@article {pmid36748690,
year = {2022},
author = {Sun, J and Prabhu, A and Aroney, STN and Rinke, C},
title = {Corrigendum: Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials.},
journal = {Microbial genomics},
volume = {8},
number = {12},
pages = {},
doi = {10.1099/mgen.0.000916},
pmid = {36748690},
issn = {2057-5858},
}

@article {pmid36748565,
year = {2022},
author = {Ghosh, A and Saha, S},
title = {Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures.},
journal = {Journal of medical microbiology},
volume = {72},
number = {12},
pages = {},
doi = {10.1099/jmm.0.001617},
pmid = {36748565},
issn = {1473-5644},
abstract = {Introduction. Studying taxonomic and functional signatures of respiratory microbiomes provide a better understanding of airway diseases.Gap Statement. Several human airway metagenomics studies have identified taxonomic and functional features restricted to a single disease condition and the findings are not comparable across airway diseases due to use of different samples, NGS platforms, and bioinformatics databases and tools.Aim. To study the microbial taxonomic and functional components of sputum microbiome across airway diseases and healthy smokers.Methodology. Here, 57 whole metagenome shotgun sequencing (WMSS) runs coming from the sputum of five airway diseases: asthma, bronchiectasis, chronic obstructive pulmonary diseases (COPD), cystic fibrosis (CF), tuberculosis (TB), and healthy smokers as the control were reanalysed using a common WMSS analysis pipeline.Results. Shannon's index (alpha diversity) of the healthy smoker group was the highest among all. The beta diversity showed that the sputum microbiome is distinct in major airway diseases such as asthma, COPD and cystic fibrosis. The microbial composition based on differential analysis showed that there are specific markers for each airway disease like Acinetobacter bereziniae as a marker for COPD and Achromobacter xylosoxidans as a marker of cystic fibrosis. Pathways and metabolites identified from the sputum microbiome of these five diseases and healthy smokers also show specific markers. 'ppGpp biosynthesis' and 'purine ribonucleosides degradation' pathways were identified as differential markers for bronchiectasis and COPD. In this meta-analysis, besides bacteria kingdom, Aspergillus fumigatus was detected in asthma and COPD, and Roseolovirus human betaherpesvirus 7 was detected in COPD. Our analysis showed that the majority of the gene families specific to the drug-resistant associated genes were detected from opportunistic pathogens across all the groups.Conclusion. In summary, the specific species in the sputum of airway diseases along with the microbial features like specific gene families, pathways, and metabolites were identified which can be explored for better diagnosis and therapy.},
}

@article {pmid36748547,
year = {2022},
author = {Stebliankin, V and Sazal, M and Valdes, C and Mathee, K and Narasimhan, G},
title = {A novel approach for combining the metagenome, metaresistome, metareplicome and causal inference to determine the microbes and their antibiotic resistance gene repertoire that contribute to dysbiosis.},
journal = {Microbial genomics},
volume = {8},
number = {12},
pages = {},
doi = {10.1099/mgen.0.000899},
pmid = {36748547},
issn = {2057-5858},
abstract = {The use of whole metagenomic data to infer the relative abundance of all its microbes is well established. The same data can be used to determine the replication rate of all eubacterial taxa with circular chromosomes. Despite their availability, the replication rate profiles (metareplicome) have not been fully exploited in microbiome analyses. Another relatively new approach is the application of causal inferencing to analyse microbiome data that goes beyond correlational studies. A novel scalable pipeline called MeRRCI (Metagenome, metaResistome, and metaReplicome for Causal Inferencing) was developed. MeRRCI combines efficient computation of the metagenome (bacterial relative abundance), metaresistome (antimicrobial gene abundance) and metareplicome (replication rates), and integrates environmental variables (metadata) for causality analysis using Bayesian networks. MeRRCI was applied to an infant gut microbiome data set to investigate the microbial community's response to antibiotics. Our analysis suggests that the current treatment stratagem contributes to preterm infant gut dysbiosis, allowing a proliferation of pathobionts. The study highlights the specific antibacterial resistance genes that may contribute to exponential cell division in the presence of antibiotics for various pathogens, namely Klebsiella pneumoniae, Citrobacter freundii, Staphylococcus epidermidis, Veilonella parvula and Clostridium perfringens. These organisms often contribute to the harmful long-term sequelae seen in these young infants.},
}

@article {pmid36748434,
year = {2022},
author = {Inglis, TJJ},
title = {Marginal notes, November 2022. From crisis to crisis.},
journal = {Journal of medical microbiology},
volume = {71},
number = {11},
pages = {},
doi = {10.1099/jmm.0.001642},
pmid = {36748434},
issn = {1473-5644},
}

@article {pmid36748431,
year = {2023},
author = {Lindgren, NR and McDaniel, MS and Novak, L and Swords, WE},
title = {Acute polymicrobial airway infections: analysis in cystic fibrosis mice.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {1},
pages = {},
doi = {10.1099/mic.0.001290},
pmid = {36748431},
issn = {1465-2080},
abstract = {Cystic fibrosis (CF) is a genetic disorder affecting epithelial ion transport, which among other impacts results in defective mucociliary clearance and innate defenses in the respiratory tract. Consequently, people with CF experience lifelong infections of the respiratory mucosa that are chronic and polymicrobial in nature. Young children with CF are initially colonized by opportunists like nontypeable Haemophilus influenzae (NTHi), which normally resides within the microbiome of the nasopharynx and upper airways and can also cause infections of the respiratory mucosa that include bronchitis and otitis media. NTHi is typically supplanted by other microbes as patients age; for example, people with CF are often chronically infected with mucoid strains of Pseudomonas aeruginosa, which prior work in our laboratory has shown to promote colonization and persistence by other opportunists that include Stenotrophomonas maltophilia. Our previous work has shown that polymicrobial infection impacts host colonization and persistence of incoming microbes via diverse mechanisms that include priming of host immunity that can promote microbial clearance, and cooperativity within polymicrobial biofilms, which can promote persistence. In infection studies with BALB/c Cftr[tm1UNC] mice, results showed, as previously observed for WT BALB/c mice, preceding infection with NTHi decreased colonization and persistence by P. aeruginosa. Likewise, polymicrobial infection of BALB/c Cftr[tm1UNC] and C57BL/6 Cftr[tm1UncTg](FABPhCFTR)1Jaw/J mice showed correlation between S. maltophilia and P. aeruginosa, with increased bacterial colonization and lung pathology. Based on these results, we conclude that our previous observations regarding polymicrobial infections with CF opportunists in WT mice are also validated using CF mice.},
}

@article {pmid36747869,
year = {2023},
author = {Voigt, AY and Walter, A and Young, T and Graham, JP and Batista Bittencourt, BM and de Mingo Pulido, A and Prieto, K and Tsai, KY and Sundberg, JP and Oh, J},
title = {Microbiome modulates immunotherapy response in cutaneous squamous cell carcinoma.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.25.525369},
pmid = {36747869},
abstract = {The gut microbiome is increasingly recognized to alter cancer risk, progression, and response to treatments such as immunotherapy, especially in cutaneous melanoma. However, whether the microbiome influences immune checkpoint inhibitor (ICI) immunotherapy response to non-melanoma skin cancer has not yet been defined. As squamous cell carcinomas (SCC) are in closest proximity to the skin microbiome, we hypothesized that the skin microbiome, which regulates cutaneous immunity, might affect SCC-associated anti-PD1 immunotherapy treatment response. We used ultraviolet radiation to induce SCC in SKH1 hairless mice. We then treated the mice with broad-band antibiotics to deplete the microbiome, followed by colonization by candidate skin and gut bacteria or persistent antibiotic treatment, all in parallel with ICI treatment. We longitudinally monitored skin and gut microbiome dynamics by 16S rRNA gene sequencing, and tumor burden by periodic tumor measurements and histologic assessment. Our study revealed that antibiotics-induced abrogation of the microbiome reduced tumor burden, suggesting a functional role of the microbiome in non-melanoma skin cancer therapy response.},
}

@article {pmid36747848,
year = {2023},
author = {Bukavina, L and Ginwala, R and Sindhani, M and Prunty, M and Geynisman, D and Pooja, G and Valentine, H and Calaway, A and Brown, JR and Correa, A and Mishra, K and Pominville, R and Plimack, E and Kutikov, A and Ghannoum, M and ElShaer, M and Retuerto, M and Uzzo, R and Ponsky, L and Abbosh, PH},
title = {Role of Gut Microbiome in Neoadjuvant Chemotherapy Response in Urothelial Carcinoma: A Multi-Institutional Prospective Cohort Evaluation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.21.525021},
pmid = {36747848},
abstract = {Treatment with neoadjuvant chemotherapy (NAC) in muscle invasive bladder cancer (MIBC) is associated with clinical benefit in urothelial carcinoma. While extensive research evaluating role of tumor mutational expression profiles and clinicopathologic factors into chemoresponse has been published, the role of gut microbiome (GM) in bladder cancer in chemoresponse has not been thoroughly evaluated. A working knowledge of the microbiome and its effect on all forms of cancer therapy in BC is critical. Here we examine gut microbiome of bladder cancer patients undergoing NAC. Overall, there was no significant difference in alpha and beta diversity by responder status. However, analysis of fecal microbiome samples showed that a higher abundance of Bacteroides within both institutional cohorts during NAC was associated with residual disease at the time of radical cystectomy regardless of chemotherapy regimen. Group community analysis revealed presence of favorable microbial subtypes in complete responders. Finally, fecal microbial composition outperformed clinical variables in prediction of complete response (AUC 0.88 vs AUC 0.50), however, no single microbial species could be regarded as a fully consistent biomarker. Microbiome-based community signature as compared to single microbial species is more likely to be associated as the link between bacterial composition and NAC response.},
}

@article {pmid36747843,
year = {2023},
author = {Johnson, KE and Heisel, T and Allert, M and Fürst, A and Yerabandi, N and Knights, D and Jacobs, KM and Lock, EF and Bode, L and Fields, DA and Rudolph, MC and Gale, CA and Albert, FW and Demerath, EW and Blekhman, R},
title = {Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.24.525211},
pmid = {36747843},
abstract = {Human milk is a complex mix of nutritional and bioactive components that provide complete nutrition for the infant. However, we lack a systematic knowledge of the factors shaping milk composition and how milk variation influences infant health. Here, we used multi-omic profiling to characterize interactions between maternal genetics, milk gene expression, milk composition, and the infant fecal microbiome in 242 exclusively breastfeeding mother-infant pairs. We identified 487 genetic loci associated with milk gene expression unique to the lactating mammary gland, including loci that impacted breast cancer risk and human milk oligosaccharide concentration. Integrative analyses uncovered connections between milk gene expression and infant gut microbiome, including an association between the expression of inflammation-related genes with IL-6 concentration in milk and the abundance of Bifidobacteria in the infant gut. Our results show how an improved understanding of the genetics and genomics of human milk connects lactation biology with maternal and infant health.},
}

@article {pmid36747842,
year = {2023},
author = {Morgan, EW and Dong, F and Annalora, A and Murray, IA and Wolfe, T and Erickson, R and Gowda, K and Amin, SG and Petersen, KS and Kris-Etherton, PM and Marcus, C and Walk, ST and Patterson, AD and Perdew, GH},
title = {Contribution of circulating host and microbial tryptophan metabolites towards Ah receptor activation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.26.525691},
pmid = {36747842},
abstract = {The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that plays an integral role in homeostatic maintenance by regulating cellular functions such as cellular differentiation, metabolism, barrier function, and immune response. An important but poorly understood class of AHR activators are compounds derived from host and bacterial metabolism of tryptophan. The commensal bacteria of the gut microbiome are major producers of tryptophan metabolites known to activate the AHR, while the host also produces AHR activators through tryptophan metabolism. We used targeted mass spectrometry-based metabolite profiling to determine the presence and metabolic source of these metabolites in the sera of conventional mice, germ-free mice, and humans. Surprisingly, sera concentrations of many tryptophan metabolites are comparable between germ-free and conventional mice. Therefore, many major AHR-activating tryptophan metabolites in mouse sera are produced by the host, despite their presence in feces and mouse cecal contents. AHR activation is rarely studied in the context of a mixture at relevant concentrations, as we present here. The AHR activation potentials of individual and pooled metabolites were explored using cell-based assays, while ligand binding competition assays and ligand docking simulations were used to assess the detected metabolites as AHR agonists. The physiological and biomedical relevance of the identified metabolites was investigated in the context of cell-based models for cancer and rheumatoid arthritis. We present data here that reframe AHR biology to include the presence of ubiquitous tryptophan metabolites, improving our understanding of homeostatic AHR activity and models of AHR-linked diseases.},
}

@article {pmid36747835,
year = {2023},
author = {Smith, S and Corbin, K and Carnero, E and Dirks, B and Igudesman, D and Yi, F and Marcus, A and Davis, T and Pratley, R and Rittmann, B and Krajmalnik-Brown, R},
title = {Reprogramming the Human Gut Microbiome Reduces Dietary Energy Harvest.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-2382790/v1},
pmid = {36747835},
abstract = {The gut microbiome is emerging as a key modulator of host energy balance1. We conducted a quantitative bioenergetics study aimed at understanding microbial and host factors contributing to energy balance. We used a Microbiome Enhancer Diet (MBD) to reprogram the gut microbiome by delivering more dietary substrates to the colon and randomized healthy participants into a within-subject crossover study with a Western Diet (WD) as a comparator. In a metabolic ward where the environment was strictly controlled, we measured energy intake, energy expenditure, and energy output (fecal, urinary, and methane)2. The primary endpoint was the within-participant difference in host metabolizable energy between experimental conditions. The MBD led to an additional 116 ± 56 kcals lost in feces daily and thus, lower metabolizable energy for the host by channeling more energy to the colon and microbes. The MBD drove significant shifts in microbial biomass, community structure, and fermentation, with parallel alterations to the host enteroendocrine system and without altering appetite or energy expenditure. Host metabolizable energy on the MBD had quantitatively significant interindividual variability, which was associated with differences in the composition of the gut microbiota experimentally and colonic transit time and short-chain fatty acid absorption in silico. Our results provide key insights into how a diet designed to optimize the gut microbiome lowers host metabolizable energy in healthy humans.},
}

@article {pmid36747827,
year = {2023},
author = {Newman, LE and Testard, C and DeCasien, AR and Chiou, KL and Watowich, MM and Janiak, MC and Pavez-Fox, MA and Sanchez Rosado, MR and Cooper, EB and Costa, CE and Petersen, RM and Montague, MJ and Platt, ML and Brent, LJN and Snyder-Mackler, N and Higham, JP},
title = {The biology of aging in a social world: insights from free-ranging rhesus macaques.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.28.525893},
pmid = {36747827},
abstract = {Social adversity can increase the age-associated risk of disease and death, yet the biological mechanisms that link social adversities to aging remain poorly understood. Long-term naturalistic studies of nonhuman animals are crucial for integrating observations of social behavior throughout an individual's life with detailed anatomical, physiological, and molecular measurements. Here, we synthesize the body of research from one such naturalistic study system, Cayo Santiago Island, which is home to the world's longest continuously monitored free-ranging population of rhesus macaques. We review recent studies of age-related variation in morphology, gene regulation, microbiome composition, and immune function. We also discuss ecological and social modifiers of age-markers in this population. In particular, we summarize how a major natural disaster, Hurricane Maria, affected rhesus macaque physiology and social structure and highlight the context-dependent and domain-specific nature of aging modifiers. Finally, we conclude by providing directions for future study, on Cayo Santiago and elsewhere, that will further our understanding of aging across different domains and how social adversity modifies aging processes.},
}

@article {pmid36747766,
year = {2023},
author = {Holcomb, L and Holman, J and Hurd, M and Lavoie, B and Colucci, L and Hunt, B and Hunt, T and Mawe, GM and Moses, PL and Perry, E and Stratigakis, A and Zhang, T and Chen, G and Ishaq, SL and Li, Y},
title = {Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.27.525953},
pmid = {36747766},
abstract = {UNLABELLED: Inflammatory Bowel Diseases (IBD) are chronic conditions characterized by inflammation of the gastrointestinal tract that heavily burden daily life, result in surgery or other complications, and disrupt the gut microbiome. How IBD influences gut microbial ecology, especially biogeographic patterns of microbial location, and how the gut microbiota can use diet components and microbial metabolites to mediate disease, are still poorly understood. Many studies on diet and IBD in mice use a chemically induced ulcerative colitis model, despite the availability of an immune-modulated Crohn's Disease model. Interleukin-10-knockout (IL-10-ko) mice on a C57BL/6 background, beginning at age 4 or 7 weeks, were fed either a control diet or one containing 10% (w/w) raw broccoli sprouts which was high in the sprout-sourced anti-inflammatory sulforaphane. Diets began 7 days prior to inoculation with Helicobacter hepaticus , which triggers Crohn's-like symptoms in these immune-impaired mice, and ran for two additional weeks. Key findings of this study suggest that the broccoli sprout diet increases sulforaphane concentration in plasma; decreases weight stagnation, fecal blood, and diarrhea associated with enterocolitis; and increases microbiota richness in the gut, especially in younger mice. Sprout diets resulted in some anatomically specific bacterial communities in younger mice, and reduced the prevalence and abundance of potentially pathogenic or otherwise-commensal bacteria which trigger inflammation in the IL-10 deficient mouse, for example, Escherichia coli and Helicobacter . Overall, the IL-10-ko mouse model is responsive to a raw broccoli sprout diet and represents an opportunity for more diet-host-microbiome research.

IMPORTANCE: A diet containing 10% raw broccoli sprouts increased the plasma concentration of the anti-inflammatory compound sulforaphane, and may be protective against negative disease characteristics of Helicobacter -induced enterocolitis in interleukin-10 knockout mice, including weight loss or stagnation, fecal blood, and diarrhea. Younger mice responded more strongly to the diet intervention, and resulted in increased gut bacterial community richness and bacterial community similarity by diet treatment and some anatomical locations in the gut, even in mice with adverse reactions to gut microbiota and a relatively short time in which they had been able to recruit them. To our knowledge, IL-10-ko mice have not previously been used to investigate the interactions of host, microbiota, and broccoli, broccoli sprouts, or broccoli bioactives in resolving symptoms of CD.},
}

@article {pmid36747646,
year = {2023},
author = {Kim, Y and Worby, CJ and Acharya, S and van Dijk, LR and Alfonsetti, D and Gromko, Z and Azimzadeh, P and Dodson, K and Gerber, G and Hultgren, S and Earl, AM and Berger, B and Gibson, TE},
title = {Strain Tracking with Uncertainty Quantification.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.25.525531},
pmid = {36747646},
abstract = {The ability to detect and quantify microbiota over time has a plethora of clinical, basic science, and public health applications. One of the primary means of tracking microbiota is through sequencing technologies. When the microorganism of interest is well characterized or known a priori , targeted sequencing is often used. In many applications, however, untargeted bulk (shotgun) sequencing is more appropriate; for instance, the tracking of infection transmission events and nucleotide variants across multiple genomic loci, or studying the role of multiple genes in a particular phenotype. Given these applications, and the observation that pathogens (e.g. Clostridioides difficile, Escherichia coli, Salmonella enterica) and other taxa of interest can reside at low relative abundance in the gastrointestinal tract, there is a critical need for algorithms that accurately track low-abundance taxa with strain level resolution. Here we present a sequence quality- and time-aware model, ChronoStrain , that introduces uncertainty quantification to gauge low-abundance species and significantly outperforms the current state-of-the-art on both real and synthetic data. ChronoStrain leverages sequences' quality scores and the samples' temporal information to produce a probability distribution over abundance trajectories for each strain tracked in the model. We demonstrate Chronostrain's improved performance in capturing post-antibiotic E. coli strain blooms among women with recurrent urinary tract infections (UTIs) from the UTI Microbiome (UMB) Project. Other strain tracking models on the same data either show inconsistent temporal colonization or can only track consistently using very coarse groupings. In contrast, our probabilistic outputs can reveal the relationship between low-confidence strains present in the sample that cannot be reliably assigned a single reference label (either due to poor coverage or novelty) while simultaneously calling high-confidence strains that can be unambiguously assigned a label. We also include and analyze newly sequenced cultured samples from the UMB Project.},
}

@article {pmid36746963,
year = {2023},
author = {Niu, J and Cui, M and Yang, X and Li, J and Yao, Y and Guo, Q and Lu, A and Qi, X and Zhou, D and Zhang, C and Zhao, L and Meng, G},
title = {Microbiota-derived acetate enhances host antiviral response via NLRP3.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {642},
pmid = {36746963},
issn = {2041-1723},
abstract = {Pathogenic viral infections represent a major challenge to human health. Host immune responses to respiratory viruses are closely associated with microbiome and metabolism via the gut-lung axis. It has been known that host defense against influenza A virus (IAV) involves activation of the NLRP3 inflammasome, however, mechanisms behind the protective function of NLRP3 are not fully known. Here we show that an isolated bacterial strain, Bifidobacterium pseudolongum NjM1, enriched in the gut microbiota of Nlrp3[-/-] mice, protects wild-type but not Nlrp3 deficient mice against IAV infection. This effect depends on the enhanced production of type I interferon (IFN-I) mediated by NjM1-derived acetate. Application of exogenous acetate reproduces the protective effect of NjM1. Mechanistically, NLRP3 bridges GPR43 and MAVS, and promotes the oligomerization and signalling of MAVS; while acetate enhances MAVS aggregation upon GPR43 engagement, leading to elevated IFN-I production. Thus, our data support a model of NLRP3 mediating enhanced induction of IFN-I via acetate-producing bacterium and suggest that the acetate-GPR43-NLRP3-MAVS-IFN-I signalling axis is a potential therapeutic target against respiratory viral infections.},
}

@article {pmid36746446,
year = {2023},
author = {Wu, HZ and Zhang, X and Cheng, XG and Yu, Q},
title = {[Saliva microbiota and metabolite in individuals with caries or periodontitis].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {58},
number = {2},
pages = {131-142},
doi = {10.3760/cma.j.cn112144-20220829-00464},
pmid = {36746446},
issn = {1002-0098},
abstract = {Objective: To detect and analyze the characteristics of oral microbiota in species composition, function and metabolism among caries, periodontitis and oral healthy individuals, hunting for the microbiome-derived biomarkers with specificity and sensitivity to estimate the occurrence of these two diseases. Methods: Saliva samples were collected from 10 patients with high caries risk [decayed-missing-filled teeth (DMFT)≥6, HC group] in Department of Endodontics, 10 patients with periodontitis of grade Ⅱ A-Ⅲ C (PG group) in Department of Periodontology and 10 oral healthy individuals (HH group) from School of Stomatology, The Fourth Military Medical University during from March 2022 to June 2022. A baseline examination was conducted on all participants, including their oral conditions of caries and periodontal health. Metagenomic sequencing (Illumina PE150 platform) and liquid chromatography-mass spectrometry were used to detect microorganisms and their metabolites in the samples respectively. The sequencing data were analyzed to obtain the information of microbial taxonomic composition, functional genes and metabolites in each group of samples. The basic oral conditions and saliva samples of subjects in each group were evaluated and collected by the same professional endodontist. Results: There were no significant difference in baseline characteristics such as age and sex among the subjects in each group (P>0.05). DMFT in HC group (9.0±1.7) was significantly higher than that in HH group (0) and PG group (0) (F=243.00, P<0.001). All participants in PG group belong to grade Ⅱ A-Ⅲ C in periodontitis stage. Sequencing data analysis showed that the taxonomic compositions of salivary microbiota in each group were mainly Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria at the phylum level, and Streptococcus, Neisseria, Rothia, Prevotella at the genus level. Differential analysis showed that, compared with the HH group, HC group and PG group had significant differences in taxonomic composition (P<0.05), and the most significant among them was Prevotella. At the species level, Prevotella pallens was the most significant change in HC group, and Porphyromonas gingivalis in PG group. Metabolite analysis showed that there were significant differences in metabolites between HC group and PG group. The results showed that, compared with the HH group, the most significant metabolite change was 3-hydroxy-1, 5-diphenylpentan-1-one in HC group (P=0.001) and N1 acetylspermine in PG group (P=0.002) respectively. Compared with the PG group, the metabolite of HC group with the most significant difference is D-glucosamine 6-phosphate (P=0.006). The metabolism gene function analysis showed that, the enrichment of carbohydrate metabolism related genes was highest in HC group, followed with HH group, and it was lowest in PG group. In addition, compared with the HH group, the abundance of functional genes related to glucose metabolism, such as ABC transporter and phosphotransferase system, were significantly decreased in PG group (P<0.05), but significantly increased in HC group (P<0.05). Conclusions: There is a significant correlation between the alternation of carbohydrate metabolism of salivary microbiota with the occurrence of caries and periodontitis. In the future, Prevotella pallens and 3-hydroxy-1, 5-diphenylpentan-1-one may be the potential biomarkers of caries; while Porphyromonas gingivalis and N1 acetylspermine work in the predictions of periodontitis.},
}

@article {pmid36746029,
year = {2023},
author = {Hong, YW and Ban, GH and Bae, D and Kim, SA},
title = {Microbial investigation of aquacultured olive flounder (Paralichthys olivaceus) from farm to table based on high-throughput sequencing.},
journal = {International journal of food microbiology},
volume = {389},
number = {},
pages = {110111},
doi = {10.1016/j.ijfoodmicro.2023.110111},
pmid = {36746029},
issn = {1879-3460},
abstract = {The microbial ecologies of fish, such as the olive flounder (Paralichthys olivaceus), one of the most widely consumed fish in East Asia, remain to be elucidated. The microbiome of olive flounder and related environmental samples (i.e., feed, water, workers' aprons and gloves) were collected from six different sources (i.e., a fish farm, a transporting truck, a Wando market and restaurant, and a Seoul market and restaurant). These samples (n = 102) were investigated at various farm-to-distribution stages based on their 16S rRNA sequences. The microbial communities of fish from the farms and trucks were dominated by Photobacterium (>86 %) and showed distinct differences from fish from the Wando and Seoul markets and restaurants. There was also a significant difference in fish microbiomes according to geographical location. The relative abundances of Shewanella, Acinetobacter, Enterobacteriaceae, and Pseudomonas increased as the distribution and consumption stages of the supply chain advanced. The percentages of Shewanella (24.74 %), Acinetobacter (18.32 %), and Enterobacteriaceae (11.24 %) in Wando, and Pseudomonas (42.98 %) in Seoul markets and restaurants implied the importance of sanitation control in these areas. Alpha and beta diversity results corresponded to taxonomic analyses and showed the division of two groups (i.e., fish from the production and transporting stage (farm and truck fish) and fish from the distribution and consumption stages (market and restaurant fish)). The present study provides an in-depth understanding of olive flounder and its environmental microbiomes and suggests control measures to improve food safety.},
}

@article {pmid36745335,
year = {2023},
author = {Won, SM and Lee, NY and Oh, KK and Gupta, H and Sharma, SP and Kim, KH and Kim, BK and Joung, HC and Jeong, JJ and Ganesan, R and Han, SH and Yoon, SJ and Kim, DJ and Suk, KT},
title = {Gut Lactobacillus and Probiotics Lactobacillus lactis/rhamnosis Ameliorate Liver Fibrosis in Prevention and Treatment.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12275-023-00014-y},
pmid = {36745335},
issn = {1976-3794},
abstract = {The progression and exacerbation of liver fibrosis are closely related to the gut microbiome. It is hypothesized that some probiotics may slow the progression of liver fibrosis. In human stool analysis [healthy group (n = 44) and cirrhosis group (n = 18)], difference in Lactobacillus genus between healthy group and cirrhosis group was observed. Based on human data, preventive and therapeutic effect of probiotics Lactobacillus lactis and L. rhamnosus was evaluated by using four mice fibrosis models. L. lactis and L. rhamnosus were supplied to 3,5-diethoxycarbonyl-1,4-dihydrocollidine or carbon tetrachloride-induced liver fibrosis C57BL/6 mouse model. Serum biochemical measurements, tissue staining, and mRNA expression in the liver were evaluated. The microbiome was analyzed in mouse cecal contents. In the mouse model, the effects of Lactobacillus in preventing and treating liver fibrosis were different for each microbe species. In case of L. lactis, all models showed preventive and therapeutic effects against liver fibrosis. In microbiome analysis in mouse models administered Lactobacillus, migration and changes in the ratio and composition of the gut microbial community were confirmed. L. lactis and L. rhamnosus showed preventive and therapeutic effects on the progression of liver fibrosis, suggesting that Lactobacillus intake may be a useful strategy for prevention and treatment.},
}

@article {pmid36744984,
year = {2023},
author = {Banerjee, P and Sarkar, A and Ghosh, K and Mazumdar, A},
title = {A Metagenomic Based Approach on Abundance and Diversity of Bacterial Communities Across the Life Stages of Culicoides peregrinus (Diptera: Ceratopogonidae) a Vector of Bluetongue Virus.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjad011},
pmid = {36744984},
issn = {1938-2928},
abstract = {During larval rearing of Culicoides peregrinus Kieffer (Diptera: Ceratopogonidae) it was obligatory to add a small quantity of mud from larval habitat to nutrient broth in culture plates. This initiated microbial growth in rearing plates which facilitated growth and development of immature. The primary aim was to enumerate gut microbial communities across the different life stages of C. peregrinus. Amplicon sequencing of the V3-V4 hypervariable region (16S rDNA) was done on Illumina Miseq platform to detect gut bacterial communities at different life stages, while ITS regions (18S rRNA) were targeted for fungal communities of the 4th instar larvae. The major findings were: 1) Phylum Proteobacteria and Firmicutes were the most abundant throughout the life stages, along with the highest bacterial alpha diversity in the egg, 2) bacterial compositions were similar to laboratory reared and field collected adults, and 3) abundant fungal phyla associated with the larval gut were Ascomycota and Basidiomycota. Furthermore, analyses of the gut microbiome with METAGENassist might be indicative of their likely function in the natural habitat. Abundant gut-associated bacteria and/or fungal genera detected in the present study could be used as dietary supplements to establish laboratory colonies for further vectorial research. While, individual roles of the bacteria or fungi in paratransgenesis are warned for their possible utilization to frame the management strategy in upcoming works.},
}

@article {pmid36747007,
year = {2021},
author = {Bowerman, KL and Knowles, SCL and Bradley, JE and Baltrūnaitė, L and Lynch, MDJ and Jones, KM and Hugenholtz, P},
title = {Effects of laboratory domestication on the rodent gut microbiome.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {49},
pmid = {36747007},
issn = {2730-6151},
abstract = {The domestication of the laboratory mouse has influenced the composition of its native gut microbiome, which is now known to differ from that of its wild ancestor. However, limited exploration of the rodent gut microbiome beyond the model species Mus musculus has made it difficult to interpret microbiome variation in a broader phylogenetic context. Here, we analyse 120 de novo and 469 public metagenomically-sequenced faecal and caecal samples from 16 rodent hosts representing wild, laboratory and captive lifestyles. Distinct gut bacterial communities were observed between rodent host genera, with broadly distributed species originating from the as-yet-uncultured bacterial genera UBA9475 and UBA2821 in the families Oscillospiraceae and Lachnospiraceae, respectively. In laboratory mice, Helicobacteraceae were generally depleted relative to wild mice and specific Muribaculaceae populations were enriched in different laboratory facilities, suggesting facility-specific outgrowths of this historically dominant rodent gut family. Several bacterial families of clinical interest, including Akkermansiaceae, Streptococcaceae and Enterobacteriaceae, were inferred to have gained over half of their representative species in mice within the laboratory environment, being undetected in most wild rodents and suggesting an association between laboratory domestication and pathobiont emergence.},
}

@article {pmid36744955,
year = {2023},
author = {Custer, GF and Gans, M and van Diepen, LTA and Dini-Andreote, F and Buerkle, CA},
title = {Comparative Analysis of Core Microbiome Assignments: Implications for Ecological Synthesis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0106622},
doi = {10.1128/msystems.01066-22},
pmid = {36744955},
issn = {2379-5077},
abstract = {The concept of a core microbiome has been broadly used to refer to the consistent presence of a set of taxa across multiple samples within a given habitat. The assignment of taxa to core microbiomes can be performed by several methods based on the abundance and occupancy (i.e., detection across samples) of individual taxa. These approaches have led to methodological inconsistencies, with direct implications for ecological interpretation. Here, we reviewed a set of methods most commonly used to infer core microbiomes in divergent systems. We applied these methods using large data sets and analyzed simulations to determine their accuracy in core microbiome assignments. Our results show that core taxa assignments vary significantly across methods and data set types, with occupancy-based methods most accurately defining true core membership. We also found the ability of these methods to accurately capture core assignments to be contingent on the distribution of taxon abundance and occupancy in the data set. Finally, we provide specific recommendations for further studies using core taxa assignments and discuss the need for unifying methodical approaches toward data processing to advance ecological synthesis. IMPORTANCE Different methods are commonly used to assign core microbiome membership, leading to methodological inconsistencies across studies. In this study, we review a set of the most commonly used core microbiome assignment methods and compare their core assignments using both simulated and empirical data. We report inconsistent classifications from commonly applied core microbiome assignment methods. Furthermore, we demonstrate the implication that variable core assignments may have on downstream ecological interpretations. Although we still lack a standardized approach to core taxa assignments, our study provides a direction to properly test core assignment methods and offers advances in model parameterization and method choice across distinct data types.},
}

@article {pmid36744910,
year = {2023},
author = {Guo, M and Wu, G and Tan, Y and Li, Y and Jin, X and Qi, W and Guo, X and Zhang, C and Zhu, Z and Zhao, L},
title = {Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0351922},
doi = {10.1128/mbio.03519-22},
pmid = {36744910},
issn = {2150-7511},
abstract = {Coronavirus disease 2019 (COVID-19) severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples from 300 in-hospital COVID-19 patients, collected at the time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), redundancy analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Co-abundance network analysis determined that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Based on average abundance difference between the two guilds, the guild-level microbiome index (GMI) classified patients from different severity groups (average AUROC [area under the receiver operating curve] = 0.83). Moreover, age-adjusted partial Spearman's correlation showed that GMIs at admission were correlated with 8 clinical parameters, which are predictors for COVID-19 prognosis, on day 7 in hospital. In addition, GMI at admission was associated with death/discharge outcome of the critical patients. We further validated that GMI was able to consistently classify patients with different COVID-19 symptom severities in different countries and differentiated COVID-19 patients from healthy subjects and pneumonia controls in four independent data sets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission. IMPORTANCE Previous reports on the associations between COVID-19 and gut microbiome have been constrained by taxonomic-level analysis and overlook the interaction between microbes. By applying a genome-resolved, reference-free, guild-based metagenomic analysis, we demonstrated that the relationship between gut microbiota and COVID-19 is genome-specific instead of taxon-specific or even species-specific. Moreover, the COVID-19-associated genomes were not independent but formed two competing guilds, with Guild 1 potentially beneficial and Guild 2 potentially more detrimental to the host based on comparative genomic analysis. The dominance of Guild 2 over Guild 1 at time of admission was associated with hospitalized COVID-19 patients at high risk for more severe outcomes. Moreover, the guild-level microbiome signature is not only correlated with the symptom severity of COVID-19 patients, but also differentiates COVID-19 patients from pneumonia controls and healthy subjects across different studies. Here, we showed the possibility of using genome-resolved and guild-level microbiome signatures to identify hospitalized COVID-19 patients with a high risk of more severe outcomes at the time of admission.},
}

@article {pmid36744900,
year = {2023},
author = {Bhandari, P and Tingley, J and Abbott, DW and Hill, JE},
title = {Glycogen-Degrading Activities of Catalytic Domains of α-Amylase and α-Amylase-Pullulanase Enzymes Conserved in Gardnerella spp. from the Vaginal Microbiome.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0039322},
doi = {10.1128/jb.00393-22},
pmid = {36744900},
issn = {1098-5530},
abstract = {Gardnerella spp. are associated with bacterial vaginosis in which normally dominant lactobacilli are replaced with facultative and anaerobic bacteria, including Gardnerella spp. Co-occurrence of multiple species of Gardnerella is common in the vagina, and competition for nutrients such as glycogen likely contributes to the differential abundances of Gardnerella spp. Glycogen must be digested into smaller components for uptake, a process that depends on the combined action of glycogen-degrading enzymes. In this study, the ability of culture supernatants of 15 isolates of Gardnerella spp. to produce glucose, maltose, maltotriose, and maltotetraose from glycogen was demonstrated. Carbohydrate-active enzymes (CAZymes) were identified bioinformatically in Gardnerella proteomes using dbCAN2. Identified proteins included a single-domain α-amylase (EC 3.2.1.1) (encoded by all 15 isolates) and an α-amylase-pullulanase (EC 3.2.1.41) containing amylase, carbohydrate binding modules, and pullulanase domains (14/15 isolates). To verify the sequence-based functional predictions, the amylase and pullulanase domains of the α-amylase-pullulanase and the single-domain α-amylase were each produced in Escherichia coli. The α-amylase domain from the α-amylase-pullulanase released maltose, maltotriose, and maltotetraose from glycogen, and the pullulanase domain released maltotriose from pullulan and maltose from glycogen, demonstrating that the Gardnerella α-amylase-pullulanase is capable of hydrolyzing α-1,4 and α-1,6 glycosidic bonds. Similarly, the single-domain α-amylase protein also produced maltose, maltotriose, and maltotetraose from glycogen. Our findings show that Gardnerella spp. produce extracellular amylase enzymes as "public goods" that can digest glycogen into maltose, maltotriose, and maltotetraose that can be used by the vaginal microbiota. IMPORTANCE Increased abundance of Gardnerella spp. is a diagnostic characteristic of bacterial vaginosis, an imbalance in the human vaginal microbiome associated with troubling symptoms, and negative reproductive health outcomes, including increased transmission of sexually transmitted infections and preterm birth. Competition for nutrients is likely an important factor in causing dramatic shifts in the vaginal microbial community, but little is known about the contribution of bacterial enzymes to the metabolism of glycogen, a major food source available to vaginal bacteria. The significance of our research is characterizing the activity of enzymes conserved in Gardnerella species that contribute to the ability of these bacteria to utilize glycogen.},
}

@article {pmid36744896,
year = {2023},
author = {Zhang, Z and Zhang, L and Zhang, G and Zhao, Z and Wang, H and Ju, F},
title = {Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0428222},
doi = {10.1128/spectrum.04282-22},
pmid = {36744896},
issn = {2165-0497},
abstract = {In the last decade, metagenomics has greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads raised mainly from the preparation of metagenomic DNA sequencing libraries and their impacts on metagenomic assembly and binning have never been brought to attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assemblies and binning based on analyses of five groups of representative metagenomes with distinct microbiome complexities. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic data sets examined thanks to the improved contig length and coverage profiling of metagenome-assembled contigs, whereas it slightly decreased the binning yields of metagenomes with low complexity (e.g., human gut metagenomes). Specifically, 411 versus 397, 331 versus 317, 104 versus 88, and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication significantly reduced the computational costs of the metagenomic assembly, including the elapsed time (9.0% to 29.9%) and the maximum memory requirement (4.3% to 37.1%). Collectively, we recommend the removal of duplicate reads in metagenomes with high complexity before assembly and binning analyses, for example, the forest soil metagenomes examined in this study. IMPORTANCE Duplicated reads in shotgun metagenomes are usually considered technical artifacts. Their presence in metagenomes would theoretically not only introduce bias into the quantitative analysis but also result in mistakes in the coverage profile, leading to adverse effects on or even failures in metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldom noticed, and its impacts on downstream essential bioinformatic procedures (e.g., assembly and binning) remained unclear. In this study, we comprehensively evaluated for the first time the implications of duplicate reads for the de novo assembly and binning of real metagenomic data sets by comparing the assembly qualities, binning yields, and requirements for computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields of metagenomes with high complexity and significantly reduced the computational costs, including the elapsed time and the maximum memory requirement, for most of the metagenomes studied. These results provide empirical references for more cost-efficient metagenomic analyses in microbiome research.},
}

@article {pmid36744308,
year = {2023},
author = {Nierengarten, MB},
title = {Association of physical exercise and a healthy gut microbiome in colorectal cancer.},
journal = {Cancer},
volume = {129},
number = {5},
pages = {655-656},
doi = {10.1002/cncr.34669},
pmid = {36744308},
issn = {1097-0142},
}

@article {pmid36744230,
year = {2022},
author = {Fritsch, DA and Jackson, MI and Wernimont, SM and Feld, GK and Badri, DV and Brejda, JJ and Cochrane, CY and Gross, KL},
title = {Adding a polyphenol-rich fiber bundle to food impacts the gastrointestinal microbiome and metabolome in dogs.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {1039032},
pmid = {36744230},
issn = {2297-1769},
abstract = {INTRODUCTION: Pet foods fortified with fermentable fibers are often indicated for dogs with gastrointestinal conditions to improve gut health through the production of beneficial post-biotics by the pet's microbiome.

METHODS: To evaluate the therapeutic underpinnings of pre-biotic fiber enrichment, we compared the fecal microbiome, the fecal metabolome, and the serum metabolome of 39 adult dogs with well-managed chronic gastroenteritis/enteritis (CGE) and healthy matched controls. The foods tested included a test food (TF1) containing a novel pre-biotic fiber bundle, a control food (CF) lacking the fiber bundle, and a commercially available therapeutic food (TF2) indicated for managing fiber-responsive conditions. In this crossover study, all dogs consumed CF for a 4-week wash-in period, were randomized to either TF1 or TF2 and fed for 4 weeks, were fed CF for a 4-week washout period, and then received the other test food for 4 weeks.

RESULTS: Meaningful differences were not observed between the healthy and CGE dogs in response to the pre-biotic fiber bundle relative to CF. Both TF1 and TF2 improved stool scores compared to CF. TF1-fed dogs showed reduced body weight and fecal ash content compared to either CF or TF2, while stools of TF2-fed dogs showed higher pH and lower moisture content vs. TF1. TF1 consumption also resulted in unique fecal and systemic metabolic signatures compared to CF and TF2. TF1-fed dogs showed suppressed signals of fecal bacterial putrefactive metabolism compared to either CF or TF2 and increased saccharolytic signatures compared to TF2. A functional analysis of fecal tryptophan metabolism indicated reductions in fecal kynurenine and indole pathway metabolites with TF1. Among the three foods, TF1 uniquely increased fecal polyphenols and the resulting post-biotics. Compared to CF, consumption of TF1 largely reduced fecal levels of endocannabinoid-like metabolites and sphingolipids while increasing both fecal and circulating polyunsaturated fatty acid profiles, suggesting that TF1 may have modulated gastrointestinal inflammation and motility. Stools of TF1-fed dogs showed reductions in phospholipid profiles, suggesting fiber-dependent changes to colonic mucosal structure.

DISCUSSION: These findings indicate that the use of a specific pre-biotic fiber bundle may be beneficial in healthy dogs and in dogs with CGE.},
}

@article {pmid36744135,
year = {2023},
author = {Sharlandjieva, V and Beristain, AG and Terry, J},
title = {Assessment of the human placental microbiome in early pregnancy.},
journal = {Frontiers in medicine},
volume = {10},
number = {},
pages = {1096262},
pmid = {36744135},
issn = {2296-858X},
abstract = {INTRODUCTION: Bacteria derived from the maternal circulation have been suggested to seed the human placenta during development leading to an intrinsic placental microbiome. This concept has become controversial as numerous studies suggest that the apparent placental microbiome is mostly, if not completely, comprised of contaminants. If the maternal circulation seeds the placenta then there should be an increase in abundance and diversity of detectable bacteria with onset of maternal perfusion of the placenta around 10 weeks gestational age; however, if only contaminants are present then there should be no significant evolution of the placental microbiome with increasing gestational age. This pilot study addresses whether bacterial abundance and diversity increase in human placenta and whether there is an associated shift in the immunophenotype of the decidual immune cell complement before and after initiation of placental perfusion.

METHODS: Human placental and decidual tissue from 5 to 19 weeks gestational age, handled aseptically to minimize contamination, is assessed by quantitative 16S polymerase chain reaction (PCR), 16S gene sequencing, and immunological flow cytometry studies.

RESULTS: A weak positive correlation between placental bacterial abundance and gestational age is identified but is not statistically significant. No significant changes in bacterial diversity are found with increasing gestational age. The proportion of decidual activated memory T helper cells increases with gestational age but no change was observed in other lymphocyte subsets.

DISCUSSION: This pilot study does not strongly support bacterial colonization of the placenta after initiation of maternal perfusion; however, the minor trends towards increases in bacterial abundance and activated memory T helper cells may represent an early stage of this process. Additional investigations in larger cohorts are warranted.},
}

@article {pmid36744088,
year = {2023},
author = {Wang, D and Tang, G and Yu, J and Li, Y and Wang, Y and Chen, L and Lei, X and Cao, Y and Yao, J},
title = {Litter size influences rumen microbiota and fermentation efficiency, thus determining host early growth in goats.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1098813},
pmid = {36744088},
issn = {1664-302X},
abstract = {INTRODUCTION: Multiple litters are accompanied by low birth weight, low survival rates, and growth rates in goats during early life. Regulating rumen microbiota structure can indirectly or directly affect host metabolism and animal growth. However, the relationship between high litter size and rumen microbiome, rumen fermentation, and growth performance in goat kids is unclear.

METHODS: In the present study, thirty 6-month-old, female goats were investigated, of which 10 goats were randomly chosen from single, twin and triplet goats respectively, and their birth weight was recorded. From birth, all goats were subjected to the same feed and management practices. Individual weaning and youth body weight were measured, and the rumen fluid samples were collected to characterize the bacterial communities and to determine the ruminal volatile fatty acids (VFA), free amino acids (AA), and free fatty acids (FA) concentration of those young goats.

RESULTS AND DISCUSSION: Compared with the single and twin goats, triplet goats have lower weaning and youth body weight and average daily gain (ADG). Ruminal propionate, butyrate, and total VFA were decreased in triplet goats. Meanwhile, ruminal AA, such as branched chain amino acids (BCAA), essential amino acids (EAA), unsaturated fatty acids (UFA), and monounsaturated fatty acids (MUFA) were decreased, while saturated fatty acids (SFA) and odd and branched chain fatty acids (OBCFA) were increased in triplet goats. Our results also revealed that litter size significantly affected the rumen bacterial communities, and triplet goats had a lower the Firmicutes: Bacteroidota ratio, the abundance of Firmicutes phylum, Rikenellaceae family, and Rikenellaceae RC9 gut group, and had a higher proportion of Prevotellaceae family, and several genera of Prevotellaceae, such as Prevotella, and unclassified f Prevotellaceae. Furthermore, Spearman's correlation network analysis showed that the changes in the rumen bacteria were associated with changes in rumen metabolites. In conclusion, this study revealed that high litter size could bring disturbances to the microbial communities and decrease the rumen fermentation efficiency and growth performance, which can be utilized to better understand variation in microbial ecology that will improve growth performance in triplet goats.},
}

@article {pmid36744087,
year = {2023},
author = {Mazumdar, T and Hänniger, S and Shukla, SP and Murali, A and Bartram, S and Heckel, DG and Boland, W},
title = {8-HQA adjusts the number and diversity of bacteria in the gut microbiome of Spodoptera littoralis.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1075557},
pmid = {36744087},
issn = {1664-302X},
abstract = {Quinolinic carboxylic acids are known for their metal ion chelating properties in insects, plants and bacteria. The larval stages of the lepidopteran pest, Spodoptera littoralis, produce 8-hydroxyquinoline-2-carboxylic acid (8-HQA) in high concentrations from tryptophan in the diet. At the same time, the larval midgut is known to harbor a bacterial population. The motivation behind the work was to investigate whether 8-HQA is controlling the bacterial community in the gut by regulating the concentration of metal ions. Knocking out the gene for kynurenine 3-monooxygenase (KMO) in the insect using CRISPR/Cas9 eliminated production of 8-HQA and significantly increased bacterial numbers and diversity in the larval midgut. Adding 8-HQA to the diet of knockout larvae caused a dose-dependent reduction of bacterial numbers with minimal effects on diversity. Enterococcus mundtii dominates the community in all treatments, probably due to its highly efficient iron uptake system and production of the colicin, mundticin. Thus host factors and bacterial properties interact to determine patterns of diversity and abundance in the insect midgut.},
}

@article {pmid36744086,
year = {2023},
author = {Li, J and Chen, L and Zhang, J and Zhang, C and Ma, D and Zhou, G and Ning, Q},
title = {Organic amendments with high proportion of heterocyclic compounds promote soil microbiome shift and microbial use efficiency of straw-C.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1087709},
pmid = {36744086},
issn = {1664-302X},
abstract = {Soil microbial use efficiency of straw carbon (C), which is the proportion of straw-C microbes assimilate into new biosynthetic material relative to C lost out of the system as CO2, is critical in increasing soil organic C (SOC) content, and hence maintaining soil fertility and productivity. However, the effect of chemical structures of the organic amendments (OAs) on the microbial use efficiency of straw-C remains unclear. The effect of the chemical structure of the OAs on microbial use efficiency of straw-C was elucidated by a combination of [13]C-straw labeling with high-throughput sequencing and pyrolysis-GC/MS. We found a strong positive correlation between the microbial use efficiency of straw-C and the proportion of heterocyclic compounds (Hete_C). The microbial use efficiency of straw-C was highest in soil supplemented with Hete_C-dominant OAs, which significantly shifted microbial community structure toward fungal dominance. Specifically, fungal-to-bacterial ratio, fungal richness, and the relative abundance of Ascomycota were higher in soil with a higher proportion of Hete_C-dominant OAs. Together, our study suggests that OAs with high proportion of Hete_C promote the microbial use efficiency of straw-C by increasing the dominance of fungi in the soil microbial community in agroecosystems.},
}

@article {pmid36743917,
year = {2022},
author = {Blancafort, C and Llácer, J},
title = {Can probiotics enhance fertility outcome? Capacity of probiotics as a single intervention to improve the feminine genital tract microbiota in non-symptomatic reproductive-aged women.},
journal = {Frontiers in endocrinology},
volume = {13},
number = {},
pages = {1081830},
pmid = {36743917},
issn = {1664-2392},
abstract = {Modifications in vaginal and endometrial microbiome and microbiota have been associated with fewer implantation rates and poorest pregnancy outcomes. Therefore, its study has emerged as a new biomarker in reproductive medicine. Despite the numerous papers published on probiotic use for vaginal dysbiosis and their actual wide empiric use especially for infertile patients, there is still no clear answer to justify their recommendation. The impact of probiotics on the vaginal or endometrial microbiota has often been investigated under a symptomatic altered vaginal microbial ecosystem, such as bacterial vaginosis. However 50% of women with bacterial vaginosis are asymptomatic. Actual clinical practice guidelines clearly recommend the use of specific antimicrobial agents for the management of symptomatic vaginal infections. Assuming this should be the management as well for an infertile population, what should be the treatment for the 50% non-symptomatic women presenting unfavorable vaginal/endometrial microbiota? The aim of this review is to assess the capacity of probiotics as a single intervention to alter the feminine genital tract microbiota in non-symptomatic reproductive-aged women.},
}

@article {pmid36743537,
year = {2022},
author = {Mushtaq, S and Shafiq, M and Tariq, MR and Sami, A and Nawaz-Ul-Rehman, MS and Bhatti, MHT and Haider, MS and Sadiq, S and Abbas, MT and Hussain, M and Shahid, MA},
title = {Interaction between bacterial endophytes and host plants.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1092105},
pmid = {36743537},
issn = {1664-462X},
abstract = {Endophytic bacteria are mainly present in the plant's root systems. Endophytic bacteria improve plant health and are sometimes necessary to fight against adverse conditions. There is an increasing trend for the use of bacterial endophytes as bio-fertilizers. However, new challenges are also arising regarding the management of these newly discovered bacterial endophytes. Plant growth-promoting bacterial endophytes exist in a wide host range as part of their microbiome, and are proven to exhibit positive effects on plant growth. Endophytic bacterial communities within plant hosts are dynamic and affected by abiotic/biotic factors such as soil conditions, geographical distribution, climate, plant species, and plant-microbe interaction at a large scale. Therefore, there is a need to evaluate the mechanism of bacterial endophytes' interaction with plants under field conditions before their application. Bacterial endophytes have both beneficial and harmful impacts on plants but the exact mechanism of interaction is poorly understood. A basic approach to exploit the potential genetic elements involved in an endophytic lifestyle is to compare the genomes of rhizospheric plant growth-promoting bacteria with endophytic bacteria. In this mini-review, we will be focused to characterize the genetic diversity and dynamics of endophyte interaction in different host plants.},
}

@article {pmid36743312,
year = {2023},
author = {Ni, B and Kong, X and Yan, Y and Fu, B and Zhou, F and Xu, S},
title = {Combined analysis of gut microbiome and serum metabolomics reveals novel biomarkers in patients with early-stage non-small cell lung cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1091825},
pmid = {36743312},
issn = {2235-2988},
abstract = {Non-small cell lung cancer (NSCLC) is the predominant form of lung cancer and is one of the most fatal cancers worldwide. Recently, the International Association for the Study of Lung Cancer (IASLC) proposed a novel grading system based on the predominant and high-grade histological patterns for invasive pulmonary adenocarcinoma (IPA). To improve outcomes for NSCLC patients, we combined serum metabolomics and fecal microbiology to screen biomarkers in patients with early-stage NSCLC and identified characteristic microbial profiles in patients with different grades of IPA. 26 genera and 123 metabolites were significantly altered in the early-stage NSCLC patients. Agathobacter, Blautia, Clostridium, and Muribaculacea were more abundant in the early-stage NSCLC patients compared with healthy controls. For the different grades of IPA, the characteristic microorganisms are as follows: Blautia and Marinobacter in IPA grade type 1; Dorea in IPA grade type 2; and Agathobacter in IPA grade type 3. In the metabolome results, the early-stage NSCLC group mainly included higher levels of sphingolipids (D-erythro-sphingosine 1-phosphate, palmitoyl sphingomyelin), fatty acyl (Avocadyne 1-acetate, 12(S)-HETE, 20-Carboxy-Leukotriene B4, Thromboxane B3, 6-Keto-prostaglandin f1alpha, Sebacic acid, Tetradecanedioic acid) and glycerophospholipids (LPC 20:2, LPC 18:0, LPC 18:4, LPE 20:2, LPC 20:1, LPC 16:1, LPC 20:0, LPA 18:2, LPC 17:1, LPC 17:2, LPC 19:0). Dysregulation of pathways, such as sphingolipid metabolism and sphingolipid signaling pathway may become an emerging therapeutic strategy for early-NSCLC. Correlation analysis showed that gut microbiota and serum metabolic profiles were closely related, while Muribaculacea and Clostridium were the core genera. These findings provide new biomarkers for the diagnosis of early-stage NSCLC and the precise grading assessment of prognostic-related IPAs, which are of clinical importance and warrant further investigation of the underlying molecular mechanisms.},
}

@article {pmid36742425,
year = {2023},
author = {Hardinsyah, H and Nurkolis, F and Kurniawan, R and Gunawan, WB and Augusta, PS and Setyawardani, A and Agustianto, RF and Al Mahira, MFN and Praditya, GN and Lailossa, DG and Yudisthira, D and Farradisya, S and Barazani, H},
title = {Can salivary microbiome become a biodetector for type-2 diabetes? Opinion for future implications and strategies.},
journal = {Frontiers in nutrition},
volume = {10},
number = {},
pages = {1113591},
pmid = {36742425},
issn = {2296-861X},
}

@article {pmid36742327,
year = {2023},
author = {Morse, ZJ and Simister, RL and Crowe, SA and Horwitz, MS and Osborne, LC},
title = {Virus induced dysbiosis promotes type 1 diabetes onset.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1096323},
pmid = {36742327},
issn = {1664-3224},
abstract = {Autoimmune disorders are complex diseases of unclear etiology, although evidence suggests that the convergence of genetic susceptibility and environmental factors are critical. In type 1 diabetes (T1D), enterovirus infection and disruption of the intestinal microbiota are two environmental factors that have been independently associated with T1D onset in both humans and animal models. However, the possible interaction between viral infection and the intestinal microbiota remains unknown. Here, we demonstrate that Coxsackievirus B4 (CVB4), an enterovirus that accelerates T1D onset in non-obese diabetic (NOD) mice, induced restructuring of the intestinal microbiome prior to T1D onset. Microbiome restructuring was associated with an eroded mucosal barrier, bacterial translocation to the pancreatic lymph node, and increased circulating and intestinal commensal-reactive antibodies. The CVB4-induced change in community composition was strikingly similar to that of uninfected NOD mice that spontaneously developed diabetes, implying a mutual "diabetogenic" microbiome. Notably, members of the Bifidobacteria and Akkermansia genera emerged as conspicuous members of this diabetogenic microbiome, implicating these taxa, among others, in diabetes onset. Further, fecal microbiome transfer (FMT) of the diabetogenic microbiota from CVB4-infected mice enhanced T1D susceptibility and led to diminished expression of the short chain fatty acid receptor GPR43 and fewer IL-10-expressing regulatory CD4[+] T cells in the intestine of naïve NOD recipients. These findings support an overlap in known environmental risk factors of T1D, and suggest that microbiome disruption and impaired intestinal homeostasis contribute to CVB-enhanced autoreactivity and T1D.},
}

@article {pmid36742316,
year = {2023},
author = {Zhang, Q and Deng, P and Chen, S and Xu, H and Zhang, Y and Chen, H and Zhang, J and Sun, H},
title = {Electroacupuncture and human iPSC-derived small extracellular vesicles regulate the gut microbiota in ischemic stroke via the brain-gut axis.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1107559},
pmid = {36742316},
issn = {1664-3224},
abstract = {Electroacupuncture (EA) and induced pluripotent stem cell (iPSC)-derived small extracellular vesicles (iPSC-EVs) have substantial beneficial effects on ischemic stroke. However, the detailed mechanisms remain unclear. Here, we explored the mechanisms underlying the regulation of EA and iPSC-EVs in the microbiome-gut-brain axis (MGBA) after ischemic stroke. Ischemic stroke mice (C57BL/6) were subjected to middle cerebral artery occlusion (MCAO) or Sham surgery. EA and iPSC-EVs treatments significantly improved neurological function and neuronal and intestinal tract injury, downregulated the levels of IL-17 expression and upregulated IL-10 levels in brain and colon tissue after cerebral ischemia-reperfusion. EA and iPSC-EVs treatments also modulated the microbiota composition and diversity as well as the differential distribution of species in the intestines of the mice after cerebral ischemia-reperfusion. Our results demonstrated that EA and iPSC-EVs treatments regulated intestinal immunity through MGBA regulation of intestinal microbes, reducing brain and colon damage following cerebral ischemia and positively impacting the outcomes of ischemic stroke. Our findings provide new insights into the application of EA combined with iPSC-EVs as a treatment for ischemic stroke.},
}

@article {pmid36742284,
year = {2023},
author = {Da, D and Zhao, Q and Zhang, H and Wu, W and Zeng, X and Liang, X and Jiang, Y and Xiao, Z and Yu, J and Ding, S and Zheng, L and Zhang, Y and Xu, X and Ding, D},
title = {Oral microbiome in older adults with mild cognitive impairment.},
journal = {Journal of oral microbiology},
volume = {15},
number = {1},
pages = {2173544},
pmid = {36742284},
issn = {2000-2297},
abstract = {The association between the oral microbiome and mild cognitive impairment (MCI) remains unclear. This study aimed to investigate such an association among Chinese older adults. Participants without dementia were recruited from the community. A battery of neuropsychological tests was administered to evaluate the cognitive function. The diagnosis of MCI was based on Peterson's criteria. The non-stimulated saliva was collected to extract sequences of the oral microbiome. Forty-seven MCI and 47 cognitively normal participants were included. There was significant difference in alpha diversity and insignificant difference in beta diversity between the two groups of participants. Compared with the cognitively normal group, Gemella haemolysans and Streptococcus gordonii were two significantly decreased species while Veillonella unclassified_Veillonella and Fusobacterium sp._HMT_203 were two significantly increased species in the MCI group. The richness of Gemella haemolysans presented the best discriminate value for MCI with the AUC (Area Under Curve) of 0.707, a cut-off value of 0.008 for relative abundance, the sensitivity of 63.8% and specificity of 70.2%. The dysbiosis of oral microbiome and relative abundance of Gemella haemolysans was significantly associated with MCI. Further studies were needed to develop new treatment strategies targeting the oral microbiome for cognitive impairment.},
}

@article {pmid36742168,
year = {2023},
author = {Bassotti, G and Fruganti, A and Stracci, F and Marconi, P and Fettucciari, K},
title = {Cytotoxic synergism of Clostridioides difficile toxin B with proinflammatory cytokines in subjects with inflammatory bowel diseases.},
journal = {World journal of gastroenterology},
volume = {29},
number = {4},
pages = {582-596},
pmid = {36742168},
issn = {2219-2840},
abstract = {Clostridioides difficile (C. difficile) is progressively colonizing humans and animals living with humans. During this process, hypervirulent strains and mutated toxin A and B of C. difficile (TcdA and TcdB) are originating and developing. While in healthy subjects colonization by C. difficile becomes a risk after the use of antibiotics that alter the microbiome, other categories of people are more susceptible to infection and at risk of relapse, such as those with inflammatory bowel disease (IBD). Recent in vitro studies suggest that this increased susceptibility could be due to the strong cytotoxic synergism between TcdB and proinflammatory cytokines the tumor necrosis factor-alpha and interferon-gamma (CKs). Therefore, in subjects with IBD the presence of an inflammatory state in the colon could be the driver that increases the susceptibility to C. difficile infection and its progression and relapses. TcdB is internalized in the cell via three receptors: chondroitin sulphate proteoglycan 4; poliovirus receptor-like 3; and Wnt receptor frizzled family. Chondroitin sulphate proteoglycan 4 and Wnt receptor frizzled family are involved in cell death by apoptosis or necrosis depending on the concentration of TcdB and cell types, while poliovirus receptor-like 3 induces only necrosis. It is possible that cytokines could also induce a greater expression of receptors for TcdB that are more involved in necrosis than in apoptosis. Therefore, in subjects with IBD there are the conditions: (1) For greater susceptibility to C. difficile infection, such as the inflammatory state, and abnormalities of the microbiome and of the immune system; (2) for the enhancement of the cytotoxic activity of TcdB +Cks; and (3) for a greater expression of TcdB receptors stimulated by cytokines that induce cell death by necrosis rather than apoptosis. The only therapeutic approach currently possible in IBD patients is monitoring of C. difficile colonization for interventions aimed at reducing tumor necrosis factor-alpha and interferon-gamma levels when the infection begins. The future perspective is to generate bacteriophages against C. difficile for targeted therapy.},
}

@article {pmid36742002,
year = {2022},
author = {Tuska, RM and Helm, SM and Graf, CF and James, C and Kong, G and Stiemsma, LT and Green, DB and Helm, SE},
title = {Surfeit folic acid, protein, and exercise modify oncogenic inflammatory biomarkers and fecal microbiota.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1060212},
pmid = {36742002},
issn = {2296-861X},
abstract = {Intestinal microbiota, diet, and physical activity are inextricably linked to inflammation occurring in the presence of tumor progression and declining neurocognition. This study aimed to explore how fecal microbiota, inflammatory biomarkers, and neurocognitive behavior are influenced by voluntary exercise and surplus dietary protein and folic acid which are common health choices. Dietary treatments provided over 8 weeks to C57BL/CJ male mice (N = 76) were: Folic Acid (FA) Protein (P) Control (FPC, 17.9% P; 2 mgFA/kg); Folic Acid Deficient (FAD); Folic Acid Supplemented (FAS; 8 mgFA/kg); Low Protein Diet (LPD, 6% P); and High Protein Diet (HPD, 48% P). FAS mice had decreased plasma HCys (p < 0.05), therefore confirming consumption of FA. Objectives included examining influence of exercise using Voluntary Wheel Running (VWR) upon fecal microbiota, inflammatory biomarkers C - reactive protein (CRP), Vascular Endothelial Growth Factor (VEGF), Interleukin-6 (IL-6), nuclear factor kappa ß subunit (NF-κßp65), Caspase-3 (CASP3), Tumor Necrosis Factor-alpha (TNF-α), and neurocognitive behavior. CRP remained stable, while a significant exercise and dietary effect was notable with decreased VEGF (p < 0.05) and increased CASP3 (p < 0.05) for exercised HPD mice. Consumption of FAS did significantly increase (p < 0.05) muscle TNF-α and the ability to build a nest (p < 0.05) was significantly decreased for both FAD and LPD exercised mice. Rearing behavior was significantly increased (p < 0.05) in mice fed HPD. An emerging pattern with increased dietary protein intake revealed more distance explored in Open Field Testing. At week 1, both weighted and unweighted UniFrac principal coordinates analysis yielded significant clustering (permanova, p ≤ 0.05) associated with the specific diets. Consumption of a HPD diet resulted in the most distinct fecal microbiota composition. At the phylum level-comparing week 1 to week 8-we report a general increase in the Firmicutes/Bacteroidetes ratio, characterized by an outgrowth of Firmicutes by week 8 in all groups except the HPD. MaAsLin2 analysis corroborates this finding and emphasizes an apparent inversion of the microbiome composition at week 8 after HPD. Explicit modification of oncogenic inflammatory biomarkers and fecal microbiome post high FA and protein intake along with voluntary exercise contributed to current underlying evidence that this diet and exercise relationship has broader effects on human health and disease-perhaps importantly as a practical modulation of cancer progression and declining neurocognition.},
}

@article {pmid36741980,
year = {2022},
author = {Amend, L and Gilbert, BTP and Pelczar, P and Böttcher, M and Huber, S and Witte, T and Finckh, A and Strowig, T},
title = {Characterization of serum biomarkers and antibody responses against Prevotella spp. in preclinical and new-onset phase of rheumatic diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1096211},
pmid = {36741980},
issn = {2235-2988},
abstract = {INTRODUCTION: The characterization of the influence of the microbiota on the development and drug responses during rheumatic diseases has intensified in recent years. The role of specific bacteria during disease development has become a central research question. Notably, several lines of evidence point to distinct microbes, e.g., Prevotella copri (P. copri) being targeted by antibodies in clinical phases of rheumatic diseases.

METHODS: In the present study, we compiled a broad collection of human serum samples from individuals at risk of developing RA, chronic RA patients as well as patients with new-onset of rheumatic diseases. We evaluated the presence of inflammatory biomarkers in our serum collection as well as serum antibody responses against novel, genetically distinct isolates of P. copri and several oral pathobionts.

RESULTS: Our analysis revealed the presence of increased levels of inflammatory markers already in pre-clinical and new onset rheumatoid arthritis. However, antibody reactivity against the microbes did not differ between patient groups. Yet, we observed high variability between the different P. copri strains. We found total serum IgG levels to slightly correlate with IgG antibody responses against P. copri, but no relation between the latter and presence or prevalence of P. copri in the intestine.

DISCUSSION: In conclusion, our work underlined the importance of strain-level characterization and its consideration during further investigations of host-microbiota interactions and the development of microbiome-based therapeutic approaches for treating rheumatic diseases.},
}

@article {pmid36741978,
year = {2022},
author = {Tsafarova, B and Hodzhev, Y and Yordanov, G and Tolchkov, V and Kalfin, R and Panaiotov, S},
title = {Morphology of blood microbiota in healthy individuals assessed by light and electron microscopy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1091341},
pmid = {36741978},
issn = {2235-2988},
abstract = {INTRODUCTION: The blood microbiome is still an enigma. The existence of blood microbiota in clinically healthy individuals was proven during the last 50 years. Indirect evidence from radiometric analysis suggested the existence of living microbial forms in erythrocytes. Recently targeted nucleic acid sequencing demonstrated rich microbial biodiversity in the blood of clinically healthy individuals. The morphology and proliferation cycle of blood microbiota in peripheral blood mononuclear cells (PBMC) isolated from freshly drawn and cultured whole blood are obscure.

METHODS: To study the life cycle of blood microbiota we focused on light, and electron microscopy analysis. Peripheral blood mononuclear cells isolated from freshly drawn blood and stress-cultured lysed whole blood at 43°C in presence of vitamin K from healthy individuals were studied.

RESULTS: Here, we demonstrated that free circulating microbiota in the PMBC fraction possess a well-defined cell wall and proliferate by budding or through a mechanism similar to the extrusion of progeny bodies. By contrast, stress-cultured lysed whole blood microbiota proliferated as cell-wall deficient microbiota by forming electron-dense or electron-transparent bodies. The electron-dense bodies proliferated by fission or produce in chains Gram-negatively stained progeny cells or enlarged and burst to release progeny cells of 180 - 200 nm size. On the other hand, electron-transparent bodies enlarged and emitted progeny cells through the membrane. A novel proliferation mechanism of blood microbiota called by us "a cell within a cell" was observed. It combines proliferation of progeny cells within a progeny cell which is growing within the "mother" cell.

DISCUSSION: The rich biodiversity of eukaryotic and prokaryotic microbiota identified in blood by next-generation sequencing technologies and our microscopy results suggest different proliferation mechanisms in whole and cultured blood. Our documented evidence and conclusions provide a more comprehensive view of the existence of normal blood microbiota in healthy individuals.},
}

@article {pmid36741975,
year = {2022},
author = {Xue, L and Ding, Y and Qin, Q and Liu, L and Ding, X and Zhou, Y and Liu, K and Singla, RK and Shen, K and Din, AU and Zhang, Y and Shen, Z and Shen, B and Miao, L},
title = {Assessment of the impact of intravenous antibiotics treatment on gut microbiota in patients: Clinical data from pre-and post-cardiac surgery.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1043971},
pmid = {36741975},
issn = {2235-2988},
abstract = {BACKGROUND AND AIMS: Surgical site infection is a common complication after surgery. Periprocedural antibiotics are necessary to prescribe for preventing or treating infections. The present study aimed to explore the effect of intravenous antibiotics on gut microbiota and menaquinone biosynthesis in patients, especially in elderly patients undergoing cardiac surgery.

METHODS: A total of 388 fecal samples were collected from 154 cardiac surgery patients. The V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced on a MiSeq PE300. The gut microbiota diversity of samples was analyzed in terms of α- and β-diversity at the OTU level. The different groups were classified according to antibiotics in combinations and single antibiotics. PICRUSt2 was used for preliminary prediction of the gut microbiota function for menaquinone biosynthesis.

RESULTS: The intravenously administered antibiotics which are excreted via bile represents the main antibiotics that could disturb the gut microbiota's composition in cardiac surgery patients, especially for elderly patients. The effect of antibiotics on gut microbiota is produced after antibiotics treatments over one week. The recovery of gut microbiota to the state of pre-antibiotics may require over two weeks of antibiotics withdrawal. Sex factor doesn't represent as an influencer in gut microbiota composition. Long-term use of cefoperazone-sulbactam may affect coagulation function.

CONCLUSIONS: The composition of the gut microbiota had a significant change post-intravenous antibiotics treatment in cardiac surgery patients. The richness and diversity of gut microbiota are increased in elderly patients.},
}

@article {pmid36741893,
year = {2022},
author = {Aguilera-Torres, C and Riveros, G and Morales, LV and Sierra-Almeida, A and Schoebitz, M and Hasbún, R},
title = {Relieving your stress: PGPB associated with Andean xerophytic plants are most abundant and active on the most extreme slopes.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1062414},
pmid = {36741893},
issn = {1664-302X},
abstract = {INTRODUCTION: Plants interact with plant growth-promoting bacteria (PGPB), especially under stress condition in natural and agricultural systems. Although a potentially beneficial microbiome has been found associated to plants from alpine systems, this plant- PGPB interaction has been scarcely studied. Nevados de Chillán Complex hold one of the southernmost xerophytic formations in Chile. Plant species living there have to cope with drought and extreme temperatures during the growing season period, microclimatic conditions that become harsher on equatorial than polar slopes, and where the interaction with PGPB could be key for plant survival. Our goal was to study the abundance and activity of different PGPB associated to two abundant plant species of Andean xerophytic formations on contrasting slopes.

METHODS: Twenty individuals of Berberis empetrifolia and Azorella prolifera shrubs were selected growing on a north and south slope nearby Las Fumarolas, at 2,050 m elevation. On each slope, microclimate based on temperature and moisture conditions were monitored throughout the growing period (oct. - apr.). Chemical properties of the soil under plant species canopies were also characterized. Bacterial abundance was measured as Log CFU g[-1] from soil samples collected from each individual and slope. Then, the most abundant bacterial colonies were selected, and different hormonal (indoleacetic acid) and enzymatic (nitrogenase, phosphatase, ACC-deaminase) mechanisms that promote plant growth were assessed and measured.

RESULTS AND DISCUSSION: Extreme temperatures were observed in the north facing slope, recording the hottest days (41 vs. 36°C) and coldest nights (-9.9 vs. 6.6°C). Moreover, air and soil moisture were lower on north than on south slope, especially late in the growing season. We found that bacterial abundance was higher in soils on north than on south slope but only under B. empetrifolia canopy. Moreover, the activity of plant growth-promoting mechanisms varied between slopes, being on average higher on north than on south slope, but with plant species-dependent trends. Our work showed how the environmental heterogeneity at microscale in alpine systems (slope and plant species identity) underlies variations in the abundance and plant growth promoting activity of the microorganisms present under the plant canopy of the Andean xerophytic formations and highlight the importance of PGPB from harsh systems as biotechnological tools for restoration.},
}

@article {pmid36741596,
year = {2023},
author = {Bezecny, JA and Bolton, E and Taylor, MH and Berry, EG},
title = {A Rare Case of Demodicosis Following Treatment With Oral Fluconazole.},
journal = {Cureus},
volume = {15},
number = {1},
pages = {e33309},
pmid = {36741596},
issn = {2168-8184},
abstract = {Demodex folliculorum and Demodex brevis are commensal human ectoparasites that reside within or near hair follicles and have been highly associated with rosacea-like papulopustular skin eruptions. We present an interesting case of recurrent, iatrogenic demodicosis in a 56-year-old man. We suspect this to have been triggered by antifungal therapy given it occurred twice closely following azole treatment. We propose that oral antifungals in the setting of immunosuppression can alter the skin microbiome, facilitating Demodex proliferation.},
}

@article {pmid36741465,
year = {2022},
author = {Cobo-López, S and Gupta, VK and Sung, J and Guimerà, R and Sales-Pardo, M},
title = {Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes.},
journal = {PNAS nexus},
volume = {1},
number = {3},
pages = {pgac055},
pmid = {36741465},
issn = {2752-6542},
abstract = {A key question in human gut microbiome research is what are the robust structural patterns underlying its taxonomic composition. Herein, we use whole metagenomic datasets from healthy human guts to show that such robust patterns do exist, albeit not in the conventional enterotype sense. We first introduce the concept of mixed-membership enterotypes using a network inference approach based on stochastic block models. We find that gut microbiomes across a group of people (hosts) display a nested structure, which has been observed in a number of ecological systems. This finding led us to designate distinct ecological roles to both microbes and hosts: generalists and specialists. Specifically, generalist hosts have microbiomes with most microbial species, while specialist hosts only have generalist microbes. Moreover, specialist microbes are only present in generalist hosts. From the nested structure of microbial taxonomies, we show that these ecological roles of microbes are generally conserved across datasets. Our results show that the taxonomic composition of healthy human gut microbiomes is associated with robustly structured combinations of generalist and specialist species.},
}

@article {pmid36741405,
year = {2022},
author = {Chen, Z and Yang, H and Fu, H and Wu, L and Liu, M and Jiang, H and Liu, Q and Wang, Y and Xiong, S and Zhou, M and Sun, X and Chen, C and Huang, L},
title = {Gut bacterial species in late trimester of pregnant sows influence the occurrence of stillborn piglet through pro-inflammation response.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1101130},
pmid = {36741405},
issn = {1664-3224},
abstract = {Maternal gut microbiota is an important regulator for the metabolism and immunity of the fetus during pregnancy. Recent studies have indicated that maternal intestinal microbiota is closely linked to the development of fetus and infant health. Some bacterial metabolites are considered to be directly involved in immunoregulation of fetus during pregnancy. However, the detailed mechanisms are largely unknown. In this study, we exploited the potential correlation between the gut microbiota of pregnant sows and the occurrence of stillborn piglets by combining the 16S rRNA gene and metagenomic sequencing data, and fecal metabolome in different cohorts. The results showed that several bacterial species from Bacteroides, potential pathogens, and LPS-producing bacteria exhibited significantly higher abundances in the gut of sows giving birth to stillborn piglets. Especially, Bacteroides fragilis stood out as the key driver in both tested cohorts and showed the most significant association with the occurrence of stillborn piglets in the DN1 cohort. However, several species producing short-chain fatty acids (SCFAs), such as Prevotella copri, Clostridium butyricum and Faecalibacterium prausnitzii were enriched in the gut of normal sows. Functional capacity analysis of gut microbiome revealed that the pathways associated with infectious diseases and immune diseases were enriched in sows giving birth to stillborn piglets. However, energy metabolism had higher abundance in normal sows. Fecal metabolome profiling analysis found that Lysophosphatidylethanolamine and phosphatidylethanolamine which are the main components of cell membrane of Gram-negative bacteria showed significantly higher concentration in stillbirth sows, while SCFAs had higher concentration in normal sows. These metabolites were significantly associated with the stillborn-associated bacterial species including Bacteroides fragilis. Lipopolysaccharide (LPS), IL-1β, IL-6, FABP2, and zonulin had higher concentration in the serum of stillbirth sows, indicating increased intestinal permeability and pro-inflammatory response. The results from this study suggested that certain sow gut bacterial species in late trimester of pregnancy, e.g., an excess abundance of Bacteroides fragilis, produced high concentration of LPS which induced sow pro-inflammatory response and might cause the death of the relatively weak piglets in a farrow. This study provided novel evidences about the effect of maternal gut microbiota on the fetus development and health.},
}

@article {pmid36741369,
year = {2022},
author = {Kayongo, A and Robertson, NM and Siddharthan, T and Ntayi, ML and Ndawula, JC and Sande, OJ and Bagaya, BS and Kirenga, B and Mayanja-Kizza, H and Joloba, ML and Forslund, SK},
title = {Airway microbiome-immune crosstalk in chronic obstructive pulmonary disease.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1085551},
pmid = {36741369},
issn = {1664-3224},
abstract = {Chronic Obstructive Pulmonary Disease (COPD) has significantly contributed to global mortality, with three million deaths reported annually. This impact is expected to increase over the next 40 years, with approximately 5 million people predicted to succumb to COPD-related deaths annually. Immune mechanisms driving disease progression have not been fully elucidated. Airway microbiota have been implicated. However, it is still unclear how changes in the airway microbiome drive persistent immune activation and consequent lung damage. Mechanisms mediating microbiome-immune crosstalk in the airways remain unclear. In this review, we examine how dysbiosis mediates airway inflammation in COPD. We give a detailed account of how airway commensal bacteria interact with the mucosal innate and adaptive immune system to regulate immune responses in healthy or diseased airways. Immune-phenotyping airway microbiota could advance COPD immunotherapeutics and identify key open questions that future research must address to further such translation.},
}

@article {pmid36740912,
year = {2023},
author = {Wang, T and Liu, L and Deng, J and Jiang, Y and Yan, X and Liu, W},
title = {Analysis of the mechanism of action of quercetin in the treatment of hyperlipidemia based on metabolomics and intestinal flora.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d2fo03509j},
pmid = {36740912},
issn = {2042-650X},
abstract = {Hyperlipidemia (HLP) is one of the main factors leading to cardiovascular diseases. Quercetin (QUE) is a naturally occurring polyhydroxy flavonoid compound that has a wide range of pharmacological effects. However, the potential mechanism for treating HLP remains unclear. Thus, the study aimed to investigate the role of QUE in HLP development and its underlying mechanisms in HLP rats based on the analysis of gut microbiota and plasma metabolomics. Following the establishment of an HLP model in rats, QUE was orally administered. Plasma samples and fecal samples were collected from HLP rats for microbiome 16S rDNA sequencing and metabolic UPLC-Q-Exactive-MS analysis. The results suggested that QUE could regulate dyslipidemia and inhibit the levels of TC, TG, and LDL-c. Additionally, histopathological findings revealed that QUE could reduce lipid deposition, ameliorate hepatic injury and steatosis in HFD-induced rats, and have a protective effect on the liver. The analysis and identification of plasma metabolomics showed that the intervention effect of QUE on HLP rats was related to 60 differential metabolites and signal pathways such as lactosamine, 11b-hydroxyprogesterone, arachidonic acid, glycerophospholipid, sphingolipid, glycerolipid, and linoleic acid metabolism. Combined with fecal microbiological analysis, it was found that QUE could significantly change the composition of intestinal flora in HLP rats, increase beneficial bacteria, and reduce the composition of harmful bacteria, attenuating the Firmicutes/Bacteroidetes ratio. The results of correlation analysis showed that the relative abundance level of Firmicutes, Deironobacterium, Fusobacterium, Bacteroides, and Escherichia coli was closely related to the change of differential metabolites. In summary, combined with metabolomics and gut microbiota studies, it is found that QUE can reduce lipid levels and improve liver function. The potential mechanism may be the regulation of metabolism and intestinal flora that play a role in reducing lipid levels, to achieve the purpose of treatment of HLP.},
}

@article {pmid36740909,
year = {2023},
author = {Brown, BRP and Goheen, JR and Newsome, SD and Pringle, RM and Palmer, TM and Leo, KM and Kartzinel, TR},
title = {Host phylogeny and functional traits differentiate gut microbiomes in a diverse natural community of small mammals.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16874},
pmid = {36740909},
issn = {1365-294X},
abstract = {Differences in the bacterial communities inhabiting mammalian gut microbiomes tend to reflect the phylogenetic relatedness of their hosts, a pattern dubbed phylosymbiosis. Although most research on this pattern has compared the gut microbiomes of host species across biomes, understanding the evolutionary and ecological processes that generate phylosymbiosis requires comparisons across phylogenetic scales and under similar ecological conditions. We analyzed the gut microbiomes of 14 sympatric small-mammal species in a semi-arid African savanna, hypothesizing that there would be a strong phylosymbiotic pattern associated with differences in their body sizes and diets. Consistent with phylosymbiosis, microbiome dissimilarity increased with phylogenetic distance among hosts, ranging from congeneric sets of mice and hares that did not differ significantly in microbiome composition to species from different taxonomic orders that had almost no gut bacteria in common. While phylosymbiosis was detected among just the 11 species of rodents, it was substantially weaker at this scale than in comparisons involving all 14 species together. In contrast, microbiome diversity and composition were generally more strongly correlated with body size, dietary breadth, and dietary overlap in comparisons restricted to rodents than in those including all lineages. The starkest divides in microbiome composition thus reflected the broad evolutionary divergence of hosts, regardless of body size or diet, while subtler microbiome differences reflected variation in ecologically important traits of closely related hosts. Strong phylosymbiotic patterns arose deep in the phylogeny, and ecological filters that promote functional differentiation of cooccurring host species may disrupt or obscure this pattern near the tips.},
}

@article {pmid36740850,
year = {2023},
author = {Larabi, AB and Masson, HLP and Bäumler, AJ},
title = {Bile acids as modulators of gut microbiota composition and function.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2172671},
doi = {10.1080/19490976.2023.2172671},
pmid = {36740850},
issn = {1949-0984},
abstract = {Changes in the composition of gut-associated microbial communities are associated with many human illnesses, but the factors driving dysbiosis remain incompletely understood. One factor governing the microbiota composition in the gut is bile. Bile acids shape the microbiota composition through their antimicrobial activity and by activating host signaling pathways that maintain gut homeostasis. Although bile acids are host-derived, their functions are integrally linked to bacterial metabolism, which shapes the composition of the intestinal bile acid pool. Conditions that change the size or composition of the bile acid pool can trigger alterations in the microbiota composition that exacerbate inflammation or favor infection with opportunistic pathogens. Therefore, manipulating the composition or size of the bile acid pool might be a promising strategy to remediate dysbiosis.},
}

@article {pmid36740846,
year = {2023},
author = {Zhu, Z and Cai, J and Hou, W and Xu, K and Wu, X and Song, Y and Bai, C and Mo, YY and Zhang, Z},
title = {Microbiome and spatially resolved metabolomics analysis reveal the anticancer role of gut Akkermansia muciniphila by crosstalk with intratumoral microbiota and reprogramming tumoral metabolism in mice.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2166700},
doi = {10.1080/19490976.2023.2166700},
pmid = {36740846},
issn = {1949-0984},
abstract = {Although gut microbiota has been linked to cancer, little is known about the crosstalk between gut- and intratumoral-microbiomes. The goal of this study was to determine whether gut Akkermansia muciniphila (Akk) is involved in the regulation of intratumoral microbiome and metabolic contexture, leading to an anticancer effect on lung cancer. We evaluated the effects of gut endogenous or gavaged exogenous Akk on the tumorigenesis using the Lewis lung cancer mouse model. Feces, blood, and tumor tissue samples were collected for 16S rDNA sequencing. We then conducted spatially resolved metabolomics profiling to discover cancer metabolites in situ directly and to characterize the overall Akk-regulated metabolic features, followed by the correlation analysis of intratumoral bacteria with metabolic network. Our results showed that both endogenous and exogenous gavaged Akk significantly inhibited tumorigenesis. Moreover, we detected increased Akk abundance in blood circulation or tumor tissue by 16S rDNA sequencing in the Akk gavaged mice, compared with the control mice. Of great interest, gavaged Akk may migrate into tumor tissue and influence the composition of intratumoral microbiome. Spatially resolved metabolomics analysis revealed that the gut-derived Akk was able to regulate tumor metabolic pathways, from metabolites to enzymes. Finally, our study identified a significant correlation between the gut Akk-regulated intratumoral bacteria and metabolic network. Together, gut-derived Akk may migrate into blood circulation, and subsequently colonize into lung cancer tissue, which contributes to the suppression of tumorigenesis by influencing tumoral symbiotic microbiome and reprogramming tumoral metabolism, although more studies are needed.},
}

@article {pmid36740845,
year = {2023},
author = {Mansour, S and Asrar, T and Elhenawy, W},
title = {The multifaceted virulence of adherent-invasive Escherichia coli.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2172669},
doi = {10.1080/19490976.2023.2172669},
pmid = {36740845},
issn = {1949-0984},
abstract = {The surge in inflammatory bowel diseases, like Crohn's disease (CD), is alarming. While the role of the gut microbiome in CD development is unresolved, the frequent isolation of adherent-invasive Escherichia coli (AIEC) strains from patient biopsies, together with their propensity to trigger gut inflammation, underpin the potential role of these bacteria as disease modifiers. In this review, we explore the spectrum of AIEC pathogenesis, including their metabolic versatility in the gut. We describe how AIEC strains hijack the host defense mechanisms to evade immune attrition and promote inflammation. Furthermore, we highlight the key traits that differentiate AIEC from commensal E. coli. Deciphering the main components of AIEC virulence is cardinal to the discovery of the next generation of antimicrobials that can selectively eradicate CD-associated bacteria.},
}

@article {pmid36740795,
year = {2023},
author = {Tu, R and Xia, J},
title = {Stroke and Vascular Cognitive Impairment: The Role of Intestinal Microbiota Metabolite TMAO.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/1871527322666230203140805},
pmid = {36740795},
issn = {1996-3181},
abstract = {The gut microbiome interacts with the brain bidirectionally through the microbiome-gut-brain axis, which plays a key role in regulating various nervous system pathophysiological processes. Trimethylamine N-oxide (TMAO) is produced by choline metabolism through intestinal microorganisms, which can cross the blood-brain barrier to act on the central nervous system. Previous studies have shown that elevated plasma TMAO concentrations increase the risk of major adverse cardiovascular events, but there are few studies on TMAO in cerebrovascular disease and vascular cognitive impairment. This review summarized a decade of research on the impact of TMAO on stroke and related cognitive impairment, with particular attention to the effects on vascular cognitive disorders. We demonstrated that TMAO has a marked impact on the occurrence, development, and prognosis of stroke by regulating cholesterol metabolism, foam cell formation, platelet hyperresponsiveness and thrombosis, and promoting inflammation and oxidative stress. TMAO can also influence the cognitive impairment caused by Alzheimer's disease and Parkinson's disease via inducing abnormal aggregation of key proteins, affecting inflammation and thrombosis. However, although clinical studies have confirmed the association between the microbiome-gut-brain axis and vascular cognitive impairment (cerebral small vessel disease and post-stroke cognitive impairment), the molecular mechanism of TMAO has not been clarified, and TMAO precursors seem to play the opposite role in the process of post-stroke cognitive impairment. In addition, several studies have also reported the possible neuroprotective effects of TMAO. Existing therapies for these diseases targeted to regulate intestinal flora and its metabolites have shown good efficacy. TMAO is probably a new target for early prediction and treatment of stroke and vascular cognitive impairment.},
}

@article {pmid36740746,
year = {2023},
author = {Ferreira Voidaleski, M and de Fátima Costa, F and de Hoog, GS and Gomes, RR and Vicente, VA},
title = {Metagenomics reveals an abundance of black yeast-like fungi in the skin microbiome.},
journal = {Mycoses},
volume = {},
number = {},
pages = {},
doi = {10.1111/myc.13574},
pmid = {36740746},
issn = {1439-0507},
abstract = {BACKGROUND: The skin is the first line of defense against communities of resident viruses, bacteria, and fungi. The composition of the microbiome might change with factors related to the environment and host. The microbiome is dominated by bacteria. Dermatophytes and yeasts are the predominant fungi that are also involved in opportunistic infections of skin, hair, and nails. Among environmental fungi, Chaetothyriales (black yeasts and relatives) are enriched by hydrocarbon pollution in domesticated habitats and comprise numerous species that cause mild-to-severe disease.

METHODS: We investigated the presence of black fungi in the skin microbiome by conducting an analysis in the publicly available metagenomic SRA database (NCBI). We focused on the causative agents of chromoblastomycosis and phaeohyphomycosis and used barcodes and padlock probe sequences as diagnostic tools.

RESULTS: A total of 132,159,577 MB was analyzed and yielded 18,360 reads that matched with 24 species of black fungi. Exophiala was the most prevalent genus, and Cyphellophora europaea was the most abundant species.

CONCLUSION: This study reveals the abundant presence of Chaetothyriales on the skin without necessarily being associated with infection. Most of the detected causal agents are known from mild skin diseases, while also species were revealed that had been reported from CARD9-deficient patients.},
}

@article {pmid36740729,
year = {2023},
author = {AminiTabrizi, R and Graf-Grachet, N and Chu, RK and Toyoda, JG and Hoyt, DW and Hamdan, R and Wilson, RM and Tfaily, MM},
title = {Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.16614},
pmid = {36740729},
issn = {1365-2486},
abstract = {Peatlands are among the largest natural sources of atmospheric methane (CH4) worldwide. Microbial processes play a key role in regulating CH4 emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH4 emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi-omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome-metabolome interactions; then explore the competition between methanogens and sulfate-reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO2 production with temperature. In contrast, the decrease in CH4 production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait-based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non-limiting sulfate concentrations at 21°C, thereby reducing CH4 emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low-molecular-weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH4 emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.},
}

@article {pmid36740577,
year = {2023},
author = {Tao, C and Wang, Z and Liu, S and Lv, N and Deng, X and Xiong, W and Shen, Z and Zhang, N and Geisen, S and Li, R and Shen, Q and Kowalchuk, GA},
title = {Additive fungal interactions drive biocontrol of Fusarium wilt disease.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18793},
pmid = {36740577},
issn = {1469-8137},
abstract = {Host-associated fungi can help protect plants from pathogens, and empirical evidence suggest that such microorganisms can be manipulated by introducing probiotic to increase disease suppression. However, we still generally lack the mechanistic knowledge of what determines the success of probiotic application, hampering the development of reliable disease suppression strategies. We conducted a 3-season consecutive microcosm experiment in which we amended banana Fusarium wilt disease-conducive soil with Trichoderma-amended biofertilizer or lacking this inoculum. High-throughput sequencing was complemented with cultivation-based methods to follow changes in fungal microbiome and explore potential links with plant health. Trichoderma application increased banana biomass by decreasing disease incidence by up to 72%, and this effect was attributed to changes in fungal microbiome, including the reduction in Fusarium oxysporum density and enrichment of pathogen-suppressing fungi (Humicola). These changes were accompanied by an expansion in microbial carbon resource utilization potential, features that contribute to disease suppression. We further demonstrated the disease suppression actions of Trichoderma-Humicola consortia, and results suggest niche overlap with pathogen and induction of plants systemic resistance may be mechanisms driving the observed biocontrol effects. Together, we demonstrate that fungal inoculants can modify the composition and functioning of the resident soil fungal microbiome to suppress soil-borne disease.},
}

@article {pmid36739987,
year = {2023},
author = {Liu, Q and Zhu, J and Wang, L and Wang, X and Huang, Z and Zhao, F and Jing, Z and Liu, Y and Ma, J},
title = {Interpreting the degradation mechanism of triclosan in microbial fuel cell by combining analysis microbiome community and degradation pathway.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {137983},
doi = {10.1016/j.chemosphere.2023.137983},
pmid = {36739987},
issn = {1879-1298},
abstract = {Microbes play a dominant role for the transformation of organic contaminants in the environment, while a significant gap exists in understanding the degradation mechanism and the function of different species. Herein, the possible bio-degradation of triclosan in microbial fuel cell was explored, with the investigation of degradation kinetics, microbial community, and possible degradation products. 5 mg/L of triclosan could be degraded within 3 days, and an intermediate degradation product (2,4-dichlorophen) could be further degraded in system. 32 kinds of dominant bacteria (relative intensity >0.5%) were identified in the biofilm, and 10 possible degradation products were identified. By analyzing the possible involved bioreactions (including decarboxylation, dehalogenation, dioxygenation, hydrolysis, hydroxylation, and ring-cleavage) of the dominant bacteria and possible degradation pathway of triclosan based on the identified products, biodegradation mechanism and function of the bacteria involved in the degradation of triclosan was clarified simultaneously. This study provides useful information for further interpreting the degradation mechanism of organic pollutants in mixed flora by combining analysis microbiome community and degradation pathway.},
}

@article {pmid36739853,
year = {2023},
author = {Yu, Y and Huang, J and Jin, L and Yu, M and Yu, X and Zhu, X and Sun, J and Zhu, L},
title = {Translocation and metabolism of tricresyl phosphate in rice and microbiome system: Isomer-specific processes and overlooked metabolites.},
journal = {Environment international},
volume = {172},
number = {},
pages = {107793},
doi = {10.1016/j.envint.2023.107793},
pmid = {36739853},
issn = {1873-6750},
abstract = {Tricresyl phosphate (TCP) is extensively used organophosphorus flame retardants and plasticizers that posed risks to organisms and human beings. In this study, the translocation and biotransformation behavior of isomers tri-p-cresyl phosphate (TpCP), tri-m-cresyl phosphate (TmCP), and tri-o-cresyl phosphate (ToCP) in rice and rhizosphere microbiome was explored by hydroponic exposure. TpCP and TmCP were found more liable to be translocated acropetally, compared with ToCP, although they have same molecular weight and similar Kow. Rhizosphere microbiome named microbial consortium GY could reduce the uptake of TpCP, TmCP, and ToCP in rice tissues, and promote rice growth. New metabolites were successfully identified in rice and microbiome, including hydrolysis, hydroxylated, methylated, demethylated, methoxylated, and glucuronide- products. The methylation, demethylation, methoxylation, and glycosylation pathways of TCP isomers were observed for the first time in organisms. What is more important is that the demethylation of TCPs could be an important and overlooked source of triphenyl phosphate (TPHP), which broke the traditional understanding of the only manmade source of toxic TPHP in the environment. Active members of the microbial consortium GY during degradation were revealed and metagenomic analysis indicated that most of active populations contained TCP-degrading genes. It is noteworthy that the strains and function genes in microbial consortium GY that responsible for TCP isomers' transformation were different. These results can improve our understanding of the translocation and transformation of organic pollutant isomers in plants and rhizosphere microbiome.},
}

@article {pmid36739820,
year = {2023},
author = {Kundu, P and Ghosh, A},
title = {Genome-scale community modeling for deciphering the inter-microbial metabolic interactions in fungus-farming termite gut microbiome.},
journal = {Computers in biology and medicine},
volume = {154},
number = {},
pages = {106600},
doi = {10.1016/j.compbiomed.2023.106600},
pmid = {36739820},
issn = {1879-0534},
abstract = {Specialized microbial communities in the fungus-farming termite gut and fungal comb microbiome help maintain host nutrition through interactive biochemical activities of complex carbohydrate degradation. Numerous research studies have been focused on identifying the microbial species in the termite gut and fungal comb microbiota, but the community-wide metabolic interaction patterns remain obscure. The inter-microbial metabolic interactions in the community environment are essential for executing biochemical processes like complex carbohydrate degradation and maintaining the host's physicochemical homeostasis. Recent progress in high-throughput sequencing techniques and mathematical modeling provides suitable platforms for constructing multispecies genome-scale community metabolic models that can render sound knowledge about microbial metabolic interaction patterns. Here, we have implemented the genome-scale metabolic modeling strategy to map the relationship between genes, proteins, and reactions of 12 key bacterial species from fungal cultivating termite gut and fungal comb microbiota. The resulting individual genome-scale metabolic models (GEMs) have been analyzed using flux balance analysis (FBA) to optimize the metabolic flux distribution pattern. Further, these individual GEMs have been integrated into genome-scale community metabolic models where a heuristics-based computational procedure has been employed to track the inter-microbial metabolic interactions. Two separate genome-scale community metabolic models were reconstructed for the O. badius gut and fungal comb microbiome. Analysis of the community models showed up to ∼167% increased flux range in lignocellulose degradation, amino acid biosynthesis, and nucleotide metabolism pathways. The inter-microbial metabolic exchange of amino acids, SCFAs, and small sugars was also upregulated in the multispecies community for maximum biomass formation. The flux variability analysis (FVA) has also been performed to calculate the feasible flux range of metabolic reactions. Furthermore, based on the calculated metabolic flux values, newly defined parameters, i.e., pairwise metabolic assistance (PMA) and community metabolic assistance (CMA) showed that the microbial species are getting up to 15% higher metabolic benefits in the multispecies community compared to pairwise growth. Assessment of the inter-microbial metabolic interaction patterns through pairwise growth support index (PGSI) indicated an increased mutualistic interaction in the termite gut environment compared to the fungal comb. Thus, this genome-scale community modeling study provides a systematic methodology to understand the inter-microbial interaction patterns with several newly defined parameters like PMA, CMA, and PGSI. The microbial metabolic assistance and interaction patterns derived from this computational approach will enhance the understanding of combinatorial microbial activities and may help develop effective synergistic microcosms to utilize complex plant polymers.},
}

@article {pmid36739424,
year = {2023},
author = {Florkowski, MR and Yorzinski, JL},
title = {Gut microbiome diversity and composition is associated with exploratory behavior in a wild-caught songbird.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {8},
pmid = {36739424},
issn = {2524-4671},
abstract = {BACKGROUND: The gut microbiome influences its host in a myriad of ways, from immune system development to nutrient utilization. However, our understanding of the relationship between the gut microbiome and behavior, especially in wild species, is still poor. One behavior that potentially interacts with the gut microbiome is exploratory behavior, which animals use to acquire new information from the environment. We hypothesized that diversity of the gut microbiome will be correlated with exploratory behavior in a wild-caught bird species. To test this hypothesis, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure the diversity of their gut microbiomes. We then introduced individuals to a novel environment and measured their exploratory behavior.

RESULTS: We found that birds with higher alpha diversity of the gut microbiome exhibited higher exploratory behavior. These results suggest that high exploratory birds encounter more types of environmental microbes that contribute to their diverse gut microbiome compared with less exploratory birds. Alternatively, increased gut microbiome diversity may contribute to increased exploratory behavior. We also found differences in beta diversity when comparing high and low exploring birds, indicating differences in microbiome community structure. When comparing predicted functional pathways of the birds' microbiomes, we found that the microbiomes of high explorers contained more pathways involved in biofilm formation and xenobiotic degradation than those of low explorers.

CONCLUSIONS: Overall, we found that the alpha and beta diversity of the gut microbiome is correlated with exploratory behavior of house sparrows. The predicted functions of the gut microbiome from high explorers differs from that of low explorers. Our study highlights the importance of considering the gut microbiome when investigating animal behavior.},
}

@article {pmid36739423,
year = {2023},
author = {Lobato-Bailón, L and García-Ulloa, M and Santos, A and Guixé, D and Camprodon, J and Florensa-Rius, X and Molleda, R and Manzano, R and P Ribas, M and Espunyes, J and Dias-Alves, A and Marco, I and Migura-Garcia, L and Martínez-Urtaza, J and Cabezón, O},
title = {The fecal bacterial microbiome of the Kuhl's pipistrelle bat (Pipistrellus kuhlii) reflects landscape anthropogenic pressure.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {7},
pmid = {36739423},
issn = {2524-4671},
abstract = {BACKGROUND: Anthropogenic disturbance has the potential to negatively affect wildlife health by altering food availability and diet composition, increasing the exposure to agrochemicals, and intensifying the contact with humans, domestic animals, and their pathogens. However, the impact of these factors on the fecal microbiome composition of wildlife hosts and its link to host health modulation remains barely explored. Here we investigated the composition of the fecal bacterial microbiome of the insectivorous bat Kuhl's pipistrelle (Pipistrellus kuhlii) dwelling in four environmental contexts with different levels of anthropogenic pressure. We analyzed their microbiome composition, structure and diversity through full-length 16S rRNA metabarcoding using the nanopore long-read sequencer MinION™. We hypothesized that the bacterial community structure of fecal samples would vary across the different scenarios, showing a decreased diversity and richness in samples from disturbed ecosystems.

RESULTS: The fecal microbiomes of 31 bats from 4 scenarios were sequenced. A total of 4,829,302 reads were obtained with a taxonomic assignment percentage of 99.9% at genus level. Most abundant genera across all scenarios were Enterococcus, Escherichia/Shigella, Bacillus and Enterobacter. Alpha diversity varied significantly between the four scenarios (p < 0.05), showing the lowest Shannon index in bats from urban and intensive agriculture landscapes, while the highest alpha diversity value was found in near pristine landscapes. Beta diversity obtained by Bray-Curtis distance showed weak statistical differentiation of bacterial taxonomic profiles among scenarios. Furthermore, core community analysis showed that 1,293 genera were shared among localities. Differential abundance analyses showed that the highest differentially abundant taxa were found in near pristine landscapes, with the exception of the family Alcaligenaceae, which was also overrepresented in urban and intensive agriculture landscapes.

CONCLUSIONS: This study suggests that near pristine and undisturbed landscapes could promote a more resilient gut microbiome in wild populations of P. kuhlii. These results highlight the potential of the fecal microbiome as a non-invasive bioindicator to assess insectivorous bats' health and as a key element of landscape conservation strategies.},
}

@article {pmid36740718,
year = {2021},
author = {Longepierre, M and Widmer, F and Keller, T and Weisskopf, P and Colombi, T and Six, J and Hartmann, M},
title = {Limited resilience of the soil microbiome to mechanical compaction within four growing seasons of agricultural management.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {44},
pmid = {36740718},
issn = {2730-6151},
abstract = {Soil compaction affects many soil functions, but we have little information on the resistance and resilience of soil microorganisms to this disturbance. Here, we present data on the response of soil microbial diversity to a single compaction event and its temporal evolution under different agricultural management systems during four growing seasons. Crop yield was reduced (up to -90%) in the first two seasons after compaction, but mostly recovered in subsequent seasons. Soil compaction increased soil bulk density (+15%), and decreased air permeability (-94%) and gas diffusion (-59%), and those properties did not fully recover within four growing seasons. Soil compaction induced cropping system-dependent shifts in microbial community structures with little resilience over the four growing seasons. Microbial taxa sensitive to soil compaction were detected in all major phyla. Overall, anaerobic prokaryotes and saprotrophic fungi increased in compacted soils, whereas aerobic prokaryotes and plant-associated fungi were mostly negatively affected. Most measured properties showed large spatial variability across the replicated blocks, demonstrating the dependence of compaction effects on initial conditions. This study demonstrates that soil compaction is a disturbance that can have long-lasting effects on soil properties and soil microorganisms, but those effects are not necessarily aligned with changes in crop yield.},
}

@article {pmid36739319,
year = {2023},
author = {Melnyk, K and Weimann, K and Conrad, TOF},
title = {Understanding microbiome dynamics via interpretable graph representation learning.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {2058},
pmid = {36739319},
issn = {2045-2322},
abstract = {Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of healthy and ill individuals can be complicated due to the large number of complex interactions among microbes. We propose to model these interactions as a time-evolving graph where nodes represent microbes and edges are interactions among them. Motivated by the need to analyse such complex interactions, we develop a method that can learn a low-dimensional representation of the time-evolving graph while maintaining the dynamics occurring in the high-dimensional space. Through our experiments, we show that we can extract graph features such as clusters of nodes or edges that have the highest impact on the model to learn the low-dimensional representation. This information is crucial for identifying microbes and interactions among them that are strongly correlated with clinical diseases. We conduct our experiments on both synthetic and real-world microbiome datasets.},
}

@article {pmid36739238,
year = {2023},
author = {Carbia, C and Bastiaanssen, TFS and Iannone, LF and García-Cabrerizo, R and Boscaini, S and Berding, K and Strain, CR and Clarke, G and Stanton, C and Dinan, TG and Cryan, JF},
title = {The Microbiome-Gut-Brain axis regulates social cognition & craving in young binge drinkers.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {104442},
doi = {10.1016/j.ebiom.2023.104442},
pmid = {36739238},
issn = {2352-3964},
abstract = {BACKGROUND: Binge drinking is the consumption of an excessive amount of alcohol in a short period of time. This pattern of consumption is highly prevalent during the crucial developmental period of adolescence. Recently, the severity of alcohol use disorders (AUDs) has been linked with microbiome alterations suggesting a role for the gut microbiome in its development. Furthermore, a strong link has emerged too between microbiome composition and socio-emotional functioning across different disorders including AUD. The aim of this study was to investigate the potential link (and its predictive value) between alcohol-related altered microbial profile, social cognition, impulsivity and craving.

METHODS: Young people (N = 71) aged 18-25 reported their alcohol use and underwent a neuropsychological evaluation. Craving was measured at baseline and three months later. Diet was controlled for. Blood, saliva and hair samples were taken for inflammatory, kynurenine and cortisol analysis. Stool samples were provided for shotgun metagenomic sequencing and short-chain fatty acids (SCFAs) were measured.

FINDINGS: Binge drinking was associated with distinct microbiome alterations and emotional recognition difficulties. Associations were found for several microbiome species with emotional processing and impulsivity. Craving showed a strong link with alterations in microbiome composition and neuroactive potential over time.

INTERPRETATION: In conclusion, this research demonstrates alterations in the gut microbiome of young binge drinkers (BDs) and identifies early biomarkers of craving. Associations between emotional processing and microbiome composition further support the growing literature on the gut microbiome as a regulator of social cognition. These findings are of relevance for new gut-derived interventions directed at improving early alcohol-related alterations during the vulnerability period of adolescence.

FUNDING: C.C. and R.G-C. received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754535. APC Microbiome Ireland is a research centre funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan [grant no. SFI/12/RC/2273_P2]. J.F.C has research support from Cremo, Pharmavite, DuPont and Nutricia. He has spoken at meetings sponsored by food and pharmaceutical companies. G.C. has received honoraria from Janssen, Probi, and Apsen as an invited speaker; is in receipt of research funding from Pharmavite, Fonterra, Nestle and Reckitt; and is a paid consultant for Yakult, Zentiva and Heel pharmaceuticals. All the authors declare no competing interests.},
}

@article {pmid36739023,
year = {2023},
author = {Obregon, D and Mafa-Attoye, T and Baskerville, M and Mitter, E and de Souza, LF and Oelbermann, M and Thevathasan, N and Tsai, SM and Dunfield, K},
title = {Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {161921},
doi = {10.1016/j.scitotenv.2023.161921},
pmid = {36739023},
issn = {1879-1026},
abstract = {Riparian buffer systems (RBS) are a common agroforestry practice that involves maintaining a forested boundary adjacent to water bodies to protect the aquatic ecosystems in agricultural landscapes. While RBS have potential for carbon sequestration, they have also can be sources of methane emissions. Our study site at Washington Creek in Southern Ontario, includes a rehabilitated tree buffer (RH), a grassed buffer (GRB), an undisturbed deciduous forest (UNF), an undisturbed coniferous forest (CF), and an adjacent agricultural field (AGR). The objective of this study was to assess the diversity and activity of CH4 cycling microbial communities in soils sampled on two hot moments of methane fluxes (July 04 and August 15). We used qPCR and high-throughput amplicon sequencing from both DNA and cDNA to target methanogen and methanotroph communities. Methanogens, including the archaeal genera Methanosaeta, Methanosarcina, Methanomassiliicoccus, and Methanoreggula, were abundant in all RBSs, but they were significantly more active in UNF soils, where CH4 emissions were highest. Methylocystis was the most prevalent taxon among methanotrophs in all the riparian sites, except for AGR soils where the methanotrophs community was composed primarily of members of rice paddy clusters (RPCs and RPC-1) and upland soil clusters (TUSC and USCα). The main factors influencing the composition and assembly of methane-cycling microbiomes were soil carbon and moisture content. We concluded that the differences in CH4 fluxes observed between RBSs were primarily caused by differences in the presence and activity of methanogens, which were influenced by total soil carbon and water content. Overall, this study emphasizes the importance of understanding the microbial drivers of CH4 fluxes in RBSs in order to maximise RBS environmental benefit.},
}

@article {pmid36738977,
year = {2023},
author = {Toh, MR and Wong Yi Ting, E and Wong Hei, S and Ng Wei Tian, A and Lit-Hsin, L and Kah Hoe Chow, P and Ngeow Yuen Yie, J},
title = {Global epidemiology and genetics of hepatocellular carcinoma.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2023.01.033},
pmid = {36738977},
issn = {1528-0012},
abstract = {Hepatocellular carcinoma (HCC) is one of the leading cancers worldwide. Classically, HCC develops in genetically susceptible individuals who are exposed to risk factors especially in the presence of liver cirrhosis. Significant temporal and geographical variations exist for HCC and its etiologies. Over time, the burden of HCC has shifted from the low-moderate to the high sociodemographic index regions, reflecting the transition from viral to non-viral causes. Geographically, the hepatitis viruses predominate as HCC causes in Asia and Africa. While there are genetic conditions that confer increased risk for HCC, these diagnoses are rarely recognized outside North America and Europe. In this review, we will evaluate the epidemiological trends and risk factors of HCC, and discuss the genetics of HCC including monogenic diseases, single-nucleotide polymorphisms, gut microbiome, and somatic mutations.},
}

@article {pmid36738892,
year = {2023},
author = {Smiline Girija, AS},
title = {Moonlighting proteins [ML proteins]: The pandora's box of insidious oro-dental diseases.},
journal = {Biochimica et biophysica acta. Molecular cell research},
volume = {},
number = {},
pages = {119435},
doi = {10.1016/j.bbamcr.2023.119435},
pmid = {36738892},
issn = {1879-2596},
abstract = {Oral pathogens survive in the harsh niche of the oral microbiome on account of a plethora of moonlighting [ML] proteins that can multitask in the oro-mucosal layers. ML proteins are considered as the complex protein hyperspace expressed in many oral bacterial pathogens and encompass many hypothetical and experimentally evidenced proteins that can efficiently assist in the initiation and progression of various oro-dental infections. With the propensity of multi-drug resistance and biofilm formation, unravelling the mysterious functions associated with the oral ML proteins could be essential in targeting the vital oral bacteria and their associated infections. This commentary thus throws insights onto the key clues on various ML proteins that can be considered for the development of therapeutic versatility to curtail the complications caused by various oral bacterial species.},
}

@article {pmid36738776,
year = {2023},
author = {Weiner, A and Turjeman, S and Koren, O},
title = {Gut microbes and host behavior: The forgotten members of the gut-microbiome.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {109453},
doi = {10.1016/j.neuropharm.2023.109453},
pmid = {36738776},
issn = {1873-7064},
abstract = {The gut microbiota refers to an entire population of microorganisms that colonize the gut. This community includes viruses, prokaryotes (bacteria and archaea), and eukaryotes (fungi and parasites). Multiple studies in the last decades described the significant involvement of gut bacteria in gut-brain axis communication; however, the involvement of other members of the gut microbiota has been neglected. Recent studies found that these 'forgotten' members of the gut microbiota may also have a role in gut-brain communication, although it is still unclear whether they have a direct effect on the brain or if their effects are mediated by gut bacteria. Here, we provide concrete suggestions for future research to tease out mechanisms of the microbiota-gut-brain axis.},
}

@article {pmid36738733,
year = {2023},
author = {Naama, M and Telpaz, S and Awad, A and Ben-Simon, S and Harshuk-Shabso, S and Modilevsky, S and Rubin, E and Sawaed, J and Zelik, L and Zigdon, M and Asulin, N and Turjeman, S and Werbner, M and Wongkuna, S and Feeney, R and Schroeder, BO and Nyska, A and Nuriel-Ohayon, M and Bel, S},
title = {Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2023.01.006},
pmid = {36738733},
issn = {1934-6069},
abstract = {Colonic goblet cells are specialized epithelial cells that secrete mucus to physically separate the host and its microbiota, thus preventing bacterial invasion and inflammation. How goblet cells control the amount of mucus they secrete is unclear. We found that constitutive activation of autophagy in mice via Beclin 1 enables the production of a thicker and less penetrable mucus layer by reducing endoplasmic reticulum (ER) stress. Accordingly, genetically inhibiting Beclin 1-induced autophagy impairs mucus secretion, while pharmacologically alleviating ER stress results in excessive mucus production. This ER-stress-mediated regulation of mucus secretion is microbiota dependent and requires the Crohn's-disease-risk gene Nod2. Overproduction of mucus alters the gut microbiome, specifically expanding mucus-utilizing bacteria, such as Akkermansia muciniphila, and protects against chemical and microbial-driven intestinal inflammation. Thus, ER stress is a cell-intrinsic switch that limits mucus secretion, whereas autophagy maintains intestinal homeostasis by relieving ER stress.},
}

@article {pmid36738429,
year = {2023},
author = {Komarnytsky, S and Wagner, C and Gutierrez, J and Shaw, OM},
title = {Berries in Microbiome-Mediated Gastrointestinal, Metabolic, and Immune Health.},
journal = {Current nutrition reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13668-023-00449-0},
pmid = {36738429},
issn = {2161-3311},
abstract = {PURPOSE OF REVIEW: Current research has shown that berry-derived polymeric substrates that resist human digestion (dietary fibers and polyphenols) are extensively metabolized in the gastrointestinal tract dominated by microbiota. This review assesses current epidemiological, experimental, and clinical evidence of how berry (strawberry, blueberry, raspberry, blackberry, cranberry, black currant, and grapes) phytochemicals interact with the microbiome and shape health or metabolic risk factor outcomes.

RECENT FINDINGS: There is a growing evidence that the compositional differences among complex carbohydrate fractions and classes of polyphenols define reversible shifts in microbial populations and human metabolome to promote gastrointestinal health. Interventions to prevent gastrointestinal inflammation and improve metabolic outcomes may be achieved with selection of berries that provide distinct polysaccharide substrates for selective multiplication of beneficial microbiota or oligomeric decoys for binding and elimination of the pathogens, as well as phenolic substrates that hold potential to modulate gastrointestinal mucins, reduce luminal oxygen, and release small phenolic metabolites signatures capable of ameliorating inflammatory and metabolic perturbations. These mechanisms may explain many of the differences in microbiota and host gastrointestinal responses associated with increased consumption of berries, and highlight potential opportunities to intentionally shift gut microbiome profiles or to modulate risk factors associated with better nutrition and health outcomes.},
}

@article {pmid36738293,
year = {2023},
author = {Lin, T and Lu, Q and Zheng, Z and Li, S and Li, S and Liu, Y and Zhu, T and Chen, L and Yang, C and Han, S},
title = {Soil cadmium stress affects phyllosphere microbiome and associated pathogen resistance differently in male and female poplars.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erad034},
pmid = {36738293},
issn = {1460-2431},
abstract = {Phyllosphere associated microorganisms play a crucial role in protecting plants from diseases, while their composition and diversity are strongly influenced by heavy metal contaminants. As dioecious plants exhibited sexual dimorphism in metal accumulation and tolerance between male and female individuals, in this study we used male and female full-sibs of Populus deltoides to investigate whether the two plant sexes will present sexual differences in the phyllosphere microbiome structure and associated pathogen resistance against a leaf pathogenic fungus after soil cadmium (Cd) exposure. We found that Cd-treated male plants grew better and accumulated more leaf Cd than females. Cd stress reduced leaf lesion area of both plant sexes after leaf pathogen infection, whereas male plants exhibited better resistance than females. More importantly, Cd exposure differentially altered the structure and function of phyllosphere microbiomes between male and female plants, with more abundant ecologically beneficial microbes but decreased pathogenic fungal taxa harbored in male plants. Further in vitro toxicity tests suggested that such sexual difference in pathogen resistance between the two plant sexes could attribute to direct Cd toxicity and indirect shifts in the phyllosphere microbiome. This study provides implication for understanding the underlying mechanism of heavy metals involved in plant-pathogen interactions.},
}

@article {pmid36737922,
year = {2023},
author = {Bhatt, S and Gupta, M},
title = {Dietary fiber from fruit waste as a potential source of metabolites in maintenance of gut milieu during ulcerative colitis: A comprehensive review.},
journal = {Food research international (Ottawa, Ont.)},
volume = {164},
number = {},
pages = {112329},
doi = {10.1016/j.foodres.2022.112329},
pmid = {36737922},
issn = {1873-7145},
abstract = {The prevalence of inflammatory bowel disease, particularly ulcerative colitis (UC), has increased dramatically in the past few years owing to a changed lifestyle. Despite various therapeutic treatments, management of the disease is still an issue due to several limitations, including cost and adverse reactions. In this regard, researchers and consumers are inclined towards natural herbal medicines and prophylactic agents. Of these, dietary fiber (DF) (polysaccharides) has become an important topic of interest owing to various putative health attributes, particularly for diseases associated with the large intestine, such as UC. To fulfil industrial and scientific demands of dietary fibers, waste utilization can prove advantageous. Here, the present review highlights recent comprehensive advances in dietary fiber from waste resources in improving UC. Additionally, their role in the gut-associated microbiome, pathway for metabolites synthesis, inflammation, and its mediators. Moreover, here we also discussed short-chain fatty acids (SCFAs) transport and epithelial barrier function along with the mechanism of inflammation regulation. Collectively, it depicts dietary fiber from waste resources that could regulate various cellular processes and molecular mechanisms involved in perpetuating UC and can be used as a promising therapeutic candidate.},
}

@article {pmid36737846,
year = {2023},
author = {Tang, D and Tang, Q and Wei, H and Zhang, Y and Tian, Y and Fu, X},
title = {Fasting: From Physiology to Pathology.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2204487},
doi = {10.1002/advs.202204487},
pmid = {36737846},
issn = {2198-3844},
abstract = {Overnutrition is a risk factor for various human diseases, including neurodegenerative diseases, metabolic disorders, and cancers. Therefore, targeting overnutrition represents a simple but attractive strategy for the treatment of these increasing public health threats. Fasting as a dietary intervention for combating overnutrition has been extensively studied. Fasting has been practiced for millennia, but only recently have its roles in the molecular clock, gut microbiome, and tissue homeostasis and function emerged. Fasting can slow aging in most species and protect against various human diseases, including neurodegenerative diseases, metabolic disorders, and cancers. These centuried and unfading adventures and explorations suggest that fasting has the potential to delay aging and help prevent and treat diseases while minimizing side effects caused by chronic dietary interventions. In this review, recent animal and human studies concerning the role and underlying mechanism of fasting in physiology and pathology are summarized, the therapeutic potential of fasting is highlighted, and the combination of pharmacological intervention and fasting is discussed as a new treatment regimen for human diseases.},
}

@article {pmid36737776,
year = {2023},
author = {Ma, J and Wang, R and Chen, Y and Wang, Z and Dong, Y},
title = {5-HT attenuates chronic stress-induced cognitive impairment in mice through intestinal flora disruption.},
journal = {Journal of neuroinflammation},
volume = {20},
number = {1},
pages = {23},
pmid = {36737776},
issn = {1742-2094},
abstract = {BACKGROUND: The microbiota-gut-brain axis plays an important role in the development of depression. The aim of this study was to investigate the effects of 5-HT on cognitive function, learning and memory induced by chronic unforeseeable mild stress stimulation (CUMS) in female mice. CUMS mice and TPH2 KO mice were used in the study. Lactococcus lactis E001-B-8 fungus powder was orally administered to mice with CUMS.

METHODS: We used the open field test, Morris water maze, tail suspension test and sucrose preference test to examine learning-related behaviours. In addition, AB-PAS staining, immunofluorescence, ELISA, qPCR, Western blotting and microbial sequencing were employed to address our hypotheses.

RESULTS: The effect of CUMS was more obvious in female mice than in male mice. Compared with female CUMS mice, extracellular serotonin levels in TPH2 KO CUMS mice were significantly reduced, and cognitive dysfunction was aggravated. Increased hippocampal autophagy levels, decreased neurotransmitter levels, reduced oxidative stress damage, increased neuroinflammatory responses and disrupted gut flora were observed. Moreover, L. lactis E001-B-8 significantly improved the cognitive behaviour of mice.

CONCLUSIONS: These results strongly suggest that L. lactis E001-B-8 but not FLX can alleviate rodent depressive and anxiety-like behaviours in response to CUMS, which is associated with the improvement of 5-HT metabolism and modulation of the gut microbiome composition.},
}

@article {pmid36737703,
year = {2023},
author = {Zhao, G and Qi, M and Wang, Q and Hu, C and Li, X and Chen, Y and Yang, J and Yu, H and Chen, H and Guo, A},
title = {Gut microbiome variations in Rhinopithecus roxellanae caused by changes in the environment.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {62},
doi = {10.1186/s12864-023-09142-6},
pmid = {36737703},
issn = {1471-2164},
abstract = {BACKGROUND: The snub-nosed monkey (Rhinopithecus roxellanae) is an endangered animal species mainly distributed in China and needs to be protected. Gut microbiome is an important determinant of animal health and population survival as it affects the adaptation of the animals to different foods and environments under kinetic changes of intrinsic and extrinsic factors. Therefore, this study aimed to elucidate gut fecal microbiome profiles of snub-nosed monkeys affected by several extrinsic and intrinsic factors, including raising patterns (captive vs. wild), age, sex, and diarrheal status to provide a reference for making protection strategies.

RESULTS: The 16S rRNA gene sequencing was firstly used to pre-check clustering of 38 fecal samples from the monkeys including 30 wild and 8 captive (5 healthy and 3 diarrheal) from three Regions of Shennongjia Nature Reserve, Hubei Province, China. Then the 24 samples with high-quality DNA from 18 wild and 6 captive (4 healthy and 2 diarrheal) monkeys were subjected to shotgun metagenomic sequencing to characterize bacterial gut microbial communities. We discovered that the raising pattern (captive and wild) rather than age and sex was the predominant factor attributed to gut microbiome structure and proportionality. Wild monkeys had significantly higher bacterial diversity and lower Bacteroidetes/Firmicutes ratios than captive animals. Moreover, the gut microbiomes in wild healthy monkeys were enriched for the genes involved in fatty acid production, while in captive animals, genes were enriched for vitamin biosynthesis and metabolism and amino acid biosynthesis from carbohydrate intermediates. Additionally, a total of 37 antibiotic resistant genes (ARG) types were detected. Unlike the microbiome diversity, the captive monkeys have a higher diversity of ARG than the wild animals.

CONCLUSION: Taken together, we highlight the importance of self-reprogramed metabolism in the snub-nosed monkey gut microbiome to help captive and wild monkeys adapt to different intrinsic and extrinsic environmental change.},
}

@article {pmid36737654,
year = {2023},
author = {Haberman, Y and Kamer, I and Amir, A and Goldenberg, S and Efroni, G and Daniel-Meshulam, I and Lobachov, A and Daher, S and Hadar, R and Gantz-Sorotsky, H and Urban, D and Braun, T and Bar, J},
title = {Gut microbial signature in lung cancer patients highlights specific taxa as predictors for durable clinical benefit.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {2007},
pmid = {36737654},
issn = {2045-2322},
abstract = {We aimed to determine microbial signature linked with lung cancer (LC) diagnosis and to define taxa linked with durable clinical benefit (DCB) of advanced LC patients. Stool samples for microbial 16S amplicon sequencing and clinical data were collected from 75 LC patients (50 of which were treated with checkpoint inhibitors) and 31 matched healthy volunteers. We compared LC to healthy controls and patients with DCB to those without. LC patients had lower α-diversity and higher between-subject diversity. Random Forests model to differentiate LC cases from controls ROC-AUC was 0.74. Clostridiales, Lachnospiraceae, and Faecalibacterium prausnitzii taxa abundance was decreased in LC compared to controls. High Akkermansia muciniphila correlated with DCB (HR 4.26, 95% CI 1.98-9.16), not only for the immunotherapy-treated patients. In addition, high Alistipes onderdonkii (HR 3.08, 95% CI 1.34-7.06) and high Ruminococcus (HR 7.76, 95% CI 3.23-18.65) correlated with DCB.Our results support the importance of gut microbiome in LC. We have validated the apparent predictive value of Akkermansia muciniphila, and highlighted Alistipes onderdonkii and Ruminococcus taxa correlation with DCB. Upon additional validations those can be used as biomarkers or as targets for future therapeutic interventions.},
}

@article {pmid36737615,
year = {2023},
author = {Zhang, T and Zhang, W and Feng, C and Kwok, LY and He, Q and Sun, Z},
title = {Author Correction: Stronger gut microbiome modulatory effects by postbiotics than probiotics in a mouse colitis model.},
journal = {NPJ science of food},
volume = {7},
number = {1},
pages = {4},
doi = {10.1038/s41538-023-00179-1},
pmid = {36737615},
issn = {2396-8370},
}

@article {pmid36737600,
year = {2023},
author = {Bagnall-Moreau, C and Spielman, B and Brimberg, L},
title = {Maternal brain reactive antibodies profile in autism spectrum disorder: an update.},
journal = {Translational psychiatry},
volume = {13},
number = {1},
pages = {37},
pmid = {36737600},
issn = {2158-3188},
abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with multifactorial etiologies involving both genetic and environmental factors. In the past two decades it has become clear that in utero exposure to toxins, inflammation, microbiome, and antibodies (Abs), may play a role in the etiology of ASD. Maternal brain-reactive Abs, present in 10-20% of mothers of a child with ASD, pose a potential risk to the developing brain because they can gain access to the brain during gestation, altering brain development during a critical period. Different maternal anti-brain Abs have been associated with ASD and have been suggested to bind extracellular or intracellular neuronal antigens. Clinical data from various cohorts support the increase in prevalence of such maternal brain-reactive Abs in mothers of a child with ASD compared to mothers of a typically developing child. Animal models of both non-human primates and rodents have provided compelling evidence supporting a pathogenic role of these Abs. In this review we summarize the data from clinical and animal models addressing the role of pathogenic maternal Abs in ASD. We propose that maternal brain-reactive Abs are an overlooked and promising field of research, representing a modifiable risk factor that may account for up to 20% of cases of ASD. More studies are needed to better characterize the Abs that contribute to the risk of having a child with ASD, to understand whether we can we predict such cases of ASD, and to better pinpoint the antigenic specificity of these Abs and their mechanisms of pathogenicity.},
}

@article {pmid36737487,
year = {2023},
author = {Poto, R and Laniro, G and de Paulis, A and Spadaro, G and Marone, G and Gasbarrini, A and Varricchi, G},
title = {Is there a role for microbiome-based approach in common variable immunodeficiency?.},
journal = {Clinical and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10238-023-01006-3},
pmid = {36737487},
issn = {1591-9528},
abstract = {Common variable immunodeficiency (CVID) is a primary immunodeficiency characterized by low levels of serum immunoglobulins and increased susceptibility to infections, autoimmune disorders and cancer. CVID embraces a plethora of heterogeneous manifestations linked to complex immune dysregulation. While CVID is thought to be due to genetic defects, the exact cause of this immune disorder is unknown in the large majority of cases. Compelling evidences support a linkage between the gut microbiome and the CVID pathogenesis, therefore a potential for microbiome-based treatments to be a therapeutic pathway for this disorder. Here we discuss the potential of treating CVID patients by developing a gut microbiome-based personalized approach, including diet, prebiotics, probiotics, postbiotics and fecal microbiota transplantation. We also highlight the need for a better understanding of microbiota-host interactions in CVID patients to prime the development of improved preventive strategies and specific therapeutic targets.},
}

@article {pmid36737018,
year = {2023},
author = {Sun, S and Ma, B and Wang, G and Tan, X},
title = {Linking microbial biogeochemical cycling genes to the rhizosphere of pioneering plants in a glacier foreland.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {161944},
doi = {10.1016/j.scitotenv.2023.161944},
pmid = {36737018},
issn = {1879-1026},
abstract = {Glacier retreat raises global concerns but brings about the moment to study soil and ecosystem development. In nutrient-limited glacier forelands, the adaptability of pioneering plant and microbial species is facilitated by their interactions, including rhizosphere effects, but the details of this adaptability are not yet understood. In the rhizosphere of five pioneering plants, we comprehensively deciphered the microbial taxonomic and functional compositions. Two nitrogen-fixing microbial genera, Bradyrhizobium and Mesorhizobium, were among the most abundant taxa in the rhizomicrobiome. Moreover, several rhizobial genera, including Rhizobium, Pararhizobium, Allohrizobium, and Sinorhizobium, head the list of major modules in microbial co-occurrence networks, highlighting the vital roles of nitrogen-cycling taxa in the rhizomicrobiome of pioneering plants. Microbial genes involved in nitrogen, sulfur, phosphorus, and methane cycles were simultaneously correlated with microbial community dissimilarity, and 12 functional pathways were detected with distinct relative abundances among soils. Zooming in on the nitrogen-cycling genes, nifW, narC, nasA, nasB, and nirA were mainly responsible for the significant differences between soils. Furthermore, soil pH and the carbon/nitrogen ratio were among the topsoil properties interacting with nitrogen and sulfur cycling gene dissimilarity. These results explicitly linked biogeochemical cycling genes to the rhizomicrobiome and soil properties, revealing the roles of these genes as microbial drivers in mediating rhizosphere soil-plant-microbiome interactions.},
}

@article {pmid36736919,
year = {2023},
author = {Krishaa, L and Ng, TKS and Wee, HN and Ching, J},
title = {Gut-brain axis through the lens of gut microbiota and their relationships with Alzheimer's disease pathology: review and recommendations.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {111787},
doi = {10.1016/j.mad.2023.111787},
pmid = {36736919},
issn = {1872-6216},
abstract = {Alzheimer's disease (AD) is a neurodegenerative disorder that affects millions of people worldwide. Growing evidence suggests that the gut microbiome (GM) plays a pivotal role in the pathogenesis of AD through the microbiota-gut-brain axis (MGB). Alterations in GM composition and diversity have been observed in both animal models and in human patients with AD. GM dysbiosis has been implicated in increased intestinal permeability, blood-brain barrier (BBB) impairment, neuroinflammation and the development of hallmarks of AD. Further elucidation of the role of GM in AD could pave way for the development of holistic predictive methods for determining AD risk and progression of disease. Furthermore, accumulating evidence suggests that GM modulation could alleviate adverse symptoms of AD or serve as a preventive measure. In addition, increasing evidence shows that Type 2 Diabetes Mellitus (T2DM) is often comorbid with AD, with common GM alterations and inflammatory response, which could chart the development of GM-related treatment interventions for both diseases. We conclude by exploring the therapeutic potential of GM in alleviating symptoms of AD and in reducing risk. Furthermore, we also propose future directions in AD research, namely fecal microbiota transplantation (FMT) and precision medicine.},
}

@article {pmid36736796,
year = {2023},
author = {Liang, Y and Xie, R and Xiong, X and Hu, Z and Mao, X and Wang, X and Zhang, J and Sun, P and Yue, Z and Wang, W and Zhang, G},
title = {Alterations of nasal microbiome in eosinophilic chronic rhinosinusitis.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2022.11.031},
pmid = {36736796},
issn = {1097-6825},
abstract = {BACKGROUND: Exposure to microbes may be important in the development of chronic rhinosinusitis. Dysbiosis of the nasal microbiome is considered to be related to chronic rhinosinusitis with nasal polyps (CRSwNP). The link between the nasal microbiota and eosinophilic CRSwNP (eCRSwNP) has rarely been studied.

OBJECTIVE: The aim of this study was to rigorously characterize nasal dysbiosis in a cohort of eCRSwNP patients and to compare the nasal microbiomes of these patients with those of healthy controls.

METHODS: We performed a cross-sectional study of 34 eCRSwNP patients, 10 noneCRSwNP patients and 44 healthy controls using 16S rRNA gene sequencing. An independent cohort of 14 eCRSwNP patients, 9 noneCRSwNP patients and 11 healthy controls was used to validate the results.

RESULTS: The nasal microbiome of eCRSwNP patients was characterized by higher alpha diversity (Shannon and Chao1 index) than that of healthy controls and a distinct composition of microbes. Notably, the distinct differences in microbial composition between eCRSwNP patients and healthy controls were significantly correlated with eCRSwNP disease status. Furthermore, in a diagnostic model generated using these differences, a combination of 15 genera could be used to distinguish eCRSwNP patients from controls, with an area under the curve of approximately 0.8 in both the exploration and validation cohorts.

CONCLUSION: Our study establishes the compositional alterations in the nasal microbiome in eCRSwNP and suggests the potential for using the nasal microbiota as a noninvasive predictive classifier for the diagnosis of eCRSwNP.},
}

@article {pmid36736649,
year = {2023},
author = {Tunç, U and Ar, CÇ and Ekren, BY and Yıldırım, Y and Yıldız, BK and Okullu, SÖ and Sezerman, OU},
title = {Corneal bacterial microbiome in patients with keratoconus using next-generation sequencing-based 16S rRNA gene analysis.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {109402},
doi = {10.1016/j.exer.2023.109402},
pmid = {36736649},
issn = {1096-0007},
abstract = {PURPOSE: To investigate the corneal bacterial microbiome in patients with keratoconus using next-generation sequencing and develop a new perspective on the pathogenesis of the disease.

METHODS: This prospective observational study included 10 patients with keratoconus who underwent corneal crosslinking procedure and 10 healthy controls who underwent photorefractive keratectomy. Patients included in the study were aged 18 years or older. The demographic and clinical characteristics of participants were recorded. Corneal epithelial samples were collected between March 2021 and June 2021. Isolated bacterial DNA from corneal epithelial samples was analyzed using 16 S ribosomal RNA gene analysis. The relative abundance rates at the phylum and genus levels were calculated. Alpha diversity parameters were assessed.

RESULTS: Eleven phyla and 521 genera of bacteria were identified in all participants. At the phylum level, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were most abundant in both groups. There were no statistical differences between the two groups except Bacteriodetes (p < 0.05). At the genus level, the relative abundance rates of twenty bacteria were significantly different between keratoconus and healthy corneas (p < 0.05). Aquabacterium was the most abundant genus in patients with keratoconus, while Shigella was the most abundant genus in healthy controls. Alpha diversity parameters were lower in patients with keratoconus, although the difference did not reach statistical significance (p > 0.05).

CONCLUSIONS: Our preliminary study revealed that there are similarities and differences in the corneal microbiome between keratoconus and healthy individuals. Further research is required on the relationship between the abnormal corneal microbiome composition and the pathogenesis of keratoconus.},
}

@article {pmid36736410,
year = {2023},
author = {Wang, J and Lou, Y and Ma, D and Feng, K and Chen, C and Zhao, L and Xing, D},
title = {Co-treatment with free nitrous acid and calcium peroxide regulates microbiome and metabolic functions of acidogenesis and methanogenesis in sludge anaerobic digestion.},
journal = {The Science of the total environment},
volume = {870},
number = {},
pages = {161924},
doi = {10.1016/j.scitotenv.2023.161924},
pmid = {36736410},
issn = {1879-1026},
abstract = {Wasted activated sludge (WAS) is a promising feedstock for carbon management because of its abundance and carbon-neutral features. Currently, the goal is to maximize the energy in WAS and avoid secondary toxic effects or accumulation of harmful substances in the environment. Chemical pretreatment is an effective strategy for enhancing WAS disintegration and production of short chain fatty acids (SCFAs). However, the role of pretreatment in shaping the core microbiome and functional metabolism of anaerobic microorganisms remains obscure. Here, the mechanisms of SCFA synthesis and microbiome response to free nitrous acid (FNA) and calcium peroxide (CaO2) co-treatment during sludge anaerobic digestion (AD) were investigated. The combination of FNA and CaO2 enriched acidogenic Macellibacteroides, Petrimonas, and Sedimentibacter to a relative abundance of 15.0%, 10.3%, and 7.3%, respectively, resulting in an apparent increase in SCFA production. Metagenome analysis indicated that FNA + CaO2 co-treatment facilitated glycolysis, phosphate acetyltransferase-acetate kinase pathway, amino acid metabolism, and acetate transport, but inhibited CO2 reduction and common pathway of methanogenesis compared with the untreated control. This work provides theoretical insights into the functional activity and interaction of microorganisms with ecological factors.},
}

@article {pmid36736321,
year = {2023},
author = {Seike, K and Kiledal, A and Fujiwara, H and Henig, I and Burgos da Silva, M and van den Brink, MRM and Hein, R and Hoostal, M and Liu, C and Oravecz-Wilson, K and Lauder, E and Li, L and Sun, Y and Schmidt, TM and Shah, YM and Jenq, RR and Dick, G and Reddy, P},
title = {Ambient oxygen levels regulate intestinal dysbiosis and GVHD severity after allogeneic stem cell transplantation.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2023.01.007},
pmid = {36736321},
issn = {1097-4180},
abstract = {The severity of T cell-mediated gastrointestinal (GI) diseases such as graft-versus-host disease (GVHD) and inflammatory bowel diseases correlates with a decrease in the diversity of the host gut microbiome composition characterized by loss of obligate anaerobic commensals. The mechanisms underpinning these changes in the microbial structure remain unknown. Here, we show in multiple specific pathogen-free (SPF), gnotobiotic, and germ-free murine models of GI GVHD that the initiation of the intestinal damage by the pathogenic T cells altered ambient oxygen levels in the GI tract and caused dysbiosis. The change in oxygen levels contributed to the severity of intestinal pathology in a host intestinal HIF-1α- and a microbiome-dependent manner. Regulation of intestinal ambient oxygen levels with oral iron chelation mitigated dysbiosis and reduced the severity of the GI GVHD. Thus, targeting ambient intestinal oxygen levels may represent a novel, non-immunosuppressive strategy to mitigate T cell-driven intestinal diseases.},
}

@article {pmid36736319,
year = {2023},
author = {Gutierrez, MW and Mercer, EM and Moossavi, S and Laforest-Lapointe, I and Reyna, ME and Becker, AB and Simons, E and Mandhane, PJ and Turvey, SE and Moraes, TJ and Sears, MR and Subbarao, P and Azad, MB and Arrieta, MC},
title = {Maturational patterns of the infant gut mycobiome are associated with early-life body mass index.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {100928},
doi = {10.1016/j.xcrm.2023.100928},
pmid = {36736319},
issn = {2666-3791},
abstract = {Unlike the bacterial microbiome, the role of early-life gut fungi in host metabolism and childhood obesity development remains poorly characterized. To address this, we investigate the relationship between the gut mycobiome of 100 infants from the Canadian Healthy Infant Longitudinal Development (CHILD) Cohort Study and body mass index Z scores (BMIz) in the first 5 years of life. An increase in fungal richness during the first year of life is linked to parental and infant BMI. The relationship between richness pattern and early-life BMIz is modified by maternal BMI, maternal diet, infant antibiotic exposure, and bacterial beta diversity. Further, the abundances of Saccharomyces, Rhodotorula, and Malassezia are differentially associated with early-life BMIz. Using structural equation modeling, we determine that the mycobiome's contribution to BMIz is likely mediated by the bacterial microbiome. This demonstrates that mycobiome maturation and infant growth trajectories are distinctly linked, advocating for inclusion of fungi in larger pediatric microbiome studies.},
}

@article {pmid36736005,
year = {2023},
author = {Fujiyoshi, S and Yarimizu, K and Perera, I and Abanto, M and Jorquera, M and Maruyama, F},
title = {Learning from mistakes: challenges in finding holobiont factors from environmental samples and the importance of methodological consistency.},
journal = {Current opinion in biotechnology},
volume = {80},
number = {},
pages = {102897},
doi = {10.1016/j.copbio.2023.102897},
pmid = {36736005},
issn = {1879-0429},
abstract = {The cause of harmful algal blooms has been a mystery, but research to elucidate its mechanism has progressed over the years thanks to genetic technologies. We have monitored toxic algae and its associated bacteria as a community, the so-called 'holobiont' in Chilean coastal waters for years from the perspective of bacteria as an algal bloom driver. This review describes the challenges of holobiont monitoring, specifically with respect to standardizing and compliance with the monitoring protocols to collect reliable and sustainable data. Further, we suggest adopting the high-throughput sequencing (HTS) standard operating procedure (SOP) by the International Human Microbiome to improve the quality and consistency of holobiont monitoring in the harmful algal world.},
}

@article {pmid36735955,
year = {2023},
author = {Rausch, P and Ellul, S and Pisani, A and Bang, C and Tabone, T and Marantidis Cordina, C and Zahra, G and Franke, A and Ellul, P},
title = {Microbial Dynamics in Newly Diagnosed and Treatment Naïve IBD Patients in the Mediterranean.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izad004},
pmid = {36735955},
issn = {1536-4844},
abstract = {BACKGROUND: Microbial communities have long been suspected to influence inflammatory processes in the gastrointestinal tract of patients with inflammatory bowel disease. However, these effects are often influenced by treatments and can rarely be analyzed in treatment-naïve onset cases. Specifically, microbial differences between IBD pathologies in new onset cases have rarely been investigated and can provide novel insight into the dynamics of the microbiota in Crohn's disease (CD) and ulcerative colitis (UC).

METHODS: Fifty-six treatment-naïve IBD onset patients (67.3% CD, 32.7% UC) and 97 healthy controls were recruited from the Maltese population. Stool samples were collected after diagnosis but before administration of anti-inflammatory treatments. Fecal microbial communities were assessed via 16S rRNA gene sequencing and subjected to ecological analyses to determine disease-specific differences between pathologies and disease subtypes or to predict future treatment options.

RESULTS: We identified significant differences in community composition, variability, and diversity between healthy and diseased individuals-but only small to no differences between the newly diagnosed, treatment-naïve UC and CD cohorts. Network analyses revealed massive turnover of bacterial interactions between healthy and diseased communities, as well as between CD and UC communities, as signs of disease-specific changes of community dynamics. Furthermore, we identified taxa and community characteristics serving as predictors for prospective treatments.

CONCLUSION: Untreated and newly diagnosed IBD shows clear differences from healthy microbial communities and an elevated level of disturbance, but only the network perspective revealed differences between pathologies. Furthermore, future IBD treatment is to some extent predictable by microbial community characteristics.},
}

@article {pmid36735849,
year = {2023},
author = {Dugan, B and Conway, J and Duggal, NA},
title = {Inflammaging as a target for healthy ageing.},
journal = {Age and ageing},
volume = {52},
number = {2},
pages = {},
doi = {10.1093/ageing/afac328},
pmid = {36735849},
issn = {1468-2834},
support = {SBF005\1132/AMS_/Academy of Medical Sciences/United Kingdom ; },
abstract = {Life expectancy has been on the rise for the past few decades, but healthy life expectancy has not kept pace, leading to a global burden of age-associated disorders. Advancing age is accompanied by a chronic increase in basal systemic inflammation, termed inflammaging, contributing towards an increased risk of developing chronic diseases in old age. This article reviews the recent literature to formulate hypotheses regarding how age-associated inflammaging plays a crucial role in driving chronic diseases and ill health in older adults. Here, we discuss how non-pharmacological intervention strategies (diet, nutraceutical supplements, phytochemicals, physical activity, microbiome-based therapies) targeting inflammaging restore health in older adults. We also consider alternative existing pharmacological interventions (Caloric restriction mimetics, p38 mitogen-activated protein kinase inhibitors) and explore novel targets (senolytics) aimed at combating inflammaging and optimising the ageing process to increase healthy lifespan.},
}

@article {pmid36735588,
year = {2023},
author = {Abdugheni, R and Li, DH and Wang, YJ and Du, MX and Zhou, N and Liu, C and Liu, SJ},
title = {Acidaminococcus homini s sp. nov., Amedibacillus hominis sp. nov., Lientehia hominis gen. nov. sp. nov., Merdimmobilis hominis gen. nov. sp. nov., and Paraeggerthella hominis sp. nov., isolated from human faeces.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.005648},
pmid = {36735588},
issn = {1466-5034},
abstract = {The human gastrointestinal tract is inhabited by various microorganisms, including thousands of bacterial taxa that have yet to be cultured and characterized. In this report, we describe the isolation, cultivation, genotypic and phenotypic characterization and taxonomy of five novel anaerobic bacterial strains that were recovered during the massive cultivation and isolation of gut microbes from human faecal samples. On the basis of the polyphasic taxonomic results, we propose two novel genera and five novel species. They are Acidaminococcus hominis sp. nov. (type strain NSJ-142[T]=CGMCC 1.17903[T]=KCTC 25346[T]), Amedibacillus hominis sp. nov. (type strain NSJ-176[T]=CGMCC 1.17933[T]=KCTC 25355[T]), Lientehia hominis gen. nov. sp. nov. (type strain NSJ-141[T]=CGMCC 1.17902[T]=KCTC 25345[T]), Merdimmobilis hominis gen. nov. sp. nov. (type strain NSJ-153[T]=CGMCC 1.17915[T]=KCTC 25350[T]) and Paraeggerthella hominis sp. nov. (type strain NSJ-152[T]=CGMCC 1.17914[T]=KCTC 25349[T]).},
}

@article {pmid36735141,
year = {2023},
author = {Frenkel, M and David, A and Sapire, K and Hausner, D},
title = {Complementary and Integrative Medicine in Pancreatic Cancer.},
journal = {Current oncology reports},
volume = {},
number = {},
pages = {},
pmid = {36735141},
issn = {1534-6269},
abstract = {PURPOSE OF REVIEW: Pancreatic cancer has high mortality and morbidity rates, associated with the issues of typically late diagnosis and the limited effectiveness of current treatments. Patients tend to experience multiple symptoms that can include anxiety, fear, depression, fatigue, weakness, peripheral neuropathy, and abdominal pain, which reduce quality of life (QoL) and may compromise the treatment continuum. Many of those symptoms are amenable to complementary and integrative medicine (CIM) therapies as a part of supportive and palliative care. This article reviews research findings on the beneficial effect of use of CIM modalities in regard to pancreatic cancer, with emphasis on pancreatic ductal adenocarcinoma (PDAC).

RECENT FINDINGS: Given the often-poor prognosis of the disease, patients with PDAC often seek integrative therapies to help manage the disease itself, to provide support through cancer treatment and its symptoms, and to provide emotional stress relief. Data is accumulating in the past few years on the potential benefits of CIM to the management of pancreatic cancer symptoms and treatment side effects, in order to augment supportive care. This data reveal that nutrition counselling; digestive enzyme therapy; microbiome support; dietary supplements; lifestyle interventions (physical activity and circadian health/sleep hygiene) appear to improve QoL of these patients through reduced symptom burden and meeting psychological needs, such as distress and fatigue. Acupuncture, mindfulness, yoga, reflexology, massage, and homeopathy may also contribute to symptom reduction, both physical and psychological, in all stages of the disease. There is supporting evidence that some CIM modalities may alleviate side effects and symptoms related to pancreatic cancer and its treatment, suggesting that practitioners might consider integrating these modalities in certain situations encountered in the treatment of pancreatic cancer. Further investigation is needed to define the optimal integration of CIM into the treatment and supportive care of patients affected by pancreatic cancer.},
}

@article {pmid36735065,
year = {2023},
author = {Graham, EB and Knelman, JE},
title = {Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-022-02155-w},
pmid = {36735065},
issn = {1432-184X},
abstract = {While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.},
}

@article {pmid36737646,
year = {2021},
author = {Segers, C and Mysara, M and Claesen, J and Baatout, S and Leys, N and Lebeer, S and Verslegers, M and Mastroleo, F},
title = {Intestinal mucositis precedes dysbiosis in a mouse model for pelvic irradiation.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {24},
pmid = {36737646},
issn = {2730-6151},
abstract = {Pelvic radiotherapy is known to evoke intestinal mucositis and dysbiosis. Currently, there are no effective therapies available to mitigate these injuries, which is partly due to a lack of insight into the events causing mucositis and dysbiosis. Here, the complex interplay between the murine host and its microbiome following pelvic irradiation was mapped by characterizing intestinal mucositis along with extensive 16S microbial profiling. We demonstrated important morphological and inflammatory implications within one day after exposure, thereby impairing intestinal functionality and inducing translocation of intraluminal bacteria into mesenteric lymph nodes as innovatively quantified by flow cytometry. Concurrent 16S microbial profiling revealed a delayed impact of pelvic irradiation on beta diversity. Analysis of composition of microbiomes identified biomarkers for pelvic irradiation. Among them, members of the families Ruminococcaceae, Lachnospiraceae and Porphyromonadaceae were differentially affected. Altogether, our unprecedented findings showed how pelvic irradiation evoked structural and functional changes in the intestine, which secondarily resulted in a microbiome shift. Therefore, the presented in vivo irradiation-gut-microbiome platform allows further research into the pathobiology of pelvic irradiation-induced intestinal mucositis and resultant dysbiosis, as well as the exploration of mitigating treatments including drugs and food supplements.},
}

@article {pmid36735064,
year = {2023},
author = {Tessler, M and Cunningham, SW and Ingala, MR and Warring, SD and Brugler, MR},
title = {An Environmental DNA Primer for Microbial and Restoration Ecology.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36735064},
issn = {1432-184X},
abstract = {Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.},
}

@article {pmid36734837,
year = {2023},
author = {Wang, X and Cui, X and Wu, J and Bao, L and Chen, C},
title = {Oral administration of silver nanomaterials affects the gut microbiota and metabolic profile altering the secretion of 5-HT in mice.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d2tb02756a},
pmid = {36734837},
issn = {2050-7518},
abstract = {Due to their excellent antibacterial ability, silver nanomaterials (Ag NMs) are the most frequently used nanomaterials. Their widespread use introduces the risk of human ingestion. However, the potential toxicity of Ag NMs to the gut microbiota and their metabolic profile are yet to be fully explored. In this study, we examined the effects of Ag NMs after oral administration (0.5 mg kg[-1] and 2.5 mg kg[-1], 14 and 28 days) on gut homeostasis by integrating tissue imaging, 16s rRNA gene sequencing and metabolomics techniques. We uncovered that silver nanoparticles (Ag NPs) and silver nanowires (Ag NWs) altered the structure (inhibiting the proliferation of Gram-negative bacteria) and decreased the diversity of gut microbiota in mice after short-term (14 days) exposure, while the microbial community tended to recover after long-term exposure (28 days), indicating that the resistance and resilience of the gut microbiome may pose a defense against the interference by reactive, exogenous nanomaterials. Interestingly, even though the gut microbiota structure recovered after 28 days of exposure, the gut metabolites significantly changed, showing increased 1H-indole-3-carboxylic acid and elevated levels of 5-HT in the gut and blood. Collectively, our results provide a piece of evidence on the association between the ingestion of exogenous nanoparticles and gut homeostasis, especially the metabolic profile of the host. This work thus provides additional insights for the continued investigation of the adverse effects of silver nanomaterials on biological hosts.},
}

@article {pmid36734518,
year = {2023},
author = {Sayin, S and Rosener, B and Li, CG and Ho, B and Ponomarova, O and Ward, DV and Walhout, AJM and Mitchell, A},
title = {Evolved bacterial resistance to the chemotherapy gemcitabine modulates its efficacy in co-cultured cells.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.83140},
pmid = {36734518},
issn = {2050-084X},
abstract = {Drug metabolism by the microbiome can influence anti-cancer treatment success. We previously suggested that chemotherapies with antimicrobial activity can select for adaptations in bacterial drug metabolism that can inadvertently influence the host's chemoresistance. We demonstrated that evolved resistance against fluoropyrimidine chemotherapy lowered its efficacy in worms feeding on drug-evolved bacteria (Rosener et al., 2020). Here we examine a model system that captures local interactions that can occur in the tumor microenvironment. Gammaproteobacteria colonizing pancreatic tumors can degrade the nucleoside-analog chemotherapy gemcitabine and, in doing so, can increase the tumor's chemoresistance. Using a genetic screen in Escherichia coli, we mapped all loss-of-function mutations conferring gemcitabine resistance. Surprisingly, we infer that one third of top resistance mutations increase or decrease bacterial drug breakdown and therefore can either lower or raise the gemcitabine load in the local environment. Experiments in three E. coli strains revealed that evolved adaptation converged to inactivation of the nucleoside permease NupC, an adaptation that increased the drug burden on co-cultured cancer cells. The two studies provide complementary insights on the potential impact of microbiome adaptation to chemotherapy by showing that bacteria-drug interactions can have local and systemic influence on drug activity.},
}

@article {pmid36734377,
year = {2023},
author = {Berasategui, A and Salem, H},
title = {Synergy in symbiosis.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.85565},
pmid = {36734377},
issn = {2050-084X},
abstract = {Honeybees rely on their microbial gut symbionts to overcome a potent toxin found in pollen and nectar.},
}

@article {pmid36734186,
year = {2023},
author = {Aiosa, N and Sinha, A and Albataineh, H and Phillips, AM and Mageeney, CM and Wilde, DS and Williams, KP and Collette, N and Branda, SS and Garg, N},
title = {Whole-cell MALDI-ToF MS coupled with untargeted metabolomics facilitates investigations of microbial chemical interactions.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/cbic.202200802},
pmid = {36734186},
issn = {1439-7633},
abstract = {The emergence of drug resistant pathogens necessitates development of new countermeasures. In this regard, the introduction of probiotics to directly attack or competitively exclude pathogens presents a useful strategy. Application of this approach requires an understanding of how a probiotic and its target pathogen interact. A key means of probiotic-pathogen interaction involves the production of small molecules called natural products (NPs). Here, we report use of whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry for characterization of NP production by candidate probiotics (mouse airway microbiome isolates) when co-cultured with respiratory pathogen Burkholderia. We found that a Bacillus velezensis strain inhibits growth of and elicits NP production by B. thailandensis. Dereplication of known NPs detected in the metabolome of this B. velezensis strain suggests that a previously unannotated bioactive compound is involved. Thus, we present use of whole-cell MALDI as a broadly applicable method for screening of NP composition of microbial co-cultures, which can be combined with other -omics methods for characterization of probiotic-pathogen, and other microbe-microbe, interactions.},
}

@article {pmid36733917,
year = {2023},
author = {Miri, S and Yeo, J and Abubaker, S and Hammami, R},
title = {Neuromicrobiology, an emerging neurometabolic facet of the gut microbiome?.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1098412},
pmid = {36733917},
issn = {1664-302X},
abstract = {The concept of the gut microbiome is emerging as a metabolic interactome influenced by diet, xenobiotics, genetics, and other environmental factors that affect the host's absorption of nutrients, metabolism, and immune system. Beyond nutrient digestion and production, the gut microbiome also functions as personalized polypharmacy, where bioactive metabolites that our microbes excrete or conjugate may reach systemic circulation and impact all organs, including the brain. Appreciable evidence shows that gut microbiota produce diverse neuroactive metabolites, particularly neurotransmitters (and their precursors), stimulating the local nervous system (i.e., enteric and vagus nerves) and affecting brain function and cognition. Several studies have demonstrated correlations between the gut microbiome and the central nervous system sparking an exciting new research field, neuromicrobiology. Microbiome-targeted interventions are seen as promising adjunctive treatments (pre-, pro-, post-, and synbiotics), but the mechanisms underlying host-microbiome interactions have yet to be established, thus preventing informed evidence-based therapeutic applications. In this paper, we review the current state of knowledge for each of the major classes of microbial neuroactive metabolites, emphasizing their biological effects on the microbiome, gut environment, and brain. Also, we discuss the biosynthesis, absorption, and transport of gut microbiota-derived neuroactive metabolites to the brain and their implication in mental disorders.},
}

@article {pmid36733427,
year = {2022},
author = {Gao, L and Wang, S and Yang, M and Wang, L and Li, Z and Yang, L and Li, G and Wen, T},
title = {Gut fungal community composition analysis of myostatin mutant cattle prepared by CRISPR/Cas9.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {1084945},
pmid = {36733427},
issn = {2297-1769},
abstract = {Myostatin (MSTN) regulates muscle development and body metabolism through a variety of pathways and is a core target gene for gene editing in livestock. Gut fungi constitute a small part of the gut microbiome and are important to host health and metabolism. The influence of MSTN mutations on bovine gut fungi remains unknown. In this study, Internal Transcribed Spacer (ITS) high-throughput sequencing was conducted to explore the composition of gut fungi in the MSTN mutant (MT) and wild-type (WT) cattle, and 5,861 operational taxonomic units (OTUs) were detected and classified into 16 phyla and 802 genera. The results of the alpha diversity analysis indicated that no notable divergence was displayed between the WT and MT cattle; however, significant differences were noticed in the composition of fungal communities. Eight phyla and 18 genera were detected. According to the prediction of fungal function, saprotroph fungi were significantly more abundant in the MT group. The correlation analysis between gut fungal and bacterial communities revealed that MSTN mutations directly changed the gut fungal composition and, at the same time, influenced some fungi and bacteria by indirectly regulating the interaction between microorganisms, which affected the host metabolism further. This study analyzed the role of MSTN mutations in regulating the host metabolism of intestinal fungi and provided a theoretical basis for the relationship between MSTN and gut fungi.},
}

@article {pmid36733397,
year = {2022},
author = {Gago, S and Mandarano, M and Floridi, C and Zelante, T},
title = {Host, pathogenic fungi and the microbiome: A genetic triangle in infection.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1078014},
pmid = {36733397},
issn = {1664-3224},
}