16S rRNA Gene Sequence Research Articles

Taklimakanibacter deserti gen. nov., sp. nov. and Taklimakanibacter lacteus sp. nov., isolated from desert soil.

Two Gram-stain-negative, aerobic, milk-white coloured, non-motile, short rod-shaped bacteria, designated as strains SYSU D60010T and SYSU D60012T, were isolated from sand samples collected from the Taklimakan Desert of Xinjiang Province in China. Both strains were positive for oxidase, catalase and nitrate reduction, but negative for amylase, H2S production, hydrolysis of gelatin and cellulase. Strains SYSU D60010T and SYSU D60012T grew well at 28 °C, at pH 7 and had the same NaCl tolerance range of 0-1 % (w/v). The major fatty acids (>5 %) of strains SYSU D60010T and SYSU D60012T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), iso-C19 : 0 cyclo ω8c, C16 : 0 and iso-C18 : 1 2-OH. Q-10 was the only respiratory ubiquinone. Strains SYSU D60010T and SYSU D60012T showed high 16S rRNA gene sequence similarities to Aestuariivirga litoralis SYSU M10001T (94.2 and 94.1 %), Rhodoligotrophos jinshengii BUT-3T (92.0 and 91.9 %) and Rhodoligotrophos appendicifer 120-1T (91.8 and 91.7 %), and the genomes were 7.4 and 5.8 Mbp in size with DNA G+C contents of 62.8 and 63.0 mol%, respectively. Phylogenetic, phenotypic and chemotaxonomic characteristics indicated that these two strains represent a novel genus and two novel species within the family Aestuariivirgaceae. We propose the name Taklimakanibacter deserti gen. nov., sp. nov. for strain SYSU D60010T, representing the type strain of this species (=KCTC 52783T =NBRC 113344T) and Taklimakanibacter lacteus gen. nov., sp. nov. for strain SYSU D60012T, representing the type strain of this species (=KCTC 52785T=NBRC 113128T).

The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host

The dominant bacteria in the hindgut of calves play an important role in their growth and health, which could even lead to lifelong consequences. However, the identification of core probiotics in the hindgut and its mechanism regulating host growth remain unclear. Here, a total of 1045 fecal samples were analyzed by 16S rRNA gene sequencing from the 408 Holstein dairy calves at the age of 0, 14, 28, 42, 56, and 70 days to characterize the dynamic changes of core taxa. Moreover, the mechanisms of nutrient metabolism of calf growth regulated by core bacteria were investigated using multi-omics analyses. Finally, fecal microbiota transplantation (FMT) in mice were conducted to illustrate the potential beneficial effects of core bacteria. Four calf enterotypes were identified and enterotypes dominated by Bifidobacterium and Oscillospiraceae_UCG-005 were representative. The frequency of enterotype conversion shifted from variable to stable. The close relationship observed between phenotype and enterotype, revealing a potential pro-growth effect of Bifidobacterium, might be implemented by promoting the use of carbohydrate, activating the synthesis of volatile fatty acids, amino acids and vitamin B6, and inhibiting methane production in the hindgut. The FMT results indicated the beneficial effect of Bifidobacterium on host growth and hindgut development. These results support the notion that the Bifidobacterium-dominated fecal microbiome would be an important driving force for promoting the host growth in the early life. Our findings provide new insights into the potential probiotic mining and application strategies to promote the growth of young animals or improve their growth retardation.

Anticandidal activity of a wild Bacillus subtilis NAM against clinical isolates of pathogenic Candida albicans

BackgroundResistance to antifungal medications poses a significant obstacle in combating fungal infections. The development of novel therapeutics for Candida albicans is necessary due to the increasing resistance of candidiasis to the existing medications. The utilization of biological control is seen as a more advantageous and less hazardous strategy therefore the objective of this study is to identify the antifungal properties of Bacillus subtilis against pathogenic C. albicans.ResultsWe conducted a study to evaluate the antifungal properties of three bacterial isolates against the human pathogen Candida albicans. One of the bacterial isolates exhibited a potent antifungal activity against this fungal pathogen. This bacterium was identified as Bacillus subtilis based on the 16Sr RNA gene sequence. It exhibited inhibitory efficacy ranging from 33.5 to 44.4% against 15 Candida isolates. The optimal incubation duration for achieving the maximum antifungal activity was determined to be 48 h, resulting in a mean inhibition zone diameter of 29 ± 0.39 mm. The Potato Dextrose agar (PDA) medium was the best medium for the most effective antifungal activity. Incubation temperature of 25oC and medium pH value of 8.0 were the most favorable conditions for maximum antagonistic activity that resulted fungal growth inhibition of 40 ± 0.16 and 36 ± 0.94 mm respectively. Furthermore, the addition of 10.5 mg/ml of bacterial filtrate to C. albicans colonies resulted in 86.51%. decrease in the number of germinated cells. The fungal cell ultrastructural responses due to exposure to B. subtilis filtrate after 48 h were investigated using transmission electron microscopy (TEM). It revealed primary a drastic abnormality that lead to cellular disintegration including folding and lysis of the cell wall, total collapse of the yeast cells, and malformed germ tube following the exposure to the filtrate. However, the control culture treatment had a characteristic morphology of the normal fungal cells featuring a consistently dense central region, a well-organized nucleus, and a cytoplasm containing several components of the endomembrane system. The cells were surrounded by a uniform and intact cell wall.ConclusionThe current study demonstrates a notable antifungal properties of B. subtilis against C. albicans as a result of production of bioactive components of the bacterial exudate. This finding could be a promising natural antifungal agent that could be utilized to combat C. albicans.

Microbial-derived Urolithin A targets GLS1 to inhibit glutaminolysis and attenuate cirrhotic portal hypertension

Background and AimsCirrhotic portal hypertension (CPH) is the leading cause of mortality in patients with cirrhosis. Over 50% patients with CPH treated with current clinical pharmacotherapy still present variceal bleeding or sometimes death owing to insufficient reduction in portal pressure. Elevated intrahepatic vascular resistance (IHVR) plays a fundamental role in increasing portal pressure. Because of its potent effect in reducing portal pressure and maintaining normal portal inflow to preserve liver function, lowering the IHVR is acknowledged as an optimal anti-CPH strategy but without clinical drugs. We aimed to investigate the protective effect of microbial-derived Urolithin A (UroA) in IHVR and CPH. MethodsCCl4 or BDL surgery was administered to mice to induce liver fibrosis and CPH. 16S rRNA gene sequencing was used for microbial analysis. Transcriptomics and metabolomics analyses were employed to study the host and cell responses. ResultsUroA was remarkably deficient in patients with CPH and was negatively correlated with disease severity. UroA deficiency was also confirmed in CPH mice and was associated with a reduced abundance of UroA-producing bacterial strain (Lactobacillus murinus, L. murinus). Glutaminolysis of hepatic stellate cells (HSCs) was identified as a previously unrecognized target of UroA. UroA inhibited the activity of glutaminase1 to suppress glutaminolysis, which counteracted fibrogenesis and contraction of HSCs and ameliorated CPH by relieving IHVR. Supplementation with UroA or L. murinus effectively ameliorated CPH in mice. ConclusionsWe for the first time identify the deficiency of gut microbial metabolite UroA as an important cause of CPH. We demonstrate that UroA exerts an excellent anti-CPH effect by suppressing HSC glutaminolysis to lower the IHVR, which highlighted its great potential as a novel therapeutic agent for CPH.

Revealing the microbial composition changes and relationship with Fusarium caused by rot disease in the Crocus sativus L.

PurposeRot disease caused by Fusarium poses a formidable threat to the growth of saffron (Crocus sativus L.), resulting in substantial damage to both yield and quality. It is paramount to delve into the root causes of rot disease in saffron to optimize both yield and quality. Existing preventive and treatment modalities have exerted deleterious effects on corms and the natural environment. Consequently, the quest for efficacious and eco-friendly methods such as biological control agents has become an urgent imperative.MethodsThe disparate distribution of microbial communities between rhizospheric microorganisms and saffron serves as the foundational exploration for uncovering the underlying causes of rot disease. Samples from various saffron organs and rhizosphere soil were gathered, and the sequencing data from the microbial communities were interpreted using 16S rRNA and ITS gene sequencing methods. This facilitated an in-depth examination of the composition and changes of microorganisms in both healthy and diseased saffron plants.ResultsThe findings indicated rot disease reduced the abundance and diversity of microorganisms in saffron, and the fungal co-occurrence networks were less stable and their communities were more sensitive to rot disease than the bacterial community. Fusarium was the predominant genus in diseased samples, accounting for 99.19% and 89.77% of the communities in diseased leaves and corms. With corms and leaves displaying heightened susceptibility to infection compared to other plant organs. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified in networks, they showed an antagonistic relationship with Fusarium, suggesting a potential for these bacteria to be used in biologically based control strategies against rot disease. These insights could prove invaluable for the development of biocontrol agents aimed at combating this plant ailment.ConclusionThese findings significantly advance our understanding of saffron-microbiome interactions and could provide fundamental and important data for improving saffron yield and quality in the process of sustainable development.

Metatranscriptomics: A Tool for Clinical Metagenomics.

In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.

Electroacupuncture at different frequencies improves visceral pain in IBS rats through different pathways.

The aim of this study was to investigate the frequency dependence of electroacupuncture (EA) in alleviating chronic visceral pain in patients with irritable bowel syndrome (IBS) and the differences in the gut microbiota and metabolites as potential mechanisms to explain frequency dependence. A visceral hyperalgesia model was established by colorectal instillation of 2,4,6-trinitrobenzene sulfonic acid in rats, and EA treatment at 2/10 Hz, 2/50 Hz and 2/100 Hz was applied at ST25. Visceral sensation was quantified by the abdominal withdrawal reflex score and the area under the curve of the rectus abdominis electromyogram in response to colorectal distension. Ultrastructural morphological damage of colonic tissue of the rats was examined by transmission electron microscopy. 16S rRNA gene sequencing and 1H-nuclear magnetic resonance spectroscopy were applied to study the differences in the gut microbiota and to perform metabonomic profiling of the colonic tissue. EA at ST25 at different frequencies attenuated chronic visceral pain, ultrastructural morphological damage to colonic tissue and disruption of the gut microbiota in IBS rats. The frequency of 2/100 Hz has more regulatory pathways than 2/10 Hz and 2/50 Hz. In addition, IBS rats exhibited colonic metabolic disorders, and pantothenate was significantly upregulated after EA treatment at different frequencies. Very low-density lipoprotein and 2-hydroxybutyrate were significantly increased in the 2/10 Hz group, while low density lipoprotein, very low-density lipoprotein, 2-hydroxybutyrate, methylmalonate and alpha-hydroxyisobutyric acid were significantly increased in the 2/100 Hz group. EA at ST25 at different frequencies attenuated chronic visceral pain through different gut microbiota and metabolic pathways.

Impact of cathodic pH and bioaugmentation on acetate and CH4 production in a microbial electrosynthesis cell.

This study compares carbon dioxide conversion in carbonate-fed microbial electrosynthesis (MES) cells operated at low (5.3), neutral (7) and high (8) pH levels and inoculated either with wild-type or bioaugmented mixed microbial populations. Two 100 mL (cathode volume) MES cells inoculated with anaerobic digester sludge were operated with a continuous supply of carbonate solution (5 g L-1 as CO3 2-). Acetate production was highest at low pH, however CH4 production still persisted, possibly due to pH gradients within the cathodic biofilm, resulting in acetate and CH4 volumetric (per cathode compartment volume) production rates of 1.0 ± 0.1 g (Lc d)-1 and 0.84 ± 0.05 L (Lc d)-1, respectively. To enhance production of carboxylic acids, four strains of acetogenic bacteria (Clostridium carboxidivorans, Clostridium ljungdahlii, Clostridium autoethanogenum, and Eubacterium limosum) were added to both MES cells. In the bioaugmented MES cells, acetate production increased to 2.0 g (Lc d)-1. However, production of other carboxylic acids such as butyrate and caproate was insignificant. Furthermore, 16S rRNA gene sequencing of cathodic biofilm and suspended biomass suggested a low density of introduced acetogenic bacteria implying that selective pressure rather than bioaugmentation led to improved acetate production.

3D printed rectal swabs for assessing the gut microbiome, metabolome and inflammation

Investigating the gut microbiome and metabolome frequently requires faecal samples, which can be difficult to obtain. Previous studies have shown that rectal swabs are comparable to faecal samples for analysing gut microbiota composition and key metabolites. In this study, 3D printed rectal swabs were compared with conventional flocked swabs and faecal samples, due to the potential advantages 3D printing as a technique offers for swab production and development. 16S rRNA gene sequencing, qPCR and metabolite profiling (using 1H-NMR spectroscopy) were performed on swab and faecal samples from healthy participants. Faecal calprotectin and total protein analysis were performed on samples from inflammatory bowel disease (IBD) patients. There were no significant differences between both swab types and faecal samples when assessing key measures of alpha and beta diversity, and differences in the abundance of major phyla. There was a strong correlation between both swab types and faecal samples for all combined metabolites detected by NMR. In IBD patients, there was no significant difference in faecal calprotectin and total protein levels between both swab types and faecal samples. These data lead us to conclude that 3D printed swabs are equivalent to flocked swabs for the analysis of the gut microbiome, metabolome and inflammation.

Early and long-term responses of intestinal microbiota and metabolites to 131I treatment in differentiated thyroid cancer patients

BackgroundMultiple high doses of 131I therapy in patients with differentiated thyroid cancer (DTC) might disrupt the balance of gut microbiota and metabolites. This study aimed to investigate the alterations of intestinal bacteria and metabolism over two courses of 131I therapy, explore the interactions, and construct diagnostic models reflecting enteric microecology based on 131I therapy.MethodsA total of 81 patients were recruited for the first 131I therapy (131I-1st), among whom 16 received a second course (131I-2nd) after half a year. Fecal samples were collected 1 day before (Pre-131I-1st/2nd) and 3 days after (Post-131I-1st/2nd) 131I therapy for microbiome (16S rRNA gene sequencing) and metabolomic (LC–MS/MS) analyses.ResultsA total of six microbial genera and 11 fecal metabolites enriched in three pathways were identified to show significant differences between Pre-131I-1st and other groups throughout the two courses of 131I treatment. In the Post-131I-1st group, the beneficial bacteria Bifidobacterium, Lachnoclostridium, uncultured_bacterium_f_Lachnospiraceae, and Lachnospiraceae_UCG004 were abundant and the radiation-sensitive pathways of linoleic acid (LA), arachidonic acid, and tryptophan metabolism were inhibited compared with the Pre-131I-1st group. Compared with the Pre-131I-1st group, the Pre-131I-2nd group exhibited a reduced diversity of flora and differentially expressed metabolites, with a low abundance of beneficial bacteria and dysregulated radiation-sensitive pathways. However, less significant differences in microbiota and metabolites were found between the Pre/Post-131I-2nd groups compared with those between the Pre/Post-131I-1st groups. A complex co-occurrence was observed between 6 genera and 11 metabolites, with Lachnoclostridium, Lachnospiraceae_UCG004, Escherichia-Shigella, and LA-related metabolites contributing the most. Furthermore, combined diagnostic models of charactered bacteria and metabolites answered well in the early, long-term, and dose-dependent responses for 131I therapy.ConclusionsDifferent stages of 131I therapy exert various effects on gut microecology, which play an essential role in regulating radiotoxicity and predicting the therapeutic response.

Miao sour soup alleviates DSS-induced colitis in mice: modulation of gut microbiota and intestinal barrier function.

Miao sour soup (MSS), a daily fermented food in Guizhou, China, is rich in microorganisms with various beneficial activities, including anti-inflammatory and antioxidant activities. However, the therapeutic effects of MSS on IBD remain unexplored. This study aimed to investigate the protective effect of MSS against colitis in mice. In this study, we examined the microbial community structure of MSS by metagenomic sequencing and also explored the protective effect of MSS on DSS-induced colitis in mice. We investigated the effects of MSS on intestinal inflammatory response and intestinal barrier function in mice. Finally, the changes in intestinal flora were analyzed based on the 16S rRNA gene sequencing results. Significantly, the experiment result shows that MSS ameliorated the severity of DSS-induced disease in mice by mitigating colitis-associated weight loss, reducing the disease activity index of IBD, alleviating colonic hemorrhagic lesions, increasing colon length, and improving colonic tissue damage. Moreover, MSS preserved intestinal barrier integrity and restored intestinal epithelial function in mice. Additionally, MSS modulated the structure and composition of the intestinal flora. Furthermore, MSS downregulated pro-inflammatory factors and attenuated the NF-κB p65 expression, thereby mitigating the inflammatory response. These findings highlight the protective effect of MSS against DSS-induced colitis, providing substantial scientific support for potential applications of MSS as a functional food.

Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter.

Two Gram-stain-negative, aerobic, motile by means of flagella, short rod-shaped bacterial strains, designated IMCC43200T and IMCC45268T, were isolated from coastal seawater samples collected from the South Sea of Korea. Strains IMCC43200T and IMCC45268T shared 98.6% 16S rRNA gene sequence similarity and were closely related to Congregibacter litoralis KT71T (98.8% and 98.7%, respectively). Complete whole-genome sequences of IMCC43200T and IMCC45268T were 3.93 and 3.86 Mb in size with DNA G + C contents of 54.8% and 54.2%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 74.5% and 23.4%, respectively, revealing that they are independent species. The two strains showed ANI values of ≤ 75.8% and dDDH values of ≤ 23.0% to the type and only species of the genus Congregibacter (C. litoralis), indicating that each strain represents a novel species. Both strains contained summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and summed feature 8 (comprising C18:1 ω6c and/or C18:1 ω7c) as major fatty acid constituents. The predominant isoprenoid quinone detected in both strains was ubiquinone-8 (Q-8). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and aminolipids. Based on the phylogenetic, genomic, and phenotypic characterization, strains IMCC43200T and IMCC45268T were considered to represent two novel species within the genus Congregibacter, for which the names Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. are proposed with IMCC43200T (= KCTC 8133T = NBRC 116295T = CCTCC AB 2023139T) and IMCC45268T (= KCTC 92921T = NBRC 116135T) as the type strains, respectively.

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.

E-Cigarette Use, Cigarette Smoking, and Sex are Associated with Nasal Microbiome Dysbiosis.

Previous research suggests that e-cigarettes can alter immune function, including in the nasal mucosa, in unique ways. The respiratory microbiome plays a key role in respiratory host defense, but the effects of e-cigarettes on the respiratory or nasal microbiome, are not well understood. Using 16S rRNA gene sequencing on nasal samples from adult e-cigarette users, smokers, and nonsmokers, we determined that e-cigarette use and cigarette smoking are associated with differential respiratory microbiome dysbiosis and substantial sex-dependent differences in the nasal microbiome, particularly in e-cigarette users. Staphylococcus aureus, a common respiratory pathogen, was more abundant in both e-cigarette users and smokers in comparison with nonsmokers, while Lactobacillus iners, often consider a protective species, was more abundant in smokers but less abundant in e-cigarette users in comparison with nonsmokers. In addition, we identified significant dysbiosis of the nasal microbiome between e-cigarette users and smokers with high versus low serum cotinine levels, an indicator of tobacco product use and toxicant exposure. We also analyzed nasal lavage fluid for immune mediators associated with host-microbiota interactions. Our analysis identified disruption of immune mediators in the nose of e-cigarette users and smokers, which is indicative of disrupted respiratory mucosal immune responses. Taken together, our data identified unique, sex-dependent host immune dysfunction associated with e-cigarette use in the nasal mucosa. More broadly, our data highlight the need for continued inclusion and careful consideration of sex as an important variable in the context of toxicant exposures. This is the first study investigating the effects of e-cigarette use and sex on the nasal microbiome, which is considered an important gatekeeper for protecting the lower respiratory tract from pathogens. We found significant sex, exposure group, and serum cotinine level associated differences in the composition of the nasal microbiome, demonstrating the importance of considering sex in future nasal microbiome studies and warranting further investigation of the mechanisms by which e-cigarette use dysregulates nasal immune homeostasis.

Q2-metnet: QIIME2 package to analyze 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota.

16S rRNA gene sequencing is the most frequent approach for the characterization of the human gut microbiota. Despite different efforts in the literature, the inference of functional and metabolic interpretations from 16S rRNA gene sequencing data is still a challenging task. High-quality metabolic reconstructions of the human gut microbiota, such as AGORA and AGREDA, constitute a curated resource to improve functional inference from 16S rRNA data, but they are not typically integrated into standard bioinformatics tools. Here, we present q2-metnet, a QIIME2 plugin that enables the contextualization of 16S rRNA gene sequencing data into AGORA and AGREDA. In particular, based on relative abundances of taxa, q2-metnet determines normalized activity scores for the reactions and subsystems involved in the selected metabolic reconstruction. Using these scores, q2-metnet allows the user to conduct differential activity analysis for reactions and subsystems, as well as exploratory analysis using PCA and hierarchical clustering. We apply q2-metnet to a dataset from our group that involves 16S rRNA data from stool samples from lean, allergic to cow's milk, obese and celiac children, and the Belgian Flemish Gut Flora Project cohort, which includes faecal 16S rRNA data from obese and normal-weight adult individuals. In the first case, q2-metnet outperforms existing algorithms in separating different clinical conditions based on predicted pathway abundances and subsystem scores. In the second case, q2-metnet complements competing approaches in predicting functional alterations in the gut microbiota of obese individuals. Overall, q2-metnet constitutes a powerful bioinformatics tool to provide metabolic context to 16S rRNA data from the human gut microbiota. Python code of q2-metnet is available in https://github.com/PlanesLab/q2-metnet and https://figshare.com/articles/dataset/q2-metnet_package/26180446. Supplementary data are available at Bioinformatics online.

Genetic characterization of Cryptosporidium spp. in the North African hedgehog (Atelerix algirus) in the Canary Islands, Spain.

The North African hedgehog (Atelerix algirus) is an introduced species from Northwest Africa and is currently distributed in the Canary Islands. This species of hedgehog has been studied as a reservoir of enteropathogens, including Cryptosporidium spp. However, there are no data at species level. Therefore, the aim of the present study was to identify the Cryptosporidium species present in a population of hedgehogs (n = 36) in the Canary Islands. Molecular screening was performed using conventional polymerase chain reaction (PCR) targeting the small subunit ribosomal RNA (18S rRNA) gene of Cryptosporidium spp. Seven of the 36 fecal samples (19.45%) were positive and confirmed by nested PCR targeting the 18S rRNA gene and Sanger sequencing. Cryptosporidium parvum and Cryptosporidium muris were identified in 11.1% (4/36) and 5.6% (2/36) of the samples, respectively, while one sample could only be identified at the genus level. The zoonotic subtypes IIdA15G1 (n = 1), IIdA16G1b (n = 1), and IIdA22G1 (n = 1) of C. parvum were identified by nested PCR followed by analysis of the 60kDa glycoprotein (gp60) gene sequence. This study is the first genetic characterization of Cryptosporidium spp. in A. algirus, identifying zoonotic species and subtypes of the parasite.

Dietary Pectin from Premna microphylla Turcz Leaves Prevents Obesity by Regulating Gut Microbiota and Lipid Metabolism in Mice Fed High-Fat Diet.

The present study was designed to investigate the protective effects of pectin extracted from Premna microphylla Turcz leaves (PTP) against high-fat-diet (HFD)-induced lipid metabolism disorders and gut microbiota dysbiosis in obese mice. PTP was made using the acid extraction method, and it was found to be an acidic pectin that had relative mole percentages of 32.1%, 29.2%, and 26.2% for galacturonic acid, arabinose, and galactose, respectively. The administration of PTP in C57BL/6J mice inhibited the HFD-induced abnormal weight gain, visceral obesity, and dyslipidemia, and also improved insulin sensitivity, as revealed by the improved insulin tolerance and the decreased glucose levels during an insulin sensitivity test. These effects were linked to increased energy expenditure, as demonstrated by the upregulation of thermogenesis-related protein UCP1 expression in the brown adipose tissue (BAT) of PTP-treated mice. 16S rRNA gene sequencing revealed that PTP dramatically improved the HFD-induced gut dysbiosis by lowering the ratio of Firmicutes to Bacteroidetes and the quantity of potentially harmful bacteria. These findings may provide a theoretical basis for us to understand the functions and usages of PTP in alleviating obesity.

Kiwifruit-Agaricus blazei intercropping effectively improved yield productivity, nutrient uptake, and rhizospheric bacterial community

Intercropping systems have garnered attention as a sustainable agricultural approach for efficient land use, increased ecological diversity in farmland, and enhanced crop yields. This study examined the effect of intercropping on the kiwifruit rhizosphere to gain a deeper understanding of the relationships between cover plants and kiwifruit in this sustainable agricultural system. Soil physicochemical properties and bacterial communities were analyzed using the Kiwifruit-Agaricus blazei intercropping System. Moreover, a combined analysis of 16S rRNA gene sequencing and metabolomic sequencing was used to identify differential microbes and metabolites in the rhizosphere. Intercropping led to an increase in soil physicochemical and enzyme activity, as well as re-shaping the bacterial community and increasing microbial diversity. Proteobacteria, Bacteroidota, Myxococcota, and Patescibacteria were the most abundant and diverse phyla in the intercropping system. Expression analysis further revealed that the bacterial genera BIrii41, Acidibacter, and Altererythrobacter were significantly upregulated in the intercropping system. Moreover, 358 differential metabolites (DMs) were identified between the monocropping and intercropping cultivation patterns, with fatty acyls, carboxylic acids and derivatives, and organooxygen compounds being significantly upregulated in the intercropping system. The KEGG metabolic pathways further revealed considerable enrichment of DMs in ABC transporters, histidine metabolism, and pyrimidine metabolism. This study identified a significant correlation between 95 bacterial genera and 79 soil metabolites, and an interactive network was constructed to explore the relationships between these differential microbes and metabolites in the rhizosphere. This study demonstrated that Kiwifruit-Agaricus blazei intercropping can be an effective, labor-saving, economic, and sustainable practice for reshaping bacterial communities and promoting the accumulation and metabolism of beneficial microorganisms in the rhizosphere.

Integrated analysis of gut microbiome and its metabolites in ACE2-knockout and ACE2-overexpressed mice.

Aberrant activation of the classic renin-angiotensin system (RAS) and intestinal micro dysbiosis adversely affect insulin resistance (IR), dyslipidemia, and other metabolic syndrome markers. However, the action of angiotensin-converting enzyme 2 (ACE2) and gut health in systemic homeostasis vary, and their interaction is not completely understood. We adopted a combinatory approach of metabolomics and fecal 16S rRNA analysis to investigate gut microbiota and metabolite in two different mouse models, ACE2 knockout (ACE2 KO) mice and the ACE2-overexpressing obese mice. 16S rRNA gene sequencing revealed that ACE2 influences microbial community composition and function, and ACE2 KO mice had increased Deferribacteres, Alcaligenaceae, Parasutterella, Catenibacterium, and Anaerotruncus, with decreased short-chain fatty acid (SCFA)-producing bacteria (Marvinbryantia and Alistipes). In contrast, ACE2-overexpressed mice exhibited increased anti-inflammatory probiotic (Oscillospiraceae, Marinifilaceae, and Bifidobacteriaceae) and SCFA-producing microbes (Rikenellaceae, Muribaculaceae, Ruminococcaceae, Odoribacter, and Alistipes) and decreased Firmicutes/Bacteroidetes, Lactobacillaceae, Erysipelotrichaceae, and Lachnospiraceae. Metabolome analysis indicated differential metabolites in ACE2 KO and ACE2-overexpression mice, especially the glucolipid metabolism-related compounds. Furthermore, correlation analysis between gut microbiota and metabolites showed a dynamic mutual influence affecting host health. Our study confirms for the first time a significant association between ACE2 status and gut microbiome and metabolome profiles, providing a novel mechanism for the positive effect of ACE2 on energy homeostasis.

Spatial Variation of Oomycetes and Bacteria on Surfaces, Solutions, and Plants from a Commercial Hydroponic Greenhouse

The spatial distribution and diversity of plant pathogens and other microbial communities in commercial operations is the first step in identifying critical control points where crops may be at risk of disease. Our objective was to characterize the spatial variation of oomycete pathogens and bacteria across the production system of a greenhouse producing lettuce in hydroponics. We utilized DNA metabarcoding to identify oomycetes and 16S rRNA gene sequencing of bacteria from different production stages and sample types (surfaces, solutions, and roots) collected from a commercial greenhouse producing lettuce in deepwater culture. Pythium was the genus with the highest relative abundance (41 to 100%) across all production stages. P. dissotocum was detected in most samples, except for sowing and seedling surfaces and municipal water, where P. myriotylum was the most abundant species. Oomycete communities showed distinct clustering by production stages and sample types, where sowing and seedling surfaces and municipal water were separated from the rest. Proteobacteria had the highest relative abundance in the surfaces at the sowing (98%) and seedling (85%) stages. Municipal water was the only sample with less than 20% relative abundance of Proteobacteria and dominated by Cyanobacteria. Negative correlations between Pythium and 13 bacteria genera point to potential antagonists in hydroponics that should be further studied. Mapping the spatial variation of oomycetes and bacterial communities in a commercial greenhouse indicates that production stage and sample type influence microbial composition and potentially the risk to disease.