and 2 partial responses (PR). In the EAP, the GI-ORR was 58% (17 CR, 9 VGPR and 4PR). The 12-month overall survival (OS) was 25% in the prospective study and 38% in the EAP. Regarding safety, five infectious complications, including 3 sepsis, could not be excluded from being related to the study procedure in HERACLES. Shotgun sequencing analyses of the identified strains suggest that none were found in MaaT013. In the EAP, 18 pharmacovigilance cases were reported among 52 treated patients, including 11 bacteraemia/sepsis. In HERACLES, we observed in stools from responding patients at D28 a higher microbiota richness and increased levels of beneficial bacteria, in particular butyrate producers, along with increased levels of short-chain fatty acid and bile acids. In contrast, stools from non-responding (NR) patients displayed increased levels of pathogenic pro-inflammatory bacteria along with increased systemic inflammatory parameters. Overall, MaaT013 was safe in this population of highly immunocompromised patients and was associated with responses in some patients with GI-aGvHD and deserves further investigation. MaaT Pharma.

Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis.

rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the commercial DNA extraction and sequencing platform SepsiTest (ST). The goal was to analyze the clinical performance of ST with a focus on nongrowing pathogens and the impact on antibiotic therapy. A literature search used PubMed/Medline, Cochrane, Science Direct, and Google Scholar. Eligibility followed PRISMA-P criteria. Quality and risk of bias were assessed drawing on QUADAS-2 (quality assessment of diagnostic accuracy studies, revised) criteria. Meta-analyses were performed regarding accuracy metrics compared to standard references and the added value of ST in terms of extra found pathogens. We identified 25 studies on sepsis, infectious endocarditis, bacterial meningitis, joint infections, pyomyositis, and various diseases from routine diagnosis. Patients with suspected infections of purportedly sterile body sites originated from various hospital wards. The overall sensitivity (79%; 95% confidence interval [CI], 73 to 84%) and specificity (83%; 95% CI, 72 to 90%) were accompanied by large effect sizes. ST-related positivity was 32% (95% CI, 30 to 34%), which was significantly higher than the culture positivity (20%; 95% CI, 18 to 22%). The overall added value of ST was 14% (95% CI, 10 to 20%) for all samples. With 130 relevant taxa, ST uncovered high microbial richness. Four studies demonstrated changes of antibiotic treatment at 12% (95% CI, 9 to 15%) of all patients upon availability of ST results. ST appears to be an approach for the diagnosis of nongrowing pathogens. The potential clinical role of this agnostic molecular diagnostic tool is discussed regarding changes of antibiotic treatment in cases where culture stays negative.

Microbial community composition in urban riverbank sediments: response to municipal effluents over spatial gradient.

Municipal effluents have adverse impacts on the aquatic ecosystem and especially the microbial community. This study described the compositions of sediment bacterial communities in the urban riverbank over the spatial gradient. Sediments were collected from seven sampling sites of the Macha River. The physicochemical parameters of sediment samples were determined. The bacterial communities in sediments were analyzed by 16S rRNA gene sequencing. The results showed that these sites were affected by different types of effluents, leading to regional variations in the bacterial community. The higher microbial richness and biodiversity at SM2 and SD1 sites were correlated with the levels of NH4+-N, organic matter, effective sulphur, electrical conductivity, and total dissolved solids (p < 0.01). Organic matter, total nitrogen, NH4+-N, NO3-N, pH, and effective sulphur were identified to be important drivers for bacterial community distribution. At the phylum level, Proteobacteria (32.8-71.7%) was predominant in sediments, and at the genus level, Serratia appeared at all sampling sites and accounted for the dominant genus. Sulphate-reducing bacteria, nitrifiers, and denitrifiers were detected and closely related to contaminants. This study expanded our understanding of municipal effluents on microbial communities in riverbank sediments, and also provided valuable information for further exploration of microbial community functions.

Comparison on biological nutrient removal and microbial community between full-scale anaerobic/anoxic/aerobic process and its upgrading processes

A comparative study was conducted for the anaerobic/anoxic/aerobic (AAO) process and its two upgrading processes, five-stage Bardenpho and AAO coupling moving bed bioreactors (AAO + MBBR), using long-term operation data of six full-scale wastewater treatment plants. The three processes all had good COD and phosphorus removal performance. The reinforcing effects of carriers on nitrification were moderate at full-scale applications, while the Bardenpho was advantageous in nitrogen removal. The AAO + MBBR and Bardenpho processes both had higher microbial richness and diversity than the AAO. The AAO + MBBR favored bacteria to degrade complex organics (Ottowia and Mycobacterium) and to form biofilms (Novosphingobium), and preferentially enriched denitrifying phosphorus-accumulating bacteria (DPB) (norank_o__Run-SP154) with the highest anoxic to aerobic phosphorus uptake rates of 65.3 % − 83.9 %. The Bardenpho enriched bacteria tolerant to varied environments (Norank_f__Blastocatellaceae, norank_o__Saccharimonadales, and norank_o__SBR103), and was more suitable for the upgrading of the AAO because of its excellent pollutant removal performance and flexible operation mode.

Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice.

Obesity places a tremendous burden on individual health and the healthcare system. The gut microbiome (GM) influences host metabolism and behaviors affecting body weight (BW) such as feeding. The GM of mice varies between suppliers and significantly influences BW. We sought to determine whether GM-associated differences in BW are associated with differences in intake, fecal energy loss, or fetal growth. Pair-housed mice colonized with a low or high microbial richness GM were weighed, and the total and BW-adjusted intake were measured at weaning and adulthood. Pups were weighed at birth to determine the effects of the maternal microbiome on fetal growth. Fecal samples were collected to assess the fecal energy loss and to characterize differences in the microbiome. The results showed that supplier-origin microbiomes were associated with profound differences in fetal growth and excessive BW-adjusted differences in intake during adulthood, with no detected difference in fecal energy loss. Agreement between the features of the maternal microbiome associated with increased birth weight here and in recent human studies supports the value of this model to investigate the mechanisms by which the maternal microbiome regulates offspring growth and food intake.

488. Association between the Respiratory Microbiota and Response to Antibiotic Therapy in Children with Macrolide-resistant Mycoplasma pneumoniae Pneumonia

Abstract Background Along with the overuse of macrolides as the empirical treatment for M. pneumoniae infection, macrolide-resistant M. pneumoniae (MRMP) emerged up to 90 prevalence rate in Asian countries. We investigated whether respiratory microbiota at the beginning of hospitalization was associated with disease severity and response to antibiotic treatment in children with MRMP pneumonia. Methods Prospectively enrolled children aged &amp;lt; 18 years with community-acquired pneumonia caused by MRMP from 2017/4-2020/3 at Linkou Chang Gung Memorial Hospital. Oropharyngeal samplings were collected within 48 hours after admission. Total 66 children were included: 23 had not received macrolide or gave response to macrolide (defined as without effective treatment group); 43 needed doxycycline treatment (defined as doxycycline treatment group). Compared the oropharyngeal microbiota between groups using the 16S-rRNA-based sequencing. Patients who were administered antibiotics other than augmentin or Azithromax were excluded. The difference in microbial composition will be examined using microbial community analysis. Statistically significant species for each group were evaluated by the linear discriminant analysis of effect size analysis to identify differentially abundant biomarkers, comparing disease severity scores, CRP and febrile days lasting. Scheme of sample collection and analyses Augmentin with or without Azithromax was the most common antimicrobial agent used. If fever persisted under the impression of suspected MRMP infection, doxycycline was used following three days of Azithromax usage. Scheme of sample collection and analyses Correlation between microbiome and clinical feature. Results Doxycycline treatment group had longer duration of total febrile days (p&amp;lt; 0.001) and total hospitalization days (p=0.002). Without effective treatment group had higher microbial richness, different overall community composition (p&amp;lt; 0.01). The lowest respiratory alpha diversity had prolonged febrile days (p=0.032). Without effective treatment group had more abundant spices or genera. Classification of samples to detect patients with effective treatment or not based on these selected microbiota genera features achieved the ROC curve of 0.86. From the list of most relatively abundant species in MRMP patient without doxycycline, Fusobacterium periodonticum most negatively correlated with total febrile days and severity score. Clinical characteristics of patients enrolled in this study Data were shown as n (%) or mean ± standard deviation. N/A, not applicable. Taxonomic assignment of the all throat swab samples. Fraction of predominant microbiota with a relative abundance of at least 2% at the order level (A) and genus level (B) in all sample. Higher respiratory microbial diversity is associated with MRMP patients without effective treatment than MRMP patients who needed doxycycline treatment Microbial richness base on the different alpha-diversity index in MRMP patients without effective treatment (blue); MRMP patients with doxycycline treatment (red). (A)(B)The box represented the interquartile range (IQR, and the midline represented the median. Tukey’s honest significance test of ANOVA, p&amp;lt;0.05.) (C)Kaplan-Meier (KM) plot of febrile time by respiratory diversity. (D)Principal coordinates analysis (PCoA) for MRMP patients without effective treatment (blue), MRMP patients with doxycycline treatment (red) by Unweighted UniFrac distance. Significant differences were observed between MRMP patients without effective treatment and MRMP patients with doxycycline treatment. A PERMANOVA (α=0.05) with 999 random permutations, p = 0.001. Conclusion Respiratory dysbiosis was associated with persistent fever and disease severity in MRMP pneumonia. In our study, F. periodoticum negatively related to fever duration and disease severity. Compositional differences in the respiratory microbiome are associated with MRMP patients without effective treatment than MRMP patients who needed doxycycline treatment by LEfSE analysis LDA scores revealed differentially abundant bacteria in the respiratory microbiome of without effective treatment (blue) and doxycycline treatment (red) groups at genus level (A) and species level (B).The mean relative abundance of genera at right side. The mean relative abundance of genera at right side. (C) Receiver operating characteristic (ROC) curves of ASVs to predict MRMP patients without effective treatment or who needed doxycycline treatment. Pairwise Spearman rank correlation heat map of significantly different taxa in throat swabs at initial sampling and clinical severity score in MRMP patients without effective treatment/with doxycycline treatment The genus (A) and species (B) level. Genus and species were in rows; the correlation was indicated by color gradient. Disclosures All Authors: No reported disclosures.

Universal drivers of cheese microbiomes

The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a systematic literature review of cheese microbiology research, we collected 16S rRNA gene amplicon sequence data from 824 cheese samples spanning 58 cheese types and 16 countries. We found a consistent, positive relationship between microbiome richness and pH, and a higher microbial richness in cheeses derived from goat milk. In contrast, we found no relationship between pasteurization, geographic location, or salinity and richness. Milk and cheese type, geographic location, and pasteurization collectively explained 65% of the variation in microbial community composition. Importantly, we identified four universal cheese microbiome types, driven by distinct dominant taxa. Our study reveals notable diversity patterns among the cheese microbiota, which are driven by geography and local environmental variables.

The high accumulation of phosphorus in high-yield paddy soils: A new insight from cutans

Phosphorus (P) is a key limiting nutrient for crops. Oscillation of redox conditions usually induces formation of Fe-enriched cutans in the plow layer of paddy soils. This study investigated P biogeochemistry in the cutans, which were collected from high-yield paddy soils in Taihu Lake region, China. Mössbauer spectroscopy showed that the content of Fe3+ was eight times higher than Fe2+ in the cutans. Based on the evidences from XRD and wet chemical analysis, the enriched Fe in the cutans mostly existed as amorphous oxides, which owned high surface areas for P sorption. In addition, the cutans were composed of spherical particles with diameters of 20–130 μm under microscopy. Moreover , the particles showed evident “trench” structures on their top surface under SEM imaging. These features caused the cutans to retain three times higher P than that in the matrix soils. Furthermore, the cutans demonstrated both high microbial richness and community diversity, in contrast to the matrix soils. In particular, the abundance of phosphate-solubilizing fungi (with relatively highly competitive saprophytic ability) was also significantly promoted. Therefore, the cutans could be considered as hotspots of P accumulation in paddy soils. The subsequent enhancement of the available P would promote rice production.

Assessing the performance and microbial structure of biofilms in membrane aerated biofilm reactor for high p-nitrophenol concentration treatment

P-nitrophenol (PNP) is a mono-nitrophenol compound that is highly toxic and difficult to degrade, causing great harm to the ecological environment and human health. In this study, a membrane aerated biofilm reactor (MABR) was used to degrade high PNP concentration without external carbon sources. This experiment mainly presented the process performance of MABR under high-load shock of PNP and variations in the community biodiversity and compositions of MABR biofilm. The experimental results showed that as the concentration of PNP in the influent gradually increased from 100 mg/L to 400 mg/L, the MABR exhibited a strong shockproof ability. The performance of the MABR peaked at an influent PNP concentration of 200 ± 50 mg/L, the removal efficiencies of PNP and chemical oxygen demand (COD) were 94.40% and 79.57%, respectively, and the removal loads were 3.644 g·m−2·d−1 and 4.975 g·m−2·d−1, respectively. The results of high-throughput sequencing revealed that MABR biofilms had high microbial richness and diversity, in which the microbial activity was not influenced by high-load shock. PNP, as a selective pressure, was used by microorganisms as the sole carbon source. The relative abundance of dominant phyla (Patescibacteria, Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidota), classes (Saccharimonadia, Clostridia, Actinobacteria, Bacilli, Gammaproteobacteria, Bacteroidia, and CPR2), and genera (TM7a, unclassified_o_Saccharimonadales, Proteiniclasticum, and norank_f_norank_o_Saccharimonadales) were different between the evaluated samples. Numerous candidate phyla radiation (CPR) bacteria were enriched in the MABR, indicating that CPR was the functional bacteria responsible for the degradation of high concentrations of PNP. The findings of this study demonstrated that the MABR system possesses great feasibility and potential for the advanced treatment of phenolic compounds.

Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance

BackgroundIn nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as a dynamic ecosystem in which players are subjected to continuous environmental and spatiotemporal stimuli.ResultsThe inspection of spontaneous sourdough metagenomes and transcriptomes revealed dominant, subdominant and satellite players that are engaged in different functional pathways. The highest microbial richness was associated with the highest number of gene copies per pathway. Based on meta-omics data collected from 8 spontaneous sourdoughs and their identified microbiota, we de novo reconstructed a synthetic microbial community SDG. We also reconstructed SMC-SD43 from scratch using the microbial composition of its spontaneous sourdough equivalent for comparison. The KEGG number of dominant players in the SDG was not affected by depletion of a single player, whereas the subdominant and satellite species fluctuated, revealing unique contributions. Compared to SMC-SD43, SDG exhibited broader transcriptome redundancy. The invariant volatilome profile of SDG after in situ long-term back slopping revealed its stability. In contrast, SMC-SD43 lost many taxon members. Dominant, subdominant and satellite players together ensured gene and transcript redundancy.ConclusionsOur study demonstrates how, by starting from spontaneous sourdoughs and reconstructing these communities synthetically, it was possible to unravel the metabolic contributions of individual players. For resilience and good performance, the sourdough metacommunity must include dominant, subdominant and satellite players, which together ensure gene and transcript redundancy. Overall, our study changes the paradigm and introduces theoretical foundations for directing food fermentations.EMEdktm6hHpuS2J-XhY8obVideo

The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system

Organic amendments are applied in organic farming systems to provide nutrients for crop uptake and to improve soil health. Compost is often favored over fresh manure for food safety reasons, while fresh manure can be a valuable source of readily available nitrogen (N). However, the potential for fresh versus composted manure to differentially affect soil microbial and N-cycling functional communities over multiple seasons remains unknown. We compared the effect of composted vs. fresh cattle manure on soil microbial communities using taxonomic and functional approaches. Soils were collected from field plots with three organic N treatments: control (no amendment), composted manure (compost, 224 kg/ha total N), and fresh manure (manure, 224 kg/ha total N) in an organic production system. Illumina amplicon sequencing was used to comprehensively assess the bacterial community (16S rRNA genes), fungal community (ITS), ureolytic community (ureC), chitinolytic community (chiA), bacterial ammonia oxidizers (AOBamoA), and nitrite oxidizers (Nitrospira nxrB). The results showed that both compost and manure treatment significantly changed the soil microbial communities. Manure had a stronger effect than compost on soil bacterial and fungal community composition, as well as on the ureolytic and chitinolytic communities, while compost treated soils had higher microbial richness than manure treated soils. Both taxonomic and functional approaches showed that the microbial community was more responsive to fresh manure than to compost. Manure treated soil also had more complex microbial interactions than compost treated soil. The abundance and community composition of N-cycling functional groups often played more limited roles than soil chemical properties (soil organic carbon, extractable organic carbon, and pH) in driving N-cycling processes. Results from our study may guide strategies for the management of organic amendments in organic farming systems and provide insights into the linkages between soil microbial communities and soil function.

Depth-depended quality comparison of light-flavor fermented grains from two fermentation rounds

To improve the utilization of raw materials, the fermentation of light-flavor Baijiu (LFB) will usually take two rounds of fermentation to the same batch of raw materials. The microorganisms involved in the fermented grains (FG) from these two fermentation rounds are the key to the quality formation of light-flavor style. Using Illumina MiSeq high-throughput sequencing and electronic-senses, it was found that the microbiota and flavor of FG for light-flavor Baijiu were mainly affected by fermentation rounds rather than depths, while the physicochemical factors were just the opposite. Starch was the most influential physiochemical factor on the microbiota. FG from the first fermentation round (FFRFG) had a higher fungal diversity, while FG from the second fermentation round (SFRFG) had a higher microbial richness and bacterial diversity. Monascus and the function of metabolism were significantly enriched in FFRFG; while Nocardia, Saccharomyces, Aspergillus and the functions of information storage and processing as well as cellular processes and signaling were significantly enriched in SFRFG. The flavor characteristics of FFRFG were mainly sourness as well as rich in sulfur organic compounds and broad range compounds, while that of SFRFG was mainly saltiness, umami, and bitterness, as well as rich in aromatic compounds. The findings could contribute to a comprehensive understanding of the role of FG in LFB fermentation from the perspective of rounds and depths.