@article {pmid36970665,
year = {2023},
author = {Gong, R and Song, S and Ai, Y and Wang, S and Dong, X and Ren, Z and Xie, H and Jiang, B and Zhao, L},
title = {Exploring the growing forest musk deer (Moschus berezovskii) dietary protein requirement based on gut microbiome.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1124163},
pmid = {36970665},
issn = {1664-302X},
abstract = {It is necessary to assess the appropriate dietary protein level of the forest musk deer (FMD), as nutritional needs are unclear. The microbiome in gastrointestinal tracts plays an important role in regulating nutrient utilization, absorption and host growth or development. Thus, we aimed to evaluate growth performance, nutrient digestibility and fecal microbiome of growing FMD supplied with different protein levels of diets. Eighteen 6-month-old male FMD with an initial weight 5.0 ± 0.2 kg were used in a 62-day trial. The animals were randomly distributed to three groups, the dietary crude protein (CP) level was 11.51% (L), 13.37% (M), and 15.48% (H). The results showed that the CP digestibility decreased as dietary CP level increased (p < 0.01). Compared with group L and H, FMD in M group has higher average daily gain, feed efficiency and neutral detergent fiber digestibility. For the fecal bacterial community, the percentage of Firmicutes was increased, Bacteroidetes was decreased and the diversity of microbiota significantly reduced (p < 0.05) with the increasing of dietary protein. The proportion of Ruminococcaceae_005, Ruminococcaceae_UCG-014 and uncultured_bacterium_f_Lachnospiraceae were significantly increased wtih rising CP, the proportions of Bacteroides and Rikenellaceae_RC9_gut_group were significantly decrease nevertheless at the genus level. The higher abundance of f_Prevotellaceae and g_Prevotellaceae_UCG_004 were found at M group by LEfSe analysis. The relative abundance of uncultured_bacterium_f_Ruminococcaceae was positively correlated with the average daily gain and feed conversion ratio (p < 0.05), whereas Family_XIII_AD3011_group was negatively correlated with feed conversion ratio (p < 0.05). The UPGMA tree showed L and M groups were closer in clustering relationship, while H group was clustered separately into a branch, which indicated that the bacterial structure had changed greatly with protein level increased from 13.37 to 15.48%. Overall, our results indicated that the optimum dietary CP for the growing FMD was 13.37%.},
}

@article {pmid36970663,
year = {2023},
author = {Zhong, X and Zhao, Y and Huang, L and Liu, J and Wang, K and Gao, X and Zhao, X and Wang, X},
title = {Remodeling of the gut microbiome by Lactobacillus johnsonii alleviates the development of acute myocardial infarction.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1140498},
pmid = {36970663},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbial community, which can be disturbed or repaired by changes in the internal environment, contributes to the development of acute myocardial infarction (AMI). Gut probiotics play a role in microbiome remodeling and nutritional intervention post-AMI. A newly isolated Lactobacillus johnsonii strain EU03 has shown potential as a probiotic. Here, we investigated the cardioprotective function and mechanism of L. johnsonii through gut microbiome remodeling in AMI rats.

METHODS: A rat model of left anterior descending coronary artery ligation (LAD)-mediated AMI was assessed with echocardiography, histology, and serum cardiac biomarkers to evaluate the beneficial effects of L. johnsonii. The immunofluorescence analysis was utilized to visualize the intestinal barrier changes. Antibiotic administration model was used for assessing the gut commensals' function in the improvement of cardiac function post-AMI. The underlying beneficial mechanism through L. johnsonii enrichment was further investigated by metagenomics and metabolomics analysis.

RESULTS: A 28-day treatment with L. johnsonii protected cardiac function, delayed cardiac pathology, suppressed myocardial injury cytokines, and improved gut barrier integrity. The microbiome composition was reprogrammed by enhancing the abundance of L. johnsonii. Microbiome dysbiosis by antibiotics abrogated the improvement of cardiac function post-AMI by L. johnsonii. L. johnsonii enrichment caused remodeling of gut microbiome by increasing the abundance of Muribaculaceae, Lactobacillus, and decreasing Romboutsia, Clostridia UCG-014, which were correlated with cardiac traits and serum metabolic biomarkers 16,16-dimethyl-PGA2, and Lithocholate 3-O-glucuronide.

CONCLUSION: These findings reveal that gut microbiome remodeling by L. johnsonii ameliorates the cardiac function post-AMI and might advance microbiome-targeted nutritional intervention.Graphical Abstract.},
}

@article {pmid36970590,
year = {2023},
author = {Dan, WY and Yang, YS and Peng, LH and Sun, G and Wang, ZK},
title = {Gastrointestinal microbiome and cholelithiasis: Current status and perspectives.},
journal = {World journal of gastroenterology},
volume = {29},
number = {10},
pages = {1589-1601},
pmid = {36970590},
issn = {2219-2840},
abstract = {Cholelithiasis is a common digestive disease affecting 10% to 15% of adults. It imposes significant global health and financial burdens. However, the pathogenesis of cholelithiasis involves several factors and is incompletely elucidated. In addition to genetic predisposition and hepatic hypersecretion, the pathogenesis of cholelithiasis might involve the gastrointestinal (GI) microbiome, consisting of microorganisms and their metabolites. High-throughput sequencing studies have elucidated the role of bile, gallstones, and the fecal microbiome in cholelithiasis, associating microbiota dysbiosis with gallstone formation. The GI microbiome may drive cholelithogenesis by regulating bile acid metabolism and related signaling pathways. This review examines the literature implicating the GI microbiome in cholelithiasis, specifically gallbladder stones, choledocholithiasis, and asymptomatic gallstones. We also discuss alterations of the GI microbiome and its influence on cholelithogenesis.},
}

@article {pmid36970461,
year = {2023},
author = {Cui, X and Guo, Y and Liu, Q},
title = {Qingfei Jiedu Granules fight influenza by regulating inflammation, immunity, metabolism, and gut microbiota.},
journal = {Journal of traditional and complementary medicine},
volume = {13},
number = {2},
pages = {170-182},
pmid = {36970461},
issn = {2225-4110},
abstract = {BACKGROUND AND AIM: Qingfei Jiedu Granules (QFJD) are a new Traditional Chinese Medicine (TCM) which has been clinically used against coronavirus pneumonia in China. In this study, the therapeutic effect and the underlying mechanisms of QFJD against influenza were investigated.

EXPERIMENTAL PROCEDURE: Pneumonia mice were induced by influenza A virus. Survival rate, weight loss, lung index and lung pathology were measured to evaluate the therapeutic effect of QFJD. The expression of inflammatory factors and lymphocytes was used to assess anti-inflammatory and immunomodulatory effect of QFJD. Gut microbiome analysis was performed to decipher the potential effect of QFJD on intestinal microbiota. Metabolomics approach was conducted to explore the overall metabolic regulation of QFJD.

RESULT AND CONCLUSION: QFJD shows a significant therapeutic effect on the treatment of influenza and the expression of many pro-inflammatory cytokines were obviously inhibited. QFJD also markedly modulates the level of T and B lymphocytes. The high-dose QFJD has shown similar therapeutic efficiency compared to positive drugs. QFJD profoundly enriched Verrucomicrobia and maintained the balance between Bacteroides and Firmicutes. QFJD associated with 12 signaling pathways in metabolomics study, 9 of which were the same as the model group and were closely related to citrate cycle and amino acid metabolism.To sum up, QFJD is a novel and promising drug against influenza. It can regulate inflammation, immunity, metabolism, and gut microbiota to fight influenza. Verrucomicrobia shows great potential to improve influenza infection and may be an important target.},
}

@article {pmid36970454,
year = {2023},
author = {Kwandee, P and Somnuk, S and Wanikorn, B and Nakphaichit, M and Tunsagool, P},
title = {Efficacy of Triphala extracts on the changes of obese fecal microbiome and metabolome in the human gut model.},
journal = {Journal of traditional and complementary medicine},
volume = {13},
number = {2},
pages = {207-217},
pmid = {36970454},
issn = {2225-4110},
abstract = {Triphala is a mixture of tree fruits obtained from Terminalia chebula, Terminalia bellerica, and Phyllanthus emblica. It is one of the Ayurveda medicinal recipes used to treat health diseases such as obesity. The chemical composition analysis of Triphala extracts obtained from an equal portion of three fruits was performed. The contents of total phenolic compounds (62.87 ± 0.21 mg gallic acid equivalent/mL), total flavonoids (0.24 ± 0.01 mg catechin equivalent/mL), hydrolyzable tannins (177.27 ± 10.09 mg gallotannin equivalent/mL), and condensed tannins (0.62 ± 0.11 mg catechin equivalent/mL) were observed in Triphala extracts. The 1 mg/mL of Triphala extracts was applied to batch culture fermentation which contained the feces from voluntarily obese female adults (body mass index of 35.0-40.0 kg/m[2]) for 24 h. The extraction of DNA and metabolites was each conducted on the samples obtained from batch culture fermentation within and without Triphala extracts treatment. The 16S rRNA gene sequencing and untargeted metabolomic analysis were carried out. There was no statistically significant difference between Triphala extracts and control treatments on the changes in microbial profiles (p-value <0.05). While the metabolomic analysis showed statistically significant differences of 305 up-regulated and 23 down-regulated metabolites in the treatment of Triphala extracts when compared with the control (p-value <0.05 and fold-change ≥2) belonging to 60 pathways. The pathway analysis revealed that Triphala extracts play an important role in the activation of phenylalanine, tyrosine and tryptophan biosynthesis. In this study, phenylalanine and tyrosine were identified metabolites which involve in the regulation of energy metabolism. The treatment of Triphala extracts possesses the induction of phenylalanine, tyrosine and tryptophan biosynthesis in fecal batch culture fermentation of obese adults and therefore it can be suggested as a probable herbal medicinal recipe for obesity treatment.},
}

@article {pmid36970450,
year = {2023},
author = {Tanelian, A and Nankova, B and Cheriyan, A and Arens, C and Hu, F and Sabban, EL},
title = {Differences in gut microbiota associated with stress resilience and susceptibility to single prolonged stress in female rodents.},
journal = {Neurobiology of stress},
volume = {24},
number = {},
pages = {100533},
pmid = {36970450},
issn = {2352-2895},
abstract = {Exposure to traumatic stress is a major risk factor for the development of neuropsychiatric disorders in a subpopulation of individuals, whereas others remain resilient. The determinants of resilience and susceptibility remain unclear. Here, we aimed to characterize the microbial, immunological, and molecular differences between stress-susceptible and stress-resilient female rats before and after exposure to a traumatic experience. Animals were randomly divided into unstressed controls (n = 10) and experimental groups (n = 16) exposed to Single Prolonged Stress (SPS), an animal model of PTSD. Fourteen days later, all rats underwent a battery of behavioral tests and were sacrificed the following day to collect different organs. Stool samples were collected before and after SPS. Behavioral analyses revealed divergent responses to SPS. The SPS treated animals were further subdivided into SPS-resilient (SPS-R) and SPS-susceptible (SPS-S) subgroups. Comparative analysis of fecal 16S sequencing before and after SPS exposure indicated significant differences in the gut microbial composition, functionality, and metabolites of the SPS-R and SPS-S subgroups. In line with the observed distinct behavioral phenotypes, the SPS-S subgroup displayed higher blood-brain barrier permeability and neuroinflammation relative to the SPS-R and/or controls. These results indicate, for the first time, pre-existing and trauma-induced differences in the gut microbial composition and functionality of female rats that relate to their ability to cope with traumatic stress. Further characterization of these factors will be crucial for understanding susceptibility and fostering resilience, especially in females, who are more likely than males to develop mood disorders.},
}

@article {pmid36970332,
year = {2023},
author = {Cui, X and Su, Y and Huang, X and Chen, J and Ma, J and Liao, P and He, X},
title = {Combined analysis of plasma metabolome and intestinal microbiome sequencing to explore jiashen prescription and its potential role in changing intestine-heart axis and effect on chronic heart failure.},
journal = {Frontiers in cardiovascular medicine},
volume = {10},
number = {},
pages = {1147438},
pmid = {36970332},
issn = {2297-055X},
abstract = {BACKGROUND: Heart failure (HF) is a syndrome with global clinical and socioeconomic burden worldwide owing to its poor prognosis. Jiashen Prescription (JSP), a traditional Chinese medicine (TCM) formula, exhibits unambiguous effects on treating HF. Previously, we have reported that underlying mechanisms of JSP by an untargeted metabolomics approach, but the contribution of gut microbiota and metabolic interaction to the cardioprotective efficacy of JSP remains to be elucidated.

MATERIALS AND METHODS: Firstly, the rat model of heart failure was established by the permanent ligation of the left anterior descending coronary artery. The efficacy evaluation of JSP in treating HF rats was per-formed by left ventricular ejection fraction (LVEF). Then, 16S rRNA gene sequencing and LC/MS-based metabolomic analysis were utilized to explore the characteristics of cecal-contents microecology and plasma metabolic profile, respectively. After that, the correlation between intestinal micro-ecological characteristics and plasma metabolic characteristics was analyzed to explore the potential mechanism of the JSP treatment in HF.

RESULTS: JSP could improve the cardiac function of heart failure rats and thus ameliorate heart failure via enhancing rat LVEF. Results of intestinal flora analysis revealed that JSP not only adjusted gut microbiota disturbances by enriching species diversity, reducing the abundance of pathogenic bacteria (such as Allobaculum, Brevinema), as well as increasing the abundance of beneficial bacteria (such as Lactobacillus, Lachnospiraceae_NK4A136_group), but also improved metabolic disorders by reversing metabolite plasma levels to normality. Through the conjoint analysis of 8 metabolites and the OTUs relative abundance data in the 16srRNA sequencing results by WGCNA method, 215 floras significantly related to the eight compounds were identified. The results of the correlation analysis demonstrated a significant association between intestinal microbiota and plasma metabolic profile, especially the significant correlation of Ruminococcaceae_UCG-014 and Protoporphyrin IX, Ruminococcaceae_UCG-005, Christensenellaceae_R-7_group and nicotinamide, dihydrofolic acid.

CONCLUSION: The present study illustrated the underlying mechanism of JSP to treat heart failure by affecting intestinal flora and plasma metabolites, provide a potential therapeutic strategy against heart failure.},
}

@article {pmid36970136,
year = {2023},
author = {Munley, JA and Nagpal, R and Hanson, NC and Mirzaie, A and Laquian, L and Mohr, AM and Efron, PA and Arnaoutakis, DJ and Cooper, MA},
title = {Chronic mesenteric ischemia-induced intestinal dysbiosis resolved after revascularization.},
journal = {Journal of vascular surgery cases and innovative techniques},
volume = {9},
number = {2},
pages = {101084},
pmid = {36970136},
issn = {2468-4287},
abstract = {OBJECTIVE: Chronic mesenteric ischemia (CMI) is a debilitating condition arising from intestinal malperfusion from mesenteric artery stenosis or occlusion. Mesenteric revascularization has been the standard of care but can result in substantial morbidity and mortality. Most of the perioperative morbidity has been secondary to postoperative multiple organ dysfunction, potentially from ischemia-reperfusion injury. The intestinal microbiome is a dense community of microorganisms in the gastrointestinal tract that help regulate pathways ranging from nutritional metabolism to the immune response. We hypothesized that patients with CMI will have microbiome perturbations that contribute to this inflammatory response and could potentially normalize in the postoperative period.

METHODS: We performed a prospective study of patients with CMI who had undergone mesenteric bypass and/or stenting from 2019 to 2020. Stool samples were collected at three time points: preoperatively at the clinic, perioperatively within 14 days after surgery, and postoperatively at the clinic at >30 days after revascularization. Stool samples from healthy controls were used for comparison. The microbiome was measured using 16S rRNA sequencing on an Illumina-MiSeq sequence platform and analyzed using the QIIME2 (quantitative insights into microbial ecology 2)-DADA2 bioinformatics pipeline with the Silva database. Beta-diversity was analyzed using a principal coordinates analysis and permutational analysis of variance. Alpha-diversity (microbial richness and evenness) was compared using the nonparametric Mann-Whitney U test. Microbial taxa unique to CMI patients vs controls were identified using linear discriminatory analysis effect size analysis. P < .05 was considered statistically significant.

RESULTS: Eight patients with CMI had undergone mesenteric revascularization (25% men; average age, 71 years). Nine healthy controls were also analyzed (78% men; average age, 55 years). Bacterial alpha-diversity (number of operational taxonomic units) was dramatically reduced preoperatively compared with that of the controls (P = .03). However, revascularization partially restored the species richness and evenness in the perioperative and postoperative phases. Beta-diversity was only different between the perioperative and postoperative groups (P = .03). Further analyses revealed increased abundance of Bacteroidetes and Clostridia taxa preoperatively and perioperatively compared with the controls, which was reduced during the postoperative period.

CONCLUSIONS: The results from the present study have shown that patients with CMI have intestinal dysbiosis that resolves after revascularization. The intestinal dysbiosis is characterized by the loss of alpha-diversity, which is restored perioperatively and maintained postoperatively. This microbiome restoration demonstrates the importance of intestinal perfusion to sustain gut homeostasis and suggests that microbiome modulation could be a possible intervention to ameliorate acute and subacute postoperative outcomes in these patients.},
}

@article {pmid36970065,
year = {2023},
author = {Bloodworth, JC and Hoji, A and Wolff, G and Mandal, RK and Schmidt, NW and Deshane, JS and Morrow, CD and Kloepfer, KM and Cook-Mills, JM},
title = {Dysbiotic lung microbial communities of neonates from allergic mothers confer neonate responsiveness to suboptimal allergen.},
journal = {Frontiers in allergy},
volume = {4},
number = {},
pages = {1135412},
pmid = {36970065},
issn = {2673-6101},
abstract = {In humans and animals, offspring of allergic mothers have increased responsiveness to allergens. This is blocked in mice by maternal supplementation with α-tocopherol (αT). Also, adults and children with allergic asthma have airway microbiome dysbiosis with increased Proteobacteria and may have decreased Bacteroidota. It is not known whether αT alters neonate development of lung microbiome dysbiosis or whether neonate lung dysbiosis modifies development of allergy. To address this, the bronchoalveolar lavage was analyzed by 16S rRNA gene analysis (bacterial microbiome) from pups of allergic and non-allergic mothers with a basal diet or αT-supplemented diet. Before and after allergen challenge, pups of allergic mothers had dysbiosis in lung microbial composition with increased Proteobacteria and decreased Bacteroidota and this was blocked by αT supplementation. We determined whether intratracheal transfer of pup lung dysbiotic microbial communities modifies the development of allergy in recipient pups early in life. Interestingly, transfer of dysbiotic lung microbial communities from neonates of allergic mothers to neonates of non-allergic mothers was sufficient to confer responsiveness to allergen in the recipient pups. In contrast, neonates of allergic mothers were not protected from development of allergy by transfer of donor lung microbial communities from either neonates of non-allergic mothers or neonates of αT-supplemented allergic mothers. These data suggest that the dysbiotic lung microbiota is dominant and sufficient for enhanced neonate responsiveness to allergen. Importantly, infants within the INHANCE cohort with an anti-inflammatory profile of tocopherol isoforms had an altered microbiome composition compared to infants with a pro-inflammatory profile of tocopherol isoforms. These data may inform design of future studies for approaches in the prevention or intervention in asthma and allergic disease early in life.},
}

@article {pmid36969858,
year = {2023},
author = {Liu, X and Dun, M and Jian, T and Sun, Y and Wang, M and Zhang, G and Ling, J},
title = {Cordyceps militaris extracts and cordycepin ameliorate type 2 diabetes mellitus by modulating the gut microbiota and metabolites.},
journal = {Frontiers in pharmacology},
volume = {14},
number = {},
pages = {1134429},
pmid = {36969858},
issn = {1663-9812},
abstract = {Introduction: Cordyceps militaris, which has many potential medicinal properties, has rarely been reported to alleviate type 2 diabetes mellitus (T2DM). Methods: The effects of C. militaris extracts (CE) and cordycepin (CCS) on high-fat diet and streptozotocin (STZ) induced T2DM mice were analysed by gut microbiome and metabolomics methods in this study. Results: The results demonstrated that glucose and lipid metabolism parameters, oxidative stress biomarkers and inflammation cytokines were down-regulated in the CCS and CE groups. A comparative analysis of the fecal samples from mice in the model and experimental groups showed that experimental groups resulted in a higher abundance of Firmicutes/Bacteroidetes. Conclusion: This study provides evidence that C. militaris can be used as a food supplement to relieve T2DM, which provides a promising prospect for new functional food in it.},
}

@article {pmid36969828,
year = {2023},
author = {Zhou, X and Ma, L and Dong, L and Li, D and Chen, F and Hu, X},
title = {Bamboo shoot dietary fiber alleviates gut microbiota dysbiosis and modulates liver fatty acid metabolism in mice with high-fat diet-induced obesity.},
journal = {Frontiers in nutrition},
volume = {10},
number = {},
pages = {1161698},
pmid = {36969828},
issn = {2296-861X},
abstract = {INTRODUCTION: Obesity is a common nutritional disorder characterized by an excessive fat accumulation. In view of the critical role of gut microbiota in the development of obesity and metabolic diseases, novel dietary therapies have been developed to manage obesity by targeting the gut microbiome. In this study, we investigated anti-obesity effects of bamboo shoot dietary fiber (BSDF) and the potential mechanisms.

METHODS: After 12 weeks of intervention with BSDF in high-fat mice, we detected obesity-related phenotypic indicators, and made transcriptomic analysis of liver tissue. Then we analyzed the changes of gut microbiota using 16S rRNA gene sequencing, explored the effect of BSDF on gut microbiota metabolites, and finally verified the importance of gut microbiota through antibiotic animal model.

RESULTS AND DISCUSSION: We found that BSDF was effective in reducing lipid accumulation in liver and adipose tissue and alleviating dyslipidemia and insulin resistance. Liver transcriptome analysis results showed that BSDF could improve lipid metabolism and liver injury by modulating peroxisome proliferator-activated receptor (PPAR) and fatty acid metabolic pathways. The 16S rRNA gene sequencing analysis of gut microbiota composition showed that BSDF significantly enriched beneficial bacteria such as Bifidobacterium, Akkermansia, Dubosiella, and Alloprevotella. Analysis of fecal metabolomics and gut microbiota metabolites revealed that BSDF increased the levels of several short-chain fatty acids and enriched bile acids, which may be important for improving lipid metabolism. Notably, the obesity-related metabolic disorders were abrogated after the abrogation of gut microbiota, suggesting that gut microbiota is a key factor in the beneficial effects of BSDF.

CONCLUSION: Our study suggests that BSDF as a prebiotic supplement has the potential to improve obesity by improving gut microbiota and modulating host PPAR and fatty acid metabolic pathways.},
}

@article {pmid36969811,
year = {2023},
author = {Chichlowski, M and van Diepen, JA and Prodan, A and Olga, L and Ong, KK and Kortman, GAM and Dunger, DB and Gross, G},
title = {Early development of infant gut microbiota in relation to breastfeeding and human milk oligosaccharides.},
journal = {Frontiers in nutrition},
volume = {10},
number = {},
pages = {1003032},
pmid = {36969811},
issn = {2296-861X},
abstract = {BACKGROUND: Infant gut microbiota composition is influenced by various factors early in life. Here, we investigate associations between infant gut microbiome development, infant age, breastfeeding duration, and human milk oligosaccharides (HMO) composition in breastmilk.

METHODS: A total of 94 mother-infant pairs were recruited as part of the Cambridge Baby Growth and Breastfeeding Study (CBGS-BF) (Cambridge, UK). Infant stool samples (n = 337) were collected at 2 week, 6 week, 3 month, and 6 month of age. The 16S rRNA V3-V4 rRNA region was sequenced using MiSeq Illumina to determine microbiota composition and diversity. Mother's hindmilk samples were collected at birth, 2 week, 6 week, 3 month, and 6 month postpartum. Concentrations of five neutral [2'FL, 3'FL, lacto-N-fucopentaose 1 (LNFP1), LNnT, LNT] and two acidic (3'SL, and 6'SL) HMOs were measured in all milk samples using High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD). We explored the associations between infant gut microbiome parameters and age, duration of exclusive breastfeeding (EBF), and levels of individual HMOs.

RESULTS: Bifidobacterium was the most abundant genus in infant stool at all-time points, irrespective of breastfeeding duration, with an overall mean relative abundance of 70%. The relative abundance of B. bifidum in stool from infants who were breastfed for longer than 6 months was significantly higher compared to the infant breastfed up to 3 months (p = 0.0285). Alpha-diversity (both Shannon and ASV-level Richness) of infant gut microbiota showed a biphasic change with infant age, decreasing from 2 weeks until 3 months and then increasing until 6 months of age. Bifidobacterium relative abundance was associated with higher concentrations of 2'FL and LNFP1 in breastmilk across all time-points (p = 0.049 and 0.017, respectively), with trends toward a higher abundance of B. longum species. No significant association with Bifidobacterium was found for breastmilk LNnT, 3'SL, and 6'SL levels.

CONCLUSION: Our study is in line with previous data demonstrating that EBF duration in the first months of life impacts infant gut microbiota composition. The observed links between specific HMOs in breastmilk and bacteria in infant stool provide evidence of how mother's milk affects infant microbiome development.},
}

@article {pmid36969810,
year = {2023},
author = {Abdolmaleky, HM and Sheng, Y and Zhou, JR},
title = {Bioactive nutraceuticals oligo-lactic acid and fermented soy extract alleviate cognitive decline in mice in part via anti-neuroinflammation and modulation of gut microbiota.},
journal = {Frontiers in nutrition},
volume = {10},
number = {},
pages = {1116278},
pmid = {36969810},
issn = {2296-861X},
abstract = {INTRODUCTION: Cognition decline is associated with aging and certain diseases, such as neurodegenerative or neuropsychiatric disorders, diabetes and chronic kidney disease. Inflammation/neuroinflammation is considered an important causal factor, and experimental evidence suggests that anti-inflammatory natural compounds may effectively prevent cognitive decline. The goal of this study was to evaluate the effects of two natural bioactive agents, oligo-lactic acid (LAP) and fermented soy extract (ImmunBalance, IMB), on cognition in an adenine-induced cognitive impairment mouse model and to investigate the modulation of related biomarkers.

METHODS: Male C57 black mice were randomly assigned into the following experimental groups and received the corresponding treatments for 2 weeks before the use of adenine for model development: (1) negative control; (2) model control: injection of adenine at 50 mg/kg daily for 4 weeks; (3, 4) IMB groups: adenine injection and IMB oral gavage at 250 and 1,000 mg/kg BW, respectively; and (5) LAP group: adenine injection and LAP oral gavage at 1,000 mg/kg BW. One week after the model was developed, mice were evaluated for cognitive performances by using Y maze test, novel object recognition test, open field test, and Barnes maze tests. At the end of the experiment, brain tissues and cecum fecal samples were collected for analysis of gene expression and gut microbiota.

RESULTS: Mice treated with LAP or IMB had significantly improved spatial working memory, spatial recognition memory (LAP only), novel object recognition, and spatial learning and memory, compared with those in the model group. Gene expression analysis showed that, among a panel of cognition related genes, six of them (ELOVL2, GLUT4, Nestein, SNCA, TGFB1, and TGFB2) were significantly altered in the model group. LAP treatment significantly reversed expression levels of inflammatory/neuroinflammatory genes (SNCA, TGFB1), and IMB significantly reversed expression levels of genes related to inflammation/neuroinflammation, neurogenesis, and energy metabolism (ELOVL2, GLUT4, Nestin, TGFB1, and TGFB2). The altered microbiome was attenuated only by IMB.

DISCUSSION: In conclusion, our data showed that LAP improved cognition associated with regulating biomarkers related to neuroinflammation and energy metabolism, whereas IMB improved cognition associated with regulating biomarkers related to neuroinflammation, energy metabolism, and neurogenesis, and modulating gut microbiota. Our results suggest that LAP and IMB may improve cognitive performance in mice via distinct mechanisms of action.},
}

@article {pmid36969543,
year = {2023},
author = {Parr McQueen, J and Gattoni, K and Gendron, EMS and Schmidt, SK and Sommers, P and Porazinska, DL},
title = {External and Internal Microbiomes of Antarctic Nematodes are Distinct, but More Similar to each other than the Surrounding Environment.},
journal = {Journal of nematology},
volume = {55},
number = {1},
pages = {20230004},
pmid = {36969543},
issn = {0022-300X},
abstract = {Host-associated microbiomes have primarily been examined in the context of their internal microbial communities, but many animal species also contain microorganisms on external host surfaces that are important to host physiology. For nematodes, single strains of bacteria are known to adhere to the cuticle (e.g., Pasteuria penetrans), but the structure of a full external microbial community is uncertain. In prior research, we showed that internal gut microbiomes of nematodes (Plectus murrayi, Eudorylaimus antarcticus) and tardigrades from Antarctica's McMurdo Dry Valleys were distinct from the surrounding environment and primarily driven by host identity. Building on this work, we extracted an additional set of individuals containing intact external microbiomes and amplified them for 16S and 18S rRNA metabarcoding. Our results showed that external bacterial microbiomes were more diverse than internal microbiomes, but less diverse than the surrounding environment. Host-specific bacterial compositional patterns were observed, and external microbiomes were most similar to their respective internal microbiomes. However, external microbiomes were more influenced by the environment than the internal microbiomes were. Non-host eukaryotic communities were similar in diversity to internal eukaryotic communities, but exhibited more stochastic patterns of assembly compared to bacterial communities, suggesting the lack of a structured external eukaryotic microbiome. Altogether, we provide evidence that nematode and tardigrade cuticles are inhabited by robust bacterial communities that are substantially influenced by the host, albeit less so than internal microbiomes are.},
}

@article {pmid36969243,
year = {2023},
author = {Ancona, G and Alagna, L and Alteri, C and Palomba, E and Tonizzo, A and Pastena, A and Muscatello, A and Gori, A and Bandera, A},
title = {Gut and airway microbiota dysbiosis and their role in COVID-19 and long-COVID.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1080043},
pmid = {36969243},
issn = {1664-3224},
abstract = {The gut microbiota plays a crucial role in human health and disease. Gut dysbiosis is known to be associated with increased susceptibility to respiratory diseases and modifications in the immune response and homeostasis of the lungs (the so-called gut-lung axis). Furthermore, recent studies have highlighted the possible role of dysbiosis in neurological disturbances, introducing the notion of the "gut-brain axis." During the last 2 years, several studies have described the presence of gut dysbiosis during coronavirus disease 2019 (COVID-19) and its relationship with disease severity, SARS-CoV-2 gastrointestinal replication, and immune inflammation. Moreover, the possible persistence of gut dysbiosis after disease resolution may be linked to long-COVID syndrome and particularly to its neurological manifestations. We reviewed recent evidence on the association between dysbiosis and COVID-19, investigating the possible epidemiologic confounding factors like age, location, sex, sample size, the severity of disease, comorbidities, therapy, and vaccination status on gut and airway microbial dysbiosis in selected studies on both COVID-19 and long-COVID. Moreover, we analyzed the confounding factors strictly related to microbiota, specifically diet investigation and previous use of antibiotics/probiotics, and the methodology used to study the microbiota (α- and β-diversity parameters and relative abundance tools). Of note, only a few studies focused on longitudinal analyses, especially for long-term observation in long-COVID. Lastly, there is a lack of knowledge regarding the role of microbiota transplantation and other therapeutic approaches and their possible impact on disease progression and severity. Preliminary data seem to suggest that gut and airway dysbiosis might play a role in COVID-19 and in long-COVID neurological symptoms. Indeed, the development and interpretation of these data could have important implications for future preventive and therapeutic strategies.},
}

@article {pmid36969224,
year = {2023},
author = {Ma, Y and Kerkar, N},
title = {Editorial: The association between HLA genes and autoimmune liver diseases.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1175342},
doi = {10.3389/fimmu.2023.1175342},
pmid = {36969224},
issn = {1664-3224},
}

@article {pmid36969214,
year = {2023},
author = {Feng, R and Zhu, Q and Li, Q and Zhai, Y and Wang, J and Qin, C and Liang, D and Zhang, R and Tian, H and Liu, H and Chen, Y and Fu, Y and Wang, X and Ding, X},
title = {Microbiota-ear-brain interaction is associated with generalized anxiety disorder through activation of inflammatory cytokine responses.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1117726},
pmid = {36969214},
issn = {1664-3224},
abstract = {INTRODUCTION: Generalized anxiety disorder (GAD) is one of the most enduring anxiety disorders, being associated with increased systemic inflammation. However, the trigger and mechanisms underlying the activation of inflammatory cytokine responses in GAD remain poorly understood.

MATERIALS AND METHODS: We characterized the ear canal microbiome in GAD patients through 16S rRNA gene sequencing and metagenomic sequencing and identified the serum inflammatory markers in GAD patients. Spearman correlations were applied to test the relationship between the microbiota changes and systemic inflammation.

RESULTS: Our findings showed the higher microbial diversity, accompanied with the significantly increased abundance of Proteobacteria, and decreased abundance of Firmicutes in the ear canal of GAD participants compared to that of the age- and sex-matched healthy controls (HC). Metagenomic sequencing showed that Pseudomonas aeruginosa were significantly increased at species-level in GAD patients. Furthermore, we observed the relative abundance of Pseudomonas aeruginosa was positively associated with elevated systemic inflammatory markers and the severity of disease, suggesting that these ear canal microbiota alterations might be correlated with GAD by activating the inflammatory response.

CONCLUSIONS: These findings indicate that microbiota-ear-brain interaction via upregulating inflammatory reaction involve in the development of GAD, as well as suggest that ear canal bacterial communities may be a target for therapeutic intervention.},
}

@article {pmid36969207,
year = {2023},
author = {Chancharoenthana, W and Kamolratanakul, S and Visitchanakun, P and Sontidejkul, S and Cheibchalard, T and Somboonna, N and Settachaimongkon, S and Leelahavanichkul, A},
title = {Lacticaseibacilli attenuated fecal dysbiosis and metabolome changes in Candida-administered bilateral nephrectomy mice.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1131447},
pmid = {36969207},
issn = {1664-3224},
abstract = {The impacts of metabolomic changes (reduced short-chain-fatty acids; SCFAs) in uremic condition is not fully understood. Once daily Candida gavage with or without probiotics (different times of administration) for 1 week prior to bilateral nephrectomy (Bil Nep) in 8-week-old C57BL6 mice as the possible models more resemble human conditions were performed. Candida-administered Bil Nep mice demonstrated more severe conditions than Bil Nep alone as indicated by mortality (n = 10/group) and other 48 h parameters (n = 6-8/group), including serum cytokines, leaky gut (FITC-dextran assay, endotoxemia, serum beta-glucan, and loss of Zona-occludens-1), and dysbiosis (increased Enterobacteriaceae with decreased diversity in microbiome analysis) (n = 3/group for fecal microbiome) without the difference in uremia (serum creatinine). With nuclear magnetic resonance metabolome analysis (n = 3-5/group), Bil Nep reduced fecal butyric (and propionic) acid and blood 3-hydroxy butyrate compared with sham and Candida-Bil Nep altered metabolomic patterns compared with Bil Nep alone. Then, Lacticaseibacillus rhamnosus dfa1 (SCFA-producing Lacticaseibacilli) (n = 8/group) attenuated the model severity (mortality, leaky gut, serum cytokines, and increased fecal butyrate) of Bil Nep mice (n = 6/group) (regardless of Candida). In enterocytes (Caco-2 cells), butyrate attenuated injury induced by indoxyl sulfate (a gut-derived uremic toxin) as indicated by transepithelial electrical resistance, supernatant IL-8, NFκB expression, and cell energy status (mitochondria and glycolysis activities by extracellular flux analysis). In conclusion, the reduced butyrate by uremia was not enhanced by Candida administration; however, the presence of Candida in the gut induced a leaky gut that was attenuated by SCFA-producing probiotics. Our data support the use of probiotics in uremia.},
}

@article {pmid36969184,
year = {2023},
author = {Wang, C and Yu, X and Lin, H and Wang, G and Liu, J and Gao, C and Qi, M and Wang, D and Wang, F},
title = {Integrating microbiome and metabolome revealed microbe-metabolism interactions in the stomach of patients with different severity of peptic ulcer disease.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1134369},
pmid = {36969184},
issn = {1664-3224},
abstract = {BACKGROUND: Peptic ulcer disease (PUD) is a multi-cause illness with an unknown role for gastric flora and metabolism in its pathogenesis. In order to further understand the pathogenesis of gastric flora and metabolism in PUD, this study used histological techniques to analyze the microbiome and metabolome of gastric biopsy tissue. In this paper, our work described the complex interactions of phenotype-microbial-metabolite-metabolic pathways in PUD patients at different pathological stages.

METHODS: Gastric biopsy tissue samples from 32 patients with chronic non-atrophic gastritis, 24 patients with mucosal erosions, and 8 patients with ulcers were collected for the microbiome. UPLC-MS metabolomics was also used to detect gastric tissue samples. These datasets were analyzed individually and integrated using various bioinformatics methods.

RESULTS: Our work found reduced diversity of gastric flora in patients with PUD. PUD patients at different pathological stages presented their own unique flora, and there were significant differences in flora phenotypes. Coprococcus_2, Phenylobacterium, Candidatus_Hepatoplasma, and other bacteria were found in the flora of people with chronic non-atrophic gastritis (HC). The representative flora of mucosal erosion (ME) had uncultured_bacterium_c_Subgroup_6, Sphingomonadaceae, Xanthobacteraceae, and uncultured_bacterium_f_Xanthobacteraceae. In comparison, the characteristic flora of the PUD group was the most numerous and complex, including Ruminococcus_2, Agathobacter, Alistipes, Helicobacter, Bacteroides and Faecalibacterium. Metabolomics identified and annotated 66 differential metabolites and 12 significantly different metabolic pathways. The comprehensive analysis correlated microorganisms with metabolites at different pathological stages and initially explored the complex interactions of phenotype-microbial-metabolite-metabolic pathways in PUD patients at different pathological stages.

CONCLUSION: Our research results provided substantial evidence to support some data on the analysis of the microbial community and its metabolism in the stomach, and they demonstrated many specific interactions between the gastric microbiome and the metabolome. Our study can help reveal the pathogenesis of PUD and indicate plausible disease-specific mechanisms for future studies from a new perspective.},
}

@article {pmid36969182,
year = {2023},
author = {Yamamoto, A and Kambara, Y and Fujiwara, H},
title = {Impact of oral microbiota on pathophysiology of GVHD.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1132983},
pmid = {36969182},
issn = {1664-3224},
abstract = {Allogeneic transplantation of hematopoietic cells is the only curative therapy for several hematopoietic disease in which patients receive cytotoxic conditioning regimens followed by infusion of hematopoietic stem cells. Although the outcomes have improved over the past decades, graft-versus-host-disease (GVHD), the most common life-threatening complication, remains a major cause of non-relapse morbidity and mortality. Pathophysiology of acute GVHD characterized by host antigen-presenting cells after tissue damage and donor T-cells is well studied, and additionally the importance of recipient microbiota in the intestine is elucidated in the GVHD setting. Oral microbiota is the second most abundant bacterial flora in the body after the intestinal tract, and it is related to chronic inflammation and carcinogenesis. Recently, composition of the oral microbiome in GVHD related to transplantation has been characterized and several common patterns, dysbiosis and enrichment of the specific bacterial groups, have been reported. This review focuses on the role of the oral microbiota in the context of GVHD.},
}

@article {pmid36969178,
year = {2023},
author = {Ling, Z and Cheng, Y and Gao, J and Lei, W and Yan, X and Hu, X and Shao, L and Liu, X and Kang, R},
title = {Alterations of the fecal and vaginal microbiomes in patients with systemic lupus erythematosus and their associations with immunological profiles.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1135861},
pmid = {36969178},
issn = {1664-3224},
abstract = {BACKGROUND: Exploring the human microbiome in multiple body niches is beneficial for clinicians to determine which microbial dysbiosis should be targeted first. We aimed to study whether both the fecal and vaginal microbiomes are disrupted in SLE patients and whether they are correlated, as well as their associations with immunological features.

METHODS: A group of 30 SLE patients and 30 BMI-age-matched healthy controls were recruited. Fecal and vaginal samples were collected, the 16S rRNA gene was sequenced to profile microbiomes, and immunological features were examined.

RESULTS: Distinct fecal and vaginal bacterial communities and decreased microbial diversity in feces compared with the vagina were found in SLE patients and controls. Altered bacterial communities were found in the feces and vaginas of patients. Compared with the controls, the SLE group had slightly lower gut bacterial diversity, which was accompanied by significantly higher bacterial diversity in their vaginas. The most predominant bacteria differed between feces and the vagina in all groups. Eleven genera differed in patients' feces; for example, Gardnerella and Lactobacillus increased, whereas Faecalibacterium decreased. Almost all the 13 genera differed in SLE patients' vaginas, showing higher abundances except for Lactobacillus. Three genera in feces and 11 genera in the vagina were biomarkers for SLE patients. The distinct immunological features were only associated with patients' vaginal microbiomes; for example, Escherichia-Shigella was negatively associated with serum C4.

CONCLUSIONS: Although SLE patients had fecal and vaginal dysbiosis, dysbiosis in the vagina was more obvious than that in feces. Additionally, only the vaginal microbiome interacted with patients' immunological features.},
}

@article {pmid36969036,
year = {2023},
author = {Yang, X and An, H and He, Y and Fu, G and Jiang, Z},
title = {Comprehensive analysis of microbiota signature across 32 cancer types.},
journal = {Frontiers in oncology},
volume = {13},
number = {},
pages = {1127225},
pmid = {36969036},
issn = {2234-943X},
abstract = {Microbial communities significantly inhabit the human body. Evidence shows the interaction between the human microbiome and host cells plays a central role in multiple physiological processes and organ microenvironments. However, the majority of related studies focus on gut microbiota or specific tissues/organs, and the component signature of intratumor microbiota across various cancer types remains unclear. Here, we systematically analyzed the correlation between intratumor microbial signature with survival outcomes, genomic features, and immune profiles across 32 cancer types based on the public databases of Bacteria in Cancer (BIC) and The Cancer Genome Atlas (TCGA). Results showed the relative abundance of microbial taxa in tumors compared to normal tissues was observed as particularly noticeable. Survival analysis found that specific candidate microbial taxa were correlated with prognosis across various cancers. Then, a microbial-based scoring system (MS), which was composed of 64 candidate prognostic microbes, was established. Further analyses showed significant differences in survival status, genomic function, and immune profiles among the distinct MS subgroups. Taken together, this study reveals the diversity and complexity of microbiomes in tumors. Classifying cancer into different subtypes based on intratumor microbial signatures might reasonably reflect genomic characteristics, immune features, and survival status.},
}

@article {pmid36968415,
year = {2023},
author = {Sharma, I and Kashyap, S and Agarwala, N},
title = {Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1132824},
pmid = {36968415},
issn = {1664-462X},
abstract = {Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.},
}

@article {pmid36968295,
year = {2023},
author = {Lundtorp Olsen, C and Markvart, M and Vendius, VFD and Damgaard, C and Belstrøm, D},
title = {Short-term sugar stress induces compositional changes and loss of diversity of the supragingival microbiota.},
journal = {Journal of oral microbiology},
volume = {15},
number = {1},
pages = {2189770},
pmid = {36968295},
issn = {2000-2297},
abstract = {Frequent intake of free sugars is a major risk factor for dental caries, but the immediate influence of sugar intake on the supragingival microbiota remains unknown. We aim to characterize the effect of 14 days of sugar rinsing on the supragingival microbiota. Forty orally and systemically healthy participants rinsed their mouth with a 10% sucrose solution, 6-8 times a day, for 14 days, followed by 14 days without sugar stress. Supragingival plaque samples were collected at baseline, and after 14, and 28 days. The supragingival microbiota was analyzed using 16S rDNA sequencing. Taxonomic classification was performed using the Human Oral Microbiome Database. After 14 days of sugar stress induced by the daily sugar rinses, a significant loss of α-diversity (p = 0.02) and a significant increase in the relative abundance of Actinomyces (6.5% to 9.6%, p = 0.006) and Corynebacterium (6.2% to 9.1%, p = 0.03) species were recorded. In addition, a significant decrease in Streptococcus (10.3% to 6.1%, p = 0.001) species was observed. Sugar-mediated changes returned to baseline conditions 14 days after the last sugar rinse. The present study shows that temporary sugar stress induces loss of diversity and compositional changes to the supragingival microbiota, which are reversible if oral care is maintained.},
}

@article {pmid36968219,
year = {2023},
author = {Um, CY and Peters, BA and Choi, HS and Oberstein, P and Beggs, DB and Usyk, M and Wu, F and Hayes, RB and Gapstur, SM and McCullough, ML and Ahn, J},
title = {Grain, Gluten, and Dietary Fiber Intake Influence Gut Microbial Diversity: Data from the Food and Microbiome Longitudinal Investigation.},
journal = {Cancer research communications},
volume = {3},
number = {1},
pages = {43-53},
pmid = {36968219},
issn = {2767-9764},
abstract = {UNLABELLED: Although short-term feeding studies demonstrated effects of grains, fiber, and gluten on gut microbiome composition, the impact of habitual intake of these dietary factors is poorly understood. We examined whether habitual intakes of whole and refined grains, fiber, and gluten are associated with gut microbiota in a cross-sectional study. This study included 779 participants from the multi-ethnic Food and Microbiome Longitudinal Investigation study. Bacterial 16SV4 rRNA gene from baseline stool was amplified and sequenced using Illumina MiSeq. Read clustering and taxonomic assignment was performed using QIIME2. Usual dietary intake was assessed by a 137-item food frequency questionnaire. Association of diet with gut microbiota was assessed with respect to overall composition and specific taxon abundances. Whole grain intake was associated with overall composition, as measured by the Jensen-Shannon divergence (multivariable-adjusted P trend for quartiles = 0.03). The highest intake quartile was associated with higher abundance of Bacteroides plebeius, Faecalibacterium prausnitzii, Blautia producta, and Erysipelotrichaceae and lower abundance of Bacteroides uniformis. These bacteria also varied by dietary fiber intake. Higher refined grain and gluten intake was associated with lower Shannon diversity (P trend < 0.05). These findings suggest that whole grain and dietary fiber are associated with overall gut microbiome structure, largely fiber-fermenting microbiota. Higher refined grain and gluten intakes may be associated with lower microbial diversity.

SIGNIFICANCE: Regular consumption of whole grains and dietary fiber was associated with greater abundance of gut bacteria that may lower risk of colorectal cancer. Further research on the association of refined grains and gluten with gut microbial composition is needed to understand their roles in health and disease.},
}

@article {pmid36968117,
year = {2023},
author = {Xiao, Y and Huang, S and Yu, W and Ni, Y and Lu, D and Wu, Q and Leng, Q and Yang, T and Ni, M and Xie, J and Zhang, X},
title = {Effects of emergency/nonemergency cervical cerclage on the vaginal microbiome of pregnant women with cervical incompetence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1072960},
pmid = {36968117},
issn = {2235-2988},
abstract = {BACKGROUND: Evaluation of the therapeutic effects of cerclage on preterm birth (PTB) caused by cervical incompetence remains challenging. The vaginal microbiome is associated with preterm births. Thus, this study aimed to analyse the vaginal microbiota of patients with cervical incompetence, explore the relationship between the composition of the vaginal microbiota before cervical cerclage and at term delivery, and assess the effect of cervical cerclage on the vaginal microbiota.

METHODS: Patients (n = 30) underwent cerclage performed by the same surgical team. Vaginal swabs were obtained pre-surgery and seven days post-surgery. A gestational age-matched cohort of healthy pregnant women (n = 20) (no particular abnormality during pregnancy, delivery at term) was used as the control group and sampled during a comparable pregnancy. All collected vaginal swabs were analysed by 16S rRNA gene sequencing.

RESULTS: When comparing the healthy control and cervical cerclage groups, the enriched microorganism in the healthy controls was G. Scardovia, and the enriched microorganism of the cerclage was G. Streptococcus. α diversity was significantly increased in patients who received cerclage with preterm delivery compared with those with full-term delivery, and the enriched microorganism was F. Enterococcus. A comparison before and after nonemergency cerclage suggested that the enriched microorganisms were G. Lactobacillus and F. Lactobacillaceae before surgery. After nonemergency cerclage, the enriched microorganisms were F. Enterobacteriaceae and C. Gammaproteobacteria. Vaginal microbiota diversity significantly increased, and the proportion of women with Lactobacillus spp.-depleted microbiomes increased after emergency cerclage. Significant differences in β diversity were found between the groups. Before the emergency cerclage, the enriched microorganisms were G. Lactobacillus, O. Alteromonadales, and P. Firmicutes. After emergency cerclage, the enriched microorganisms were P. Actinobacteria, C. Actinobacteria, P. Proteobacteria, F. Bifidobacteriaceae, O. Bifidobacteriales, G. Gardnerella, and G. Veillonella.

CONCLUSION: Cerclage (particularly emergency cerclage) may alter the vaginal microbiota by increasing microbiota diversity, decreasing vaginal Lactobacillus abundance, and increasing the abundance of pathogenic bacteria that are not conducive to pregnancy maintenance, thereby affecting surgical efficacy. Therefore, the role of the vaginal microbiome should be considered when developing treatment strategies for pregnant women with cervical incompetence.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn, identifier ChiCTR2100046305.},
}

@article {pmid36968114,
year = {2023},
author = {Homayouni Rad, A and Pourjafar, H and Mirzakhani, E},
title = {A comprehensive review of the application of probiotics and postbiotics in oral health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1120995},
pmid = {36968114},
issn = {2235-2988},
abstract = {Oral diseases are among the most common diseases around the world that people usually suffer from during their lifetime. Tooth decay is a multifactorial disease, and the composition of oral microbiota is a critical factor in its development. Also, Streptococcus mutans is considered the most important caries-causing species. It is expected that probiotics, as they adjust the intestinal microbiota and reduce the number of pathogenic bacteria in the human intestine, can exert their health-giving effects, especially the anti-pathogenic effect, in the oral cavity, which is part of the human gastrointestinal tract. Therefore, numerous in vitro and in vivo studies have been conducted on the role of probiotics in the prevention of tooth decay. In this review, while investigating the effect of different strains of probiotics Lactobacillus and Bifidobacteria on oral diseases, including dental caries, candida yeast infections, periodontal diseases, and halitosis, we have also discussed postbiotics as novel non-living biological compounds derived from probiotics.},
}

@article {pmid36968080,
year = {2023},
author = {Wang, M and Li, L and Qian, J and Wang, N and Bao, J and Lu, J and Chen, F and Li, Y and Zhang, Y and Yan, F},
title = {Periodontitis salivary microbiota exacerbates nonalcoholic fatty liver disease in high-fat diet-induced obese mice.},
journal = {iScience},
volume = {26},
number = {4},
pages = {106346},
pmid = {36968080},
issn = {2589-0042},
abstract = {Periodontitis may aggravate the development of nonalcoholic fatty liver disease (NAFLD); however, the precise mechanism is unknown. In this study, salivary microbiota collected from patients with periodontitis was transferred intragastrically to obese mice induced by high-fat diet. Microbiomics and metabolomics analysis were performed to assess the influence of periodontitis salivary microbiota on gut microbiome and liver metabolism. Periodontitis salivary microbiota altered gut microbiota composition and exacerbated intestinal barrier dysfunction in obese mice. Subsequently, the bacterial lipopolysaccharide transported to liver may activate the toll-like receptor 4 signaling and cause the release of pro-inflammatory factors. Moreover, the tryptophan-kynurenine-AhR signal axis was upregulated in liver, which may be related to aggravated hepatic steatosis and glucolipid metabolism dysregulation during NAFLD development. This study indicated that in the context of obesity, periodontitis salivary microbiota may aggravate the pathological progression of NAFLD, in which the tryptophan-AhR pathway may play a key role.},
}

@article {pmid36967532,
year = {2023},
author = {You, X and Rani, A and Özcan, E and Lyu, Y and Sela, DA},
title = {Bifidobacterium longum subsp. infantis utilizes human milk urea to recycle nitrogen within the infant gut microbiome.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2192546},
doi = {10.1080/19490976.2023.2192546},
pmid = {36967532},
issn = {1949-0984},
abstract = {Human milk guides the structure and function of microbial commensal communities that colonize the nursing infant gut. Indigestible molecules dissolved in human milk establish a microbiome often dominated by bifidobacteria capable of utilizing these substrates. Interestingly, urea accounts for ~15% of total human milk nitrogen, representing a potential reservoir for microbiota that may be salvaged for critical metabolic operations during lactation and neonatal development. Accordingly, B. infantis strains are competent for urea nitrogen utilization, constituting a previously hypothetical phenotype in commensal bacteria hosted by humans. Urease gene expression, downstream nitrogen metabolic pathways, and enzymatic activity are induced during urea utilization to yield elevated ammonia concentrations. Moreover, biosynthetic networks relevant to infant nutrition and development are transcriptionally responsive to urea utilization including branched chain and other essential amino acids. Importantly, isotopically labeled urea nitrogen is broadly distributed throughout the expressed B. infantis proteome. This incisively demonstrates that the previously inaccessible urea nitrogen is incorporated into microbial products available for infant host utilization. In aggregate, B. infantis possesses the requisite phenotypic foundation to participate in human milk urea nitrogen recycling within its infant host and thus may be a key contributor to nitrogen homeostasis early in life.},
}

@article {pmid36967434,
year = {2023},
author = {Ma, X and Jia, X and Peng, Y and Li, X and Wang, C and Yu, K},
title = {Gut microbiota disruption during sepsis and the influence of innate metabolites on sepsis prognosis.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {36967434},
issn = {1618-1905},
abstract = {Sepsis causes high mortality in intensive care units. Although there have been many studies on the gut microbiota in patients with sepsis, the impact of sepsis on the gut microbiota has not been directly determined because the treatment of sepsis also affects the gut microbiota. Therefore, we designed this animal experiment to explore gut microbiota alterations during sepsis. Mice were divided into two groups, mice that survived less than 3 days and mice that survived more than 3 days. Fecal samples collected on the day of cecal ligation and puncture (CLP), as well as on the 3rd and 7th days after CLP, were subjected to microbial community analysis and nontargeted metabolomics analysis. The results showed significantly lower bacterial diversity in fecal samples after CLP. At the genus level, the fecal samples obtained on the 3rd and 7th days after CLP exhibited significantly increased relative abundances of Bacteroides, Helicobacter, etc., and significantly decreased relative abundances of Alloprevotella, Prevotella, etc. Innate metabolite levels were significantly different in mice that survived less than 3 days and mice that survived more than 3 days. In conclusion, CLP-induced sepsis in mice changes the structure of the gut microbiome, and innate metabolites affect the prognosis of septic mice.},
}

@article {pmid36967379,
year = {2023},
author = {Sun, Y and Zhang, X and Jin, C and Yue, K and Sheng, D and Zhang, T and Dou, X and Liu, J and Jing, H and Zhang, L and Yue, J},
title = {Prospective, longitudinal analysis of the gut microbiome in patients with locally advanced rectal cancer predicts response to neoadjuvant concurrent chemoradiotherapy.},
journal = {Journal of translational medicine},
volume = {21},
number = {1},
pages = {221},
pmid = {36967379},
issn = {1479-5876},
abstract = {BACKGROUND: Neoadjuvant concurrent chemoradiotherapy (nCCRT) is a standard treatment for locally advanced rectal cancer (LARC). The gut microbiome may be reshaped by radiotherapy through its effects on microbial composition, mucosal immunity, and the systemic immune system. We sought to clarify dynamic, longitudinal changes in the gut microbiome and blood immunomodulators throughout nCCRT and to explore the relationship of such changes with outcomes after nCCRT.

METHODS: A total of 39 patients with LARC were recruited for this study. Fecal samples and peripheral blood samples were collected from all 39 patients before nCCRT, during nCCRT (at week 3), and after nCCRT (at week 5). The gut microbiota and the microbial community structure were analyzed by 16S rRNA sequencing of the V3-V4 region. Levels of blood immunomodulatory proteins were measured with a Millipore HCKPMAG-11 K kit and Luminex 200 platform (Luminex, USA).

RESULTS: Cross-sectional and longitudinal analyses revealed that the gut microbiome profile and enterotype exhibited characteristic variations that could distinguish patients with good response (AJCC TRG classification 0-1) vs poor response (TRG 2-3) to nCCRT. Sparse partial least squares regression and canonical correspondence analyses showed multivariate associations between specific microbial taxa, host immunomodulatory proteins, immune cells, and outcomes after nCCRT. An integrated model consisting of baseline Clostridium sensu stricto 1 levels, fold changes in Intestinimonas, blood levels of the herpesvirus entry mediator (HVEM/CD270), and lymphocyte counts could predict good vs poor outcome after nCCRT [area under the receiver-operating characteristics curve (AUC)= 0.821; area under the precision-recall curve [AUPR] = 0.911].

CONCLUSIONS: Our results showed that longitudinal variations in specific gut taxa, associated host immune cells, and immunomodulatory proteins before and during nCCRT could be useful for early predictions of the efficacy of nCCRT, which could guide the choice of individualized treatment for patients with LARC.},
}

@article {pmid36967101,
year = {2023},
author = {Thanawala, SU and Kaplan, DE and Falk, GW and Beveridge, CA and Schaubel, D and Serper, M and Yang, YX},
title = {Antibiotic exposure is associated with a risk of esophageal adenocarcinoma.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2023.03.012},
pmid = {36967101},
issn = {1542-7714},
abstract = {BACKGROUND & AIMS: Antibiotic exposure leads to changes in the gut microbiota. Our objective was to evaluate the association between antibiotic exposure and esophageal adenocarcinoma (EAC) risk.

METHODS: We performed a nested case-control study using data from the Veterans Health Administration from 2004 through 2020. Cases group consisted of patients who received an incident diagnosis of EAC. For each case, up to 20 matched controls were selected using incidence density sampling. Our primary exposure of interest was any oral or intravenous antibiotic use. Our secondary exposures included cumulative number of days of exposure and classification of antibiotics by various subgroups. Conditional logistic regression was used to estimate the crude and adjusted odds ratios (aOR) for the risk of EAC associated with antibiotic exposure.

RESULTS: The case-control analysis included 8,226 EAC cases and 140,670 matched controls. Exposure to any antibiotic was associated with an aOR for EAC of 1.74 (95% CI: 1.65-1.83) versus no antibiotic exposure. Compared to no antibiotic exposure, the aOR for EAC was 1.63 (95% CI:1.52-1.74, p<0.001) for cumulative exposure to any antibiotic for 1-15 days, 1.77 (95% CI 1.65-1.89, p<0.001) for 16-47 days, and 1.87 (95% CI 1.75-2.01, p<0.001) for ≥48 days, respectively (p for trend <0.001).

CONCLUSION: Exposure to any antibiotic is associated with an increased risk of EAC, and this risk increases as the cumulative days of exposure increases. This novel finding is hypothesis-generating for potential mechanisms that may play a role in the development or progression of EAC.},
}

@article {pmid36967089,
year = {2023},
author = {Cui, SS and Jiang, QW and Chen, SD},
title = {Sex difference in biological change and mechanism of Alzheimer's disease: from macro- to micro-landscape.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {101918},
doi = {10.1016/j.arr.2023.101918},
pmid = {36967089},
issn = {1872-9649},
abstract = {Alzheimer's disease (AD) is the most common form of dementia and numerous studies reported a higher prevalence and incidence of AD among women. Although women have longer lifetime, longevity does not wholly explain the higher frequency and lifetime risk in women. It is important to understand sex differences in AD pathophysiology and pathogenesis, which could provide foundation for future clinical AD research. Here, we review the most recent and relevant literature on sex differences in biological change of AD from macroscopical neuroimaging to microscopical pathologic change (neuronal degeneration, synaptic dysfunction, amyloid-beta and tau accumulation). We also discussed sex differences in cellular mechanisms related to AD (neuroinflammation, mitochondria dysfunction, oxygen stress, apoptosis, autophagy, blood-brain-barrier dysfunction, gut microbiome alteration, bulk and single cell/nucleus omics) and possible causes underlying these differences including sex-chromosome, sex hormone and hypothalamic-pituitary- adrenal (HPA) axis effects.},
}

@article {pmid36966625,
year = {2023},
author = {He, LX and He, LY and Gao, FZ and Zhang, M and Chen, J and Jia, WL and Ye, P and Jia, YW and Hong, B and Liu, SS and Liu, YS and Zhao, JL and Ying, GG},
title = {Mariculture affects antibiotic resistome and microbiome in the coastal environment.},
journal = {Journal of hazardous materials},
volume = {452},
number = {},
pages = {131208},
doi = {10.1016/j.jhazmat.2023.131208},
pmid = {36966625},
issn = {1873-3336},
abstract = {Antibiotics are increasingly used and released into the marine environment due to the rapid development of mariculture, resulting in spread of antibiotic resistance. The pollution, distribution, and characteristics of antibiotics, antibiotic resistance genes (ARGs) and microbiomes have been investigated in this study. Results showed that 20 antibiotics were detected in Chinese coastal environment, with predominance of erythromycin-H2O, enrofloxacin and oxytetracycline. In coastal mariculture sites, antibiotic concentrations were significantly higher than in control sites, and more types of antibiotics were detected in the South than in the North of China. Residues of enrofloxacin, ciprofloxacin and sulfadiazine posed high resistance selection risks. β-Lactam, multi-drug and tetracycline resistance genes were frequently detected with significantly higher abundance in the mariculture sites. Of the 262 detected ARGs, 10, 26, and 19 were ranked as high-risk, current-risk, future-risk, respectively. The main bacterial phyla were Proteobacteria and Bacteroidetes, of which 25 genera were zoonotic pathogens, with Arcobacter and Vibrio in particular ranking in the top10. Opportunistic pathogens were more widely distributed in the northern mariculture sites. Phyla of Proteobacteria and Bacteroidetes were the potential hosts of high-risk ARGs, while the conditional pathogens were associated with future-risk ARGs, indicating a potential threat to human health.},
}

@article {pmid36966280,
year = {2023},
author = {Zhao, Y and Yi, J and Xiang, J and Jia, W and Chen, A and Chen, L and Zheng, L and Zhou, W and Wu, M and Yu, Z and Tang, J},
title = {Exploration of lung mycobiome in the patients with non-small-cell lung cancer.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {81},
pmid = {36966280},
issn = {1471-2180},
abstract = {As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi.},
}

@article {pmid36966246,
year = {2023},
author = {Hall, MW and Wellappuli, NC and Huang, RC and Wu, K and Lam, DK and Glogauer, M and Beiko, RG and Senadheera, DB},
title = {Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {23},
pmid = {36966246},
issn = {2730-6151},
abstract = {Experimentally induced gingivitis is associated with inflammatory and microbiological changes in an otherwise healthy subject, demonstrating the impacts of discontinuing oral hygiene routines. Understanding the bacterial dynamics during the induction and resolution of gingival inflammation will aid in the development of bacterial prognostic tests and probiotics for severe oral disease. We profiled the bacterial community in 15 healthy subjects who suspended all oral-hygiene practices for three weeks. Saliva, tongue, subgingival, and supragingival plaque samples were collected over seven weeks and showed a return to community baseline after oral hygiene practices were resumed. Stronger temporal changes in subgingival and supragingival plaque suggest these sample types may be preferred over saliva or tongue plaque for future prognostics. Taxonomic groups spanning ten phyla demonstrated consistent abundance shifts, including a significant decrease in Streptococcus, Neisseria, and Actinomyces populations, and an increase in Prevotella, Fusobacterium, and Porphyromonas populations. With four distinct oral sites surveyed and results mapped to the Human Oral Microbiome Database reference set, this work provides a comprehensive taxonomic catalog of the bacterial shifts observed during the onset and resolution of gingival inflammation.},
}

@article {pmid36966207,
year = {2023},
author = {Bickel, S and Or, D},
title = {Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {322},
pmid = {36966207},
issn = {2399-3642},
abstract = {Earth's diverse soil microbiomes host bacteria within dynamic and fragmented aqueous habitats that occupy complex pore spaces and restrict the spatial range of ecological interactions. Yet, the spatial distributions of bacterial cells in soil communities remain underexplored. Here, we propose a modelling framework representing submillimeter-scale distributions of soil bacteria based on physical constraints supported by individual-based model results and direct observations. The spatial distribution of bacterial cell clusters modulates various metabolic interactions and soil microbiome functioning. Dry soils with long diffusion times limit localized interactions of the sparse communities. Frequently wet soils enable long-range trophic interactions between dense cell clusters through connected aqueous pathways. Biomes with high carbon inputs promote large and dense cell clusters where anoxic microsites form even in aerated soils. Micro-geographic considerations of difficult-to-observe microbial processes can improve the interpretation of data from bulk soil samples.},
}

@article {pmid36965559,
year = {2023},
author = {Jiang, S and Xu, H and Zhao, C and Zhong, F and Li, D},
title = {Oyster polysaccharides relieve DSS-induced colitis via anti-inflammatory and maintaining the physiological hypoxia.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {124150},
doi = {10.1016/j.ijbiomac.2023.124150},
pmid = {36965559},
issn = {1879-0003},
abstract = {Oyster polysaccharides (OPS) possess potent anti-inflammatory properties and mediate gut microbiome. The research aimed to investigate the beneficial effect of OPS on attenuating colitis. OPS administration decreased the disease activity index and suppressed the increase in colon length. Hematoxylin and eosin staining results displayed that OPS restored the DSS-induced histopathological damage. After oral administration of OPS, myeloperoxidase activity and pro-inflammatory cytokines (TNF-α) in colitis mice were inhibited, while IL-10 was elevated. Western blotting results revealed that OPS improved the expression of tight junction proteins (ZO-1, Claudin-4, and Occludin). Additionally, OPS stabilized the expression of hypoxia-inducible factor-1α (HIF-1α) and prevented the levels of bacterial endotoxin (lipopolysaccharides). OPS activated barrier-protective genes (intestinal trefoil factor) via mediating HIF-1α. These results indicated that OPS alleviated DSS-induced colitis by inhibiting inflammation and regulating HIF-1α. OPS would be a potential candidate to alleviate DSS-induced colitis.},
}

@article {pmid36965522,
year = {2023},
author = {Luo, L and Chang, Y and Sheng, L},
title = {Gut-liver axis in the progression of nonalcoholic fatty liver disease: From the microbial derivatives-centered perspective.},
journal = {Life sciences},
volume = {},
number = {},
pages = {121614},
doi = {10.1016/j.lfs.2023.121614},
pmid = {36965522},
issn = {1879-0631},
abstract = {Nonalcoholic fatty liver disease (NAFLD) is one of the world's most common chronic liver diseases. However, its pathogenesis remains unclear. With the deepening of research, NAFLD is considered a metabolic syndrome associated with the environment, heredity, and metabolic disorders. Recently, the close relationship between the intestinal microbiome and NAFLD has been discovered, and the theory of the "gut-liver axis" has been proposed. In short, the gut bacteria directly reach the liver via the portal vein through the damaged intestinal wall or indirectly participate in the development of NAFLD through signaling pathways mediated by their components and metabolites. This review focuses on the roles of microbiota-derived lipopolysaccharide, DNA, peptidoglycan, bile acids, short-chain fatty acids, endogenous ethanol, choline and its metabolites, indole and its derivatives, and bilirubin and its metabolites in the progression of NAFLD, which may provide significative insights into the pathogenesis, diagnosis, and treatment for this highly prevalent liver disease.},
}

@article {pmid36965327,
year = {2023},
author = {Lin, D and Medeiros, DM},
title = {The microbiome as a major function of the gastrointestinal tract and its implication in micronutrient metabolism and chronic diseases.},
journal = {Nutrition research (New York, N.Y.)},
volume = {112},
number = {},
pages = {30-45},
doi = {10.1016/j.nutres.2023.02.007},
pmid = {36965327},
issn = {1879-0739},
abstract = {The composition and function of microbes harbored in the human gastrointestinal lumen have been underestimated for centuries because of the underdevelopment of nucleotide sequencing techniques and the lack of humanized gnotobiotic models. Now, we appreciate that the gut microbiome is an integral part of the human body and exerts considerable roles in host health and diseases. Dietary factors can induce changes in the microbial community composition, metabolism, and function, thereby altering the host immune response, and consequently, may influence disease risks. An imbalance of gut microbiome homeostasis (i.e., dysbiosis) has been linked to several chronic diseases, such as inflammatory bowel diseases, obesity, and diabetes. Remarkable progress has recently been made in better understanding the extent to which the influence of the diet-microbiota interaction on host health outcomes in both animal models and human participants. However, the exact causality of the gut microbiome on the development of diseases is still controversial. In this review, we will briefly describe the general structure and function of the intestine and the process of nutrient absorption in humans. This is followed by a summarization of the recent updates on interactions between gut microbiota and individual micronutrients, including carotenoids, vitamin A, vitamin D, vitamin C, folate, iron, and zinc. In the opinion of the authors, these nutrients were identified as representative of vitamins and minerals with sufficient research on their roles in the microbiome. The host responses to the gut microbiome will also be discussed. Future direction in microbiome research, for example, precision microbiome, will be proposed.},
}

@article {pmid36965240,
year = {2023},
author = {Cassotta, M and Cianciosi, D and De Giuseppe, R and Navarro-Hortal, MD and Armas Diaz, Y and Forbes-Hernández, TY and Pifarre, KT and Pascual Barrera, AE and Grosso, G and Xiao, J and Battino, M and Giampieri, F},
title = {Possible role of nutrition in the prevention of inflammatory bowel disease-related colorectal cancer: A focus on human studies.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {110},
number = {},
pages = {111980},
doi = {10.1016/j.nut.2023.111980},
pmid = {36965240},
issn = {1873-1244},
abstract = {Patients with inflammatory bowel disease (IBD) are at substantially high risk for colorectal cancer (CRC). IBD-associated CRC accounts for roughly 10% to 15% of the annual mortality in patients with IBD. IBD-related CRC also affects younger patients compared with sporadic CRC, with a 5-y survival rate of 50%. Regardless of medical therapies, the persistent inflammatory state characterizing IBD raises the risk for precancerous changes and CRC, with additional input from several elements, including genetic and environmental risk factors, IBD-associated comorbidities, intestinal barrier dysfunction, and gut microbiota modifications. It is well known that nutritional habits and dietary bioactive compounds can influence IBD-associated inflammation, microbiome abundance and composition, oxidative stress balance, and gut permeability. Additionally, in recent years, results from broad epidemiologic and experimental studies have associated certain foods or nutritional patterns with the risk for colorectal neoplasia. The present study aimed to review the possible role of nutrition in preventing IBD-related CRC, focusing specifically on human studies. It emerges that nutritional interventions based on healthy, nutrient-dense dietary patterns characterized by a high intake of fiber, vegetables, fruit, ω-3 polyunsaturated fatty acids, and a low amount of animal proteins, processed foods, and alcohol, combined with probiotic supplementation have the potential of reducing IBD-activity and preventing the risk of IBD-related CRC through different mechanisms, suggesting that targeted nutritional interventions may represent a novel promising approach for the prevention and management of IBD-associated CRC.},
}

@article {pmid36965002,
year = {2023},
author = {Martiny, JBH and Martiny, AC and Brodie, E and Chase, AB and Rodríguez-Verdugo, A and Treseder, KK and Allison, SD},
title = {Investigating the eco-evolutionary response of microbiomes to environmental change.},
journal = {Ecology letters},
volume = {},
number = {},
pages = {},
doi = {10.1111/ele.14209},
pmid = {36965002},
issn = {1461-0248},
abstract = {Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.},
}

@article {pmid36964865,
year = {2023},
author = {Kitamura, N and Hashida, Y and Higuchi, T and Ohno, S and Sento, S and Sasabe, E and Murakami, I and Yamamoto, T and Daibata, M},
title = {Detection of Merkel cell polyomavirus in multiple primary oral squamous cell carcinomas.},
journal = {Odontology},
volume = {},
number = {},
pages = {},
pmid = {36964865},
issn = {1618-1255},
abstract = {Oral microbiome studies have mainly focussed on bacteria, with the relationship between viruses and oral cancers remaining poorly understood. Oral cancers can develop even in the absence of any history of daily smoking or drinking. Oral cancer patients frequently have multiple primary cancers in the oral cavity and other organs, such as the upper gastrointestinal tract. Merkel cell polyomavirus (MCPyV) is a novel oncovirus identified from a subtype of skin cancer in 2008. In this study, we investigated the potential involvement of MCPyV in the pathogenesis of oral squamous cell carcinoma (OSCC). Participants comprised 115 Japanese patients with OSCC (single primary: 109 tumours in 109 patients; multiple primaries: 16 tumours in 6 patients) treated in our department between 2014 and 2017. DNA was extracted from formalin-fixed paraffin-embedded specimens of primary lesions. MCPyV DNA copy counts were analysed by quantitative real-time polymerase chain reaction. Twenty-four of the 115 patients (20.9%) were positive for MCPyV DNA. No association was found between presence or absence of MCPyV DNA and clinical characteristics other than number of primary lesions. The MCPyV DNA-positive rate was significantly higher for multiple primary OSCCs (62.5%, 10/16 tumours) than for single primary OSCCs (16.5%, 18/109 tumours; P < 0.001). Furthermore, MCPyV DNA load was significantly higher for patients with multiple primaries (P < 0.05). MCPyV was observed more frequently and DNA load was significantly higher with multiple primary OSCCs than with single primary OSCC. MCPyV may play some role as an oncovirus for multiple primary OSCCs.},
}

@article {pmid36964623,
year = {2023},
author = {Manabe, Y and Ishibashi, T and Asano, R and Tonomura, S and Maeda, Y and Motooka, D and Ueda, J and Yanagawa, M and Edamoto-Taira, Y and Chikaishi-Kirino, T and Masaki, T and Inagaki, T and Nakamura, S and Katada, Y and Okazawa, M and Narazaki, M and Ogo, T and Kumanogoh, A and Nakaoka, Y},
title = {Gut dysbiosis is associated with aortic aneurysm formation and progression in Takayasu arteritis.},
journal = {Arthritis research & therapy},
volume = {25},
number = {1},
pages = {46},
pmid = {36964623},
issn = {1478-6362},
abstract = {BACKGROUND: Takayasu arteritis (TAK) is an autoimmune large vessel vasculitis that affects the aorta and its major branches, eventually leading to the development of aortic aneurysm and vascular stenosis or occlusion. This retrospective and prospective study aimed to investigate whether the gut dysbiosis exists in patients with TAK and to identify specific gut microorganisms related to aortic aneurysm formation/progression in TAK.

METHODS: We analysed the faecal microbiome of 76 patients with TAK and 56 healthy controls (HCs) using 16S ribosomal RNA sequencing. We examined the relationship between the composition of the gut microbiota and clinical parameters.

RESULTS: The patients with TAK showed an altered gut microbiota with a higher abundance of oral-derived bacteria, such as Streptococcus and Campylobacter, regardless of the disease activity, than HCs. This increase was significantly associated with the administration of a proton pump inhibitor used for preventing gastric ulcers in patients treated with aspirin and glucocorticoids. Among patients taking a proton pump inhibitor, Campylobacter was more frequently detected in those who underwent vascular surgeries and endovascular therapy for aortic dilatation than in those who did not. Among the genus of Campylobacter, Campylobacter gracilis in the gut microbiome was significantly associated with clinical events related to aortic aneurysm formation/worsening in patients with TAK. In a prospective analysis, patients with a gut microbiome positive for Campylobacter were significantly more likely to require interventions for aortic dilatation than those who were negative for Campylobacter. Furthermore, patients with TAK who were positive for C. gracilis by polymerase chain reaction showed a tendency to have severe aortic aneurysms.

CONCLUSIONS: A specific increase in oral-derived Campylobacter in the gut may be a novel predictor of aortic aneurysm formation/progression in patients with TAK.},
}

@article {pmid36964325,
year = {2023},
author = {Gu, C and Zhang, F and Lu, K and Sun, X and Guo, W and Shao, Q},
title = {Response of microbial community in the soil of halophyte after contamination with tetrabromobisphenol A.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {36964325},
issn = {1678-4405},
abstract = {Coastal wetlands are subjected to increasing tetrabromobisphenol A (TBBPA) pollution, whereas knowledge of TBBPA degradation in marine environments is lacking. The changes of bacterial communities in TBBPA-polluted soil covered with halophytes were investigated. TBBPA could be degraded in the halophyte-covered saline-alkali soil in a microcosm experiment. Higher TBBPA removal occurred in the soil of Kandelia obovata compared with soils covered with Suaeda australis and Phragmites australis within 56 days of cultivation. The rhizosphere soils of S. australis, P. australis, and K. obovata mainly involved the classes of Bacteroidia, Gammaproteobacteria, Alphaproteobacteria, and Anaerolineae. Additionally, manganese oxidation, aerobic anoxygenic phototrophy, and fermentation functions were higher in the rhizosphere soil of K. obovata after TBBPA addition. This study supports that using suitable local halophytic plants is a promising approach for degrading TBBPA-contaminated coastal soil.},
}

@article {pmid36964264,
year = {2023},
author = {Bélteky, M and Milletich, PL and Ahrens, AP and Triplett, EW and Ludvigsson, J},
title = {Infant gut microbiome composition correlated with type 1 diabetes acquisition in the general population: the ABIS study.},
journal = {Diabetologia},
volume = {},
number = {},
pages = {},
pmid = {36964264},
issn = {1432-0428},
abstract = {AIMS/HYPOTHESIS: While autoantibodies are traditional markers for type 1 diabetes development, we identified gut microbial biomarkers in 1-year-old infants associated with future type 1 diabetes up to 20 years before diagnosis.

METHODS: Infants enrolled in the longitudinal general population cohort All Babies In Southeast Sweden (ABIS) provided a stool sample at a mean age of 12.5 months. Samples (future type 1 diabetes, n=16; healthy controls, n=268) were subjected to 16S ribosomal RNA (rRNA) sequencing and quantitative PCR. Microbial differences at the taxonomic and core microbiome levels were assessed. PICRUSt was used to predict functional content from the 16S rRNA amplicons. Sixteen infants, with a future diagnosis of type 1 diabetes at a mean age of 13.3±5.4 years, and one hundred iterations of 32 matched control infants, who remained healthy up to 20 years of age, were analysed.

RESULTS: Parasutterella and Eubacterium were more abundant in healthy control infants, while Porphyromonas was differentially more abundant in infants with future type 1 diabetes diagnosis. Ruminococcus was a strong determinant in differentiating both control infants and those with future type 1 diabetes using random forest analysis and had differing trends of abundance when comparing control infants and those with future type 1 diabetes. Flavonifractor and UBA1819 were the strongest factors for differentiating control infants, showing higher abundance in control infants compared with those with future type 1 diabetes. Alternatively, Alistipes (more abundant in control infants) and Fusicatenibacter (mixed abundance patterns when comparing case and control infants) were the strongest factors for differentiating future type 1 diabetes. Predicted gene content regarding butyrate production and pyruvate fermentation was differentially observed to be higher in healthy control infants.

CONCLUSIONS/INTERPRETATION: This investigation suggests that microbial biomarkers for type 1 diabetes may be present as early as 1 year of age, as reflected in the taxonomic and functional differences of the microbial communities. The possibility of preventing disease onset by altering or promoting a 'healthy' gut microbiome is appealing.

DATA AVAILABILITY: The forward and reverse 16S raw sequencing data generated in this study are available through the NCBI Sequence Read Archive under BioProject PRJNA875929. Associated sample metadata used for statistical comparison are available in the source data file. R codes used for statistical comparisons and figure generation are available at: https://github.com/PMilletich/T1D_Pipeline .},
}

@article {pmid36964135,
year = {2023},
author = {McLaughlin, S and Zhalnina, K and Kosina, S and Northen, TR and Sasse, J},
title = {The core metabolome and root exudation dynamics of three phylogenetically distinct plant species.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1649},
pmid = {36964135},
issn = {2041-1723},
abstract = {Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.},
}

@article {pmid36964133,
year = {2023},
author = {Ruze, R and Song, J and Yin, X and Chen, Y and Xu, R and Wang, C and Zhao, Y},
title = {Mechanisms of obesity- and diabetes mellitus-related pancreatic carcinogenesis: a comprehensive and systematic review.},
journal = {Signal transduction and targeted therapy},
volume = {8},
number = {1},
pages = {139},
pmid = {36964133},
issn = {2059-3635},
abstract = {Research on obesity- and diabetes mellitus (DM)-related carcinogenesis has expanded exponentially since these two diseases were recognized as important risk factors for cancers. The growing interest in this area is prominently actuated by the increasing obesity and DM prevalence, which is partially responsible for the slight but constant increase in pancreatic cancer (PC) occurrence. PC is a highly lethal malignancy characterized by its insidious symptoms, delayed diagnosis, and devastating prognosis. The intricate process of obesity and DM promoting pancreatic carcinogenesis involves their local impact on the pancreas and concurrent whole-body systemic changes that are suitable for cancer initiation. The main mechanisms involved in this process include the excessive accumulation of various nutrients and metabolites promoting carcinogenesis directly while also aggravating mutagenic and carcinogenic metabolic disorders by affecting multiple pathways. Detrimental alterations in gastrointestinal and sex hormone levels and microbiome dysfunction further compromise immunometabolic regulation and contribute to the establishment of an immunosuppressive tumor microenvironment (TME) for carcinogenesis, which can be exacerbated by several crucial pathophysiological processes and TME components, such as autophagy, endoplasmic reticulum stress, oxidative stress, epithelial-mesenchymal transition, and exosome secretion. This review provides a comprehensive and critical analysis of the immunometabolic mechanisms of obesity- and DM-related pancreatic carcinogenesis and dissects how metabolic disorders impair anticancer immunity and influence pathophysiological processes to favor cancer initiation.},
}

@article {pmid36963900,
year = {2023},
author = {Elghannam, MT and Hassanien, MH and Ameen, YA and Turky, EA and Elattar, GM and ElRay, AA and Eltalkawy, MD},
title = {Oral microbiota and liver diseases.},
journal = {Clinical nutrition ESPEN},
volume = {54},
number = {},
pages = {68-72},
doi = {10.1016/j.clnesp.2022.12.030},
pmid = {36963900},
issn = {2405-4577},
abstract = {Gut microbiota plays a crucial role in our health and particularly liver diseases, including NAFLD, cirrhosis, and HCC. Oral microbiome and its role in health and disease represent an active field of research. Several lines of evidence have suggested that oral microbiota dysbiosis represents a major factor contributing to the occurrence and progression of many liver diseases. The human microbiome is valuable to the diagnosis of cancer and provides a novel strategy for targeted therapy of HCC. The most studied liver disease in relation to oral-gut-liver axis dysbiosis includes MAFLD; however, other diseases include Precancerous liver disease as viral liver diseases, liver cirrhosis, AIH and liver carcinoma (HCC). It seems that restoring populations of beneficial organisms and correcting dysbiosis appears to improve outcomes in liver disorders. We discuss the possible role of oral microbiota in these diseases.},
}

@article {pmid36963861,
year = {2023},
author = {St-Amant, A and Bergdahl, A},
title = {A systematic review and meta-analysis of randomized controlled trials investigating the effects of probiotics on oxidative stress in healthy adults.},
journal = {Clinical nutrition ESPEN},
volume = {54},
number = {},
pages = {180-186},
doi = {10.1016/j.clnesp.2023.01.016},
pmid = {36963861},
issn = {2405-4577},
abstract = {BACKGROUND: The oxidative stress (OS) theory of disease stipulates that a chronic imbalance in the ratio of oxidants to antioxidants in the cellular environment leads to a variety of debilitating conditions, including type 2 diabetes, cardiovascular and liver diseases. Metabolites in the gut microbiome have been associated with increases in reactive oxygen species (ROS). Many randomized controlled trials (RCTs) have thus investigated the potential of probiotics as a nutraceutical intervention to improve parameters of OS.

AIM: The objective of this paper is to review relevant human RCTs exploring the potential of probiotic supplementation to prevent OS in metabolically healthy individuals.

METHODS: This systematic review and meta-analysis was registered on PROSPERO (CRD42021297210). The PubMed database was searched using keywords related to probiotics and OS. In total, out of the 652 studies were screened, 9 respected the inclusion criteria.

RESULTS: Total antioxidant capacity (TAC) (SMD: 0.83 mmol/L, 95% CI: 0.25-1.40, p = 0.005) and glutathione (GSH) (SMD: 0.45, 95% CI: 0.13-0.77, p = 0.006) are improved with probiotic ingestion, although there are no alterations in superoxide dismutase (SOD) (SMD: 0.33, 95% CI: -0.27-0.93, p = 0.28). Decreases in plasma concentrations of the OS biomarker malondialdehyde (MDA) (SMD: -0.55, 95% CI: -1.11-0.00, p = 0.05) are also detected.

CONCLUSION: Probiotics improve AS and OS in metabolically healthy individuals. However, more studies are needed to address the moderate to high degree of heterogeneity in methodology.},
}

@article {pmid36963683,
year = {2023},
author = {Perdomo-González, A and Pérez-Reverón, R and Goberna, M and León-Barrios, M and Fernández-López, M and Villadas, PJ and Reyes-Betancort, JA and Díaz-Peña, FJ},
title = {How harmful are exotic plantations for soils and its microbiome? A case study in an arid island.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163030},
doi = {10.1016/j.scitotenv.2023.163030},
pmid = {36963683},
issn = {1879-1026},
abstract = {The plantation of exotic species has been a common practice in (semi-) arid areas worldwide aiming to restore highly degraded habitats. The effects of these plantations on plant cover or soil erosion have been widely studied, while little attention has been paid to the consequences on soil quality and belowground biological communities. This study evaluates the long-term (>60 years) effects of the exotic species Acacia cyclops and Pinus halepensis revegetation on soil properties, including microbiome, in an arid island. Soils under exotic plantation were compared to both degraded soils with a very low cover of native species and soils with well-preserved native plant communities. Seven scenarios were selected in a small area (~25 ha) with similar soil type but differing in the plant cover. Topsoils (0-15 cm) were analyzed for physical, chemical and biochemical properties, and amplicon sequencing of bacterial and fungal communities. Microbial diversity was similar among soils with exotic plants and native vegetation (Shannon's index = 5.26 and 5.34, respectively), while the most eroded soils exhibited significantly lower diversity levels (Shannon's index = 4.72). Bacterial and fungal communities' composition in degraded soils greatly differed from those in vegetated soils (Canberra index = 0.85 and 0.92, respectively) likely due to high soil sodicity, fine textures and compaction. Microbial communities' composition also differed in soils covered with exotic and native species, to a greater extent for fungi than for bacteria (Canberra index = 0.94 and 0.89, respectively), due to higher levels of nutrients, microbial biomass and activity in soils with native species. Results suggest that reforestation succeeded in avoiding further soil degradation but still leading to relevant changes in soil microbial community that may have negative effects on ecosystem stability. Information gained in this research could be useful for environmental agencies and decision makers about the controversial replacement of exotic plants in insular territories.},
}

@article {pmid36963629,
year = {2023},
author = {Lincke, JB and Christe, L and Unterlauft, JD and Zinkernagel, MS and Zysset-Burri, DC},
title = {Microbiome and retinal vascular diseases.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2023.02.017},
pmid = {36963629},
issn = {1525-2191},
abstract = {The gut microbiome consists of more than thousand different microbes and their associated genes and microbial metabolites. It influences various host metabolic pathways and is therefore important for homeostasis. In recent years, its influence on health and disease was extensively researched. In case of a microbiome disequilibrium called dysbiosis, the gut microbiome is associated with several diseases. Consequent chronic inflammation may lead to or promote inflammatory bowel disease, obesity, diabetes mellitus, atherosclerosis, alcoholic and non-alcoholic liver disease, cirrhosis, hepatocellular carcinoma and other diseases. The pathogenesis of the three most common retinal vascular diseases, diabetic retinopathy, retinal vein and artery occlusion, may also be influenced by an altered microbiome and associated risk factors such as diabetes mellitus, atherosclerosis, hypertension and obesity. Direct cause-effect relationships remain less well understood. A potential prevention or treatment modality for these diseases could be targeting and modulating the individual's gut microbiome.},
}

@article {pmid36963568,
year = {2023},
author = {Weil, PP and Reincke, S and Hirsch, CA and Giachero, F and Aydin, M and Scholz, J and Jönsson, F and Hagedorn, C and Nguyen, DN and Thymann, T and Pembaur, A and Orth, V and Wünsche, V and Jiang, PP and Wirth, S and Jenke, ACW and Sangild, PT and Kreppel, F and Postberg, J},
title = {Uncovering the gastrointestinal passage, intestinal epithelial cellular uptake and AGO2 loading of milk miRNAs in neonates using xenomiRs as tracers.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2023.03.016},
pmid = {36963568},
issn = {1938-3207},
abstract = {BACKGROUND: Human breast milk has a high microRNA (miRNA) content. It remains unknown whether and how milk miRNAs might affect intestinal gene regulation and homeostasis of the developing microbiome after initiation of enteral nutrition. However, this requires that relevant milk miRNA amounts survive gastrointestinal passage, are taken up by cells, and become available to the RNA interference (RNAi) machinery. It seems important to dissect the fate of these miRNAs after oral ingestion and gastrointestinal passage.

OBJECTIVE: Our goal was to analyze the potential transmissibility of milk miRNAs via the gastrointestinal system in neonate humans and a porcine model in vivo to contribute to the discussion whether milk miRNAs could influence gene regulation in neonates and thus might vertically transmit developmental relevant signals.

DESIGN: We performed cross-species profiling of miRNAs via deep-sequencing and utilized dietary xenobiotic taxon-specific milk miRNA (xenomiRs) as tracers in human and porcine neonates, followed by functional studies in primary human fetal intestinal epithelial cells (HIEC-6) using Ad5-mediated miRNA-gene transfer.

RESULTS: Mammals share many milk miRNAs yet exhibit taxon-specific miRNA fingerprints. We traced bovine-specific miRNAs from formula-nutrition in human preterm stool and 9 days after onset of enteral feeding in intestinal cells of preterm piglets. Thereafter, several xenomiRs accumulated in the intestinal cells. Moreover, few hours after introducing enteral feeding in preterm piglets with supplemented reporter miRNAs (cel-miR-39-5p/-3p), we observed their enrichment in blood serum and in AGO2-immunocomplexes from intestinal biopsies.

CONCLUSIONS: Milk-derived miRNAs survived gastrointestinal passage in human and porcine neonates. Bovine-specific miRNAs accumulated in intestinal cells of preterm piglets after enteral feeding with bovine colostrum/formula. In piglets, colostrum supplementation with cel-miR-39-5p/-3p resulted in increased blood levels of cel-miR-39-3p and argonaute RISC catalytic component 2 (AGO2) loading in intestinal cells. This suggests the possibility of vertical transmission of miRNA signaling from milk through the neonatal digestive tract.},
}

@article {pmid36970453,
year = {2023},
author = {Panyod, S and Wu, WK and Chen, CC and Wu, MS and Ho, CT and Sheen, LY},
title = {Modulation of gut microbiota by foods and herbs to prevent cardiovascular diseases.},
journal = {Journal of traditional and complementary medicine},
volume = {13},
number = {2},
pages = {107-118},
pmid = {36970453},
issn = {2225-4110},
abstract = {UNLABELLED: Dietary nutrients are associated with the development of cardiovascular disease (CVD) both through traditional pathways (inducing hyperlipidemia and chronic inflammation) and through the emergence of a metaorganism-pathogenesis pathway (through the gut microbiota, its metabolites, and host). Several molecules from food play an important role as CVD risk-factor precursors either themselves or through the metabolism of the gut microbiome. Animal-based dietary proteins are the primary source of CVD risk-factor precursors; however, some plants also possess these precursors, though at relatively low levels compared with animal-source food products. Various medications have been developed to treat CVD through the gut-microbiota-circulation axis, and they exhibit potent effects in CVD treatment. Nevertheless, such medicines are still being improved, and there are many research gaps that need to be addressed. Furthermore, some medications have unpleasant or adverse effects. Numerous foods and herbs impart beneficial effects upon health and disease. In the past decade, many studies have focused on treating and preventing CVD by modulating the gut microbiota and their metabolites. This review provides an overview of the available information, summarizes current research related to the gut-microbiota-heart axis, enumerates the foods and herbs that are CVD-risk precursors, and illustrates how metabolites become CVD risk factors through the metabolism of gut microbiota. Moreover, we present perspectives on the application of foods and herbs-including prebiotics, probiotics, synbiotics, postbiotics, and antibiotic-like substances-as CVD prevention agents to modulate gut microbiota by inhibiting gut-derived CVD risk factors.

Cardiovascular disease, gut microbiota, herbal medicine, preventive medicine, dietary therapy, nutrition supplements.},
}

@article {pmid36963522,
year = {2023},
author = {Pezzini, MF and Rampelotto, PH and Dall'Agnol, J and Guerreiro, GTS and Longo, L and Suarez Uribe, ND and Lange, EC and Álvares-da-Silva, MR and Joveleviths, D},
title = {Changes in the gut microbiota of rats after exposure to the fungicide Mancozeb.},
journal = {Toxicology and applied pharmacology},
volume = {},
number = {},
pages = {116480},
doi = {10.1016/j.taap.2023.116480},
pmid = {36963522},
issn = {1096-0333},
abstract = {Mancozeb is a fungicide commonly used in pest control programs, especially to protect vineyards. Its toxicity has already been evidenced in several studies. However, its influence on the composition and diversity of the gut microbiota remains unknown. In this work, the adverse impact of Mancozeb on the intestinal microbiota was investigated using a rodent model. Adult male Sprague Dawley rats were randomized into three groups: Control (standard diet), MZ1 (Mancozeb dose: 250 mg/kg bw/day), and MZ2 (Mancozeb dose: 500 mg/kg bw/day). After 12 weeks of experiment, animals were euthanized, and feces present in the intestine were collected. After fecal DNA extraction, the V4 region of the 16S rRNA gene was amplified followed by sequencing in an Ion S5™ System. Alpha and beta diversity analysis showed significant differences between Control and Mancozeb groups (MZ1 e MZ2), but no difference between MZ1 and MZ2 was observed. Seven genera significantly increased in abundance following Mancozeb exposure, while five genera decreased. Co-occurrence analyses revealed that the topological properties of the microbial networks, which can be used to infer co-occurrence interaction patterns among microorganisms, were significantly lower in both groups exposed to Mancozeb when compared to Control. In addition, 23 differentially abundant microbial metabolic pathways were identified in Mancozeb-treated groups mainly related to a change in energy metabolism, LPS biosynthesis, and nucleotide biosynthesis. In conclusion, the exposure to Mancozeb presented side effects by changing the composition of the microbiota in rats, increasing bacterial diversity regardless of the dose used, reducing the interaction patterns of the microbial communities, and changing microbial metabolic pathways.},
}

@article {pmid36963394,
year = {2023},
author = {Chen, H and Tong, T and Lu, SY and Ji, L and Xuan, B and Zhao, G and Yan, Y and Song, L and Zhao, L and Xie, Y and Leng, X and Zhang, X and Cui, Y and Chen, X and Xiong, H and Yu, T and Li, X and Sun, T and Wang, Z and Chen, J and Chen, YX and Hong, J and Fang, JY},
title = {Urea cycle activation triggered by host-microbiota maladaptation driving colorectal tumorigenesis.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2023.03.003},
pmid = {36963394},
issn = {1932-7420},
abstract = {Maladaptation of host-microbiota metabolic interplay plays a critical role in colorectal cancer initiation. Here, through a combination of single-cell transcriptomics, microbiome profiling, metabonomics, and clinical analysis on colorectal adenoma and carcinoma tissues, we demonstrate that host's urea cycle metabolism is significantly activated during colorectal tumorigenesis, accompanied by the absence of beneficial bacteria with ureolytic capacity, such as Bifidobacterium, and the overabundance of pathogenic bacteria lacking ureolytic function. Urea could enter into macrophages, inhibit the binding efficiency of p-STAT1 to SAT1 promotor region, and further skew macrophages toward a pro-tumoral phenotype characterized by the accumulation of polyamines. Treating a murine model using urea cycle inhibitors or Bifidobacterium-based supplements could mitigate urea-mediated tumorigenesis. Collectively, this study highlights the utility of urea cycle inhibitors or therapeutically manipulating microbial composition using probiotics to prevent colorectal cancer.},
}

@article {pmid36963360,
year = {2023},
author = {Zhang, X and Pan, Z and Wang, Y and Liu, P and Hu, K},
title = {Taraxacum officinale-derived exosome-like nanovesicles modulate gut metabolites to prevent intermittent hypoxia-induced hypertension.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {161},
number = {},
pages = {114572},
doi = {10.1016/j.biopha.2023.114572},
pmid = {36963360},
issn = {1950-6007},
abstract = {BACKGROUND: We aimed to investigate whether Taraxacum officinale (T. officinale)-derived exosome-like nanovesicles (ELNs) exerted hypotensive effects in intermittent hypoxia (IH)-induced hypertensive disorders and their potential mechanisms.

RESULTS: In this study, we developed T. officinale-derived natural nanoparticles with ideal size and stable negative surface charge, containing large amount of lipids and some functional proteins. We found that ELNs effectively reduced IH-induced hypertension, exhibited local anti-inflammatory effects on intestinal tissues in a rat model of IH-induced hypertension, and reduced intestinal tissue damage, including loss of goblet cells and barrier integrity damage, and ultimately inhibited the systemic inflammatory response. In addition, we evaluated intestinal microbial composition and SCFAs content and found significant changes in the structure and diversity of intestinal microbes, where butyrate was identified as the most important cause of the overall differences in the flora. Therefore, we further evaluated whether butyrate was a key target for ELNs to exert their effects in IH-induced hypertensive disease. We found that butyrate intervention further inhibited systemic inflammatory response and vascular wall remodeling by improving the intestinal microenvironment in IH rats, thereby attenuating IH-induced hypertension.

CONCLUSIONS: T. officinale-derived ELNs were effective in the treatment of IH-induced hypertensive disease, whereas butyrate played a major role in mediating the effects of ELNs in anti-IH-induced hypertensive disease.},
}

@article {pmid36963248,
year = {2023},
author = {Descamps, A and Van der Borght, K and De Spiegeleer, A and Wynendaele, E and De Spiegeleer, B},
title = {Peptidomics: LC-MS operational parameters do matter.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {229},
number = {},
pages = {115348},
doi = {10.1016/j.jpba.2023.115348},
pmid = {36963248},
issn = {1873-264X},
abstract = {The sensitive and specific detection of peptides at low levels in biofluids is critical to increase the lab-to-human translation of peptidomic research. An interesting group of peptides with increasing evidence for involvement in human diseases are quorum sensing peptides. To obtain more reliable conclusions on peptide measurands in biofluids, a selection of often neglected parts of the analytical process using LC-MS were investigated, with novel approaches recommended for each part. Quorum sensing peptides were used as the main model-peptides. The peptidomic parts investigated and discussed here are: Our work addresses aQbD-approached solutions to these challenges, encompassing sample stabilization measures, a suitable peptide anti-adsorption tool, judicious choice of injection solvent versus gradient system and optimal duty cycle parameters. Our recommendations will improve the peptidomics bio-analytics of not only quorum sensing peptides, but can also be of value for other measurands at low concentrations.},
}

@article {pmid36963164,
year = {2023},
author = {Beliaeva, MA and Wilmanns, M and Zimmermann, M},
title = {Decipher enzymes from human microbiota for drug discovery and development.},
journal = {Current opinion in structural biology},
volume = {80},
number = {},
pages = {102567},
doi = {10.1016/j.sbi.2023.102567},
pmid = {36963164},
issn = {1879-033X},
abstract = {The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.},
}

@article {pmid36961872,
year = {2023},
author = {Janker, L and Schuster, D and Bortel, P and Hagn, G and Meier-Menches, SM and Mohr, T and Mader, JC and Slany, A and Bileck, A and Brunmair, J and Madl, C and Unger, L and Hennlich, B and Weitmayr, B and Del Favero, G and Pils, D and Pukrop, T and Pfisterer, N and Feichtenschlager, T and Gerner, C},
title = {Multi-omics empowered deep phenotyping of ulcerative colitis identifies biomarker signatures reporting functional remission states.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjad052},
pmid = {36961872},
issn = {1876-4479},
abstract = {INTRODUCTION: Ulcerative colitis (UC) is a chronic disease with rising incidence and unclear etiology. Deep molecular phenotyping by multi omics analyses may provide novel insights into disease processes and characteristic features of remission states.

METHODS: UC pathomechanisms were assessed by proteome profiling of human tissue specimen, obtained from five distinct colon locations for each of the 12 patients included in the study. Systemic disease-associated alterations were evaluated thanks to a cross-sectional setting of mass spectrometry-based multi-omics analyses comprising proteins, metabolites and eicosanoids of plasma obtained from UC patients during acute episodes and upon remission in comparison to healthy controls.

RESULTS: Tissue proteome profiling indicated colitis-associated activation of neutrophils, macrophages, B- and T-cells, fibroblasts, endothelial cells and platelets, and hypoxic stress, and suggested a general down-regulation of mitochondrial proteins accompanying the establishment of apparent wound healing-promoting activities including scar formation. While pro-inflammatory proteins were apparently upregulated by immune cells, the colitis-associated epithelial cells, fibroblasts, endothelial cells and platelets seemed to predominantly contribute anti-inflammatory and wound healing-promoting proteins. Blood plasma proteomics indicated chronic inflammation and platelet activation, whereas plasma metabolomics identified disease-associated deregulations of gut and gut microbiome-derived metabolites. Upon remission, several, but not all, molecular candidate biomarker levels recovered back to normal.

CONCLUSIONS: The findings may indicate that microvascular damage and platelet deregulation hardly resolve upon remission but apparently persist as disease-associated molecular signature. This study presents local and systemic molecular alterations integrated in a model for UC pathomechanisms potentially supporting the assessment of disease and remission states in UC patients.},
}

@article {pmid36961605,
year = {2023},
author = {Basiru, S and Ait Si Mhand, K and Hijri, M},
title = {Disentangling arbuscular mycorrhizal fungi and bacteria at the soil-root interface.},
journal = {Mycorrhiza},
volume = {},
number = {},
pages = {},
pmid = {36961605},
issn = {1432-1890},
abstract = {Arbuscular mycorrhizal fungi (AMF) are essential components of the plant root mycobiome and are found in approximately 80% of land plants. As obligate plant symbionts, AMF harbor their own microbiota, both inside and outside the plant root system. AMF-associated bacteria (AAB) possess various functional traits, including nitrogen fixation, organic and inorganic phosphate mobilization, growth hormone production, biofilm production, enzymatic capabilities, and biocontrol against pathogen attacks, which not only contribute to the health of the arbuscular mycorrhizal symbiosis but also promote plant growth. Because of this, there is increasing interest in the diversity, functioning, and mechanisms that underlie the complex interactions between AMF, AAB, and plant hosts. This review critically examines AMF-associated bacteria, focusing on AAB diversity, the factors driving richness and community composition of these bacteria across various ecosystems, along with the physical, chemical, and biological connections that enable AMF to select and recruit beneficial bacterial symbionts on and within their structures and hyphospheres. Additionally, potential applications of these bacteria in agriculture are discussed, emphasizing the potential importance of AMF fungal highways in engineering plant rhizosphere and endophyte bacteria communities, and the importance of a functional core of AAB taxa as a promising tool to improve plant and soil productivity. Thus, AMF and their highly diverse bacterial taxa represent important tools that could be efficiently explored in sustainable agriculture, carbon sequestration, and reduction of greenhouse gas emissions related to nitrogen fertilizer applications. Nevertheless, future studies adopting integrated multidisciplinary approaches are crucial to better understand AAB functional diversity and the mechanisms that govern these tripartite relationships.},
}

@article {pmid36961604,
year = {2023},
author = {Nöltner, C and Bulashevska, A and Hübscher, K and Haberstroh, H and Grimbacher, B and Proietti, M},
title = {Fecal Immunoglobulin Levels as a Modifier of the Gut Microbiome in Patients with Common Variable Immunodeficiency.},
journal = {Journal of clinical immunology},
volume = {},
number = {},
pages = {},
pmid = {36961604},
issn = {1573-2592},
abstract = {OBJECTIVE: Common variable immunodeficiency (CVID) is the most common clinically relevant entity of inborn errors of immunity. In these patients, an altered gut microbiome composition with reduced diversity has been described. We sought to investigate the fecal immunoglobulin levels and their impact on the gut microflora in patients with CVID.

METHODS: We analyzed the gut microbiome of 28 CVID patients and 42 healthy donors (HDs), including 21 healthy household controls, by sequencing the V3 and V4 regions of the bacterial 16S rRNA gene extracted from stool samples. The fecal levels of immunoglobulin A, M, and G of 27 CVID patients and 41 HDs were measured in the supernatant by ELISA and normalized for protein concentration.

RESULTS: We measured decreased IgA and increased IgG in stool samples from CVID patients compared to HDs. Decreased levels of fecal IgA and IgM were associated with reduced microbial diversity and increased dysbiosis. We identified a large number of significantly differentially abundant taxa, especially in patients with decreased IgA levels, but also in patients with decreased IgM levels compared to their counterparts.

CONCLUSIONS: CVID patients have an altered gut microbiota composition, which is most prevalent in patients with decreased fecal IgA and IgM levels. In this study, we identify fecal immunoglobulins as a potential modifier of the gut microbiome in CVID patients.},
}

@article {pmid36961409,
year = {2023},
author = {Vishnoi, V and Morey, T and Hoedt, EC and Keely, S and Pockney, P and Smith, SR},
title = {A Systematic Review and Meta-Analysis of Intra-Operative Surgical Site Sampling: Culture versus Culture-Independent Techniques in Predicting Downstream Surgical Site Infection.},
journal = {Surgical infections},
volume = {},
number = {},
pages = {},
doi = {10.1089/sur.2023.012},
pmid = {36961409},
issn = {1557-8674},
abstract = {Background: Surgical site infection remains a significant cause of morbidity and mortality. Traditionally, the causation has been inferred from the organism(s) detected in the post-operative setting. However, the intra-operative surgical site and the bacteria it harbors have been scarcely studied. Compared with culture-dependent methods, the development of genomic technology provides a new sensitive tool that could aid in characterizing the bacteria within the surgical site. The purpose of this literature review is to establish if there is a predictive role of sampling the intra-operative surgical site. Methods: A systematic literature review was conducted identifying relevant literature reporting on studies that sampled the intra-operative surgical site of any specialty, using either traditional culture or a culture-independent genomic sequencing-based technique and correlation with infection was attempted. The review identified studies between 1959 and 2021 in MEDLINE, EMBASE and Cochrane. Results: The initial search identified 7,835 articles; 36 remained after screening. Thirty-one articles focused on culture-dependent techniques, five on culture-independent. Subgroup meta-analysis demonstrates that a positive intra-operative culture carries a risk of downstream infection with an odds ratio of 8.6, however limited by a high false-positive and inability to correlate the intra-operative culture with the post-operative infection. In contrast, culture-independent studies through genomic sequencing are not predictive but suggest that the surgical incision is a complex microbial community with a shift toward dysbiosis in certain patients. Conclusion: The intra-operative surgical site clearly harbors bacteria. Both techniques give rise to separate explanations underpinning the role of bacteria in surgical site infection. It is possible there is a more complex dynamic community within the incision that makes a patient susceptible to infection. Characterizing this microbial community in large scale studies, including patients with infections may enhance our ability to predict and prevent incisional surgical site infections in patients undergoing surgical procedures.},
}

@article {pmid36960914,
year = {2023},
author = {Cable, J and Rathmell, JC and Pearce, EL and Ho, PC and Haigis, MC and Mamedov, MR and Wu, MJ and Kaech, SM and Lynch, L and Febbraio, MA and Bapat, SP and Hong, HS and Zou, W and Belkaid, Y and Sullivan, ZA and Keller, A and Wculek, SK and Green, DR and Postic, C and Amit, I and Benitah, SA and Jones, RG and Reina-Campos, M and Torres, SV and Beyaz, S and Brennan, D and O'Neill, LAJ and Perry, RJ and Brenner, D},
title = {Immunometabolism at the crossroads of obesity and cancer-a Keystone Symposia report.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.14976},
pmid = {36960914},
issn = {1749-6632},
support = {/NH/NIH HHS/United States ; },
abstract = {Immunometabolism considers the relationship between metabolism and immunity. Typically, researchers focus on either the metabolic pathways within immune cells that affect their function or the impact of immune cells on systemic metabolism. A more holistic approach that considers both these viewpoints is needed. On September 5-8, 2022, experts in the field of immunometabolism met for the Keystone symposium "Immunometabolism at the Crossroads of Obesity and Cancer" to present recent research across the field of immunometabolism, with the setting of obesity and cancer as an ideal example of the complex interplay between metabolism, immunity, and cancer. Speakers highlighted new insights on the metabolic links between tumor cells and immune cells, with a focus on leveraging unique metabolic vulnerabilities of different cell types in the tumor microenvironment as therapeutic targets and demonstrated the effects of diet, the microbiome, and obesity on immune system function and cancer pathogenesis and therapy. Finally, speakers presented new technologies to interrogate the immune system and uncover novel metabolic pathways important for immunity.},
}

@article {pmid36960491,
year = {2023},
author = {Johnston, W and Rosier, BT and Carda-Diéguez, M and Paterson, M and Watson, P and Piela, K and Goulding, M and Ramage, G and Baranyia, D and Chen, T and Al-Hebshi, N and Mira, A and Culshaw, S},
title = {Longitudinal changes in subgingival biofilm composition following periodontal treatment.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/JPER.22-0749},
pmid = {36960491},
issn = {1943-3670},
abstract = {BACKGROUND: Current periodontal treatment involves instrumentation using hand and/or ultrasonic instruments, which are used either alone or in combination based on patient and clinician preference, with comparable clinical outcomes. This study sought to investigate early and later changes in the subgingival biofilm following periodontal treatment; to identify whether these changes were associated with treatment outcomes; and to investigate whether the biofilm responded differently to hand compared with ultrasonic instruments.

METHODS: This was a secondary-outcome analysis of a randomised controlled trial. Thirty-eight periodontitis patients received full-mouth subgingival instrumentation using hand (n = 20) or ultrasonic instrumentation (n = 18). Subgingival plaque was sampled at baseline and 1, 7 and 90 days following treatment. Bacterial DNA was analysed using 16S rRNA sequencing. Periodontal clinical parameters were evaluated before and after treatment.

RESULTS: Biofilm composition was comparable in both (hand and ultrasonics) treatment groups at all timepoints (all genus and species; p[adjusted]>0.05). Large-scale changes were observed within-groups across timepoints. At days 1 and 7, taxonomic diversity and dysbiosis were reduced, with an increase in health-associated genera including Streptococcus and Rothia equating to 30-40% of the relative abundance. When reassessed at day 90 a subset of samples reformed a microbiome more comparable with baseline, which was independent of instrumentation choice and residual disease.

CONCLUSIONS: Hand and ultrasonic instruments induced comparable impacts on the subgingival plaque microbiome. There were marked early changes in the subgingival biofilm composition, although there was limited evidence that community shifts associated with treatment outcomes. This article is protected by copyright. All rights reserved.},
}

@article {pmid36960395,
year = {2023},
author = {Uzuner, C and Mak, J and El-Assaad, F and Condous, G},
title = {The bidirectional relationship between endometriosis and microbiome.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1110824},
pmid = {36960395},
issn = {1664-2392},
abstract = {Endometriosis has been described by many different theories of pathogenesis over the years. It is now also appreciated to be a state of chronic inflammation, and the role of immune dysfunction in its development has been proven. There is increasing evidence to support the role of the microbiome in the formation and progression of endometriosis via inflammatory pathways. The dysbiosis seen in endometriosis is thought to be both causative and a consequence of the pathogenesis. Gut, peritoneal fluid and female reproductive tract microbiota has been studied to understand if there are any microbiome signatures specific to endometriosis. New research on how to manipulate the microbiome for better detection and treatment of endometriosis is emerging.},
}

@article {pmid36960288,
year = {2023},
author = {Zeng, Q and Man, X and Huang, Z and Zhuang, L and Yang, H and Sha, Y},
title = {Effects of rice blast biocontrol strain Pseudomonas alcaliphila Ej2 on the endophytic microbiome and proteome of rice under salt stress.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1129614},
pmid = {36960288},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil salinity is a prevalent environmental stress in agricultural production. Microbial inoculants could effectively help plants to alleviate salt stress. However, there is little knowledge of the biocontrol strain Pseudomonas alcaliphila Ej2 mechanisms aiding rice plants to reduce the adverse effects caused by salt stress.

METHODS: We performed integrated field and greenhouse experiments, microbial community profiling, and rice proteomic analysis to systematically investigate the Ej2 mechanism of action.

RESULTS: The results displayed that biocontrol strain Ej2 increased shoot/root length and fresh/dry weight compared with control under salt stress. Meanwhile, strain Ej2 has the ability to control rice blast disease and promote rice growth. Furthermore, the microbial community analysis revealed that the alpha-diversity of Ej2-inoculated plants was higher than the control plants, expect the Shannon index of the bacterial microbiome and the Ej2-inoculated samples clustered and separated from the control samples based on beta-diversity analysis. Importantly, the enriched and specific OTUs after Ej2 inoculation at the genus level were Streptomyces, Pseudomonas, Flavobacterium, and Bacillus. Moreover, we observed that Ej2 inoculation influenced the rice proteomic profile, including metabolism, plant-pathogen interactions, and biosynthesis of unsaturated fatty acids. These results provide comprehensive evidence that Ej2 inoculation induced the rice endophytic microbiome and proteomic profiles to promote plant growth under salt stress.

DISCUSSION: Understanding the biocontrol strain effects on the endophytic microbiome and rice proteomics will help us better understand the complex interactions between plants and microorganisms under salt stress. Furthermore, unraveling the mechanisms underlying salt tolerance will help us more efficiently ameliorate saline soils.},
}

@article {pmid36960281,
year = {2023},
author = {Kapinusova, G and Lopez Marin, MA and Uhlik, O},
title = {Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1089630},
pmid = {36960281},
issn = {1664-302X},
abstract = {In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.},
}

@article {pmid36960045,
year = {2023},
author = {Yang, Z and Cai, T and Li, Y and Jiang, D and Luo, J and Zhou, Z},
title = {Effects of topical fluoride application on oral microbiota in young children with severe dental caries.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1104343},
pmid = {36960045},
issn = {2235-2988},
abstract = {While the effect of fluoride on severe early childhood caries (S-ECC) is clear, knowledge of how it influences the oral microbiota and the consequential effects on oral health is limited. In this cohort study, we investigated the changes introduced in the oral ecosystem before and after using fluoride varnish in 54- to 66-month-old individuals (n=90: 18 children were sampled at 5 different time points). 16S rDNA was amplified from bacterial samples using polymerase chain reaction, and high-throughput sequencing was performed using Illumina MiSeq platforms. Many pronounced microbial changes were related to the effects of fluoride varnishing. The health-associated Bacteroides and Uncultured_bacterium_f_Enterobacteriaceae were enriched in the saliva microbiome following treatment with fluoride varnishing. Co-occurrence network analysis of the dominant genera showed that different groups clearly showed different bacterial correlations. The PICRUSt algorithm was used to predict the function of the microbial communities from saliva samples. The results showed that starch and sucrose metabolism was greater after fluoride use. BugBase was used to determine phenotypes present in microbial community samples. The results showed that Haemophilus and Neisseria (phylum Proteobacteria) was greater before fluoride use. We conclude that the changes in oral microbiology play a role in fluoride prevention of S-ECC.},
}

@article {pmid36960044,
year = {2023},
author = {Zhao, H and Chen, Y and Zheng, Y and Xu, J and Zhang, C and Fu, M and Xiong, K},
title = {Conjunctival sac microbiome in anophthalmic patients: Flora diversity and the impact of ocular prosthesis materials.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1117673},
pmid = {36960044},
issn = {2235-2988},
abstract = {PURPOSE: To explore the changes of bacterial flora in anophthalmic patients wearing ocular prosthesis (OP) and the microbiome diversity in conditions of different OP materials.

METHODS: A cross-sectional clinical study was conducted, involving 19 OP patients and 23 healthy subjects. Samples were collected from the upper, lower palpebral, caruncle, and fornix conjunctiva. 16S rRNA sequencing was applied to identify the bacterial flora in the samples. The eye comfort of each OP patient was determined by a questionnaire. In addition, demographics information of each participant was also collected.

RESULTS: The diversity and richness of ocular flora in OP patients were significantly higher than that in healthy subjects. The results of flora species analysis also indicated that in OP patients, pathogenic microorganisms such as Escherichia Shigella and Fusobacterium increased significantly, while the resident flora of Lactobacillus and Lactococcus decreased significantly. Within the self-comparison of OP patients, compared with Polymethyl Methacrylate (PMMA), prosthetic material of glass will lead to the increased colonization of opportunistic pathogens such as Alcaligenes, Dermabacter and Spirochaetes, while gender and age have no significant impact on ocular flora.

CONCLUSIONS: The ocular flora of OP patients was significantly different from that of healthy people. Abundant colonization of pathogenic microorganisms may have an important potential relationship with eye discomfort and eye diseases of OP patients. PMMA, as an artificial eye material, demonstrated potential advantages in reducing the colonization of opportunistic pathogens.},
}

@article {pmid36960043,
year = {2023},
author = {Lin, T},
title = {Editorial: New techniques in microbiome research.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1158392},
doi = {10.3389/fcimb.2023.1158392},
pmid = {36960043},
issn = {2235-2988},
}

@article {pmid36959989,
year = {2022},
author = {Khanna, HN and Roy, S and Shaikh, A and Bandi, V},
title = {Emerging Role and Place of Probiotics in the Management of Pediatric Neurodevelopmental Disorders.},
journal = {Euroasian journal of hepato-gastroenterology},
volume = {12},
number = {2},
pages = {102-108},
pmid = {36959989},
issn = {2231-5047},
abstract = {UNLABELLED: The current decade has witnessed significant developments with the latest therapeutic agents for managing various infectious diseases to complex hemato-oncological conditions, leading to a decrease in morbidity and mortality, while improving the quality of life (QoL), and increasing the life span. Non-communicable diseases (NCDs), which are on the rise across all age-groups, are being driven by unhealthy lifestyles and improved mental health issues. The current therapeutic agents were found to offer only symptomatic relief of varying efficacy and significant adverse effects, leading clinicians to evaluate other options for the management of both neurodevelopmental and neurodegenerative disorders. The role of gut microbiota has emerged as a potential target for the treatment of both neurodegenerative diseases and neurodevelopmental disorders like attention-deficit hyperactivity disorder (ADHD)/autism spectrum disorders (ASD) as a result of the decoding of the human genome and advances in our understanding of the human gut microbiome, including its interactions with the human brain. This review has been undertaken to understand on date level of understanding of human microbiota and towards identifying probiotic strains with proven efficacy and safety. According to recent investigations, several lactobacillus strains, including L. Paracasei 37, L. Planetarium 128, L. reuteri DSM 17938, and Bifidobacterium longum, have been effective in treating children's neurodevelopmental disorders such as ASD and ADHD. Future clinical studies are nonetheless required to confirm the long-term safety and effectiveness of probiotic strains in managing the primary and comorbid symptoms, hence improving patient and family quality of life.

HOW TO CITE THIS ARTICLE: Khanna HN, Roy S, Shaikh A, et al. Emerging Role and Place of Probiotics in the Management of Pediatric Neurodevelopmental Disorders. Euroasian J Hepato-Gastroenterol 2022;12(2):102-108.},
}

@article {pmid36959951,
year = {2023},
author = {Mundra, S and Shockey, J and Morsy, M},
title = {Editorial: Plant microbiome: Ecology, functions, and application trends.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1175556},
pmid = {36959951},
issn = {1664-462X},
}

@article {pmid36959686,
year = {2023},
author = {Yang, Y and Han, Z and Gao, Z and Chen, J and Song, C and Xu, J and Wang, H and Huang, A and Shi, J and Gu, J},
title = {Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {36959686},
issn = {2542-5641},
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is an independent risk factor for colorectal cancer (CRC), and the patients with CRC and T2DM have worse survival. The human gut microbiota (GM) is linked to the development of CRC and T2DM, respectively. However, the GM characteristics in patients with CRC and T2DM remain unclear.

METHODS: We performed fecal metagenomic and targeted metabolomics studies on 36 samples from CRC patients with T2DM (DCRC group, n = 12), CRC patients without diabetes (CRC group, n = 12), and healthy controls (Health group, n = 12). We analyzed the fecal microbiomes, characterized the composition and function based on the metagenomics of DCRC patients, and detected the short-chain fatty acids (SCFAs) and bile acids (BAs) levels in all fecal samples. Finally, we performed a correlation analysis of the differential bacteria and metabolites between different groups.

RESULTS: Compared with the CRC group, LefSe analysis showed that there is a specific GM community in DCRC group, including an increased abundance of Eggerthella, Hungatella, Peptostreptococcus, and Parvimonas, and decreased Butyricicoccus, Lactobacillus, and Paraprevotella. The metabolomics analysis results revealed that the butyric acid level was lower but the deoxycholic acid and 12-keto-lithocholic acid levels were higher in the DCRC group than other groups (P < 0.05). The correlation analysis showed that the dominant bacterial abundance in the DCRC group (Parvimonas, Desulfurispora, Sebaldella, and Veillonellales, among others) was negatively correlated with butyric acid, hyodeoxycholic acid, ursodeoxycholic acid, glycochenodeoxycholic acid, chenodeoxycholic acid, cholic acid and glycocholate. However, the abundance of mostly inferior bacteria was positively correlated with these metabolic acid levels, including Faecalibacterium, Thermococci, and Cellulophaga.

CONCLUSIONS: Unique fecal microbiome signatures exist in CRC patients with T2DM compared to those with non-diabetic CRC. Alterations in GM composition and SCFAs and secondary BAs levels may promote CRC development.},
}

@article {pmid36959568,
year = {2023},
author = {Ivashkin, V and Shifrin, O and Maslennikov, R and Poluektova, E and Korolev, A and Kudryavtseva, A and Krasnov, G and Benuni, N and Barbara, G},
title = {Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study.},
journal = {BMC gastroenterology},
volume = {23},
number = {1},
pages = {82},
pmid = {36959568},
issn = {1471-230X},
abstract = {BACKGROUND: Rifaximin effectively treats symptomatic uncomplicated diverticular disease (SUDD) and has shown eubiotic potential (i.e., an increase in resident microbial elements with potential beneficial effects) in other diseases. This study investigated changes in the fecal microbiome of patients with SUDD after repeated monthly treatment with rifaximin and the association of these changes with the severity of abdominal pain.

METHODS: This was a single-center, prospective, observational, uncontrolled cohort study. Patients received rifaximin 400 mg twice a day for 7 days per month for 6 months. Abdominal pain (assessed on a 4-point scale from 0 [no pain] to 3 [severe pain]) and fecal microbiome (assessed using 16 S rRNA gene sequencing) were assessed at inclusion (baseline) and 3 and 6 months. The Spearman's rank test analyzed the relationship between changes in the gut microbiome and the severity of abdominal pain. A p-value ≤ 0.05 was considered statistically significant.

RESULTS: Of the 23 patients enrolled, 12 patients completed the study and were included in the analysis. Baseline abdominal pain levels decreased significantly after 3 (p = 0.036) and 6 (p = 0.008) months of treatment with rifaximin. The abundance of Akkermansia in the fecal microbiome was significantly higher at 3 (p = 0.017) and 6 (p = 0.015) months versus baseline. The abundance of Ruminococcaceae (p = 0.034), Veillonellaceae (p = 0.028), and Dialister (p = 0.036) were significantly increased at 6 months versus baseline, whereas Anaerostipes (p = 0.049) was significantly decreased. The severity of abdominal pain was negatively correlated with the abundance of Akkermansia (r=-0.482; p = 0.003) and Ruminococcaceae (r=-0.371; p = 0.026) but not with Veillonellaceae, Dialister, or Anaerostipes. After 3 months of rifaximin, abdominal pain was significantly less in patients with Akkermansia in their fecal microbiome than in patients without Akkermansia (p = 0.022).

CONCLUSION: The eubiotic effect of rifaximin was associated with decreased abdominal pain in patients with SUDD.},
}

@article {pmid36959296,
year = {2023},
author = {Bernard, NJ},
title = {Microbiome checkpoint.},
journal = {Nature immunology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41590-023-01486-1},
pmid = {36959296},
issn = {1529-2916},
}

@article {pmid36959286,
year = {2023},
author = {Ye, W and Xing, J and Yu, Z and Hu, X and Zhao, Y},
title = {Mechanism and treatments of antipsychotic-induced weight gain.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {36959286},
issn = {1476-5497},
abstract = {The long-term use of antipsychotics (APs) may cause a variety of diseases, such as metabolic syndrome, antipsychotic-induced weight gain (AIWG), and even obesity. This paper reviews the various mechanisms of AIWG and obesity in detail, involving genetics, the central nervous system, the neuroendocrine system, and the gut microbiome. The common drug and non-drug therapies used in clinical practice are also introduced, providing the basis for research on the molecular mechanisms and the future selection of treatments.},
}

@article {pmid36959210,
year = {2023},
author = {Wu, CM and Wheeler, KM and Cárcamo-Oyarce, G and Aoki, K and McShane, A and Datta, SS and Mark Welch, JL and Tiemeyer, M and Griffen, AL and Ribbeck, K},
title = {Mucin glycans drive oral microbial community composition and function.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {11},
pmid = {36959210},
issn = {2055-5008},
abstract = {Human microbiome composition is closely tied to health, but how the host manages its microbial inhabitants remains unclear. One important, but understudied, factor is the natural host environment: mucus, which contains gel-forming glycoproteins (mucins) that display hundreds of glycan structures with potential regulatory function. Leveraging a tractable culture-based system to study how mucins influence oral microbial communities, we found that mucin glycans enable the coexistence of diverse microbes, while resisting disease-associated compositional shifts. Mucins from tissues with unique glycosylation differentially tuned microbial composition, as did isolated mucin glycan libraries, uncovering the importance of specific glycan patterns in microbiome modulation. We found that mucins shape microbial communities in several ways: serving as nutrients to support metabolic diversity, organizing spatial structure through reduced aggregation, and possibly limiting antagonism between competing taxa. Overall, this work identifies mucin glycans as a natural host mechanism and potential therapeutic intervention to maintain healthy microbial communities.},
}

@article {pmid36959041,
year = {2023},
author = {Ait-Zenati, F and Djoudi, F and Mehelleb, D and Madaoui, M},
title = {Involvement of the human microbiome in frequent cancers, current knowledge and carcinogenesis mechanisms.},
journal = {Bulletin du cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bulcan.2023.01.022},
pmid = {36959041},
issn = {1769-6917},
abstract = {The human body is home to a complex microbial community, living in symbiosis. However, when an imbalance occurs, known as dysbiosis, it can lead to organic diseases such as cancers. Helicobacter pylori is commonly recognized as the causative agent of gastric cancer. Numerous studies have explored the potential role of other microorganisms in cancers. For example, the role of intestinal microbiota in the hepatocellular carcinoma formation and progression, the microbiota in breast cancer and the interaction between the microbiome and TP53 in human lung carcinogenesis. In this review, we highlight the latest findings on the microbiome involved in the most common cancers and the suggested mechanisms of carcinogenesis.},
}

@article {pmid36958817,
year = {2023},
author = {Vich Vila, A and Hu, S and Andreu-Sánchez, S and Collij, V and Jansen, BH and Augustijn, HE and Bolte, LA and Ruigrok, RAAA and Abu-Ali, G and Giallourakis, C and Schneider, J and Parkinson, J and Al-Garawi, A and Zhernakova, A and Gacesa, R and Fu, J and Weersma, RK},
title = {Faecal metabolome and its determinants in inflammatory bowel disease.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2022-328048},
pmid = {36958817},
issn = {1468-3288},
abstract = {OBJECTIVE: Inflammatory bowel disease (IBD) is a multifactorial immune-mediated inflammatory disease of the intestine, comprising Crohn's disease and ulcerative colitis. By characterising metabolites in faeces, combined with faecal metagenomics, host genetics and clinical characteristics, we aimed to unravel metabolic alterations in IBD.

DESIGN: We measured 1684 different faecal metabolites and 8 short-chain and branched-chain fatty acids in stool samples of 424 patients with IBD and 255 non-IBD controls. Regression analyses were used to compare concentrations of metabolites between cases and controls and determine the relationship between metabolites and each participant's lifestyle, clinical characteristics and gut microbiota composition. Moreover, genome-wide association analysis was conducted on faecal metabolite levels.

RESULTS: We identified over 300 molecules that were differentially abundant in the faeces of patients with IBD. The ratio between a sphingolipid and L-urobilin could discriminate between IBD and non-IBD samples (AUC=0.85). We found changes in the bile acid pool in patients with dysbiotic microbial communities and a strong association between faecal metabolome and gut microbiota. For example, the abundance of Ruminococcus gnavus was positively associated with tryptamine levels. In addition, we found 158 associations between metabolites and dietary patterns, and polymorphisms near NAT2 strongly associated with coffee metabolism.

CONCLUSION: In this large-scale analysis, we identified alterations in the metabolome of patients with IBD that are independent of commonly overlooked confounders such as diet and surgical history. Considering the influence of the microbiome on faecal metabolites, our results pave the way for future interventions targeting intestinal inflammation.},
}

@article {pmid36958642,
year = {2023},
author = {Detcharoen, M and Jiggins, FM and Schlick-Steiner, BC and Steiner, FM},
title = {Wolbachia endosymbiotic bacteria alter the gut microbiome in the fly Drosophila nigrosparsa.},
journal = {Journal of invertebrate pathology},
volume = {198},
number = {},
pages = {107915},
doi = {10.1016/j.jip.2023.107915},
pmid = {36958642},
issn = {1096-0805},
abstract = {Wolbachia are known to cause reproductive manipulations and in some arthropod species, Wolbachia were reported to cause changes in gut microbiome. However, the effects of Wolbachia bacteria on the microbiomes of their hosts, including Drosophila flies, have not been fully accessed. Here, we checked the bacterial microbiome in guts of Wolbachia-uninfected and of Wolbachia-infected Drosophila nigrosparsa, both separated into a bleach-only (embryos bleached) and a gnotobiotic (embryos bleached and inoculated with bacteria) treatment. We observed a clear separation between the Wolbachia-infected and the Wolbachia-uninfected samples, and the infected samples had higher variation in alpha diversity than the uninfected ones. There were reductions in the abundances of Proteobacteria (Pseudomonadota), especially Acetobacter, in the infected samples of both treatments. These findings highlight that Wolbachia change the gut microbiome in D. nigrosparsa as well as that the interactions between Wolbachia and bacteria like Acetobacter need to be investigated.},
}

@article {pmid36958561,
year = {2023},
author = {Mancuso, FP and Morrissey, KL and De Clerck, O and Airoldi, L},
title = {Warming and nutrient enrichment can trigger seaweed loss by dysregulation of the microbiome structure and predicted function.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {162919},
doi = {10.1016/j.scitotenv.2023.162919},
pmid = {36958561},
issn = {1879-1026},
abstract = {Warming and nutrient enrichment are key pervasive drivers of ecological shifts in both aquatic and terrestrial ecosystems, impairing the physiology and survival of a wide range of foundation species. But the underlying mechanisms often remain unclear, and experiments have overlooked the potential effects mediated by changes in the microbial communities. We experimentally tested in the field orthogonal stress combinations from simulated air warming and nutrient enrichment on the intertidal foundation seaweed Cystoseira compressa, and its associated bacterial communities. A total of 523 Amplicon Sequence Variance (ASVs) formed the bacterial community on C. compressa, with 222 ASVs assigned to 69 taxa at the genus level. Most bacteria taxa experienced changes in abundance as a result of additive (65 %) and antagonistic (30 %) interactions between the two stressors, with synergies (5 %) occurring less frequently. The analysis of the predicted bacterial functional profile identified 160 metabolic pathways, and showed that these were mostly affected by additive interactions (74 %) between air warming and nutrient enrichment, while antagonisms (20 %) and synergisms (6 %) were less frequent. Overall, the two stressors combined increased functions associated with seaweed disease or degradation of major cell-wall polymers and other algicidal processes, and decreased functions associated with Quorum Quenching and photosynthetic response. We conclude that warming and nutrient enrichment can dysregulate the microbiome of seaweeds, providing a plausible mechanism for their ongoing loss, and encourage more research into the effects of human impacts on crucial but yet largely unstudied host-microbiome relationships in different aquatic and terrestrial species.},
}

@article {pmid36958158,
year = {2023},
author = {Saha, S and Xiong, JQ and Patil, SM and Ha, GS and Hoh, JK and Park, HK and Chung, W and Chang, SW and Khan, MA and Park, HB and Jeon, BH},
title = {Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate.},
journal = {Journal of hazardous materials},
volume = {452},
number = {},
pages = {131200},
doi = {10.1016/j.jhazmat.2023.131200},
pmid = {36958158},
issn = {1873-3336},
abstract = {The preeminence of sulfonamide drug resistance genes in food waste (FW) and the increased utilization of high-strength organic FW in anaerobic digestion (AD) to enhance methane production have raised severe public health concerns in wastewater treatment plants worldwide. In this regard, the dissemination patterns of different sulfonamide resistance genes (sul1 and sul2) and their impact on the digester core microbiota during AD of FW leachate (FWL) were evaluated. The presence of various sulfonamide antibiotics (SAs) in FWL digesters improved the final methane yield by 37 % during AD compared with FWL digesters without SAs. Microbial population shifts towards hydrolytic, acidogenic, and acetogenic bacteria in the phyla Actinobacteriota, Bacteroidota, Chloroflexi, Firmicutes, Proteobacteria, and Synergistota occurred due to SA induced substrate digestion and absorption through active transport; butanoate, propanoate, and pyruvate metabolism; glycolysis; gluconeogenesis; the citrate cycle; and pentose phosphate pathway. The initial dominance of Methanosaeta (89-96 %) declined to 47-53 % as AD progressed and shifted towards Methanosarcina (40 %) in digesters with the highest SA concentrations at the end of AD. Dissemination of sul1 depended on class 1 integron gene (intl1)-based horizontal gene transfer to pathogenic members of Chloroflexi, Firmicutes, and Patescibacteria, whereas sul2 was transmitted to Synergistota independent of intl1. Low susceptibility and ability to utilize SAs during methanogenesis shielded methanogenic archaea against selection pressure, thus preventing them from interacting with sul or intl1 genes, thereby minimizing the risk of antibiotic resistance development. The observed emergence of cationic antimicrobial peptide, vancomycin, and β-lactam resistance in the core microbiota during AD of FWL in the presence of SAs suggests that multidrug resistance caused by bacterial transformation could lead to an increase in the environmental resistome through wastewater sludge treatment.},
}

@article {pmid36870434,
year = {2023},
author = {Maves, RC and Kalil, AC},
title = {Which trial do we need? Doxycycline in combination with ceftriaxone for the treatment of community-acquired pneumonia.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2023.02.020},
pmid = {36870434},
issn = {1469-0691},
}

@article {pmid36957979,
year = {2023},
author = {Kato, I and Sun, J},
title = {Microbiome and Diet in Colon Cancer Development and Treatment.},
journal = {Cancer journal (Sudbury, Mass.)},
volume = {29},
number = {2},
pages = {89-97},
pmid = {36957979},
issn = {1540-336X},
abstract = {Diet plays critical roles in defining our immune responses, microbiome, and progression of human diseases. With recent progress in sequencing and bioinformatic techniques, increasing evidence indicates the importance of diet-microbial interactions in cancer development and therapeutic outcome. Here, we focus on the epidemiological studies on diet-bacterial interactions in the colon cancer. We also review the progress of mechanistic studies using the experimental models. Finally, we discuss the limits and future directions in the research of microbiome and diet in cancer development and therapeutic outcome. Now, it is clear that microbes can influence the efficacy of cancer therapies. These research results open new possibilities for the diagnosis, prevention, and treatment of cancer. However, there are still big gaps to apply these new findings to the clinical practice.},
}

@article {pmid36957978,
year = {2023},
author = {Amit, U and Facciabene, A and Ben-Josef, E},
title = {Radiation Therapy and the Microbiome; More Than a Gut Feeling.},
journal = {Cancer journal (Sudbury, Mass.)},
volume = {29},
number = {2},
pages = {84-88},
doi = {10.1097/PPO.0000000000000650},
pmid = {36957978},
issn = {1540-336X},
abstract = {It is increasingly recognized that heterogeneities in tumor response and severity of adverse effects in irradiated patients can be attributed to the tumor microenvironment and host-related factors. Among the latter, a growing body of literature in recent years has demonstrated the role of the patient's microbiome in modulating both tumor and normal tissue response to radiotherapy (RT). Upon contact with the environment after birth, the infant's gastrointestinal tract is rapidly colonized by microbiota, which is low in diversity and predominantly characterized by 2 dominant species, Actinobacteria and Proteobacteria. With time, intestinal microbiota diversity increases, and colonization of Firmicutes and Bacteroidetes becomes dominant. By the time a child reaches 3 years, the gut microbiota composition has been reshaped and is relatively similar to that of an adult. The microbiome colonizing the different body organs comprises various species and abundances, which may impact human health. Although the adult microbiome composition is thought to remain stable in health, microbiome diversity and composition respond to different environmental and pathological conditions, including pharmaceutical interventions and RT. Our review focuses on how the gut microbiota modulates normal tissue toxicity and tumor control. Readers who want to learn more about how RT shapes gut microbiome diversity and composition are referred to several excellent recently published reviews.},
}

@article {pmid36957977,
year = {2023},
author = {Malard, F and Jenq, RR},
title = {The Microbiome and Its Impact on Allogeneic Hematopoietic Cell Transplantation.},
journal = {Cancer journal (Sudbury, Mass.)},
volume = {29},
number = {2},
pages = {75-83},
pmid = {36957977},
issn = {1540-336X},
abstract = {Allogeneic hematopoietic cell transplantation (alloHCT) is a standard curative therapy for a variety of benign and malignant hematological diseases. Previously, patients who underwent alloHCT were at high risk for complications with potentially life-threatening toxicities, including a variety of opportunistic infections as well as acute and chronic manifestations of graft-versus-host disease (GVHD), where the transplanted immune system can produce inflammatory damage to the patient. With recent advances, including newer conditioning regimens, advances in viral and fungal infection prophylaxis, and novel GVHD prophylactic and treatment strategies, improvements in clinical outcomes have steadily improved. One modality with great potential that has yet to be fully realized is targeting the microbiome to further improve clinical outcomes.In recent years, the intestinal microbiota, which includes bacteria, fungi, viruses, and other microbes that reside within the intestinal tract, has become established as a potent modulator of alloHCT outcomes. The composition of intestinal bacteria, in particular, has been found in large multicenter prospective studies to be strongly associated with GVHD, treatment-related mortality, and overall survival. Murine studies have demonstrated a causal relationship between intestinal microbiota injury and aggravated GVHD, and more recently, clinical interventional studies of repleting the intestinal microbiota with fecal microbiota transplantation have emerged as effective therapies for GVHD. How the composition of the intestinal bacterial microbiota, which is often highly variable in alloHCT patients, can modulate GVHD and other outcomes is not fully understood. Recent studies, however, have begun to make substantial headway, including identifying particular bacterial subsets and/or bacterial-derived metabolites that can mediate harm or benefit. Here, the authors review recent studies that have improved our mechanistic understanding of the relationship between the microbiota and alloHCT outcomes, as well as studies that are beginning to establish strategies to modulate the microbiota with the hope of optimizing clinical outcomes.},
}

@article {pmid36957976,
year = {2023},
author = {Jiminez, V and Yusuf, N},
title = {Role of the Microbiome in Immunotherapy of Melanoma.},
journal = {Cancer journal (Sudbury, Mass.)},
volume = {29},
number = {2},
pages = {70-74},
pmid = {36957976},
issn = {1540-336X},
abstract = {Novel immunotherapeutics for advanced melanoma have drastically changed survival rates and management strategies in recent years. Immune checkpoint inhibitors have emerged as efficacious agents for some patients but have not been proven to be as beneficial in other patient cohorts. Recent investigation into this observation has implicated the gut microbiome as a potential immunomodulator in regulating patient response to therapy. Numerous studies have provided evidence for this link. Bacterial colonization patterns have been associated with therapeutic outcomes, under the notion that favorable commensal organisms improve host immune response. This review aims to report the most recent and pertinent findings related to the relationship between gut microbial communities and melanoma therapy efficacy. This article also highlights the emerging frontier of artificial intelligence in its application regarding patient microbial composition evaluation, predictive models for therapy response, and recommendations for the future of probiotics and dietary interventions to optimize melanoma survival and outcomes.},
}

@article {pmid36957975,
year = {2023},
author = {Kennedy, K and Khaddour, K and Ramnath, N and Weinberg, F},
title = {The Lung Microbiome in Carcinogenesis and Immunotherapy Treatment.},
journal = {Cancer journal (Sudbury, Mass.)},
volume = {29},
number = {2},
pages = {61-69},
pmid = {36957975},
issn = {1540-336X},
abstract = {Lung cancer is the leading cause of cancer-related deaths. Over the past 10 years, significant advances in treatment modalities, including immune checkpoint inhibitor (ICI) blockade, have led to improved outcomes. Elucidating predicative biomarkers in responders and nonresponders to ICI will lead to development of therapeutic targets that could enhance ICI efficacy. Recently, the gut microbiome was identified as a predictive biomarker for ICI in patients with multiple cancer types. However, it is unclear how other host microbiomes influence tumorigenesis and response to ICI. Other groups have explored the lung microbiome as it relates to carcinogenesis and immunotherapy efficacy. In this review, we explore the role of the lung microbiome in health and disease. We also review the current state of lung microbiome research as it relates to tumorigenesis and treatments and provide potential insights into how the lung microbiome could improve outcomes in patients with cancer.},
}

@article {pmid36957974,
year = {2023},
author = {Myojin, Y and Greten, TF},
title = {The Microbiome and Liver Cancer.},
journal = {Cancer journal (Sudbury, Mass.)},
volume = {29},
number = {2},
pages = {57-60},
pmid = {36957974},
issn = {1540-336X},
abstract = {The gut microbiome and liver are anatomically and functionally connected. The impact of the gut microbiota or microbial metabolites on liver cancer progression via immune cells has been recently revealed across various preclinical models. Commensal gut microbes of liver cancer patients differ from control subjects, and their composition is affected by the etiology of the hepatocellular carcinoma. The gut microbiota represents a potential novel target for intervention as shown in patients with melanoma, but we still lack data in patients with hepatocellular carcinoma. Fecal microbiota transplantation and dietary approaches may improve immunotherapy efficacy, and a couple of clinical trials are ongoing. In liver cancer, the ongoing recognition of interactions between gut microbes and the tumor immune microenvironment provides an exciting therapeutic avenue to complement established immunotherapy.},
}

@article {pmid36957973,
year = {2023},
author = {Attebury, H and Daley, D},
title = {The Gut Microbiome and Pancreatic Cancer Development and Treatment.},
journal = {Cancer journal (Sudbury, Mass.)},
volume = {29},
number = {2},
pages = {49-56},
pmid = {36957973},
issn = {1540-336X},
abstract = {Changes in the gut microbiome have been increasingly shown to accompany oncogenesis across various tumors. Similarly, microbial dysbiosis was found to be associated with pancreatic cancer progression and survival outcomes, expanding the field of tumor microenvironment research in pancreatic cancer. Mechanistic studies in pancreatic cancer models implicate components of the gut and pancreatic cancer microbiome in regulating tumorigenesis by altering cancer cell signaling, modulating immune function, and influencing the efficacy of current therapies in pancreatic cancer. This review discusses the outcomes of microbial modulation across various preclinical and clinical studies and highlights ongoing trials targeting the microbiome for pancreatic cancer therapy.},
}

@article {pmid36957972,
year = {2023},
author = {Chen, GY},
title = {The Human Microbiome and Cancer.},
journal = {Cancer journal (Sudbury, Mass.)},
volume = {29},
number = {2},
pages = {47-48},
doi = {10.1097/PPO.0000000000000653},
pmid = {36957972},
issn = {1540-336X},
}

@article {pmid36952261,
year = {2023},
author = {Ryan, E and Joyce, SA and Clarke, DJ},
title = {Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {3},
pages = {},
doi = {10.1099/mic.0.001315},
pmid = {36952261},
issn = {1465-2080},
abstract = {Bacteria produce an array of diverse, dynamic and often complex lipid structures, some of which function beyond their typical role in membrane structure. The model organism, E. coli, has three major membrane lipids, which are glycerophosphoglycerol (phosphatidylglycerol), glycerophosphoethanolamine (phosphatidylethanolamine) and cardiolipin. However, it is now appreciated that some bacteria have the capacity to synthesize a range of lipids, including glycerophosphocholines, glycerophosphoinositols, 'phosphorous-free' N-acyl amines, sphingolipids and plasmalogens. In recent years, some of these bacterial lipids have emerged as influential contributors to the microbe-host molecular dialogue. This review outlines our current knowledge of bacterial lipid diversity, with a focus on the membrane lipids of microbiome-associated bacteria that have documented roles as signalling molecules.},
}

@article {pmid36951975,
year = {2023},
author = {Long, X and Mu, S and Zhang, J and Xiang, H and Wei, W and Sun, J and Kuang, Z and Yang, Y and Chen, Y and Zhao, H and Dong, Y and Yin, J and Zheng, H and Song, Z},
title = {Global signatures of the microbiome and metabolome during hospitalization of septic patients.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002117},
pmid = {36951975},
issn = {1540-0514},
abstract = {BACKGROUND: The gut plays an important role in the development of sepsis and acts as one of the possible drivers of multiple organ dysfunction syndrome (MODS). This study aimed to explore the dynamic alterations in the gut microbiota and its metabolites in septic patients at different stages of ICU admission.

METHODS: In this prospective observational study, a total of 109 fecal samples from 23 septic patients, 16 non-septic ICU patients and 10 healthy controls were analyzed. 16S rRNA gene sequencing and UPLC-MS/MS targeted metabolomics were used for microbiota and metabolome analysis. A prediction model combining the SOFA score, Klebsiella , taurocholic acid, and butyric acid was used to predict the prognosis of sepsis.

RESULTS: The diversity and dominant species of the gut microbiota of septic patients were significantly disturbed. The proportions of normal gut microbiota, such as Firmicutes on the phylum level, as well as Faecalibacterium, Subdoligranulum , Ruminococcus , Agathobacter , and Blautia on the genus level, were decreased at different stages of ICU admission, while the proportions of potential pathogenic bacteria, such as Proteobacteria on the phylum level, and Enterococcus and Stenotrophomonas on the genus level were significantly increased. In addition, the amount of short-chain fatty acids and secondary bile acids decreased in septic patients, while that of the primary bile acids increased markedly. Bacterial richness and diversity were lower in the non-surviving patients than those in the surviving patients in the later stage of ICU admission. In the nomogram model, the higher abundance of Klebsiella , concentration of taurocholic acid and SOFA score, combined with a lower butyric acid concentration, could predict a higher probability of death from sepsis.

CONCLUSION: Our study indicated that the dynamical alterations of gut microbiota and its metabolites were associated with the prognosis of the sepsis. Based on these alterations and clinical indicators, a nomogram model to predict the prognosis of septic patients was performed.},
}

@article {pmid36951585,
year = {2023},
author = {Singavarapu, B and Du, J and Beugnon, R and Cesarz, S and Eisenhauer, N and Xue, K and Wang, Y and Bruelheide, H and Wubet, T},
title = {Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0457822},
doi = {10.1128/spectrum.04578-22},
pmid = {36951585},
issn = {2165-0497},
abstract = {Soil microbial communities play crucial roles in the earth's biogeochemical cycles. Yet, their genomic potential for nutrient cycling in association with tree mycorrhizal type and tree-tree interactions remained unclear, especially in diverse tree communities. Here, we studied the genomic potential of soil fungi and bacteria with arbuscular (AM) and ectomycorrhizal (EcM) conspecific tree species pairs (TSPs) at three tree diversity levels in a subtropical tree diversity experiment (BEF-China). The soil fungi and bacteria of the TSPs' interaction zone were characterized by amplicon sequencing, and their subcommunities were determined using a microbial interkingdom co-occurrence network approach. Their potential genomic functions were predicted with regard to the three major nutrients carbon (C), nitrogen (N), and phosphorus (P) and their combinations. We found the microbial subcommunities that were significantly responding to different soil characteristics. The tree mycorrhizal type significantly influenced the functional composition of these co-occurring subcommunities in monospecific stands mixtures and two-tree-species mixtures but not in mixtures with more than three tree species (here multi-tree-species mixtures). Differentiation of subcommunities was driven by differentially abundant taxa producing different sets of nutrient cycling enzymes across the tree diversity levels, predominantly enzymes of the P (n = 11 and 16) cycles, followed by the N (n = 9) and C (n = 9) cycles, in monospecific stands and two-tree-species mixtures, respectively. Fungi of the Agaricomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes and bacteria of the Verrucomicrobia, Acidobacteria, Alphaproteobacteria, and Actinobacteria were the major differential contributors (48% to 62%) to the nutrient cycling functional abundances of soil microbial communities across tree diversity levels. Our study demonstrated the versatility and significance of microbial subcommunities in different soil nutrient cycling processes of forest ecosystems. IMPORTANCE Loss of multifunctional microbial communities can negatively affect ecosystem services, especially forest soil nutrient cycling. Therefore, exploration of the genomic potential of soil microbial communities, particularly their constituting subcommunities and taxa for nutrient cycling, is vital to get an in-depth mechanistic understanding for better management of forest soil ecosystems. This study revealed soil microbes with rich nutrient cycling potential, organized in subcommunities that are functionally resilient and abundant. Such microbial communities mainly found in multi-tree-species mixtures associated with different mycorrhizal partners can foster soil microbiome stability. A stable and functionally rich soil microbiome is involved in the cycling of nutrients, such as carbon, nitrogen, and phosphorus, and their combinations could have positive effects on ecosystem functioning, including increased forest productivity. The new findings could be highly relevant for afforestation and reforestation regimes, notably in the face of growing deforestation and global warming scenarios.},
}

@article {pmid36951567,
year = {2023},
author = {Goswami, A and Adkins-Jablonsky, SJ and Barreto Filho, MM and Shilling, MD and Dawson, A and Heiser, S and O'Connor, A and Walker, M and Roberts, Q and Morris, JJ},
title = {Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0242622},
doi = {10.1128/spectrum.02426-22},
pmid = {36951567},
issn = {2165-0497},
abstract = {Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease. IMPORTANCE Heavy metals cross-select for antimicrobial resistance in laboratory experiments, but few studies have documented this effect in polluted soils. Moreover, despite decades of awareness of heavy metal contamination at the EPA Superfund site in North Birmingham, Alabama, this is the first analysis of the impact of this pollution on the soil microbiome. Specifically, this work advances the understanding of the relationship between heavy metals, microbial diversity, and patterns of antibiotic resistance in North Birmingham soils. Our results suggest that polluted soils carry a risk of increased exposure to antibiotic-resistant infections in addition to the direct health consequences of heavy metals. Our work provides important information relevant to both political and scientific efforts to advance environmental justice for the communities that call Superfund neighborhoods home.},
}

@article {pmid36951555,
year = {2023},
author = {Chu, Y and Meng, Q and Yu, J and Zhang, J and Chen, J and Kang, Y},
title = {Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0455122},
doi = {10.1128/spectrum.04551-22},
pmid = {36951555},
issn = {2165-0497},
abstract = {The vast population of bacterial phages or viruses (virome) plays pivotal roles in the ecology of human microbial flora and health conditions. Obstacles, including poor viral sequence inference, strain-sensitive virus-host relationship, and the high diversity among individuals, hinder the in-depth understanding of the human virome. We conducted longitudinal studies of the virome based on constructing a high-quality personal reference metagenome (PRM). By applying long-read sequencing for representative samples, we could build a PRM of high continuity that allows accurate annotation and abundance estimation of viruses and bacterial species in all samples of the same individual by aligning short sequencing reads to the PRM. We applied this approach to a series of fecal samples collected for 6 months from a 2-year-old boy who had experienced a 2-month flare-up of atopic eczema (dermatitis) in this period. We identified 31 viral strains in the patient's gut microbiota and deciphered their strain-level relationship to their bacterial hosts. Among them, a lytic crAssphage developed into a dozen substrains and coordinated downregulation in the catabolism of aromatic amino acids (AAAs) in their host bacteria which govern the production of immune-active AAA derivates. The metabolic alterations confirmed based on metabolomic assays cooccurred with symptom remission. Our PRM-based analysis provides an easy approach for deciphering the dynamics of the strain-level human gut virome in the context of entire microbiota. Close temporal correlations among virome alteration, microbial metabolism, and disease remission suggest a potential mechanism for how bacterial phages in microbiota are intimately related to human health. IMPORTANCE The vast populations of viruses or bacteriophages in human gut flora remain mysterious. However, poor annotation and abundance estimation remain obstacles to strain-level analysis and clarification of their roles in microbiome ecology and metabolism associated with human health and diseases. We demonstrate that a personal reference metagenome (PRM)-based approach provides strain-level resolution for analyzing the gut microbiota-associated virome. When applying such an approach to longitudinal samples collected from a 2-year-old boy who has experienced a 2-month flare-up of atopic eczema, we observed thriving substrains of a lytic crAssphage, showing temporal correlation with downregulated catabolism of aromatic amino acids, lower production of immune-active metabolites, and remission of the disease. The PRM-based approach is practical and powerful for strain-centric analysis of the human gut virome, and the underlying mechanism of how strain-level virome dynamics affect disease deserves further investigation.},
}

@article {pmid36951547,
year = {2023},
author = {Yang, Q and Wang, B and Zheng, Q and Li, H and Meng, X and Zhou, F and Zhang, L},
title = {A Review of Gut Microbiota-Derived Metabolites in Tumor Progression and Cancer Therapy.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2207366},
doi = {10.1002/advs.202207366},
pmid = {36951547},
issn = {2198-3844},
abstract = {Gut microbiota-derived metabolites are key hubs connecting the gut microbiome and cancer progression, primarily by remodeling the tumor microenvironment and regulating key signaling pathways in cancer cells and multiple immune cells. The use of microbial metabolites in radiotherapy and chemotherapy mitigates the severe side effects from treatment and improves the efficacy of treatment. Immunotherapy combined with microbial metabolites effectively activates the immune system to kill tumors and overcomes drug resistance. Consequently, various novel strategies have been developed to modulate microbial metabolites. Manipulation of genes involved in microbial metabolism using synthetic biology approaches directly affects levels of microbial metabolites, while fecal microbial transplantation and phage strategies affect levels of microbial metabolites by altering the composition of the microbiome. However, some microbial metabolites harbor paradoxical functions depending on the context (e.g., type of cancer). Furthermore, the metabolic effects of microorganisms on certain anticancer drugs such as irinotecan and gemcitabine, render the drugs ineffective or exacerbate their adverse effects. Therefore, a personalized and comprehensive consideration of the patient's condition is required when employing microbial metabolites to treat cancer. The purpose of this review is to summarize the correlation between gut microbiota-derived metabolites and cancer, and to provide fresh ideas for future scientific research.},
}

@article {pmid36951501,
year = {2023},
author = {Latour, YL and Allaman, MM and Barry, DP and Smith, TM and Williams, KJ and McNamara, KM and Jacobse, J and Goettel, JA and Delgado, AG and Piazuelo, MB and Zhao, S and Gobert, AP and Wilson, KT},
title = {Epithelial talin-1 protects mice from citrobacter rodentium-induced colitis by restricting bacterial crypt intrusion and enhancing t cell immunity.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2192623},
doi = {10.1080/19490976.2023.2192623},
pmid = {36951501},
issn = {1949-0984},
abstract = {Pathogenic enteric Escherichia coli present a significant burden to global health. Food-borne enteropathogenic E. coli (EPEC) and Shiga toxin-producing E. coli (STEC) utilize attaching and effacing (A/E) lesions and actin-dense pedestal formation to colonize the gastrointestinal tract. Talin-1 is a large structural protein that links the actin cytoskeleton to the extracellular matrix though direct influence on integrins. Here we show that mice lacking talin-1 in intestinal epithelial cells (Tln1[Δepi]) have heightened susceptibility to colonic disease caused by the A/E murine pathogen Citrobacter rodentium. Tln1[Δepi] mice exhibit decreased survival, and increased colonization, colon weight, and histologic colitis compared to littermate Tln1[fl/fl] controls. These findings were associated with decreased actin polymerization and increased infiltration of innate myeloperoxidase-expressing immune cells, confirmed as neutrophils by flow cytometry, but more bacterial dissemination deep into colonic crypts. Further evaluation of the immune population recruited to the mucosa in response to C. rodentium revealed that loss of Tln1 in colonic epithelial cells (CECs) results in impaired recruitment and activation of T cells. C. rodentium infection-induced colonic mucosal hyperplasia was exacerbated in Tln1[Δepi] mice compared to littermate controls. We demonstrate that this is associated with decreased CEC apoptosis and crowding of proliferating cells in the base of the glands. Taken together, talin-1 expression by CECs is important in the regulation of both epithelial renewal and the inflammatory T cell response in the setting of colitis caused by C. rodentium, suggesting that this protein functions in CECs to limit, rather than contribute to the pathogenesis of this enteric infection.},
}

@article {pmid36951379,
year = {2023},
author = {Rak, MB and Moyers, TD and Price, JM and Whittemore, JC},
title = {Clinicopathologic and gastrointestinal effects of administration of prednisone, prednisone with omeprazole, or prednisone with probiotics to dogs: A double-blind randomized trial.},
journal = {Journal of veterinary internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/jvim.16672},
pmid = {36951379},
issn = {1939-1676},
abstract = {BACKGROUND: The efffect of administering of probiotics or twice-daily omeprazole on glucocorticoid-induced gastric bleeding in dogs is unknown.

HYPOTHESIS: Compare gastrointestinal bleeding among dogs administered placebo, prednisone (2 mg/kg q24h), prednisone with omeprazole (1 mg/kg q12h), or prednisone with probiotics (Visbiome, 11.2-22.5 billion CFU/kg q24h) for 28 days.

ANIMALS: Twenty-four healthy research dogs.

METHODS: Double-blinded, placebo-controlled randomized trial. Clinical signs and endoscopic gastrointestinal mucosal lesion scores at baseline (t1), day 14 (t2), and day 28 (t3) were compared using split-plot repeated-measures mixed-model ANOVAs.

RESULTS: Fecal score differed by treatment-by-time (F[6,40] = 2.65, P < .03), with higher scores in groups receiving prednisone at t3 than t1 . Nineteen of thirty-three episodes of diarrhea occurred in the prednisone with omeprazole group. Gastric mucosal lesion scores differed by treatment-by-time (F[6,60] = 2.86, P = .05), among treatment groups (F[3,60] = 4.9, P = .004), and over time (F[2,60] = 16.5, P < .001). Post hoc analysis revealed lesion scores increased over time for all groups receiving prednisone. At t3 , scores for the prednisone (8.7 ± 4.9) and prednisone with probiotics (8.7 ± 4.9) groups differed significantly from placebo (1.8 ± 1.8; P ≤ .04), whereas scores for the prednisone with omeprazole (6.5 ± 5.5) group did not differ from placebo (P = .7). Ulcers occurred only in dogs receiving prednisone.

Prednisone-induced gastric bleeding. Co-administration of omeprazole partially mitigated bleeding, but a similar protective benefit was not demonstrated by co-administration of the evaluated probiotic.},
}