@article {pmid35051873,
year = {2021},
author = {Gomaa, F and Utter, DR and Loo, W and Lahr, DJG and Cavanaugh, CM},
title = {Exploring the protist microbiome: The diversity of bacterial communities associated with Arcella spp. (Tubulina: Amoebozoa).},
journal = {European journal of protistology},
volume = {82},
number = {},
pages = {125861},
doi = {10.1016/j.ejop.2021.125861},
pmid = {35051873},
issn = {1618-0429},
abstract = {Research on protist-bacteria interactions is increasingly relevant as these associations are now known to play important roles in ecosystem and human health. Free-living amoebae are abundant in all environments and are frequent hosts for bacterial endosymbionts including pathogenic bacteria. However, to date, only a small fraction of these symbionts have been identified, while the structure and composition of the total symbiotic bacterial communities still remains largely unknown. Here, we use the testate amoeba Arcella spp. as model organisms to investigate the specificity and diversity of Arcella-associated microbial communities. High-throughputamplicon sequencing from the V4 region of the 16S rRNA gene revealed high diversity in the bacterial communities associated with the wild Arcella spp. To investigate the specificity of the associated bacterial community with greater precision, we investigated the bacterial communities of two lab-cultured Arcella species, A. hemispherica and A. intermedia, grown in two different media types. Our results suggest that Arcella-bacteria associations are species-specific, and that the associated bacterial community of lab-cultured Arcella spp. remains distinct from that of the surrounding media. Further, each host Arcella species could be distinguished based on its bacterial composition. Our findings provide insight into the understanding of eukaryotic-bacterial symbiosis.},
}

@article {pmid35051672,
year = {2021},
author = {Chen, S and Yan, C and Liu, W and Chen, K and Xing, L and Li, H and Zhao, X},
title = {Research Note: Integrated gut microbiome and short-chain fatty acids responds to dominance hierarchy in roosters.},
journal = {Poultry science},
volume = {101},
number = {3},
pages = {101670},
doi = {10.1016/j.psj.2021.101670},
pmid = {35051672},
issn = {1525-3171},
abstract = {The dominant chickens have priority over the use of resources, such as resting places and the announcement of dawn. While cooperation from the subdominant animal is of great help to reduce conflict and maintain the sustainability of a group. However, whether the dominance hierarchy is associated with individuals' health is not yet known. In this study, we first determined the dominance hierarchy within a group of roosters, to figure out its effects on individuals' health status by the determination of microbial composition and short-chain fatty acids (SCFAs). Sixteen Weining roosters were kept in a group in order to fix and determine the ranking of dominance hierarchy, as R1 (the highest-ranking rooster), R2, R3, and R4. Results show that the R1 roosters had the highest aggression behavior followed by R2, R3 and R4 (P < 0.05). The alpha diversity of R1, R2, and R4 was higher than R3 roosters (P < 0.05). There were several top 10 phylum and genus microbes among the different ranking roosters (P < 0.05). The acetic acid, propionic acid, butyric acid, and valerate acid concentrations were higher, while isobutyric acid concentration was lower in the higher rank roosters (R1 and R2) than the lower rank roosters, respectively (R3 and R4) (P < 0.05). Our results show that the variation of dominance hierarchy contributes to changes of microbial composition, diversity and metabolites. Dominant roosters seem to benefit from SCFAs activities while subdominant roosters profit from microbial functions.},
}

@article {pmid35051423,
year = {2022},
author = {Bandala-Sanchez, E and Roth-Schulze, AJ and Oakey, H and Penno, MAS and Bediaga, NG and Naselli, G and Ngui, KM and Smith, AD and Huang, D and Zozaya-Valdes, E and Thomson, RL and Brown, JD and Vuillermin, PJ and Barry, SC and Craig, ME and Rawlinson, WD and Davis, EA and Harris, M and Soldatos, G and Colman, PG and Wentworth, JM and Haynes, A and Morahan, G and Sinnott, RO and Papenfuss, AT and Couper, JJ and Harrison, LC and , },
title = {Women with type 1 diabetes exhibit a progressive increase in gut Saccharomyces cerevisiae in pregnancy associated with evidence of gut inflammation.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {109189},
doi = {10.1016/j.diabres.2022.109189},
pmid = {35051423},
issn = {1872-8227},
abstract = {AIMS: Studies of the gut microbiome have focused on its bacterial composition. We aimed to characterize the gut fungal microbiome (mycobiome) across pregnancy in women with and without type 1 diabetes.

METHODS: Faecal samples (n=162) were collected from 70 pregnant women (45 with and 25 without type 1 diabetes) across all trimesters. Fungi were analysed by internal transcribed spacer 1 amplicon sequencing. Markers of intestinal inflammation (faecal calprotectin) and intestinal epithelial integrity (serum intestinal fatty acid binding protein; I-FABP), and serum antibodies to Saccharomyces cerevisiae (ASCA) were measured.

RESULTS: Women with type 1 diabetes had decreased fungal alpha diversity by the third trimester, associated with an increased abundance of Saccharomyces cerevisiae that was inversely related to the abundance of the anti-inflammatory butyrate-producing bacterium Faecalibacterium prausnitzii. Women with type 1 diabetes had higher concentrations of calprotectin, I-FABP and ASCA.

CONCLUSIONS: Women with type 1 diabetes exhibit a shift in the gut mycobiome across pregnancy associated with evidence of gut inflammation and impaired intestinal barrier function. The relevance of these findings to the higher rate of pregnancy complications in type 1 diabetes warrants further study.},
}

@article {pmid35051422,
year = {2022},
author = {Volodina, DE and Gureev, AP and Shaforostova, EA and Gryaznova, MV and Ignatyeva, DA and Popov, VN},
title = {Effect of l-carnitine and mildronate on the mitochondrial metabolism of heart and bacterial composition of the gut microbiome in ageing mice.},
journal = {Life sciences},
volume = {},
number = {},
pages = {120333},
doi = {10.1016/j.lfs.2022.120333},
pmid = {35051422},
issn = {1879-0631},
abstract = {Ageing is the most significant risk factor for cardiovascular diseases. l-Carnitine has a potent cardioprotective effect and its synthesis decreases during ageing. At the same time, there are pharmaceuticals, such as mildronate which, on the contrary, are aimed at reducing the concentration of l-carnitine in the heart and lead to slows down the oxidation of fatty acids in mitochondria. Despite this, both l-carnitine and mildronate are positioned as cardio protectors. We showed that l-carnitine supplementation to the diet of 15-month-old mice increased expression of the PGC-1α gene, which is responsible for the regulation of fatty acid oxidation, and the Nrf2 gene, which is responsible for protecting mitochondria by regulating the expression of antioxidants and mitophagy, in the heart. Mildronate activated the expression of genes that regulate glucose metabolism. Probably, this metabolic shift may protect the mitochondria of the heart from the accumulation of acyl-carnitine, which occurs during the oxidation of fatty acids under oxygen deficiency. Both pharmaceuticals impacted the gut microbiome bacterial composition. l-Carnitine increased the level of Lachnoanaerobaculum and [Eubacterium] hallii group, mildronate increased the level of Bifidobacterium, Rikinella, Christensenellaceae. Considered, that these bacteria for protection the organism from various pathogens and chronic inflammation. Thus, we suggested that the positive effects of both drugs on the mitochondria metabolism and gut microbiome bacterial composition may contribute to the protection of the heart during ageing.},
}

@article {pmid35051369,
year = {2022},
author = {Jin, WB and Li, TT and Huo, D and Qu, S and Li, XV and Arifuzzaman, M and Lima, SF and Shi, HQ and Wang, A and Putzel, GG and Longman, RS and Artis, D and Guo, CJ},
title = {Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2021.12.035},
pmid = {35051369},
issn = {1097-4172},
abstract = {Hundreds of microbiota genes are associated with host biology/disease. Unraveling the causal contribution of a microbiota gene to host biology remains difficult because many are encoded by nonmodel gut commensals and not genetically targetable. A general approach to identify their gene transfer methodology and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. We developed a pipeline that identifies the gene transfer methods for multiple nonmodel microbes spanning five phyla, and we demonstrated the utility of their genetic tools by modulating microbiome-derived short-chain fatty acids and bile acids in vitro and in the host. In a proof-of-principle study, by deleting a commensal gene for bile acid synthesis in a complex microbiome, we discovered an intriguing role of this gene in regulating colon inflammation. This technology will enable genetically engineering the nonmodel gut microbiome and facilitate mechanistic dissection of microbiota-host interactions.},
}

@article {pmid35051291,
year = {2022},
author = {Zhang, W and Mason, GA},
title = {Modulating the rhizosphere microbiome by altering the cocktail of root secretions.},
journal = {Plant physiology},
volume = {188},
number = {1},
pages = {12-13},
doi = {10.1093/plphys/kiab480},
pmid = {35051291},
issn = {1532-2548},
}

@article {pmid35051217,
year = {2022},
author = {Bodie, AR and Dittoe, DK and Feye, KM and Knueven, CJ and Ovall, C and Ricke, SC},
title = {Comparison of ready-to-eat "organic" antimicrobials, sodium bisulfate, and sodium lactate, on Listeria monocytogenes and the indigenous microbiome of organic uncured beef frankfurters stored under refrigeration for three weeks.},
journal = {PloS one},
volume = {17},
number = {1},
pages = {e0262167},
doi = {10.1371/journal.pone.0262167},
pmid = {35051217},
issn = {1932-6203},
abstract = {Listeria monocytogenes has been implicated in several ready-to-eat (RTE) foodborne outbreaks, due in part to its ability to survive under refrigerated conditions. Thus, the objective of this study was to evaluate the effects of sodium bisulfate (SBS), sodium lactate (SL), and their combination as short-duration antimicrobial dips (10-s) on L. monocytogenes and the microbiome of inoculated organic frankfurters (8 Log10 CFU/g). Frankfurters were treated with tap water (TW), SBS0.39%, SBS0.78%, SL0.78%, SL1.56%, SBS+SL0.39%, SBS+SL0.78%. In addition, frankfurters were treated with frankfurter solution water (HDW)+SBS0.78%, HDW+SL1.56%, and HDW+SBS+SL0.78%. After treatment, frankfurters were vacuum packaged and stored at 4°C. Bacterial enumeration and 16S rDNA sequencing occurred on d 0, 7, 14, 21. Counts were Log10 transformed and calculated as growth potential from d 0 to d 7, 14, and 21. Data were analyzed in R using mixed-effects model and One-Way ANOVA (by day) with differences separated using Tukey's HSD at P ≤ 0.05. The 16S rDNA was sequenced on an Illumina MiSeq and analyzed in Qiime2-2018.8 with significance at P ≤ 0.05 and Q ≤ 0.05 for main and pairwise effects. An interaction of treatment and time was observed among the microbiological plate data with all experimental treatments reducing the growth potential of Listeria across time (P < 0.0001). Efficacy of treatments was inconsistent across time; however, on d 21, SBS0.39% treated franks had the lowest growth potential compared to the control. Among diversity metrics, time had no effect on the microbiota (P > 0.05), but treatment did (P < 0.05). Thus, the treatments potentially promoted a stable microbiota across time. Using ANCOM, Listeria was the only significantly different taxa at the genus level (P < 0.05, W = 52). Therefore, the results suggest incorporating SBS over SL as an alternative antimicrobial for the control of L. monocytogenes in organic frankfurters without negatively impacting the microbiota. However, further research using multiple L. monocytogenes strains will need to be utilized in order to determine the scope of SBS use in the production of RTE meat.},
}

@article {pmid35050830,
year = {2022},
author = {Shoemark, A and Shteinberg, M and De Soyza, A and Haworth, C and Richardson, H and Gao, Y and Perea, L and Dicker, AJ and Goeminne, PC and Cant, E and Polverino, E and Altenburg, J and Keir, HR and Loebinger, MR and Blasi, F and Welte, T and Sibila, O and Aliberti, S and Chalmers, JD},
title = {Characterisation of Eosinophilic Bronchiectasis: A European Multicohort Study.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202108-1889OC},
pmid = {35050830},
issn = {1535-4970},
abstract = {RATIONALE: Bronchiectasis is classically considered a neutrophilic disorder but eosinophilic subtypes have recently been described.

OBJECTIVES: To use multiple datasets available through the EMBARC consortium to characterise eosinophilic bronchiectasis as a clinical entity focussing on the impact of eosinophils on bronchiectasis exacerbations.

METHODS: Patients were included from 5 countries to examine the relationships between blood eosinophil counts and clinical phenotypes after excluded co-existing asthma. 16S rRNA sequencing was used to examine relationships between eosinophil counts and the sputum microbiome. A posthoc analysis of the PROMIS phase-2 trial was used to examine the impact of blood eosinophil counts on exacerbations in patients with P.aeruginosa infection.

MEASUREMENTS AND MAIN RESULTS: A relationship between sputum and blood eosinophil counts was demonstrated in 2 cohorts. In analysis of 1007 patients from 5 countries, 22.6% of patients had blood eosinophil counts >300cells/ul. Counts<100cells/ul were associated with higher bronchiectasis severity and increased mortality. There was no clear relationship with exacerbations. Blood eosinophil counts >300cells/ul were associated with both Streptococcus and Pseudomonas dominated microbiome profiles. To investigate the relationship of eosinophil counts with exacerbations after controlling for the confounding effects of infection, 144 patients were studied in a clinical trial following treatment with antipseudomonal antibiotics. Compared to patients with blood eosinophil counts<100cells(reference), elevated eosinophil counts 100-300cells/ul (HR 2.38 95%CI 1.33-4.25,p=0.003) and >300cells/ul (HR 3.99 95%CI 2.20-7.85,p<0.0001) were associated with shorter time to exacerbation.

CONCLUSION: Eosinophilic bronchiectasis affects approximately 20% of patients. After accounting for infection status, raised blood eosinophil counts are associated with shortened time to exacerbation.},
}

@article {pmid35050355,
year = {2022},
author = {Liu, S and D'Amico, D and Shankland, E and Bhayana, S and Garcia, JM and Aebischer, P and Rinsch, C and Singh, A and Marcinek, DJ},
title = {Effect of Urolithin A Supplementation on Muscle Endurance and Mitochondrial Health in Older Adults: A Randomized Clinical Trial.},
journal = {JAMA network open},
volume = {5},
number = {1},
pages = {e2144279},
doi = {10.1001/jamanetworkopen.2021.44279},
pmid = {35050355},
issn = {2574-3805},
abstract = {Importance: Aging is associated with a decline in mitochondrial function and reduced exercise capacity. Urolithin A is a natural gut microbiome-derived food metabolite that has been shown to stimulate mitophagy and improve muscle function in older animals and to induce mitochondrial gene expression in older humans.

Objective: To investigate whether oral administration of urolithin A improved the 6-minute walk distance, muscle endurance in hand and leg muscles, and biomarkers associated with mitochondrial and cellular health.

This double-blind, placebo-controlled randomized clinical trial in adults aged 65 to 90 years was conducted at a medical center and a cancer research center in Seattle, Washington, from March 1, 2018, to July 30, 2020. Muscle fatigue tests and plasma analysis of biomarkers were assessed at baseline, 2 months, and 4 months. Six-minute walk distance and maximal ATP production were assessed using magnetic resonance spectroscopy at baseline and at the end of study at 4 months. The analysis used an intention-to-treat approach.

Interventions: Participants were randomized to receive daily oral supplementation with either 1000 mg urolithin A or placebo for 4 months.

Main Outcomes and Measures: The primary end point was change from baseline in the 6-minute walk distance and change from baseline to 4 months in maximal ATP production in the hand skeletal muscle. The secondary end points were change in muscle endurance of 2 skeletal muscles (tibialis anterior [TA] in the leg and first dorsal interosseus [FDI] in the hand). Cellular health biomarkers were investigated via plasma metabolomics. Adverse events were recorded and compared between the 2 groups during the intervention period.

Results: A total of 66 participants were randomized to either the urolithin A (n = 33) or the placebo (n = 33) intervention group. These participants had a mean (SD) age of 71.7 (4.94) years, were predominantly women (50 [75.8%]), and were all White individuals. Urolithin A, compared with placebo, significantly improved muscle endurance (ie, increase in the number of muscle contractions until fatigue from baseline) in the FDI and TA at 2 months (urolithin A: FDI, 95.3 [115.5] and TA, 41.4 [65.5]; placebo: FDI, 11.6 [147.4] and TA, 5.7 [127.1]). Plasma levels of several acylcarnitines, ceramides, and C-reactive protein were decreased by urolithin A, compared with placebo, at 4 months (baseline vs 4 mo: urolithin A, 2.14 [2.15] vs 2.07 [1.46]; placebo, 2.17 [2.52] vs 2.65 [1.86]). The mean (SD) increase from baseline in the 6-minute walk distance was 60.8 (67.2) m in the urolithin A group and 42.5 (73.3) m in the placebo group. The mean (SD) change from baseline to 4 months in maximal ATP production in the FDI was 0.07 (0.23) mM/s in the urolithin A group and 0.06 (0.20) mM/s in the placebo group; for the TA, it was -0.03 (0.10) mM/s in the urolithin A group and 0.03 (0.10) mM/s in the placebo group. These results showed no significant improvement with urolithin A supplementation compared with placebo. No statistical differences in adverse events were observed between the 2 groups.

Conclusions and Relevance: This randomized clinical trial found that urolithin A supplementation was safe and well tolerated in the assessed population. Although the improvements in the 6-minute walk distance and maximal ATP production in the hand muscle were not significant in the urolithin A group vs the placebo group, long-term urolithin A supplementation was beneficial for muscle endurance and plasma biomarkers, suggesting that urolithin A may counteract age-associated muscle decline; however, future work is needed to confirm this finding.

Trial Registration: ClinicalTrials.gov Identifier: NCT03283462.},
}

@article {pmid35050187,
year = {2022},
author = {Callender, C and Attaye, I and Nieuwdorp, M},
title = {The Interaction between the Gut Microbiome and Bile Acids in Cardiometabolic Diseases.},
journal = {Metabolites},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/metabo12010065},
pmid = {35050187},
issn = {2218-1989},
support = {09150182010020//ZonMW VICI 2020/ ; },
abstract = {Cardio-metabolic diseases (CMD) are a spectrum of diseases (e.g., type 2 diabetes, atherosclerosis, non-alcohol fatty liver disease (NAFLD), and metabolic syndrome) that are among the leading causes of morbidity and mortality worldwide. It has long been known that bile acids (BA), which are endogenously produced signalling molecules from cholesterol, can affect CMD risk and progression and directly affect the gut microbiome (GM). Moreover, studies focusing on the GM and CMD risk have dramatically increased in the past decade. It has also become clear that the GM can function as a "new" endocrine organ. BA and GM have a complex and interdependent relationship with several CMD pathways. This review aims to provide a comprehensive overview of the interplay between BA metabolism, the GM, and CMD risk and progression.},
}

@article {pmid35050132,
year = {2021},
author = {Lu, Y and Chong, J and Shen, S and Chammas, JB and Chalifour, L and Xia, J},
title = {TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome.},
journal = {Metabolites},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/metabo12010010},
pmid = {35050132},
issn = {2218-1989},
abstract = {Crosstalk between the gut microbiome and the host plays an important role in animal development and health. Small compounds are key mediators in this host-gut microbiome dialogue. For instance, tryptophan metabolites, generated by biotransformation of tryptophan through complex host-microbiome co-metabolism can trigger immune, metabolic, and neuronal effects at local and distant sites. However, the origin of tryptophan metabolites and the underlying tryptophan metabolic pathway(s) are not well characterized in the current literature. A large number of the microbial contributors of tryptophan metabolism remain unknown, and there is a growing interest in predicting tryptophan metabolites for a given microbiome. Here, we introduce TrpNet, a comprehensive database and analytics platform dedicated to tryptophan metabolism within the context of host (human and mouse) and gut microbiome interactions. TrpNet contains data on tryptophan metabolism involving 130 reactions, 108 metabolites and 91 enzymes across 1246 human gut bacterial species and 88 mouse gut bacterial species. Users can browse, search, and highlight the tryptophan metabolic pathway, as well as predict tryptophan metabolites on the basis of a given taxonomy profile using a Bayesian logistic regression model. We validated our approach using two gut microbiome metabolomics studies and demonstrated that TrpNet was able to better predict alterations in in indole derivatives compared to other established methods.},
}

@article {pmid35050030,
year = {2022},
author = {Liu, D and Cai, J and He, H and Yang, S and Chater, CCC and Yu, F},
title = {Anemochore Seeds Harbor Distinct Fungal and Bacterial Abundance, Composition, and Functional Profiles.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/jof8010089},
pmid = {35050030},
issn = {2309-608X},
support = {202103AC100003//Key R & D program of Yunnan Province, China/ ; },
abstract = {Many plants adapted to harsh environments have evolved low seed mass ('light seeds') with specific dispersal strategies, primarily either by wind (anemochory) or water (hydrochory). However, the role of their seed microbiota in their survival, and their seed microbial abundance and structure, remain insufficiently studied. Herein, we studied the light seed microbiome of eight anemochores and two hydrochores (as controls) collected from four provinces in China, using qPCR and metagenomic sequencing targeting both bacteria and fungi. Substantial variations were found for seed endophytic fungi (9.9 × 1010~7.3 × 102 gene copy numbers per seed) and bacteria (1.7 × 1010~8.0 × 106). Seed microbial diversity and structure were mainly driven by the plant genotype (species), with weak influences from their host plant classification level or dispersal mode. Seed microbial composition differences were clear at the microbial phylum level, with dominant proportions (~75%) for Proteobacteria and Ascomycota. The light seeds studied harbored unique microbial signatures, sharing only two Halomonas amplicon sequence variants (ASVs) and two fungal ASVs affiliated to Alternaria and Cladosporium. A genome-level functional profile analysis revealed that seed bacterial microbiota were enriched in amino acid, nucleoside, and nucleotide biosynthesis, while in fungal communities the generation of precursor metabolites and respiration were more highly represented. Together, these novel insights provide a deeper understanding of highly diversified plant-specific light seed microbiota and ecological strategies for plants in harsh environments.},
}

@article {pmid35049792,
year = {2022},
author = {Pantoja-Don Juan, CA and Gómez-Verduzco, G and Márquez-Mota, CC and Téllez-Isaías, G and Kwon, YM and Cortés-Cuevas, A and Arce-Menocal, J and Martínez-Gómez, D and Ávila-González, E},
title = {Productive Performance and Cecum Microbiota Analysis of Broiler Chickens Supplemented with β-Mannanases and Bacteriophages-A Pilot Study.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/ani12020169},
pmid = {35049792},
issn = {2076-2615},
abstract = {This study was conducted to evaluate the productive performance, intestinal health, and description of the cecum microbiota in broilers supplemented with β-mannanases (MNs) and bacteriophages (BPs). Six hundred one-day-old broilers were divided into four groups and fed one of the following diets: CON-corn-soybean meal + 10 ppm enramycin (ENR); MN: CON + 500 ppm MN; BP: CON + 500 ppm BP; MN + BP: BP + 500 ppm MN. The BP and MN factors showed similar performances to ENR. MN improved the concentration of IgA in the jejunum at 35 days of age. The morphometric index (IM) of the thymus increased by adding MN, while BP increased the liver and thymus IM. The histological analysis showed that BP and MN improved the intestinal morphology. MN + BP showed a tendency to decrease the abundance of Proteobacteria and increase the abundance of Bacteroidetes, indicating better microbiota function. In conclusion, our results demonstrate that the combination of MN + BP has potential in poultry nutrition; however, we highly recommend further experiments to confirm this hypothesis.},
}

@article {pmid35049773,
year = {2022},
author = {Fu, H and Li, W},
title = {Metagenomic Comparisons between Soft and Hard Feces of Plateau Pikas (Ochotona curzoniae).},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/ani12020149},
pmid = {35049773},
issn = {2076-2615},
support = {no. 2017-ZJ-714//Applied Basic Research Programs of Qinghai Province/ ; },
abstract = {The division of hard and soft feces is an effective digestion strategy in the order Lagomorpha. Although previous studies have reported that hard and soft feces differ in morphology and component, the discrepancy in the microbiome remains unclear. This study explored the microbiomes of hard and soft feces in plateau pikas by sequencing the V3 and V4 regions of 16S rDNA. We found that hard feces harbored higher Firmicutes, while soft feces harbored higher Akkermansia. Increased rare bacterial taxa were observed in hard feces compared with soft feces. Moreover, hard and soft feces displayed a greater difference in terms of core operational taxonomy units (OTUs) compared to the total OTUs. The soft feces showed enhancements in all predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functions, indicating an advancing microbial metabolism compared to hard feces. The significantly upregulated pathways in soft feces were mainly enriched in metabolism of energy and carbohydrate, glycan biosynthesis, cofactors and vitamins, and amino acids-all of which are associated with increased contents of microbial proteins, vitamins, and short-chain fatty acids. Our study reports, for the first time, the differential microbiomes between hard and soft feces of pikas and provides direction for the future studies on cecotrophy.},
}

@article {pmid35049722,
year = {2022},
author = {Arthur, R and Antonczyk, S and Off, S and Scherer, PA},
title = {Mesophilic and Thermophilic Anaerobic Digestion of Wheat Straw in a CSTR System with 'Synthetic Manure': Impact of Nickel and Tungsten on Methane Yields, Cell Count, and Microbiome.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/bioengineering9010013},
pmid = {35049722},
issn = {2306-5354},
abstract = {Lignocellulosic residues, such as straw, are currently considered as candidates for biogas production. Therefore, straw fermentations were performed to quantitatively estimate methane yields and cell counts, as well as to qualitatively determine the microbiome. Six fully automated, continuously stirred biogas reactors were used: three mesophilic (41 °C) and three thermophilic (58 °C). They were fed every 8 h with milled wheat straw suspension in a defined, buffered salt solution, called 'synthetic manure'. Total reflection X-ray fluorescence spectrometry analyses showed nickel and tungsten deficiency in the straw suspension. Supplementation of nickel and subsequently tungsten, or with an increasing combined dosage of both elements, resulted in a final concentration of approximately 0.1 mg/L active, dissolved tungsten ions, which caused an increase of the specific methane production, up to 63% under mesophilic and 31% under thermophilic conditions. That is the same optimal range for pure cultures of methanogens or bacteria found in literature. A simultaneous decrease of volatile fatty acids occurred. The Ni/W effect occurred with all three organic loading rates, being 4.5, 7.5, and 9.0 g volatile solids per litre and day, with a concomitant hydraulic retention time of 18, 10, or 8 days, respectively. A maximum specific methane production of 0.254 m3 CH4, under standard temperature and pressure per kg volatile solids (almost 90% degradation), was obtained. After the final supplementation of tungsten, the cell counts of methanogens increased by 300%, while the total microbial cell counts increased by only 3-62%. The mesophilic methanogenic microflora was shifted from the acetotrophic Methanosaeta to the hydrogenotrophic Methanoculleus (85%) by tungsten, whereas the H2-CO2-converter, Methanothermobacter, always dominated in the thermophilic fermenters.},
}

@article {pmid35049252,
year = {2022},
author = {Frese, C and Reissfelder, LS and Kilian, S and Felten, A and Laurisch, L and Schoilew, K and Boutin, S},
title = {Can the Acid-formation Potential of Saliva Detect a Caries-related Shift in the Oral Microbiome?.},
journal = {Oral health & preventive dentistry},
volume = {20},
number = {1},
pages = {51-60},
doi = {10.3290/j.ohpd.b2573053},
pmid = {35049252},
issn = {1757-9996},
abstract = {PURPOSE: To determine acid-formation potential of saliva and evaluate whether this method corresponds with microbiome composition of individuals with and without caries.

MATERIALS AND METHODS: A clinical, controlled pilot study was performed with two groups: individuals without caries (n = 25; DMFT = 0) and individuals with at least one active carious lesion (n = 25; DMFT>0). A detailed intraoral examination was performed, and the gingival bleeding index (GBI) and plaque index (PI) were recorded. The acid-formation potential was measured (ΔpH) after 1 h. Streptococcus mutans (SM) and lactobacilli (LB) were also quantified. Intergroup comparisons were made using the Mann-Whitney U-test. The diagnostic value was evaluated using the receiver operating characteristics (ROC) method and area under the curve (AUC) values were calculated. The saliva microbiome was analysed by 16S rDNA next-generation sequencing.

RESULTS: A statistically significant difference was found in ΔpH, with the 'caries' group showing a higher mean value after 1 h ('healthy' = 1.1,'caries' = 1.4; p = 0.035). The AUC values were moderate to good (ΔpH = 0.67; SM = 0.83; LB = 0.83;1 = ideal). Streptococcus mutans and Lactobacilli were more frequently detected in the 'caries' group (p < 0.001), as were statistically significantly higher GBI (p = 0.006) and PI (p = 0.001). The saliva microbiome had a higher α-diversity and greater richness in individuals with active caries. The incidence of the genera Alloprevotella, Prevotella, Campylobacter and Veillonella was statistically significantly higher in the 'healthy' group. The incidence of the genera Fretibacterium, Lactobacillus, and Leptotrichia, as well as the phyla Spirochaetes and Synergistetes, was statistically significantly higher in the 'caries' group.

CONCLUSION: Further studies must be carried out to determine the extent to which both tests are suitable for predicting future caries development.},
}

@article {pmid35049120,
year = {2022},
author = {Youngblut, ND and de la Cuesta-Zuluaga, J and Ley, RE},
title = {Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15910},
pmid = {35049120},
issn = {1462-2920},
abstract = {Tree-based diversity measures incorporate phylogenetic or functional relatedness into comparisons of microbial communities. This can improve the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g., 16S rRNA gene). Utilizing the Genome Taxonomy Database (GTDB) for species-level metagenome profiling allows for functional diversity measures based on genomic content or traits inferred from it. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or function into measures of diversity. We assessed this by measuring phylogeny-based, function-based, and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 30 studies and 2943 samples. We found tree-based measures to explain phenotypic variation (e.g., westernization, disease status, and gender) better or equivalent to tree-agnostic measures. Ecophylogenetic and functional diversity measures provided unique insight into how microbiome diversity was partitioned by phenotype. Tree-based measures greatly improved machine learning model performance for predicting westernization, disease status, and gender, relative to models trained solely on tree-agnostic measures. Our findings illustrate the usefulness of tree- and function-based measures for metagenomic assessments of microbial diversity, which is a fundamental component of microbiome science. This article is protected by copyright. All rights reserved.},
}

@article {pmid35049092,
year = {2022},
author = {Furuhashi, H and Takayasu, L and Isshi, K and Hara, Y and Ono, S and Kato, M and Sumiyama, K and Suda, W},
title = {Effect of storage temperature and flash-freezing on salivary microbiota profiles based on 16S rRNA-targeted sequencing.},
journal = {European journal of oral sciences},
volume = {},
number = {},
pages = {e12852},
doi = {10.1111/eos.12852},
pmid = {35049092},
issn = {1600-0722},
support = {//RIKEN Integrated Symbiology/ ; },
abstract = {The sample storage environment affects gut microbial profiles as assessed using 16S rRNA sequencing. However, the influence of storage condition on human salivary microbial profiles has not been well characterized. Here, we performed an observational study to assess the robustness of microbiota profiles in three different storage environments (-80°C after flash-freezing, -80°C, and -15°C; all for 14 days) compared to immediate DNA extraction using the MiSeq Illumina platform. Notably, the 16S rRNA V1-V2 region amplicon sequencing revealed no difference in microbiota profiles between the immediate extraction and each of three storage conditions. An almost perfect correlation was shown between the immediate extraction and the -15°C storage group for relative abundance at the genus and operational taxonomic unit levels. The intraindividual UniFrac distances among storage methods were significantly shorter than those of interindividual distances. None of the amount of extracted DNA, the α-diversity indices, or the relative abundance at the phylum/genus/operational taxonomic unit level differed among storage methods. These findings indicate that a storage temperature of -15°C without flash-freezing may be optimal in terms of cost advantage and simplicity in 16S rRNA sequencing-based salivary microbial research.},
}

@article {pmid35048923,
year = {2022},
author = {Saeb, A and Grundmann, SM and Gessner, DK and Schuchardt, S and Most, E and Wen, G and Eder, K and Ringseis, R},
title = {Feeding of cuticles from Tenebrio molitor larvae modulates the gut microbiota and attenuates hepatic steatosis in obese Zucker rats.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d1fo03920b},
pmid = {35048923},
issn = {2042-650X},
abstract = {Insect biomass obtained from large-scale mass-rearing of insect larvae has gained considerable attention in recent years as an alternative and sustainable source of food and feed. A byproduct from mass-rearing of insect larvae is the shed cuticles - the most external components of insects which are a relevant source of the polysaccharide chitin. While it has been shown that chitin modulates the gut microbiota and ameliorates lipid metabolic disorders in obese rodent models, feeding studies dealing with isolated insects' cuticles are completely lacking. Thus, the present study tested the hypothesis that dietary insects' cuticles modulate the gut microbiome and improve hepatic lipid metabolism in obese Zucker rats. To test this hypothesis, three groups of obese Zucker rats were fed a nutrient-adequate, semisynthetic basal diet which was supplemented with either 0% (group O), 1.5% (group O1.5) or 3.0% (group O3.0) Tenebrio molitor cuticles at the expense of cellulose. Oil red O-stained liver sections showed a marked lipid accumulation, but lipid accumulation was clearly less in group O3.0 than in groups O and O1.5. In line with this, hepatic lipid concentrations were 30% lower in group O3.0 than in group O (p < 0.05). No differences were observed across the obese groups regarding liver concentrations of methionine, S-adenosylmethionine and homocysteine. Analysis of cecal microbial community at the family level revealed that the relative abundances of Bifidobacteriaceae, Coriobacteriaceae Erysipelotrichaceae, Lactobacillaceae, Prevotellaceae, Sutterellaceae, unknown Deltaproteobacteria and unknown Firmicutes were higher and those of Anaeroplasmataceae, Desulfovibrionaceae, Eubacteriaceae, Ruminococcaceae, Saccharibacteria and unknown Clostridiales were lower in group O3.0 compared to group O (p < 0.05). Cecal digesta concentrations of total short-chain fatty acids, acetate and butyrate were higher in group O3.0 than in group O (p < 0.05). Targeted plasma metabolomics revealed 53 metabolites differing between groups, amongst which two indole metabolites, indole-3-propionic acid and 3-indoxylsulfate, were markedly elevated in group O3.0 compared to groups O1.5 and O. Regarding that increased abundances of bacteria of the Actinobacteria phylum and Lactobacillaceae family in the gut have been reported to be associated with antisteatotic, hepatoprotective and antiinflammatory effects, the pronounced increases of Bifidobacteriaceae and Coriobacteriaceae (both Actinobacteria), and of Lactobacillaceae in group O3.0 might have contributed to the amelioration of fatty liver.},
}

@article {pmid35048920,
year = {2022},
author = {Chen, W and Zhu, R and Ye, X and Sun, Y and Tang, Q and Liu, Y and Yan, F and Yu, T and Zheng, X and Tu, P},
title = {Food-derived cyanidin-3-O-glucoside reverses microplastic toxicity via promoting discharge and modulating the gut microbiota in mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d1fo02983e},
pmid = {35048920},
issn = {2042-650X},
abstract = {Microplastics (MPs) ingested and accumulated by organisms would ultimately pose a threat to humans via the food chain. A balanced gut microbiota contributes to many health benefits, which is readily influenced by environmental chemicals such as MPs. Cyanidin-3-O-glucoside (C3G), a bioactive compound of the anthocyanin family, possesses a variety of functional effects including anti-oxidant and anti-inflammatory, as well as gut microbiota modulation. C3G has been demonstrated to prevent polystyrene (PS) induced toxicities in Caco-2 cells and Caenorhabditis elegans (C. elegans) via activating autophagy and promoting discharge. In the present study, we aimed to explore the alleviation effect of C3G on PS induced toxicities in C57BL/6 mice. Our results showed that the supplementation of C3G effectively reduced the tissue accumulation and promoted the fecal PS discharge, leading to alleviation of the PS-caused oxidative stress and inflammatory response. Meanwhile, C3G modulated PS-associated gut microbiome perturbations and regulated functional bacteria in inflammation such as Desulfovibrio, Helicobacter, Oscillospiraceae and Lachnoclostridium. Also, C3G administration initiated alterations in functional pathways in response to xenobiotic PS, and reduced bacterial functional genes related to inflammation and human diseases. These findings may offer evidence for the protective role of C3G in the intervention of PS-induced toxicity and gut dysbiosis.},
}

@article {pmid35048549,
year = {2022},
author = {Khitan, ZJ and Chin, KV and Sodhi, K and Kheetan, M and Alsanani, A and Shapiro, JI},
title = {Gut Microbiome and Diet in Populations with Obesity: Role of the Na+/K+-ATPase Transporter Signaling in Severe COVID-19.},
journal = {Obesity (Silver Spring, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/oby.23387},
pmid = {35048549},
issn = {1930-739X},
abstract = {OBJECTIVES: The triad of obesity, high protein diet from animal sources and disturbed gut microbiota have been linked to poor clinical outcome in COVID-19 patients. In this report, we are exploring the effect of oxidative stress resulting from the Na+ /K+ -ATPase transporter signaling cascade as a driver to this poor clinical outcome.

METHODS: Protein-protein interactions with SARS-CoV-2 proteome were identified from the interactome data for ATP1A1, EGFR, and ERBB2, using the curated data from the BioGRID Database of Protein Interactions. Data for gene expression pattern of inflammatory response was from the Gene Expression Omnibus (GEO) database for cardiomyocytes post SARS-CoV-2 infection (number GSE151879).

RESULTS: The ATP1A1 subunit of the Na+ /K+ -ATPase transporter is targeted by multiple SARS-CoV-2 proteins. Further, receptor proteins associated with inflammatory response including EGFR and ERBB2, which interact with ATP1A1, are also targeted by some SARS-CoV-2 proteins. This heightened interaction likely triggers a cytokine release that increases the severity of the viral infection in obese individuals.

CONCLUSIONS: The similarities between the effects of SARS-CoV2 proteins and indoxyl sulphate on the Na+ /K+ -ATPase transporter signaling cascade suggest the possibility of augmentation of gene changes seen with COVID-19 infection that can result in a hyper-induction of cytokine release in individuals with obesity.},
}

@article {pmid35048535,
year = {2022},
author = {Thapa, S and Luna, RA and Chumpitazi, BP and Oezguen, N and Abdel-Rahman, SM and Garg, U and Musaad, S and Versalovic, J and Kearns, GL and Shulman, RJ},
title = {Peppermint oil effects on the gut microbiome in children with functional abdominal pain.},
journal = {Clinical and translational science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cts.13224},
pmid = {35048535},
issn = {1752-8062},
support = {//US Government/ ; },
abstract = {Peppermint oil (PMO) is effective in the treatment of functional abdominal pain disorders, but its mechanism of action is unclear. Evidence suggests PMO has microbicidal activity. We investigated the effect of three different doses of PMO on gut microbiome composition. Thirty children (7-12 years of age) with functional abdominal pain provided a baseline stool sample prior to randomization to 180, 360, or 540 mg of enteric coated PMO (10 participants per dose). They took their respective dose of PMO (180 mg once, 180 mg twice, or 180 mg thrice daily) for 1 week, after which the stool collection was repeated. Baseline and post-PMO stools were analyzed for microbiome composition. There was no difference in alpha diversity of the gut microbiome between the baseline and post-PMO treatment. Principal coordinate analysis revealed no significant difference in overall bacterial composition between baseline and post-PMO samples, as well as between the PMO dose groups. However, the very low abundant Collinsella genus and three operational taxonomic units (one belonging to Collinsella) were significantly different in samples before and after PMO treatment. The Firmicutes/Bacteroidetes ratio was lower in children who received 540 mg of PMO compared to the 180 mg and 360 mg dose groups (p = 0.04). Network analysis revealed separation between pre- and post-PMO fecal samples with the genus Collinsella driving the post-PMO clusters. PMO administration appeared to impact only low abundance bacteria. The 540 mg PMO dose differentially impacted the Firmicutes/Bacteroidetes ratio. A higher dose and/or longer duration of treatment might yield different results.},
}

@article {pmid35048307,
year = {2022},
author = {Xia, J and Wang, M and Jiang, W},
title = {New insights into pathogenesis of IgA nephropathy.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {35048307},
issn = {1573-2584},
abstract = {IgA nephropathy (IgAN) is the usual form of glomerulonephritis worldwide; however, the pathogenesis remains complex and uncertain. The interactions of gene, immune and environment lead to the variability of IgAN clinical presentations. Except for gene, it is still a question that what kind of the external factors that may cause IgAN. We summarized exposome, microbiome and infectome may be involved in the pathogenesis of IgAN through literature. Based on the above discoveries, we proposed a hypothesis of the course of IgAN that gene determines the internal cause, while skin and mucosa inflammations are the conditions of inducing immune disorders, the low point of immune disorders and change of immune status caused by internal and external environment lead to the disease onset. Therefore, a more detailed clinical phemomics of IgAN was required to be collected for further study.},
}

@article {pmid35048279,
year = {2022},
author = {Serag, AM and Abdel-Sabour, MS and El-Hadidi, M and Maged, M and Magdy, M and Ramadan, MF and Refaat, MH},
title = {Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {35048279},
issn = {1559-0291},
abstract = {Nile tilapia, Oreochromis niloticus, is the principal fish bred in Egypt. A pilot study was designed to analyze the bacterial composition of the Nile tilapia fish guts from two saltwater lakes in Northern Egypt. Fish samples were obtained from two Delta lakes: Manzala (ML) and Borollus (BL). DNA was extracted, and the bacterial communities in the stomach content were classified (down to the species level) using the 16S rRNA-based analysis. From the two metagenomics libraries in this study, 1,426,740 reads of the amplicon sequence corresponding to 508 total taxonomic operational units were recorded. The most prevalent bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Synergistetes in all samples. Some of the strains identified belong to classes of pathogenic zoonotic bacteria. A notable difference was observed between gut bacteria of Nile tilapia fish obtained from BL and ML. There is a remarkable indication that Nile tilapia fish living in BL is heavily burdened with pathogenic microbes most remarkably those involved with methylation of mercury and its accumulation in fish organs. These pathogenic microbes could have clinical implications and correlated with many diseases. This result was also consistent with the metagenomic data's functional prediction that indicated that Nile tilapia species harboring these two Egyptian northern lakes may be exposed to numerous anthropogenic pollutants. The findings show that the host environment has a significant impact on the composition of its microbiota. The first step towards exploring the better management of this profit-making fish is recognizing the structure of the microbiome.},
}

@article {pmid35048168,
year = {2022},
author = {Boscaro, V and Manassero, V and Keeling, PJ and Vannini, C},
title = {Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35048168},
issn = {1432-184X},
abstract = {Protist-bacteria associations are extremely common. Among them, those involving ciliates of the genus Euplotes are emerging as models for symbioses between prokaryotes and eukaryotes, and a great deal of information is available from cultured representatives of this system. Even so, as for most known microbial symbioses, data on natural populations is lacking, and their ecology remains largely unexplored; how well lab cultures represent actual diversity is untested. Here, we describe a survey on natural populations of Euplotes based on a single-cell microbiomic approach, focusing on taxa that include known endosymbionts of this ciliate. The results reveal an unexpected variability in symbiotic communities, with individual hosts of the same population harboring different sets of bacterial endosymbionts. Co-occurring Euplotes individuals of the same population can even have different essential symbionts, Polynucleobacter and "Candidatus Protistobacter," which might suggest that replacement events could be more frequent in nature than previously hypothesized. Accessory symbionts are even more variable: some showed a strong affinity for one host species, some for a sampling site, and two ("Candidatus Cyrtobacter" and "Candidatus Anadelfobacter") displayed an unusual pattern of competitive exclusion. These data represent the first insight into the prevalence and patterns of bacterial symbionts in natural populations of free-living protists.},
}

@article {pmid35048081,
year = {2021},
author = {Belibasakis, GN and Hajishengallis, G},
title = {Frontiers in Oral Mucosal Immunity and the Microbiome.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {821148},
doi = {10.3389/froh.2021.821148},
pmid = {35048081},
issn = {2673-4842},
abstract = {The 2nd International Conference on Oral Mucosal Immunity and the Microbiome (OMIM) took place at the Grecotel Kos Imperial Hotel, Kos, Greece, between 25th and 30th September 2021, under the auspices of the Aegean Conferences. This has only been the second Aegean Conference of this thematic, the first one having taken place in 2018 in Crete, during the same period of the year. Given the hardships in travel and heightened infection transmission risks amid the COVID-19 pandemic, the Conference was well attended by 29 international speakers across the world. For many of the participants, this was the first conference travel in the post-pandemic era, and quite significant that it has taken place on the island of Hippocrates. Stringent regional health and safety regulations had to be followed to accomplish for this in-person Conference to take place. Frontiers in Oral Health has hosted papers from presentations of the Conference, whereas the present article serves as the proceedings of the Conference with summaries of the presentations.},
}

@article {pmid35048077,
year = {2021},
author = {Uranga, C and Nelson, KE and Edlund, A and Baker, JL},
title = {Tetramic Acids Mutanocyclin and Reutericyclin A, Produced by Streptococcus mutans Strain B04Sm5 Modulate the Ecology of an in vitro Oral Biofilm.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {796140},
doi = {10.3389/froh.2021.796140},
pmid = {35048077},
issn = {2673-4842},
abstract = {The human oral microbiome consists of diverse microbes actively communicating and interacting through a variety of biochemical mechanisms. Dental caries is a major public health issue caused by fermentable carbohydrate consumption that leads to dysbiosis of the oral microbiome. Streptococcus mutans is a known major contributor to caries pathogenesis, due to its exceptional ability to form biofilms in the presence of sucrose, as well as to its acidophilic lifestyle. S. mutans can also kill competing bacteria, which are typically health associated, through the production of bacteriocins and other small molecules. A subset of S. mutans strains encode the muc biosynthetic gene cluster (BGC), which was recently shown to produce the tetramic acids, mutanocyclin and reutericyclins A, B, and C. Reutericyclin A displayed strong antimicrobial activity and mutanocyclin appeared to be anti-inflammatory; however the effect of these compounds, and the carriage of muc by S. mutans, on the ecology of the oral microbiota is not known, and was examined here using a previously developed in vitro biofilm model derived from human saliva. While reutericyclin significantly inhibited in vitro biofilm formation and acid production at sub-nanomolar concentrations, mutanocyclin did not present any activity until the high micromolar range. 16S rRNA gene sequencing revealed that reutericyclin drastically altered the biofilm community composition, while mutanocyclin showed a more specific effect, reducing the relative abundance of cariogenic Limosilactobacillus fermentum. Mutanocyclin or reutericyclin produced by the S. mutans strains amended to the community did not appear to affect the community in the same way as the purified compounds, although the results were somewhat confounded by the differing growth rates of the S. mutans strains. Regardless of the strain added, the addition of S. mutans to the in vitro community significantly increased the abundance of S. mutans and Veillonella infantium, only. Overall, this study illustrates that reutericyclin A and mutanocyclin do impact the ecology of a complex in vitro oral biofilm; however, further research is needed to determine the extent to which the production of these compounds affects the virulence of S. mutans.},
}

@article {pmid35048073,
year = {2021},
author = {Zhou, P and Manoil, D and Belibasakis, GN and Kotsakis, GA},
title = {Veillonellae: Beyond Bridging Species in Oral Biofilm Ecology.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {774115},
doi = {10.3389/froh.2021.774115},
pmid = {35048073},
issn = {2673-4842},
abstract = {The genus Veillonella comprises 16 characterized species, among which eight are commonly found in the human oral cavity. The high abundance of Veillonella species in the microbiome of both supra- and sub-gingival biofilms, and their interdependent relationship with a multitude of other bacterial species, suggest veillonellae to play an important role in oral biofilm ecology. Development of oral biofilms relies on an incremental coaggregation process between early, bridging and later bacterial colonizers, ultimately forming multispecies communities. As early colonizer and bridging species, veillonellae are critical in guiding the development of multispecies communities in the human oral microenvironment. Their ability to establish mutualistic relationships with other members of the oral microbiome has emerged as a crucial factor that may contribute to health equilibrium. Here, we review the general characteristics, taxonomy, physiology, genomic and genetics of veillonellae, as well as their bridging role in the development of oral biofilms. We further discuss the role of Veillonella spp. as potential "accessory pathogens" in the human oral cavity, capable of supporting colonization by other, more pathogenic species. The relationship between Veillonella spp. and dental caries, periodontitis, and peri-implantitis is also recapitulated in this review. We finally highlight areas of future research required to better understand the intergeneric signaling employed by veillonellae during their bridging activities and interspecies mutualism. With the recent discoveries of large species and strain-specific variation within the genus in biological and virulence characteristics, the study of Veillonella as an example of highly adaptive microorganisms that indirectly participates in dysbiosis holds great promise for broadening our understanding of polymicrobial disease pathogenesis.},
}

@article {pmid35048071,
year = {2021},
author = {Dame-Teixeira, N and de Lima, AKA and Do, T and Stefani, CM},
title = {Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {770917},
doi = {10.3389/froh.2021.770917},
pmid = {35048071},
issn = {2673-4842},
abstract = {Objectives: In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the Veillonella genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of Veillonella species in dental caries in studies using NGS data. Materials and Methods: Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality. Results: Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of Veillonella spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54-3.90); p = 0.01]. Conclusions: Veillonella spp. is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.},
}

@article {pmid35048063,
year = {2021},
author = {Gui, Q and Lyons, DJ and Deeb, JG and Belvin, BR and Hoffman, PS and Lewis, JP},
title = {Non-human Primate Macaca mulatta as an Animal Model for Testing Efficacy of Amixicile as a Targeted Anti-periodontitis Therapy.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {752929},
doi = {10.3389/froh.2021.752929},
pmid = {35048063},
issn = {2673-4842},
abstract = {Periodontitis is an inflammatory condition triggered by selected oral microbiota; thus treatment strategies should be aimed at reducing the abundance of the pathogenic bacteria. An obstacle to preclinical testing of such strategies is the availability of reliable animal models. Here, a non-human primate (NHP), Macaca mulatta, was used to examine the effectiveness of a novel antimicrobial, amixicile, which inhibits pyruvate-ferredoxin oxidoreductase (PFOR) present in anaerobic bacteria. Animals were assessed for their periodontal health, including radiography, clinical attachment loss (CAL), presence of plaque (PI), bleeding on probing (BOP) and pocket depth (PD), and sampled for saliva, gingival crevicular fluid (GCF), and subgingival plaque to determine their baseline clinical status. Amixicile was then administered for 2 weeks (40 mg/kg/day) and the animals were monitored for periodontal health immediately after the antibiotic treatment, then at 1 month-, 3 months-, and 6-months posttreatment. Microbial species present in plaque and saliva were determined through 16S rDNA sequencing. Baseline assessment of the microbiome has shown a significant proportion of bacteria belonging to the Streptococcus, Haemophilus, Porphyromonas, Gemella, and Fusobacterium genera. The abundance of Porphyromonas and Fusobacterium was reduced following treatment with amixicile, whereas that of Escherichia, Haemophilus, and Gemella were elevated. CAL, PD, and BOP were also significantly reduced following the treatment. In conclusion, the NHP model proves useful for preclinical studies of strategies targeting selected members of the oral microbiome. We show that amixicile reduces the levels of anaerobic bacteria under in vivo conditions, correlating with a reduction in CAL, PD, and BOP, thus validating its usefulness as an antimicrobial strategy.},
}

@article {pmid35048056,
year = {2021},
author = {Kurago, Z and Loveless, J},
title = {Microbial Colonization and Inflammation as Potential Contributors to the Lack of Therapeutic Success in Oral Squamous Cell Carcinoma.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {739499},
doi = {10.3389/froh.2021.739499},
pmid = {35048056},
issn = {2673-4842},
abstract = {This review discusses the microenvironment of evolving and established conventional oral squamous cell carcinoma, by far the most common oral cancer. The focus of this paper is mainly on the more recent data that describe the role of microorganisms, host-microbial interactions, and in particular, the contributions of cell-surface toll-like receptors on immune system cells and on normal and malignant epithelial cells to their functions that support carcinogenesis. Because carcinomas arising at various host surfaces share much in common, additional information available from studies of other carcinomas is included in the discussion. Accumulating evidence reveals the complex toll-like receptor-mediated tumor-supporting input into many aspects of carcinogenesis via malignant cells, stromal immune cells and non-immune cells, complicating the search for effective treatments.},
}

@article {pmid35048055,
year = {2021},
author = {Widyarman, AS and Theodorea, CF and Udawatte, NS and Drestia, AM and Bachtiar, EW and Astoeti, TE and Bachtiar, BM},
title = {Diversity of Oral Microbiome of Women From Urban and Rural Areas of Indonesia: A Pilot Study.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {738306},
doi = {10.3389/froh.2021.738306},
pmid = {35048055},
issn = {2673-4842},
abstract = {Objective: The studies on the influence of geographical and socio-economic factors on the oral microbiome remain underrepresented. The Indonesia basic health research (RISKESDAS) 2018, showed an increasing trend in non-communicable diseases compared with the previous report in 2013. The prevalence of diabetes, heart disease, hypertension, and obesity are reported to be higher in urban areas than in rural areas. Interestingly, non-communicable diseases were found to be more prevalent in women than men. This pilot study aimed to examine the oral health and oral microbiome derived from tongue samples of healthy Indonesian women from urban and rural areas. Methods: Twenty women aged 21-47 years old from West Jakarta, residents of DKI Jakarta (n = 10) as representative of the urban area, and residents of Ende, Nangapanda, East Nusa Tenggara (n = 10) as representative of the rural area were recruited for this pilot study. The participants were evaluated by the Simplified Oral Hygiene Index (OHI-S) according to the criteria of Greene and Vermillion and divided into three groups. High-throughput DNA sequencing was performed on an Illumina iSeq 100 platform. Results: The principal component analysis displayed a marked difference in the bacterial community profiles between the urban and rural localities. The presence of manifest was associated with increased diversity and an altered oral bacterial community profile in the urban women. Two bacterial taxa were present at significantly higher levels (adjusted p < 0.01) in the urban oral microflora (Genus Prevotella and Leptotricia) could account for this difference irrespective of the individual oral hygiene status. The linear discriminant analysis effect size (LEfSe) analysis revealed several distinct urban biomarkers. At the species level, Leptotrichia wadei, Prevotella melaninogenica, Prevotella jejuni, and P. histicola, show an excellent discriminatory potential for distinguishing the oral microflora in women between urban and rural areas. Further, using SparCC co-occurrence network analysis, the co-occurrence pattern in the dominant core oral microbiome assembly was observed to be specific to its ecological niche between two populations. Conclusions: This is the first pilot study demonstrating the characterization of the oral microbiome in Indonesian women in urban and rural areas. We found that the oral microbiome in women displays distinct patterns consistent with geographic locality. The specific characterization of the microbiota of Indonesian women is likely linked to geographical specific dietary habits, cultural habits, and socio-economic status or the population studied.},
}

@article {pmid35048048,
year = {2021},
author = {Ebersole, JL and Nagarajan, R and Kirakodu, S and Gonzalez, OA},
title = {Oral Microbiome and Gingival Gene Expression of Inflammatory Biomolecules With Aging and Periodontitis.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {725115},
doi = {10.3389/froh.2021.725115},
pmid = {35048048},
issn = {2673-4842},
abstract = {Although data describe the presence and increase of inflammatory mediators in the local environment in periodontitis vs. health in humans, details regarding how these responses evolve in the transition from health to disease, changes during disease progression, and features of a resolved lesion remain unknown. This study used a nonhuman primate model of ligature-induced periodontitis in young, adolescent, adult, and aged animals to document features of inflammatory response affected by age. Rhesus monkeys had ligatures tied and provided gingival tissue biopsy specimens at baseline, 0.5, 1, and 3 months of disease and at 5 months of the study, which was 2 months post-ligature removal for clinically resolved tissues. The transcriptome was assessed using microarrays for chemokine (n = 41), cytokine (n = 45), chemokine receptor (n = 21), cytokine receptor (n = 37), and lipid mediator (n = 31) genes. Limited differences were noted in healthy tissues for chemokine expression with age; however, chemokine receptor genes were decreased in young but elevated in aged samples. IL1A, IL36A, and IL36G cytokines were decreased in the younger groups, with IL36A elevated in aged animals. IL10RA/IL10RB cytokine receptors were altered with age. Striking variation in the lipid mediator genes in health was observed with nearly 60% of these genes altered with age. A specific repertoire of chemokine and chemokine receptor genes was affected by the disease process, predominated by changes during disease initiation. Cytokine/cytokine receptor genes were also elevated with disease initiation, albeit IL36B, IL36G, and IL36RN were all significantly decreased throughout disease and resolution. Significant changes were observed in similar lipid mediator genes with disease and resolution across the age groups. Examination of the microbiome links to the inflammatory genes demonstrated that specific microbes, including Fusobacterium, P. gingivalis, F. alocis, Pasteurellaceae, and Prevotella are most frequently significantly correlated. These correlations were generally positive in older animals and negative in younger specimens. Gene expression and microbiome patterns from baseline were distinctly different from disease and resolution. These results demonstrate patterns of inflammatory gene expression throughout the phases of the induction of a periodontal disease lesion. The patterns show a very different relationship to specific members of the oral microbiome in younger compared with older animals.},
}

@article {pmid35048045,
year = {2021},
author = {Kawamoto, D and Borges, R and Ribeiro, RA and de Souza, RF and Amado, PPP and Saraiva, L and Horliana, ACRT and Faveri, M and Mayer, MPA},
title = {Oral Dysbiosis in Severe Forms of Periodontitis Is Associated With Gut Dysbiosis and Correlated With Salivary Inflammatory Mediators: A Preliminary Study.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {722495},
doi = {10.3389/froh.2021.722495},
pmid = {35048045},
issn = {2673-4842},
abstract = {Inflammation is a driven force in modulating microbial communities, but little is known about the interplay between colonizing microorganisms and the immune response in periodontitis. Since local and systemic inflammation may play a whole role in disease, we aimed to evaluate the oral and fecal microbiome of patients with periodontitis and to correlate the oral microbiome data with levels of inflammatory mediator in saliva. Methods: Nine patients with periodontitis (P) in Stage 3/Grade B and nine age-matched non-affected controls (H) were evaluated. Microbial communities of oral biofilms (the supra and subgingival from affected and non-affected sites) and feces were determined by sequencing analysis of the 16SrRNA V3-V4 region. Salivary levels of 40 chemokines and cytokines were correlated with oral microbiome data. Results: Supragingival microbial communities of P differed from H (Pielou's evenness index, and Beta diversity, and weighted UniFrac), since relative abundance (RA) of Defluviitaleaceae, Desulfobulbaceae, Mycoplasmataceae, Peptostreococcales-Tissierellales, and Campylobacteraceae was higher in P, whereas Muribaculaceae and Streptococcaceae were more abundant in H. Subgingival non-affected sites of P did not differ from H, except for a lower abundance of Gemellaceae. The microbiome of affected periodontitis sites (PD ≥ 4 mm) clustered apart from the subgingival sites of H. Oral pathobionts was more abundant in sub and supragingival biofilms of P than H. Fecal samples of P were enriched with Acidaminococcus, Clostridium, Lactobacillus, Bifidobacterium, Megasphaera, and Romboutsia when compared to H. The salivary levels of interleukin 6 (IL-6) and inflammatory chemokines were positively correlated with the RA of several recognized and putative pathobionts, whereas the RA of beneficial species, such as Rothia aeria and Haemophilus parainfluenzae was negatively correlated with the levels of Chemokine C-C motif Ligand 2 (CCL2), which is considered protective. Dysbiosis in patients with periodontitis was not restricted to periodontal pockets but was also seen in the supragingival and subgingival non-affected sites and feces. Subgingival dysbiosis revealed microbial signatures characteristic of different immune profiles, suggesting a role for candidate pathogens and beneficial organisms in the inflammatory process of periodontitis.},
}

@article {pmid35048037,
year = {2021},
author = {Negrini, TC and Carlos, IZ and Duque, C and Caiaffa, KS and Arthur, RA},
title = {Interplay Among the Oral Microbiome, Oral Cavity Conditions, the Host Immune Response, Diabetes Mellitus, and Its Associated-Risk Factors-An Overview.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {697428},
doi = {10.3389/froh.2021.697428},
pmid = {35048037},
issn = {2673-4842},
abstract = {This comprehensive review of the literature aimed to investigate the interplay between the oral microbiome, oral cavity conditions, and host immune response in Diabetes mellitus (DM). Moreover, this review also aimed to investigate how DM related risk factors, such as advanced age, hyperglycemia, hyperlipidemia, obesity, hypertension and polycystic ovary syndrome (PCOS), act in promoting or modifying specific mechanisms that could potentially perpetuate both altered systemic and oral conditions. We found that poorly controlled glycemic index may exert a negative effect on the immune system of affected individuals, leading to a deficient immune response or to an exacerbation of the inflammatory response exacerbating DM-related complications. Hyperglycemia induces alterations in the oral microbiome since poor glycemic control is associated with increased levels and frequencies of periodontal pathogens in the subgingival biofilm of individuals with DM. A bidirectional relationship between periodontal diseases and DM has been suggested: DM patients may have an exaggerated inflammatory response, poor repair and bone resorption that aggravates periodontal disease whereas the increased levels of systemic pro-inflammatory mediators found in individuals affected with periodontal disease exacerbates insulin resistance. SARS-CoV-2 infection may represent an aggravating factor for individuals with DM. Individuals with DM tend to have low salivary flow and a high prevalence of xerostomia, but the association between prevalence/experience of dental caries and DM is still unclear. DM has also been associated to the development of lesions in the oral mucosa, especially potentially malignant ones and those associated with fungal infections. Obesity plays an important role in the induction and progression of DM. Co-affected obese and DM individuals tend to present worse oral health conditions. A decrease in HDL and, an increase in triglycerides bloodstream levels seem to be associated with an increase on the load of periodontopathogens on oral cavity. Moreover, DM may increase the likelihood of halitosis. Prevalence of impaired taste perception and impaired smell recognition tend to be greater in DM patients. An important interplay among oral cavity microbiome, DM, obesity and hypertension has been proposed as the reduction of nitrate into nitrite, in addition to contribute to lowering of blood pressure, reduces oxidative stress and increases insulin secretion, being these effects desirable for the control of obesity and DM. Women with PCOS tend to present a distinct oral microbial composition and an elevated systemic response to selective members of this microbial community, but the association between oral microbiome, PCOS are DM is still unknown. The results of the studies presented in this review suggest the interplay among the oral microbiome, oral cavity conditions, host immune response and DM and some of the DM associated risk factors exist. DM individuals need to be encouraged and motivated for an adequate oral health care. In addition, these results show the importance of adopting multidisciplinary management of DM and of strengthening physicians-dentists relationship focusing on both systemic and on oral cavity conditions of DM patients.},
}

@article {pmid35048036,
year = {2021},
author = {Ruff, RR and Paul, B and Sierra, MA and Xu, F and Li, X and Crystal, YO and Saxena, D},
title = {Predicting Treatment Nonresponse in Hispanic/Latino Children Receiving Silver Diamine Fluoride for Caries Arrest: A Pilot Study Using Machine Learning.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {695759},
doi = {10.3389/froh.2021.695759},
pmid = {35048036},
issn = {2673-4842},
abstract = {Objectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment non-response using machine learning. Methods: An observational pilot study (N = 20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment non-response was assessed using lasso regression and artificial neural networks. Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between non-responders and those who responded to SDF therapy. No differences were found between non-responders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron. Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.},
}

@article {pmid35048035,
year = {2021},
author = {Bamashmous, S and Kotsakis, GA and Jain, S and Chang, AM and McLean, JS and Darveau, RP},
title = {Clinically Healthy Human Gingival Tissues Show Significant Inter-individual Variability in GCF Chemokine Expression and Subgingival Plaque Microbial Composition.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {689475},
doi = {10.3389/froh.2021.689475},
pmid = {35048035},
issn = {2673-4842},
abstract = {Aim: Clinically healthy gingival tissue is maintained through controlled regulation of host defense mechanisms against plaque biofilm overgrowth. One key component is the transit of neutrophils from the vasculature into gingival tissue where the expression of different neutrophil chemokines are tightly regulated. This cross-sectional study examines the inter-individual variability in chemokine profiles within gingival crevicular fluid (GCF) in relation to the subgingival bacterial community in a state of gingival health. Methods: Gingival crevicular fluid and subgingival plaque samples were collected from mesiobuccal surfaces of all six Ramfjord teeth of 20 systemically healthy individuals (14.55 ± 1.67 years). A multiplex immunoassay was carried out to quantify the expression of 40 different chemokines in the healthy gingival tissue. Neutrophils were assessed indirectly by myeloperoxidase (MPO) in GCF using traditional ELISA. Characterization of healthy subgingival plaque was conducted with the Illumina Miseq targeting the 16S rRNA gene. Results: In health, there are distinct variations within individual gingival crevicular fluid chemokine expression profiles, as well as in the concentration of neutrophils, that divided the participants into high or low chemokine expressing groups. Specifically, key differences were identified within MIF (2683.54 ± 985.82 pg per 30-s sample), IL-8/CXCL8 (170.98 ± 176.96 pg per 30-s sample), Gro-α/CXCL1 (160.42 ± 94.21 pg per 30-s sample), ENA-78/CXCL5 (137.76 ± 76.02 pg per 30-s sample), IL-1β (51.39 ± 37.23 pg per 30-s sample), TNF-α (1.76 ± 1.79 pg per 30-s sample), and IFN-γ (0.92 ± 0.54 pg per 30-s sample). Of these identified chemokines, the highest correlation was associated between IL-8/CXCL8 and neutrophils (r = 0.54, p = 0.014). Furthermore, species characterization of healthy subgingival plaque revealed significant inter-individual variability that identified two unique groups unrelated to the previously identified chemokine groups. Conclusion: The lack of concordance between the microbial composition and chemokine profile during health may be a reflection of the unique microbial composition of each individual coupled with variations within their host response, emphasizing the vast complexity of the defense mechanisms in place to maintain gingival health.},
}

@article {pmid35048033,
year = {2021},
author = {Vazquez-Munoz, R and Dongari-Bagtzoglou, A},
title = {Anticandidal Activities by Lactobacillus Species: An Update on Mechanisms of Action.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {689382},
doi = {10.3389/froh.2021.689382},
pmid = {35048033},
issn = {2673-4842},
abstract = {Lactobacilli are among the most studied bacteria in the microbiome of the orodigestive and genitourinary tracts. As probiotics, lactobacilli may provide various benefits to the host. These benefits include regulating the composition of the resident microbiota, preventing - or even potentially reverting- a dysbiotic state. Candida albicans is an opportunistic pathogen that can influence and be influenced by other members of the mucosal microbiota and, under immune-compromising conditions, can cause disease. Lactobacillus and Candida species can colonize the same mucosal sites; however, certain Lactobacillus species display antifungal activities that can contribute to low Candida burdens and prevent fungal infection. Lactobacilli can produce metabolites with direct anticandidal function or enhance the host defense mechanisms against fungi. Most of the Lactobacillus spp. anticandidal mechanisms of action remain underexplored. This work aims to comprehensively review and provide an update on the current knowledge regarding these anticandidal mechanisms.},
}

@article {pmid35048015,
year = {2021},
author = {Wong, J and Manoil, D and Näsman, P and Belibasakis, GN and Neelakantan, P},
title = {Microbiological Aspects of Root Canal Infections and Disinfection Strategies: An Update Review on the Current Knowledge and Challenges.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {672887},
doi = {10.3389/froh.2021.672887},
pmid = {35048015},
issn = {2673-4842},
abstract = {The oral cavity is the habitat of several hundreds of microbial taxa that have evolved to coexist in multispecies communities in this unique ecosystem. By contrast, the internal tissue of the tooth, i.e., the dental pulp, is a physiologically sterile connective tissue in which any microbial invasion is a pathological sign. It results in inflammation of the pulp tissue and eventually to pulp death and spread of inflammation/infection to the periradicular tissues. Over the past few decades, substantial emphasis has been placed on understanding the pathobiology of root canal infections, including the microbial composition, biofilm biology and host responses to infections. To develop clinically effective treatment regimens as well as preventive therapies, such extensive understanding is necessary. Rather surprisingly, despite the definitive realization that root canal infections are biofilm mediated, clinical strategies have been focused more on preparing canals to radiographically impeccable levels, while much is left desired on the debridement of these complex root canal systems. Hence, solely focusing on "canal shaping" largely misses the point of endodontic treatment as the current understanding of the microbial aetiopathogenesis of apical periodontitis calls for the emphasis to be placed on "canal cleaning" and chemo-mechanical disinfection. In this review, we dissect in great detail, the current knowledge on the root canal microbiome, both in terms of its composition and functional characteristics. We also describe the challenges in root canal disinfection and the novel strategies that attempt to address this challenge. Finally, we provide some critical pointers for areas of future research, which will serve as an important area for consideration in Frontiers in Oral Health.},
}

@article {pmid35048007,
year = {2021},
author = {Adibi, S and Seferovic, D and Tribble, GD and Alcorn, JL and Fakhouri, WD},
title = {Surfactant Protein A and Microbiome Composition in Patients With Atraumatic Intraoral Lesions.},
journal = {Frontiers in oral health},
volume = {2},
number = {},
pages = {663483},
doi = {10.3389/froh.2021.663483},
pmid = {35048007},
issn = {2673-4842},
abstract = {Oral ulcers are lesions that occur due to disruption of epithelial integrity of the mucosa of the oral cavity. Intraoral ulcers are often associated with pain, redness, symptoms of discomfort, and blood hemorrhage. The etiology for many oral ulcers is local trauma, systemic health conditions, or medication; for other ulcers the cause is less clear. This pilot study aims to evaluate the salivary components and microbiome in patients with atraumatic pre-ulcerous and ulcerous oral lesions compared to control individuals, while considering three common risk factors for atraumatic ulcers, smoking, stress, and gender. This study uses matched age, sex, and ethnicity samples from healthy otherwise and oral lesion patients to investigate the changes in salivary surfactant protein A (SP-A) and examines the prevalence and diversity of the salivary oral microflora. The goal is to determine if there are factors in saliva that have the potential to be used as biomarkers for risk of developing atraumatic oral ulcers. Our data show that the average level of SP-A is significantly reduced in female smokers compared to non-smoker healthy females. The average level of SP-A in female oral lesion patients is reduced compared to controls. The microbiome composition is significantly affected by smoking and the level of SP-A. Comparing the control participants and oral lesion patients, there are 16 species of bacteria that are significantly different, and all of these bacteria are significantly affected by smoking and SP-A. LEfSe analysis identified five bacteria that may represent potential biomarkers. This preliminary study demonstrates the potential of the oral microbiome to act as a biomarker for oral ulcer risk and infers potential mechanistic links between risk factors and alterations in innate immune mechanisms such as SP-A levels.},
}

@article {pmid35047812,
year = {2022},
author = {Banerjee, K and Chen, J and Zhan, X},
title = {Adaptive and powerful microbiome multivariate association analysis via feature selection.},
journal = {NAR genomics and bioinformatics},
volume = {4},
number = {1},
pages = {lqab120},
doi = {10.1093/nargab/lqab120},
pmid = {35047812},
issn = {2631-9268},
abstract = {The important role of human microbiome is being increasingly recognized in health and disease conditions. Since microbiome data is typically high dimensional, one popular mode of statistical association analysis for microbiome data is to pool individual microbial features into a group, and then conduct group-based multivariate association analysis. A corresponding challenge within this approach is to achieve adequate power to detect an association signal between a group of microbial features and the outcome of interest across a wide range of scenarios. Recognizing some existing methods' susceptibility to the adverse effects of noise accumulation, we introduce the Adaptive Microbiome Association Test (AMAT), a novel and powerful tool for multivariate microbiome association analysis, which unifies both blessings of feature selection in high-dimensional inference and robustness of adaptive statistical association testing. AMAT first alleviates the burden of noise accumulation via distance correlation learning, and then conducts a data-adaptive association test under the flexible generalized linear model framework. Extensive simulation studies and real data applications demonstrate that AMAT is highly robust and often more powerful than several existing methods, while preserving the correct type I error rate. A free implementation of AMAT in R computing environment is available at https://github.com/kzb193/AMAT.},
}

@article {pmid35047681,
year = {2019},
author = {Bannach-Brown, A and Tillmann, S and MacLeod, MR and Wegener, G},
title = {Administration of galacto-oligosaccharide prebiotics in the Flinders Sensitive Line animal model of depression.},
journal = {BMJ open science},
volume = {3},
number = {1},
pages = {e000017},
doi = {10.1136/bmjos-2018-000017},
pmid = {35047681},
issn = {2398-8703},
abstract = {Introduction: Major depressive disorder is the leading source of disability globally and current pharmacological treatments are less than adequate. Animal models such as the Flinders Sensitive Line (FSL) rats are used to mimic aspects of the phenotype in the human disorder and to characterise candidate antidepressant agents. Communication between the gut microbiome and the brain may play an important role in psychiatric disorders such as depression. Interventions targeting the gut microbiota may serve as potential treatments for depression, and this drives increasing research into the effect of probiotics and prebiotics in neuropsychiatric disorders. Prebiotics, galacto-oligosaccharides and fructooligosaccharides that stimulate the activity of gut bacteria have been reported to have a positive impact, reducing anxiety and depressive-like phenotypes and stress-related physiology in mice and rats, as well as in humans. Bimuno, the commercially available beta-galacto-oligosaccharide, has been shown to increase gut microbiota diversity.

Aim: Here, we aim to investigate the effect of Bimuno on rat anxiety-like and depressive-like behaviour and gut microbiota composition in the FSL model, a genetic model of depression, in comparison to their control, the Flinders Resistant Line (FRL) rats.

Methods: Sixty-four male rats aged 5-7 weeks, 32 FSL and 32 FRL rats, will be randomised to receive Bimuno or control (4 g/kg) daily for 4 weeks. Animals will be tested by an experimenter unaware of group allocation on the forced swim test to assessed depressive-like behaviour, the elevated plus maze to assess anxiety-like behaviour and the open field test to assess locomotion. Animals will be weighed and food and water intake, per kilogram of bodyweight, will be recorded. Faeces will be collected from each animal prior to the start of the experiment and on the final day to assess the bacterial diversity and relative abundance of bacterial genera in the gut. All outcomes and statistical analysis will be carried out blinded to group allocation, group assignments will be revealed after raw data have been uploaded to Open Science Framework. Two-way analysis of variance will be carried out to investigate the effect of treatment (control or prebiotic) and strain (FSL or FRL) on depressive-like and anxiety-like behaviours.},
}

@article {pmid35047580,
year = {2021},
author = {Hu, X and Zhou, R and Li, H and Zhao, X and Sun, Y and Fan, Y and Zhang, S},
title = {Alterations of Gut Microbiome and Serum Metabolome in Coronary Artery Disease Patients Complicated With Non-alcoholic Fatty Liver Disease Are Associated With Adverse Cardiovascular Outcomes.},
journal = {Frontiers in cardiovascular medicine},
volume = {8},
number = {},
pages = {805812},
doi = {10.3389/fcvm.2021.805812},
pmid = {35047580},
issn = {2297-055X},
abstract = {Rationale: Patients suffering from coronary artery disease (CAD) complicated with nonalcoholic fatty liver disease (NAFLD) present worse cardiovascular outcomes than CAD patients without NAFLD. The progression of CAD is recently reported to be associated with gut microbiota and microbe-derived metabolites. However, it remains unclear how the complication of NAFLD will affect gut microbiota and microbe-derived metabolites in CAD patients, and whether or not this interplay is related to the worse cardiovascular outcomes in CAD-NAFLD patients. Methods: We performed 16S rRNA sequencing and serum metabolomic analysis in 27 CAD patients with NAFLD, 81 CAD patients without NAFLD, and 24 matched healthy volunteers. Predicted functional profiling was achieved using PICRUSt2. The occurrence of cardiovascular events was assessed by a follow-up study. The association of alterations in the gut microbiome and metabolome with adverse cardiovascular events and clinical indicators was revealed by Spearman correlation analysis. Results: We discovered that the complication of NAFLD was associated with worse clinical outcomes in CAD patients and critical serum metabolome shifts. We identified 25 metabolite modules that were correlated with poor clinical outcome in CAD-NAFLD patients compared with non-NAFLD patients, represented by increased cardiac-toxic metabolites including prochloraz, brofaromine, aristolochic acid, triethanolamine, and reduced potentially beneficial metabolites including estradiol, chitotriose, palmitelaidic acid, and moxisylyte. In addition, the gut microbiome of individuals with CAD-NAFLD was changed and characterized by increased abundances of Oscillibacter ruminantium and Dialister invisus, and decreased abundances of Fusicatenibacter saccharivorans, Bacteroides ovatus and Prevotella copri. PICRUSt2 further confirmed an increase of potential pathogenic bacteria in CAD-NAFLD. Moreover, we found that variations of gut microbiota were critically correlated with changed circulating metabolites and clinical outcomes, which revealed that aberrant gut microbiota in CAD-NAFLD patients may sculpt a detrimental metabolome which results in adverse cardiovascular outcomes. Conclusions: Our findings suggest that CAD patients complicated with NAFLD result in worse clinical outcomes possibly by modulating the features of the gut microbiota and circulating metabolites. We introduce "liver-gut microbiota-heart axis" as a possible mechanism underlying this interrelationship. Our study provides new insights on the contribution of gut microbiota heterogeneity to CAD-NAFLD progression and suggests novel strategies for disease therapy.},
}

@article {pmid35047454,
year = {2021},
author = {Choi, SI and Kim, N and Nam, RH and Park, JH and Nho, H and Yu, JE and Song, CH and Lee, SM and Lee, DH},
title = {Fecal Microbial Enterotypes Differentially Respond to a High-fat Diet Based on Sex in Fischer-344 Rats.},
journal = {Journal of cancer prevention},
volume = {26},
number = {4},
pages = {277-288},
doi = {10.15430/JCP.2021.26.4.277},
pmid = {35047454},
issn = {2288-3649},
abstract = {The gut microbiota interacts with the host gut environment, which is influenced by such factors as sex, age, and host diet. These factors induce changes in the microbial composition. The aim of this study was to identify differences in the gut microbiome of Fisher-344 (F344) rats fed a high-fat diet (HFD), depending on their age and sex. Fecal microbiomes from 6-, 31-, and 74-week-old, and 2-year-old both male and female rats (corresponding to 5-, 30-, 60-, and 80-year-old humans) were analyzed using 16S rRNA gene sequencing, phylogenetic investigation of communities by reconstruction of unobserved states, and enterotype (E) assessment. Moreover, the effect of an HFD on colonic epithelial cells was measured using real-time quantitative PCR. Alpha diversity decreased in the HFD group regardless of age and sex. Based on the enterotype clustering of the whole fecal microbiome, clusters from male rats were divided into E1 and E2 enterotypes, while clusters from female rats were divided into E1, E2, and E3 enterotypes. The female E3 group showed a significantly high abundance in the Ruminococcus genus and expression of Tlr2 mRNA, which may reflect compensation to the HFD. Moreover, the female E3 group showed a lower ratio of opportunistic pathogenic strains to commensal strains compared to the female E2 group. Administration of an HFD influenced the rat fecal microbiota in all assessed age groups, which could be further differentiated by sex. In particular, female rats showed a compensatory enterotype response to an HFD compared to male rats.},
}

@article {pmid35047354,
year = {2022},
author = {Filippelli, M and dell'Omo, R and Amoruso, A and Paiano, I and Pane, M and Napolitano, P and Campagna, G and Bartollino, S and Costagliola, C},
title = {Effectiveness of oral probiotics supplementation in the treatment of adult small chalazion.},
journal = {International journal of ophthalmology},
volume = {15},
number = {1},
pages = {40-44},
doi = {10.18240/ijo.2022.01.06},
pmid = {35047354},
issn = {2222-3959},
abstract = {AIM: To define the possible beneficial impact of probiotics oral supplementation on patients affected by chalazion.

METHODS: Prospective comparative pilot study on 20 adults suffering from chalazion randomly divided into two groups. The first group (n=10) received conservative treatment with lid hygiene, warm compression, and dexamethasone/tobramycin ointment for at least 20d. The second group (n=10), in addition to the conservative treatment, received a mixture of probiotic microorganisms of Streptococcus thermophilus ST10 (DSM 25246), Lactococcus lactis LLC02 (DSM 29536) and Lactobacillus delbrueckii (DSM 16606) once a day up to 3mo. Chalazia were classified according to their size into three groups: small (<2 mm), medium (≥2 to <4 mm), or large (≥4 mm). When conservative treatment with and without probiotics supplementation failed to resolve the lesion, invasive methods were used, intralesional steroid injection in medium size chalazion and surgical incision and curettage for the largest ones.

RESULTS: Medical treatment with or without probiotics supplementation was effective only on the small size chalazia. There was a significant difference in the time taken for complete resolution of small size chalazia between the two groups in favor of the patients receiving probiotics (38.50±9.04d vs 21.00±7.00d, P=0.039). Medium and large size chalazia did not respond to medical treatment with or without probiotics supplementation over the follow-up period (3mo). The treatment did not induce any complications in both groups and no recurrence of chalaziosis was recorded in both groups.

CONCLUSION: The considerable difference in time taken for complete resolution of small chalazia between the two groups in favor of the experimental one confirms the presence of a gut-eye axis.},
}

@article {pmid35047301,
year = {2021},
author = {Penumetcha, SS and Ahluwalia, S and Irfan, R and Khan, SA and Rohit Reddy, S and Vasquez Lopez, ME and Zahid, M and Busmail, A and Mohammed, L},
title = {The Efficacy of Probiotics in the Management of Helicobacter Pylori: A Systematic Review.},
journal = {Cureus},
volume = {13},
number = {12},
pages = {e20483},
doi = {10.7759/cureus.20483},
pmid = {35047301},
issn = {2168-8184},
abstract = {Helicobacter pylori is a Gram-negative microorganism that causes chronic dyspepsia, gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, and gastric adenocarcinoma. Various antibiotic regimens are employed to eradicate it; however, antibiotic resistance has skyrocketed in recent years, resulting in a reduction in eradication rates. As a result, numerous novel therapeutic approaches are being adopted in clinical practice, and probiotics are being extensively investigated. Probiotics are living bacteria that, when consumed, offer many medicinal advantages that may be accomplished by altering the amount or activity of gut flora. Their beneficial influence on gut health, immune system modulation, and cancer therapy is the subject of extensive investigation. This is owing to their perceived safety and simplicity of use. The primary objective of this review is to learn about and investigate the function of probiotics in the eradication of H. pylori, either alone or in conjunction with traditional treatments. Data have been collected from PubMed, PubMed Central, Medline, Cochrane, and Google Scholar, and relevant articles have been chosen following the PRISMA guidelines. Our search resulted in 2489 records, of which 123 full-text articles were screened for eligibility. Two reviewers independently performed the quality appraisal of 16 relevant articles, and ultimately 11 high-quality studies are included in this review. In conclusion, probiotic monotherapy does not have a significant effect on the eradication rates of H. pylori, but in conjunction with standard treatment regimens, there was mild improvement in the eradication rates but a significant reduction of side effects due to antibiotics.},
}

@article {pmid35046983,
year = {2021},
author = {Cai, S and Jia, J and He, C and Zeng, L and Fang, Y and Qiu, G and Lan, X and Su, J and He, X},
title = {Multi-Omics of Pine Wood Nematode Pathogenicity Associated With Culturable Associated Microbiota Through an Artificial Assembly Approach.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {798539},
doi = {10.3389/fpls.2021.798539},
pmid = {35046983},
issn = {1664-462X},
abstract = {Pinewood nematode (PWN), the causal agent of pine wilt disease (PWD), causes massive global losses of Pinus species each year. Bacteria and fungi existing in symbiosis with PWN are closely linked with the pathogenesis of PWD, but the relationship between PWN pathogenicity and the associated microbiota is still ambiguous. This study explored the relationship between microbes and the pathogenicity of PWN by establishing a PWN-associated microbe library, and used this library to generate five artificial PWN-microbe symbiont (APMS) assemblies with gnotobiotic PWNs. The fungal and bacterial communities of different APMSs (the microbiome) were explored by next-generation sequencing. Furthermore, different APMSs were used to inoculate the same Masson pine (Pinus massoniana) cultivar, and multi-omics (metabolome, phenomics, and transcriptome) data were obtained to represent the pathogenicity of different APMSs at 14 days post-inoculation (dpi). Significant positive correlations were observed between microbiome and transcriptome or metabolome data, but microbiome data were negatively correlated with the reactive oxygen species (ROS) level in the host. Five response genes, four fungal genera, four bacterial genera, and nineteen induced metabolites were positively correlated with the ROS level, while seven induced metabolites were negatively correlated. To further explore the function of PWN-associated microbes, single genera of functional microbes (Mb1-Mb8) were reloaded onto gnotobiotic PWNs and used to inoculate pine tree seedlings. Three of the genera (Cladophialophora, Ochroconis, and Flavobacterium) decreased the ROS level of the host pine trees, while only one genus (Penicillium) significantly increased the ROS level of the host pine tree seedlings. These results demonstrate a clear relationship between associated microbes and the pathogenicity of PWN, and expand the knowledge on the interaction between PWD-induced forest decline and the PWN-associated microbiome.},
}

@article {pmid35046950,
year = {2021},
author = {Gong, X and Liu, Y and Liu, X and Li, A and Guo, K and Zhou, D and Hong, Z},
title = {Disturbance of Gut Bacteria and Metabolites Are Associated with Disease Severity and Predict Outcome of NMDAR Encephalitis: A Prospective Case-Control Study.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {791780},
doi = {10.3389/fimmu.2021.791780},
pmid = {35046950},
issn = {1664-3224},
abstract = {Objective: We aimed to investigate the associations between the intestinal microbiota, metabolites, cytokines, and clinical severity in anti-N-methyl-d-aspartate receptor (NMDAR) encephalitis and to further determine the predictive value of the intestinal microbiota or metabolites in clinical prognosis.

Methods: In this prospective observational cohort study of 58 NMDAR encephalitis patients and 49 healthy controls, fecal microbiota, metabolites, and cytokines were quantified and characterized by16S rRNA gene sequencing, liquid chromatography-mass spectrometry, and the Luminex assay, respectively.

Results: There were marked variations in the gut microbiota composition and metabolites in critically ill patients. We identified 8 metabolite modules (mainly characterized by fatty acid, glycerophosphoethanolamines, and glycerophosphocholines) that were distinctly classified as negatively or positively associated with bacterial co-abundance groups (CAGs). These CAGs were mainly composed of Bacteroides, Eubacterium_hallii_group, Anaerostipes, Ruminococcus, Butyricicoccus, and Faecalibacterium, which were substantially altered in patients. In addition, these fecal and serum metabolic modules were further correlated with the serum cytokines. Additionally, the combination of clinical features, microbial marker (Granulicatella), and a panel of metabolic markers could further enhance the performance of prognosis discrimination significantly, which yielded an area under the receiver operating characteristic curve of (AUC) of 0.94 (95%CI = 0.7-0.9). Patients with low bacterial diversity are more likely to develop relapse than those with higher bacterial diversity (log-rank p = 0.04, HR = 2.7, 95%CI = 1.0-7.0).

Interpretation: The associations between the multi-omics data suggested that certain bacteria might affect the pathogenesis of NMDAR encephalitis by modulating the metabolic pathways of the host and affecting the production of pro-inflammatory cytokines. Furthermore, the disturbance of fecal bacteria may predict the long-term outcome and relapse in NMDAR encephalitis.},
}

@article {pmid35046929,
year = {2021},
author = {König, RS and Albrich, WC and Kahlert, CR and Bahr, LS and Löber, U and Vernazza, P and Scheibenbogen, C and Forslund, SK},
title = {The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS).},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {628741},
doi = {10.3389/fimmu.2021.628741},
pmid = {35046929},
issn = {1664-3224},
abstract = {Myalgic encephalomyelitis (ME) or Chronic Fatigue Syndrome (CFS) is a neglected, debilitating multi-systemic disease without diagnostic marker or therapy. Despite evidence for neurological, immunological, infectious, muscular and endocrine pathophysiological abnormalities, the etiology and a clear pathophysiology remains unclear. The gut microbiome gained much attention in the last decade with manifold implications in health and disease. Here we review the current state of knowledge on the interplay between ME/CFS and the microbiome, to identify potential diagnostic or interventional approaches, and propose areas where further research is needed. We iteratively selected and elaborated on key theories about a correlation between microbiome state and ME/CFS pathology, developing further hypotheses. Based on the literature we hypothesize that antibiotic use throughout life favours an intestinal microbiota composition which might be a risk factor for ME/CFS. Main proposed pathomechanisms include gut dysbiosis, altered gut-brain axis activity, increased gut permeability with concomitant bacterial translocation and reduced levels of short-chain-fatty acids, D-lactic acidosis, an abnormal tryptophan metabolism and low activity of the kynurenine pathway. We review options for microbiome manipulation in ME/CFS patients including probiotic and dietary interventions as well as fecal microbiota transplantations. Beyond increasing gut permeability and bacterial translocation, specific dysbiosis may modify fermentation products, affecting peripheral mitochondria. Considering the gut-brain axis we strongly suspect that the microbiome may contribute to neurocognitive impairments of ME/CFS patients. Further larger studies are needed, above all to clarify whether D-lactic acidosis and early-life antibiotic use may be part of ME/CFS etiology and what role changes in the tryptophan metabolism might play. An association between the gut microbiome and the disease ME/CFS is plausible. As causality remains unclear, we recommend longitudinal studies. Activity levels, bedridden hours and disease progression should be compared to antibiotic exposure, drug intakes and alterations in the composition of the microbiota. The therapeutic potential of fecal microbiota transfer and of targeted dietary interventions should be systematically evaluated.},
}

@article {pmid35046924,
year = {2021},
author = {Qiao, Y and Zhang, Z and Zhai, Y and Yan, X and Zhou, W and Liu, H and Guan, L and Peng, L},
title = {Apigenin Alleviates Obesity-Associated Metabolic Syndrome by Regulating the Composition of the Gut Microbiome.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {805827},
doi = {10.3389/fmicb.2021.805827},
pmid = {35046924},
issn = {1664-302X},
abstract = {The gut microbiota, often viewed as a "digestive organ," can influence the development of obesity and related metabolic disorders. Diet is significantly important in shaping the structure and modulating the function of the gut microbiota. Apigenin (Api) widely exists in fruits and vegetables as a naturally occurring flavonoid and has anti-obesogenic, anti-inflammatory, and anti-carcinogenic properties. Its low bioavailability means it has enough time to interact with the intestine thus becomes a potential substrate for the gut intestine; thus, contributing to gut health. Here, we show that Api reduces whole-body weight, low-grade inflammation, and insulin resistance in high-fat diet (HFD)-induced obese mice. Our results reflect that Api supplementation can substantially improve intestinal dysbiosis triggered by HFD and restores gut barrier damage by alleviating metabolic endotoxemia. Augmentation of Akkermansia and Incertae_Sedis along with reduction of Faecalibaculum and Dubosiella at the genus level potentially mediated the protective effects of Api on metabolic syndrome. Furthermore, we show that the impact of Api on the reduction of body weight and the modification of gut microbiota could be transferred from Api-administered mice to HFD-feeding mice via horizontal fecal microbiota transplantation. Taken together, our data highlight the prebiotic role of Api and show its contribution to the restraint of gut dysbiosis and metabolic deterioration associated with obesity in mice.},
}

@article {pmid35046910,
year = {2021},
author = {Blais, MA and Matveev, A and Lovejoy, C and Vincent, WF},
title = {Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {760282},
doi = {10.3389/fmicb.2021.760282},
pmid = {35046910},
issn = {1664-302X},
abstract = {Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.},
}

@article {pmid35046693,
year = {2022},
author = {He, Y and Yu, W and Ning, P and Luo, Q and Zhao, L and Xie, Y and Yu, Y and Ma, X and Chen, L and Zheng, Y and Gao, Z},
title = {Shared and Specific Lung Microbiota with Metabolic Profiles in Bronchoalveolar Lavage Fluid Between Infectious and Inflammatory Respiratory Diseases.},
journal = {Journal of inflammation research},
volume = {15},
number = {},
pages = {187-198},
doi = {10.2147/JIR.S342462},
pmid = {35046693},
issn = {1178-7031},
abstract = {Background: Infiltration of the lower respiratory tract (LRT) microenvironment could be significantly associated with respiratory diseases. However, alterations in the LRT microbiome and metabolome in infectious and inflammatory respiratory diseases and their correlation with inflammation still need to be explored.

Methods: Bronchoalveolar lavage samples from 44 community-acquired pneumonia (CAP) patients, 29 connective tissue disease-associated interstitial disease (CTD-ILD) patients, and 30 healthy volunteers were used to detect microbiota and metabolites through 16S rRNA gene sequencing and untargeted high-performance liquid chromatography with mass spectrometry.

Results: The composition of the LRT microbial communities and metabolites differed in disease states. CAP patients showed a significantly low abundance and both diseases presented a depletion of some genera of the phylum Bacteroidetes, including Prevotella, Porphyromonas, and health-associated metabolites, such as sphingosine (d16:1), which were negatively correlated with infectious indicators. In contrast, Bacillus and Mycoplasma were both enriched in the disease groups. Streptococcus was specifically increased in CTD-ILD. In addition, co-elevated metabolites such as FA (22:4) and pyruvic acid represented hypoxia and inflammation in the diseases. Significantly increased levels of amino acids and succinate, as well as decreased itaconic acid levels, were observed in CAP patients, whereas CTD-ILD patients showed only a handful of specific metabolic alterations. Functions related to microbial lipid and amino acid metabolism were significantly altered, indicating the possible contributions of microbial metabolism. Dual omics analysis showed a moderate positive correlation between the microbiome and metabolome. The levels of L-isoleucine and L-arginine were negatively correlated with Streptococcus, and itaconic acid positively correlated with Streptococcus.

Conclusion: In the LRT microenvironment, shared and specific alterations occurred in CAP and CTD-ILD patients, which were associated with inflammatory and immune reactions, which may provide a new direction for future studies aiming to elucidate the mechanism, improve the diagnosis, and develop therapies for different respiratory diseases.},
}

@article {pmid35046416,
year = {2022},
author = {Clavijo, V and Morales, T and Vives-Flores, MJ and Reyes Muñoz, A},
title = {The gut microbiota of chickens in a commercial farm treated with a Salmonella phage cocktail.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {991},
pmid = {35046416},
issn = {2045-2322},
support = {0845-2013//Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS)/ ; INV-2017-25-1117//Facultad de Ciencias, Universidad de los Andes/ ; INV-2018-48-1342//Facultad de Ciencias, Universidad de los Andes/ ; INV-2018-50-1399//Facultad de Ciencias, Universidad de los Andes/ ; },
abstract = {The microbiota in broiler chicken intestines affects the animals' health, metabolism, and immunity both positively and negatively. Accordingly, it has a significant impact on animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The purpose of this study is to further characterize the commensal microbial community at production scale in broiler chickens treated with a Salmonella phage treatment. We evaluated the cecal microbiota of broilers reared in a commercial farming system where a phage cocktail against Salmonella, SalmoFree was supplied to animals. To do so, two field trials were conducted, incorporating three doses of phages in the broilers' drinking water. Our results showed that the core microbiome (taxa that were present in more than 50% of samples) contained species that are key to microbiota adaptation in the last stage of the production cycle. Among these, there are some important degraders of complex polysaccharides and producers of short chain fatty acids (SCFA) such as Eisenbergiella and Lachnoclostridium. The phage cocktail did not affect the normal development of the microbiota's structure. The addition of the phage cocktail resulted in a significant reduction in Campylobacter and an increase in Butyricimonas, Helicobacter and Rikenellaceae, which are common inhabitants in chicken gut with known negative and positive effects on their health and metabolism. Altogether, we consider that these results contribute valuable information to the implementation of large-scale phage therapy technologies.},
}

@article {pmid35045853,
year = {2022},
author = {Sun, Z and Song, ZG and Liu, C and Tan, S and Lin, S and Zhu, J and Dai, FH and Gao, J and She, JL and Mei, Z and Lou, T and Zheng, JJ and Liu, Y and He, J and Zheng, Y and Ding, C and Qian, F and Zheng, Y and Chen, YM},
title = {Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients.},
journal = {BMC medicine},
volume = {20},
number = {1},
pages = {24},
pmid = {35045853},
issn = {1741-7015},
support = {2017SHZDZX01//Science and Technology Commission of Shanghai Municipality/ ; 20490780100//Science and Technology Commission of Shanghai Municipality for International Partnership Project/ ; 31741072//National Natural Science Foundation of China/ ; 81973032//National Natural Science Foundation of China/ ; 32041004//National Natural Science Foundation of China/ ; 31930001//National Natural Science Foundation of China/ ; 3213000167//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: COVID-19 is an infectious disease characterized by multiple respiratory and extrapulmonary manifestations, including gastrointestinal symptoms. Although recent studies have linked gut microbiota to infectious diseases such as influenza, little is known about the role of the gut microbiota in COVID-19 pathophysiology.

METHODS: To better understand the host-gut microbiota interactions in COVID-19, we characterized the gut microbial community and gut barrier function using metagenomic and metaproteomic approaches in 63 COVID-19 patients and 8 non-infected controls. Both immunohematological parameters and transcriptional profiles were measured to reflect the immune response in COVID-19 patients.

RESULTS: Altered gut microbial composition was observed in COVID-19 patients, which was characterized by decreased commensal species and increased opportunistic pathogenic species. Severe illness was associated with higher abundance of four microbial species (i.e., Burkholderia contaminans, Bacteroides nordii, Bifidobacterium longum, and Blautia sp. CAG 257), six microbial pathways (e.g., glycolysis and fermentation), and 10 virulence genes. These severity-related microbial features were further associated with host immune response. For example, the abundance of Bu. contaminans was associated with higher levels of inflammation biomarkers and lower levels of immune cells. Furthermore, human-origin proteins identified from both blood and fecal samples suggested gut barrier dysfunction in COVID-19 patients. The circulating levels of lipopolysaccharide-binding protein increased in patients with severe illness and were associated with circulating inflammation biomarkers and immune cells. Besides, proteins of disease-related bacteria (e.g., B. longum) were detectable in blood samples from patients.

CONCLUSIONS: Our results suggest that the dysbiosis of the gut microbiome and the dysfunction of the gut barrier might play a role in the pathophysiology of COVID-19 by affecting host immune homeostasis.},
}

@article {pmid35045306,
year = {2022},
author = {Huang, G and Wang, L and Li, J and Hou, R and Wang, M and Wang, Z and Qu, Q and Zhou, W and Nie, Y and Hu, Y and Ma, Y and Yan, L and Wei, H and Wei, F},
title = {Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda.},
journal = {Cell reports},
volume = {38},
number = {3},
pages = {110203},
doi = {10.1016/j.celrep.2021.110203},
pmid = {35045306},
issn = {2211-1247},
abstract = {Characteristics of the gut microbiome vary synchronously with changes in host diet. However, the underlying effects of these fluctuations remain unclear. Here, we performed fecal microbiota transplantation (FMT) of diet-specific feces from an endangered mammal (the giant panda) into a germ-free mouse model. We demonstrated that the butyrate-producing bacterium Clostridium butyricum was more abundant during shoot-eating season than during the leaf-eating season, congruent with the significant increase in host body mass. Following season-specific FMT, the microbiota of the mouse model resembled that of the donor, and mice transplanted with the microbiota from the shoot-eating season grew faster and stored more fat. Mechanistic investigations revealed that butyrate extended the upregulation of hepatic circadian gene Per2, subsequently increasing phospholipid biosynthesis. Validation experiments further confirmed this causal relationship. This study demonstrated that seasonal shifts in the gut microbiome affect growth performance, facilitating a deeper understanding of host-microbe interactions in wild mammals.},
}

@article {pmid35045228,
year = {2022},
author = {Feuerstadt, P and Louie, TJ and Lashner, B and Wang, EEL and Diao, L and Bryant, JA and Sims, M and Kraft, CS and Cohen, SH and Berenson, CS and Korman, LY and Ford, CB and Litcofsky, KD and Lombardo, MJ and Wortman, JR and Wu, H and Auniņš, JG and McChalicher, CWJ and Winkler, JA and McGovern, BH and Trucksis, M and Henn, MR and von Moltke, L},
title = {SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection.},
journal = {The New England journal of medicine},
volume = {386},
number = {3},
pages = {220-229},
doi = {10.1056/NEJMoa2106516},
pmid = {35045228},
issn = {1533-4406},
abstract = {BACKGROUND: Current therapies for recurrent Clostridioides difficile infection do not address the disrupted microbiome, which supports C. difficile spore germination into toxin-producing bacteria. SER-109 is an investigational microbiome therapeutic composed of purified Firmicutes spores for the treatment of recurrent C. difficile infection.

METHODS: We conducted a phase 3, double-blind, randomized, placebo-controlled trial in which patients who had had three or more episodes of C. difficile infection (inclusive of the qualifying acute episode) received SER-109 or placebo (four capsules daily for 3 days) after standard-of-care antibiotic treatment. The primary efficacy objective was to show superiority of SER-109 as compared with placebo in reducing the risk of C. difficile infection recurrence up to 8 weeks after treatment. Diagnosis by toxin testing was performed at trial entry, and randomization was stratified according to age and antibiotic agent received. Analyses of safety, microbiome engraftment, and metabolites were also performed.

RESULTS: Among the 281 patients screened, 182 were enrolled. The percentage of patients with recurrence of C. difficile infection was 12% in the SER-109 group and 40% in the placebo group (relative risk, 0.32; 95% confidence interval [CI], 0.18 to 0.58; P<0.001 for a relative risk of <1.0; P<0.001 for a relative risk of <0.833). SER-109 led to less frequent recurrence than placebo in analyses stratified according to age stratum (relative risk, 0.24 [95% CI, 0.07 to 0.78] for patients <65 years of age and 0.36 [95% CI, 0.18 to 0.72] for those ≥65 years) and antibiotic received (relative risk, 0.41 [95% CI, 0.22 to 0.79] with vancomycin and 0.09 [95% CI, 0.01 to 0.63] with fidaxomicin). Most adverse events were mild to moderate and were gastrointestinal in nature, with similar numbers in the two groups. SER-109 dose species were detected as early as week 1 and were associated with bile-acid profiles that are known to inhibit C. difficile spore germination.

CONCLUSIONS: In patients with symptom resolution of C. difficile infection after treatment with standard-of-care antibiotics, oral administration of SER-109 was superior to placebo in reducing the risk of recurrent infection. The observed safety profile of SER-109 was similar to that of placebo. (Funded by Seres Therapeutics; ECOSPOR III ClinicalTrials.gov number, NCT03183128.).},
}

@article {pmid35045174,
year = {2022},
author = {Shilo, S and Godneva, A and Rachmiel, M and Korem, T and Bussi, Y and Kolobkov, D and Karady, T and Bar, N and Wolf, BC and Glantz-Gashai, Y and Cohen, M and Levin, NZ and Shehadeh, N and Gruber, N and Levran, N and Koren, S and Weinberger, A and Pinhas-Hamiel, O and Segal, E},
title = {The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control.},
journal = {Diabetes care},
volume = {},
number = {},
pages = {},
doi = {10.2337/dc21-1656},
pmid = {35045174},
issn = {1935-5548},
abstract = {OBJECTIVE: Previous studies have demonstrated an association between gut microbiota composition and type 1 diabetes (T1D) pathogenesis. However, little is known about the composition and function of the gut microbiome in adults with longstanding T1D or its association with host glycemic control.

RESEARCH DESIGN AND METHODS: We performed a metagenomic analysis of the gut microbiome obtained from fecal samples of 74 adults with T1D, 14.6 ± 9.6 years following diagnosis, and compared their microbial composition and function to 296 age-matched healthy control subjects (1:4 ratio). We further analyzed the association between microbial taxa and indices of glycemic control derived from continuous glucose monitoring measurements and blood tests and constructed a prediction model that solely takes microbiome features as input to evaluate the discriminative power of microbial composition for distinguishing individuals with T1D from control subjects.

RESULTS: Adults with T1D had a distinct microbial signature that separated them from control subjects when using prediction algorithms on held-out subjects (area under the receiver operating characteristic curve = 0.89 ± 0.03). Linear discriminant analysis showed several bacterial species with significantly higher scores in T1D, including Prevotella copri and Eubacterium siraeum, and species with higher scores in control subjects, including Firmicutes bacterium and Faecalibacterium prausnitzii (P < 0.05, false discovery rate corrected for all). On the functional level, several metabolic pathways were significantly lower in adults with T1D. Several bacterial taxa and metabolic pathways were associated with the host's glycemic control.

CONCLUSIONS: We identified a distinct gut microbial signature in adults with longstanding T1D and associations between microbial taxa, metabolic pathways, and glycemic control indices. Additional mechanistic studies are needed to identify the role of these bacteria for potential therapeutic strategies.},
}

@article {pmid35045086,
year = {2022},
author = {Price, CA and Jospin, G and Brownell, K and Eisen, JA and Laraia, B and Epel, ES},
title = {Differences in gut microbiome by insulin sensitivity status in Black and White women of the National Growth and Health Study (NGHS): A pilot study.},
journal = {PloS one},
volume = {17},
number = {1},
pages = {e0259889},
doi = {10.1371/journal.pone.0259889},
pmid = {35045086},
issn = {1932-6203},
abstract = {The prevalence of overweight and obesity is greatest amongst Black women in the U.S., contributing to disproportionately higher type 2 diabetes prevalence compared to White women. Insulin resistance, independent of body mass index, tends to be greater in Black compared to White women, yet the mechanisms to explain these differences are not completely understood. The gut microbiome is implicated in the pathophysiology of obesity, insulin resistance and cardiometabolic disease. Only two studies have examined race differences in Black and White women, however none characterizing the gut microbiome based on insulin sensitivity by race and sex. Our objective was to determine if gut microbiome profiles differ between Black and White women and if so, determine if these race differences persisted when accounting for insulin sensitivity status. In a pilot cross-sectional analysis, we measured the relative abundance of bacteria in fecal samples collected from a subset of 168 Black (n = 94) and White (n = 74) women of the National Growth and Health Study (NGHS). We conducted analyses by self-identified race and by race plus insulin sensitivity status (e.g. insulin sensitive versus insulin resistant as determined by HOMA-IR). A greater proportion of Black women were classified as IR (50%) compared to White women (30%). Alpha diversity did not differ by race nor by race and insulin sensitivity status. Beta diversity at the family level was significantly different by race (p = 0.033) and by the combination of race plus insulin sensitivity (p = 0.038). Black women, regardless of insulin sensitivity, had a greater relative abundance of the phylum Actinobacteria (p = 0.003), compared to White women. There was an interaction between race and insulin sensitivity for Verrucomicrobia (p = 0.008), where among those with insulin resistance, Black women had four fold higher abundance than White women. At the family level, we observed significant interactions between race and insulin sensitivity for Lachnospiraceae (p = 0.007) and Clostridiales Family XIII (p = 0.01). Our findings suggest that the gut microbiome, particularly lower beta diversity and greater Actinobacteria, one of the most abundant species, may play an important role in driving cardiometabolic health disparities of Black women, indicating an influence of social and environmental factors on the gut microbiome.},
}

@article {pmid35044852,
year = {2022},
author = {Craft, J and Eddington, H and Christman, N and Pryor, W and Chaston, JM and Erickson, D and Wilson, E},
title = {Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {AEM0142321},
doi = {10.1128/AEM.01423-21},
pmid = {35044852},
issn = {1098-5336},
abstract = {Turkeys (Meleagris gallopavo) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminant antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compared the cecal microbiota of wild and domestic turkeys, hypothesizing that environmental pressures faced by wild birds may select for a disease-resistant microbial community. Sequence analysis of 16S rRNA genes amplified from cecal samples indicate that free-roaming wild turkeys carry a rich and variable microbiota compared to domestic turkeys raised on large-scale poultry farms. Wild turkeys also had very low levels of Staphylococcus, Salmonella and E. coli when compared to domestic turkeys. E. coli strains isolated from wild or domestic turkey cecal samples also belong to distinct phylogenetic backgrounds and differ in their propensity to carry virulence genes. E. coli strains isolated from factory-raised turkeys were far more likely to carry genes for capsule (kpsII, kpsIII) or siderophore (iroN, fyuA) synthesis than those isolated from wild turkeys. These results suggest that the microbiota of wild turkeys may provide colonization resistance against common poultry pathogens. Importance Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compare the microbiota of wild and domestic turkeys. Results suggest that free ranging wild turkeys carry a distinct microbiome when compared to farm raised turkeys. The microbiome of wild birds contains very low levels of poultry pathogens compared to farm raised birds. The microbiomes of wild turkeys may be used to guide development of new ways to control disease in large scale poultry production.},
}

@article {pmid35044669,
year = {2022},
author = {Kumar, RS and Mishra, N and Kumar, A},
title = {Characterization of Tobacco Microbiome by Metagenomics Approach.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2413},
number = {},
pages = {229-244},
pmid = {35044669},
issn = {1940-6029},
abstract = {Chronic consumption of tobacco in all forms, either smoked/smokeless forms, causes major health hazards to humans that include cancer, cardiovascular, lung diseases, diabetes, fertility issues, etc. Among tobacco-mediated cancers, the prominent one being the oral cancers are caused due to chronic tobacco chewing. The biochemicals present in tobacco are involved in carcinogenesis, and their presence is partly mediated by the existence of microbes in tobacco products. The microbial characterization has been evolved from classical microscopical observation to the recent development of 16S rRNA sequencing by next-generation sequencing methods. The metagenomics approach using 16S rRNA-based next-generation sequencing methods enables the detection and characterization of the complete microbial community of tobacco, including both cultivable and non-cultivable microorganisms. Identification of microbes will help in devising strategies to limit the carcinogenic compounds present in tobacco.},
}

@article {pmid35044528,
year = {2022},
author = {Chakrabarti, A and Geurts, L and Hoyles, L and Iozzo, P and Kraneveld, AD and La Fata, G and Miani, M and Patterson, E and Pot, B and Shortt, C and Vauzour, D},
title = {The microbiota-gut-brain axis: pathways to better brain health. Perspectives on what we know, what we need to investigate and how to put knowledge into practice.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {79},
number = {2},
pages = {80},
pmid = {35044528},
issn = {1420-9071},
abstract = {The gut and brain link via various metabolic and signalling pathways, each with the potential to influence mental, brain and cognitive health. Over the past decade, the involvement of the gut microbiota in gut-brain communication has become the focus of increased scientific interest, establishing the microbiota-gut-brain axis as a field of research. There is a growing number of association studies exploring the gut microbiota's possible role in memory, learning, anxiety, stress, neurodevelopmental and neurodegenerative disorders. Consequently, attention is now turning to how the microbiota can become the target of nutritional and therapeutic strategies for improved brain health and well-being. However, while such strategies that target the gut microbiota to influence brain health and function are currently under development with varying levels of success, still very little is yet known about the triggers and mechanisms underlying the gut microbiota's apparent influence on cognitive or brain function and most evidence comes from pre-clinical studies rather than well controlled clinical trials/investigations. Filling the knowledge gaps requires establishing a standardised methodology for human studies, including strong guidance for specific focus areas of the microbiota-gut-brain axis, the need for more extensive biological sample analyses, and identification of relevant biomarkers. Other urgent requirements are new advanced models for in vitro and in vivo studies of relevant mechanisms, and a greater focus on omics technologies with supporting bioinformatics resources (training, tools) to efficiently translate study findings, as well as the identification of relevant targets in study populations. The key to building a validated evidence base rely on increasing knowledge sharing and multi-disciplinary collaborations, along with continued public-private funding support. This will allow microbiota-gut-brain axis research to move to its next phase so we can identify realistic opportunities to modulate the microbiota for better brain health.},
}

@article {pmid35044342,
year = {2022},
author = {Delbeke, H and Casteels, I and Joossens, M},
title = {Concerning the Paper "Ocular Surface Microbiome in Health and Disease".},
journal = {Asia-Pacific journal of ophthalmology (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/APO.0000000000000463},
pmid = {35044342},
issn = {2162-0989},
}

@article {pmid35044233,
year = {2022},
author = {Wells, J and Bai, J and Tsementzi, D and Jhaney, CI and Foster, A and Bruner, DW and Gillespie, T and Li, Y and Hu, YJ},
title = {Exploring the Anal Microbiome in HIV positive and high risk HIV negative Women.},
journal = {AIDS research and human retroviruses},
volume = {},
number = {},
pages = {},
doi = {10.1089/AID.2020.0245},
pmid = {35044233},
issn = {1931-8405},
abstract = {BACKGROUND: This exploratory study sought to characterize the anal microbiome and explore associations among the anal microbiome, risk factors for anal cancer, and clinical factors.

SETTING: A pilot sample of 50 HIV infected and high-risk HIV negative women were recruited from the former Women's Interagency HIV Study.

METHODS: Microbiome characterization by 16S rRNA gene sequencing and datasets were analyzed using QIIME 2TM. Composition of the anal microbiome and its associations with anal cancer risk factors and clinical factors were analyzed using linear decomposition model and permuational multivariate analysis of variance.

RESULTS: Composition of the anal microbiome among HIV positive and high-risk negative women was dominated by Bacteroides, Prevotella, and Campylobacter. The overall taxonomic composition and microbial diversity of the anal microbiome did not significantly differ by HIV status. However, the abundance of Ruminococcus 1 belonging to the Rumincoccaceae family was associated with HIV status (q = 0.05). No anal cancer risk factors were associated with the anal microbiome composition. Clinical factors marginally associated with the anal microbiome composition included BMI (p=0.05) and Hepatitis C (HCV; p=0.05).

CONCLUSIONS: Although HIV and risk factors for anal cancer were not associated with the composition of the anal microbiome in this pilot sample, other clinical factors such as BMI and HCV, may be worth further investigation in a larger study. Future research can build on these findings to explore the role of the microbiome and HIV comorbidities in women.},
}

@article {pmid35044201,
year = {2022},
author = {Zhang, Z and Hou, Q and Wang, Y and Xiang, F and Guo, Z},
title = {Evaluation of Bacterial Diversity and Evolutionary Dynamics of Gut Bifidobacterium longum Isolates Obtained from Older Individuals in Hubei Province, China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0144221},
doi = {10.1128/spectrum.01442-21},
pmid = {35044201},
issn = {2165-0497},
abstract = {Bifidobacterium longum predominates in the human gut throughout the life span, from birth to old age, and could alter the intestinal microbial population and immune function in the elderly. We investigated the intestinal bacterial diversity in the elderly, and further evaluated the genetic diversity and population structure of B. longum. The results revealed a distinct difference in gut bacterial populations between the elderly from Xiangyang and its neighboring region, Enshi city. A total of 62 bifidobacterial strains were isolated, 30 of which were found to be B. longum. The multilocus sequence typing (MLST) analysis also revealed that 437 B. longum isolates from diverse regions worldwide, including the 30 isolated in this study, could be classified into 341 sequence types (STs). They could be further clustered into 10 clonal complexes and 127 singleton STs, indicating a highly genetic diversity among B. longum isolates. Two putative clone complexes (CCs) containing the isolates from Xiangyang were found to be geographically specific, and a 213-bp recombination fragment was detected. Phylogenetic trees divided these 437 isolates into three lineages, corresponding to the three subspecies of B. longum. It is noteworthy that two isolates from the elderly were identified to be B. longum subsp. suis, while the others were B. longum subsp. longum. Together, our study characterized the intestinal bacterial diversity and evolution of B. longum in the elderly, and it could contribute to further studies on the genotyping and discrimination of B. longum. IMPORTANCE Bifidobacterium longum are common inhabitants of the human gut throughout the life span, and have been associated with health-promoting effects, yet little is known about the genotype profile and evolution of these isolates. Our study showed that there was significant difference in gut bacterial community and abundance of B. longum between the elderly from two neighboring cities. Furthermore, the possible geographically specific STs, CCs, and intraspecies recombination fragment were found among the B. longum isolates from elderly.},
}

@article {pmid35043999,
year = {2022},
author = {Murata, H and Barnhill, LM and Bronstein, JM},
title = {Air Pollution and the Risk of Parkinson's Disease: A Review.},
journal = {Movement disorders : official journal of the Movement Disorder Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/mds.28922},
pmid = {35043999},
issn = {1531-8257},
support = {T32ES015457/ES/NIEHS NIH HHS/United States ; //Parkinson Alliance/ ; //The Levine Foundation/ ; },
abstract = {Parkinson's disease, as well as other neurodegenerative disorders, are primarily characterized by pathological accumulation of proteins, inflammation, and neuron loss. Although there are some known genetic risk factors, most cases cannot be explained by genetics alone. Therefore, it is important to determine the environmental factors that confer risk and the mechanisms by which they act. Recent epidemiological studies have found that exposure to air pollution is associated with an increased risk for development of Parkinson's disease, although not all results are uniform. The variability between these studies is likely due to differences in what components of air pollution are measured, timing and methods used to determine exposures, and correction for other variables. There are several potential mechanisms by which air pollution could act to increase the risk for development of Parkinson's disease, including direct neuronal toxicity, induction of systemic inflammation leading to central nervous system inflammation, and alterations in gut physiology and the microbiome. Taken together, air pollution is an emerging risk factor in the development of Parkinson's disease. A number of potential mechanisms have been implicated by which it promotes neuropathology providing biological plausibility, and these mechanisms are likely relevant to the development of other neurodegenerative disorders such as Alzheimer's disease. This field is in its early stages, but a better understanding of how environmental exposures influence the pathogenesis of neurodegeneration is essential for reducing the incidence of disease and finding disease-modifying therapies. © 2022 International Parkinson and Movement Disorder Society.},
}

@article {pmid35043984,
year = {2022},
author = {Keyes, S and van Veelen, A and McKay Fletcher, D and Scotson, C and Koebernick, N and Petroselli, C and Williams, K and Ruiz, S and Cooper, L and Mayon, R and Duncan, S and Dumont, M and Jakobsen, I and Oldroyd, G and Tkacz, A and Poole, P and Mosselmans, F and Borca, C and Huthwelker, T and Jones, DL and Roose, T},
title = {Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of mycorrhizal fungi.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.17980},
pmid = {35043984},
issn = {1469-8137},
abstract = {Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore-space, and models of AMF-enhanced P-uptake are poorly validated. We used synchrotron X-ray computed tomography (SXRCT) to visualize mycorrhizas in soil, and synchrotron X-ray fluorescence (XRF/XANES) elemental mapping for phosphorus (P), sulphur (S) and aluminium (Al), in combination with modelling. We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Results showed that AMF co-locate with areas of high P and low Al, andpreferentially associate with organic-type P species in preference to Al-rich inorganic P. We discovered that AMF avoid Al-rich areas as a source of P. S-rich regions correlated with higher hyphal density and an increased organic-associated P-pool, whilst oxidized S-species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome-related. Our experimentally-validated model led to an estimate of P-uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated; a result with significant implications for modelling of plant-soil-AMF interactions.},
}

@article {pmid35043621,
year = {2022},
author = {Kalani Roy, M and La Carpia, F and Cendali, F and Fernando, S and Moriconi, C and Wojczyk, BS and Wang, L and Nemkov, T and Hod, EA and D'Alessandro, A},
title = {Irradiation Causes Alterations of Polyamine, Purine, and Sulfur Metabolism in Red Blood Cells and Multiple Organs.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.1c00912},
pmid = {35043621},
issn = {1535-3907},
abstract = {Investigating the metabolic effects of radiation is critical to understand the impact of radiotherapy, space travel, and exposure to environmental radiation. In patients undergoing hemopoietic stem cell transplantation, iron overload is a common risk factor for poor outcomes. However, no studies have interrogated the multiorgan effects of these treatments concurrently. Herein, we use a model that recapitulates transfusional iron overload, a condition often observed in chronically transfused patients. We applied an omics approach to investigate the impact of both the iron load and irradiation on the host metabolome. The results revealed dose-dependent effects of irradiation in the red blood cells, plasma, spleen, and liver energy and redox metabolism. Increases in polyamines and purine salvage metabolites were observed in organs with high oxygen consumption including the heart, kidneys, and brain. Irradiation also impacted the metabolism of the duodenum, colon, and stool, suggesting a potential effect on the microbiome. Iron infusion affected the response to radiation in the organs and blood, especially in erythrocyte polyamines and spleen antioxidant metabolism, and affected glucose, methionine, and glutathione systems and tryptophan metabolism in the liver, stool, and the brain. Together, the results suggest that radiation impacts metabolism on a multiorgan level with a significant interaction of the host iron status.},
}

@article {pmid35043537,
year = {2022},
author = {Warne, RW and Dallas, J},
title = {Microbiome mediation of animal life histories via metabolites and insulin-like signalling.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.12833},
pmid = {35043537},
issn = {1469-185X},
abstract = {The regulatory pathways by which gut microbiota potentially shape host life histories remain largely untested, however, a constellation of research suggests that gut bacteria likely have significant effects on their hosts via metabolites. In this article we review known and hypothesized pathways by which gut microbiota influence host life histories through interfacing with the neuroendocrine system, with a focus on the insulin-like growth factor (IGF) signalling pathway. Bacterially derived metabolites including short-chain fatty acids (SCFAs), polyamines, and peptides likely impact host life histories as metabolic substrates, essential nutrients, and via molecular signalling with well-studied neuroendocrine pathways. The hypothalamus-pituitary axis and insulin-like signalling (ILS) pathways are central regulatory networks for development, growth, reproductive maturity, reproduction, and senescence and are likely targets for tests of how gut bacterial metabolites shape host life histories. SCFAs in particular, as metabolites derived from bacterial fermentation, are implicated as significant microbiome signalling molecules shown to interface with the ILS pathway as well as to bind to receptors on neuroendocrine and peripheral nervous tissues. For example, experimental increases of SCFA production have been shown to affect IGF-1 levels in circulation and are associated with robust development, growth, reproduction, and delayed senescence. Finally, emerging -omics approaches are providing integrative ways to test and detail the potential diverse ways in which gut microbiota interact with their hosts and the likely important roles they play in shaping host life-history responses to varied environmental conditions.},
}

@article {pmid35043436,
year = {2022},
author = {Hinchliffe, T and Pauline, ML and Wizzard, PR and Jovel, J and Nation, PN and Wales, PW and Madsen, KL and Turner, JM},
title = {The effect of fecal microbial transplant on intestinal microbial composition in short bowel neonatal piglets.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.2333},
pmid = {35043436},
issn = {1941-2444},
abstract = {BACKGROUND: Short bowel syndrome (SBS) in neonates is associated with microbial dysbiosis due to intestinal surgery, prolonged hospitalization, enteral nutrition, and repeated antibiotic exposure. Sepsis and liver disease, leading causes of morbidity and mortality in SBS, may relate to such intestinal dysbiosis. We investigated the safety and feasibility of fecal microbial transplant (FMT) to alter intestinal microbial composition in SBS piglets.

METHODS: Following a 75% distal small intestinal resection, piglets were fed parenteral nutrition (PN) and elemental diet (ED), and randomized to saline (SAL, n=12) or FMT (n=12) treatments delivered by gastric tube on day 2 (d2). FMT donor was a healthy adult pig. Comparisons were also made to healthy sow-fed littermate controls (SOW, n=6). Stool samples were collected daily, and tissue samples were collected at baseline and termination. Microbial DNA was extracted from stool and analyzed using 16S rRNA sequencing.

RESULTS: All piglets survived to the endpoint. On d2-4, FMT piglets had some differences in microbiota composition, compared to SAL, SOW, and donor. Between base and term, there were transitory changes to alpha and beta diversity in FMT and SAL.

CONCLUSION: FMT treatment in post-surgical neonatal piglets with SBS appears safe, with no increase in sepsis and no mortality. In SBS piglets, FMT induced transient changes to the intestinal microbiota. However, these changes did not persist long-term. This article is protected by copyright. All rights reserved.},
}

@article {pmid35043293,
year = {2022},
author = {De Filippis, F and Esposito, A and Ercolini, D},
title = {Outlook on next-generation probiotics from the human gut.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {79},
number = {2},
pages = {76},
pmid = {35043293},
issn = {1420-9071},
support = {GR-2016-02362975//Ministero della Salute/ ; 818368//European Commission/ ; 20174FHBWR_005//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; DOT1718749//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; CUP E65F21003630003//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; },
abstract = {Probiotics currently available on the market generally belong to a narrow range of microbial species. However, recent studies about the importance of the gut microbial commensals on human health highlighted that the gut microbiome is an unexplored reservoir of potentially beneficial microbes. For this reason, academic and industrial research is focused on identifying and testing novel microbial strains of gut origin for the development of next-generation probiotics. Although several of these are promising for the prevention and treatment of many chronic diseases, studies on human subjects are still scarce and approval from regulatory agencies is, therefore, rare. In addition, some issues need to be overcome before implementing their wide application on the market, such as the best methods for cultivation and storage of these oxygen-sensitive taxa. This review summarizes the most recent evidence related to NGPs and provides an outlook to the main issues that still limit their wide employment.},
}

@article {pmid35043221,
year = {2022},
author = {Kanisan, DP and Quek, ZBR and Oh, RM and Afiq-Rosli, L and Lee, JN and Huang, D and Wainwright, BJ},
title = {Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35043221},
issn = {1432-184X},
abstract = {Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.},
}

@article {pmid35043188,
year = {2022},
author = {Liu, J and Abdelfattah, A and Wasserman, B and Wisniewski, M and Droby, S and Fazio, G and Mazzola, M and Wu, X},
title = {Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks.},
journal = {Horticulture research},
volume = {9},
number = {},
pages = {},
doi = {10.1093/hr/uhab013},
pmid = {35043188},
issn = {2662-6810},
abstract = {The endophytic microbiome of plants is believed to have a significant impact on its physiology and disease resistance, however, the role of host genotype in determining the composition of the endophytic microbiome of apple root systems remains an open question that has important implications for defining breeding objectives. In the current study, the bacterial and fungal microbiota associated with four different apple rootstocks planted in April, 2018 in the same soil environment and harvested in May, 2019 were evaluated to determine the role of genotype on the composition of both the bacterial and fungal communities. Results demonstrated a clear impact of genotype and root size on microbial composition and diversity. The fungal community was more affected by plant genotype whereas the bacterial community was shaped by root size. Fungal and bacterial abundance was equal between different-sized roots however, significantly higher microbial counts were detected in rhizosphere samples compared to root endosphere samples. This study provides information that can be used to develop a comprehensive and readily applicable understanding of the impact of genotype and environmental factors on the establishment of plant microbiome, as well as its potential function and impact on host physiology.},
}

@article {pmid35042975,
year = {2022},
author = {Zhu, Q and Hou, Q and Huang, S and Ou, Q and Huo, D and Vázquez-Baeza, Y and Cen, C and Cantu, V and Estaki, M and Chang, H and Belda-Ferre, P and Kim, HC and Chen, K and Knight, R and Zhang, J},
title = {Correction to: Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-021-01040-7},
pmid = {35042975},
issn = {1751-7370},
}

@article {pmid35042542,
year = {2022},
author = {Galiwango, RM and Park, DE and Huibner, S and Onos, A and Aziz, M and Roach, K and Anok, A and Nnamutete, J and Isabirye, Y and Wasswa, JB and Male, D and Kigozi, G and Tobian, AAR and Prodger, JL and Liu, CM and Kaul, R},
title = {Immune milieu and microbiome of the distal urethra in Ugandan men: impact of penile circumcision and implications for HIV susceptibility.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {7},
pmid = {35042542},
issn = {2049-2618},
abstract = {BACKGROUND: Coronal sulcus (CS) anaerobe abundance and IL-8 levels are linked to HIV acquisition, and are dramatically reduced after penile circumcision (PC). The distal urethra may be the site of some HIV acquisition before PC, and presumably most acquisition post PC. We describe the immune milieu and microbiome of the distal urethra in uncircumcised Ugandan men, and define the impact of PC. Participants consisted of HIV-negative, genital symptom-free adult Ugandan men undergoing PC (n = 51). Urethral and coronal sulcus swabs were collected at baseline and at 6- and 12-months post-PC. Soluble immune factors were quantified by multiplex ELISA, and bacterial abundance assessed by 16S rRNA qPCR and sequencing.

RESULTS: At baseline, the urethra was enriched compared to the CS for most cytokines (including IL-8 and MIP-1β) and soluble E-cadherin (sE-cadherin, an epithelial disruption marker), although CS levels of IL-1α and IL-1β were higher. Baseline total bacterial abundance was ≥ 20-fold higher in the CS than the urethra (median 27,100 vs. 1200 gene copies/swab, p = 0.001), and anaerobes comprised 58% of CS bacteria vs. 42% of urethral bacteria. PC did not alter urethral IL-8 (median 806 at baseline vs. 1130 pg/ml at 12 months; p = 0.062) and urethral sE-cadherin increased (113,223 vs. 158,385 pg/ml, p = 0.009), despite five- and sevenfold drops in total bacterial and anaerobe abundance after PC, respectively. However, PC dramatically reduced CS levels of sE-cadherin (15,843 vs. 837 pg/ml, p < 0.001) and most cytokines (IL-8; 34 vs. 3 pg/ml, p < 0.001), while reducing total bacterial and anaerobe abundance by 13-fold and 60-fold, respectively (both P ≤ 0.004).

CONCLUSIONS: The urethra is immunologically rich with characteristics of an HIV-susceptible tissue site. However, PC had no impact on urethral immunology and may have reduced epithelial integrity, despite modest reductions in total bacteria and anaerobes, suggesting that HIV protection from PC is not mediated via immune or microbiome alterations in the urethra. Video abstract.},
}

@article {pmid35042457,
year = {2022},
author = {Latino, C and Gianatti, EJ and Mehta, S and Lo, J and Devine, A and Christophersen, C},
title = {Does a high dietary intake of resistant starch affect glycaemic control and alter the gut microbiome in women with gestational diabetes? A randomised control trial protocol.},
journal = {BMC pregnancy and childbirth},
volume = {22},
number = {1},
pages = {46},
pmid = {35042457},
issn = {1471-2393},
support = {Enabling Allied Health Research Capacity 2020//Department of Health, Government of Western Australia/ ; G1005941//Spinnaker Health Research Foundation/ ; },
abstract = {BACKGROUND: Gestational Diabetes Mellitus (GDM) is prevalent with lasting health implications for the mother and offspring. Medical nutrition therapy is the foundation of GDM management yet achieving optimal glycaemic control often requires treatment with medications, like insulin. New dietary strategies to improve GDM management and outcomes are required. Gut dysbiosis is a feature of GDM pregnancies, therefore, dietary manipulation of the gut microbiota may offer a new avenue for management. Resistant starch is a fermentable dietary fibre known to alter the gut microbiota and enhance production of short-chain fatty acids. Evidence suggests that short-chain fatty acids improve glycaemia via multiple mechanisms, however, this has not been evaluated in GDM.

METHODS: An open-label, parallel-group design study will investigate whether a high dietary resistant starch intake or resistant starch supplement improves glycaemic control and changes the gut microbiome compared with standard dietary advice in women with newly diagnosed GDM. Ninety women will be randomised to one of three groups - standard dietary treatment for GDM (Control), a high resistant starch diet or a high resistant starch diet plus a 16 g resistant starch supplement. Measurements taken at Baseline (24 to 30-weeks' gestation), Day 10 and Day 56 (approximately 36 weeks' gestation) will include fasting plasma glucose levels, microbial composition and short-chain fatty acid concentrations in stool, 3-day dietary intake records and bowel symptoms questionnaires. One-week post-natal data collection will include microbial composition and short-chain fatty acid concentrations of maternal and neonatal stools, microbial composition of breastmilk, birthweight, maternal and neonatal outcomes. Mixed model analysis of variance will assess change in glycaemia and permutation-based multivariate analysis of variance will assess changes in microbial composition within and between intervention groups. Distance-based linear modelling will identify correlation between change in stool microbiota, short-chain fatty acids and measures of glycaemia.

DISCUSSION: To improve outcomes for GDM dyads, evaluation of a high dietary intake of resistant starch to improve glycaemia through the gut microbiome needs to be established. This will expand the dietary interventions available to manage GDM without medication.

TRIAL REGISTRATION: Australian New Zealand Clinical Trial Registry, ACTRN12620000968976p . Registered 28 September 2020.},
}

@article {pmid35042252,
year = {2022},
author = {Schnabl, B and Arteel, GE and Stickel, F and Hengstler, J and Vartak, N and Ghallab, A and Dooley, S and Li, Y and Schwabe, RF},
title = {Liver specific, systemic and genetic contributors to alcohol-related liver disease progression.},
journal = {Zeitschrift fur Gastroenterologie},
volume = {60},
number = {1},
pages = {36-44},
doi = {10.1055/a-1714-9330},
pmid = {35042252},
issn = {1439-7803},
support = {Biomedical Laboratory Research and Development, VA Office of Research and Development//BX004594/ ; Bundesministerium für Bildung und Forschung//PTJ-031L0043,PTJ-031L0257A/ ; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung//SNF no. 310030_169196/ ; National Institutes of Health//P30 DK120515,P30 DK120531,P50 AA011999,R01 AA020703,R01 AA021978,R01 AA24726,R01 CA262424,U01 AA026939/ ; Deutsche Forschungsgemeinschaft//DO 373/20-1/ ; },
abstract = {Alcohol-related liver disease (ALD) impacts millions of patients worldwide each year and the numbers are increasing. Disease stages range from steatosis via steatohepatitis and fibrosis to cirrhosis, severe alcohol-associated hepatitis and liver cancer. ALD is usually diagnosed at an advanced stage of progression with no effective therapies. A major research goal is to improve diagnosis, prognosis and also treatments for early ALD. This however needs prioritization of this disease for financial investment in basic and clinical research to more deeply investigate mechanisms and identify biomarkers and therapeutic targets for early detection and intervention. Topics of interest are communication of the liver with other organs of the body, especially the gut microbiome, the individual genetic constitution, systemic and liver innate inflammation, including bacterial infections, as well as fate and number of hepatic stellate cells and the composition of the extracellular matrix in the liver. Additionally, mechanical forces and damaging stresses towards the sophisticated vessel system of the liver, including the especially equipped sinusoidal endothelium and the biliary tract, work together to mediate hepatocytic import and export of nutritional and toxic substances, adapting to chronic liver disease by morphological and functional changes. All the aforementioned parameters contribute to the outcome of alcohol use disorder and the risk to develop advanced disease stages including cirrhosis, severe alcoholic hepatitis and liver cancer. In the present collection, we summarize current knowledge on these alcohol-related liver disease parameters, excluding the aspect of inflammation, which is presented in the accompanying review article by Lotersztajn and colleagues.},
}

@article {pmid35042220,
year = {2022},
author = {van Mierlo, MMF and Pardo, LM and Fieten, KB and van den Broek, TJ and Schuren, FHJ and van Geel, M and Pasmans, SGMA},
title = {The Skin and Nose Microbiome and Its Association with Filaggrin Gene Mutations in Pediatric Atopic Dermatitis.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000520978},
pmid = {35042220},
issn = {1421-9832},
abstract = {BACKGROUND: Interactions between the skin barrier, immune system, and microbiome underlie the development of atopic dermatitis (AD).

OBJECTIVE: To investigate the skin and nasal microbiome in relation to filaggrin gene (FLG) mutations.

METHODS: A cross-sectional study including 77 children with difficult-to-treat AD. The entire encoding region of FLG was screened for mutations using single molecule molecular inversion probes and next-generation sequencing. Bacterial swabs from the anterior nares, lesional and nonlesional skin were analyzed using 16S rRNA sequencing. For skin samples, additional qPCR was performed for Staphylococcus aureus and Staphylococcus epidermidis.

RESULTS: The prevalence of patients with a mutation in FLG was 40%, including 10 different mutations. Analyzing bacterial swabs from all three niches showed a significant effect for both niche and FLG mutation status on the overall microbiome composition. Using a subset analysis to test the effect of FLG mutation status per niche separately did not show a significant association to the microbiome. Shannon diversity and S. aureus abundance were significantly affected by the niche, but not by the presence of an FLG mutation.

CONCLUSIONS: Our results suggest only a minor role for FLG mutation status on the overall microbiome, which is rather caused by differences in the present genera than by microbe richness and evenness.},
}

@article {pmid35042212,
year = {2022},
author = {Scorza, FA and de Almeida, AG and Fiorini, AC and Finsterer, J},
title = {THE MICROBIOTA IN PARKINSON'S DISEASE: RANKING THE RISK OF HEART DISEASE.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1159/000521992},
pmid = {35042212},
issn = {1421-9697},
abstract = {This letter is a commenting on the article recently published in Annals of Nutrition and Metabolism entitled "Parkinson's Disease and Gut Microbiota" by Hirayama and Ohno published in your esteemed journal. In brief, the authors properly discussed the recent research on possible mechanisms of how gut dysbiosis is causally associated with the development and progression of Parkinson's Disease. However, we would like to add some thoughts that may open the debate about the relationship between gut microbiome dysbiosis and cardiac disorders, highlighting the possible role of this association with the occurrence of some cases of sudden death in Parkinson's Disease.},
}

@article {pmid35042114,
year = {2022},
author = {Ruiz-Rico, M and Renwick, S and Allen-Vercoe, E and Barat, JM},
title = {In vitro susceptibility of human gut microbes to potential food preservatives based on immobilized phenolic compounds.},
journal = {Food chemistry},
volume = {378},
number = {},
pages = {132136},
doi = {10.1016/j.foodchem.2022.132136},
pmid = {35042114},
issn = {1873-7072},
abstract = {The development of novel food preservatives based on natural antimicrobials such as phenolic compounds is increasing, but their safety should be established before use, including evaluating their impact on the gut microbiota. This work explored the influence of antimicrobial phenolics presented in different forms on selected human gut microbiota members through in vitro susceptibility tests. The bacteria tested exhibited a wide range of susceptibilities to phenolics depending on the molecule structure and mode of administration. Agathobacter rectalis and Clostridium spiroforme, members of the phylum Firmicutes, were the most sensitive strains. Susceptibility was strain- and species-specific, suggesting that it may not be possible to easily extrapolate results across the human microbiome in general. Species of other phyla including Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia were more resistant than Firmicutes, with growth of some strains even enhanced. Our results provide insights into the biocompatibility of free and immobilized phenolics as potential food additives.},
}

@article {pmid35041811,
year = {2022},
author = {Contino, KF and Yadav, H and Shiozawa, Y},
title = {The gut microbiome can be a potential regulator and treatment target of bone metastasis.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {114916},
doi = {10.1016/j.bcp.2022.114916},
pmid = {35041811},
issn = {1873-2968},
abstract = {The gut microbiota, an often forgotten organ, have a tremendous impact on human health. It has long been known that the gut microbiota are implicated in cancer development, and more recently, the gut microbiota have been shown to influence cancer metastasis to distant organs. Although one of the most common sites of distant metastasis is the bone, and the skeletal system has been shown to be a subject of interactions with the gut microbiota to regulate bone homeostasis, little research has been done regarding how the gut microbiota control the development of bone metastasis. This review will discuss the mechanisms through which the gut microbiota and derived microbial compounds (i) regulate gastrointestinal cancer disease progression and metastasis, (ii) influence skeletal remodeling and potentially modulate bone metastasis, and (iii) affect and potentially enhance immunotherapeutic treatments for bone metastasis.},
}

@article {pmid35041771,
year = {2022},
author = {Ahearn-Ford, S and Berrington, JE and Stewart, CJ},
title = {Development of the gut microbiome in early life.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP089919},
pmid = {35041771},
issn = {1469-445X},
abstract = {NEW FINDINGS: What is the topic of this review? This symposium report discusses the importance of the early life gut microbiome, with a focus on preterm infants and microbially-related diseases. Current techniques to study the preterm gut microbiome are appraised, and the potential of recent methodological advancements is discussed. What advances does it highlight? Recent findings in the field achieved by the application of advanced technologies are acknowledged. The review also highlights the applicability of intestinal-derived organoid models to study host-microbiome interactions in the preterm gut, and recent developments in enhancing the physiological relevance of such models. Preterm intestinal-derived organoids may provide novel insights into the mechanisms underlying preterm disease, as well as diagnosis and treatment opportunities. These models have huge translational potential, offering a step towards precision medicine.

ABSTRACT: Accumulating evidence affirms the importance of the gut microbiome in both health and disease. In early life, there exists a critical period in which the composition of gut microbes is particularly malleable and subject to a wide range of influencing factors. Disturbances to microbial communities during this time may be beneficial or detrimental to short and long-term health outcomes. For infants born prematurely, naïve immune systems, immature gastrointestinal tracts and additional clinical needs put this population at high risk of abnormal microbial colonisation, resulting in an increased susceptibility to diseases including necrotising enterocolitis (NEC) and late-onset sepsis (LOS). Traditional cell culture methods, gnotobiotic animals, molecular sequencing techniques (16S rRNA gene sequencing and metagenomics) and advanced "omics" technologies (transcriptomics, proteomics and metabolomics) have been fundamental in exploring the associations between diet, gut microbes, microbial functions, and disease. Despite significant investment and ongoing research efforts, prevention and treatment strategies in NEC and LOS remain limited. Recent endeavours have focused on searching for new, more physiologically relevant models to simulate the preterm intestine. Preterm intestinal-derived organoids represent a promising in vitro approach in the study of host-microbial interactions in the preterm infant gut, offering new and exciting possibilities in this field. This article is protected by copyright. All rights reserved.},
}

@article {pmid35041070,
year = {2022},
author = {Runge, P and Ventura, F and Kemen, E and Stam, R},
title = {Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35041070},
issn = {1432-184X},
support = {ERC-2018-COG 820124/ERC_/European Research Council/International ; ERC-2018-COG 820124/ERC_/European Research Council/International ; STA1547/2//german science foundation/ ; },
abstract = {Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.},
}

@article {pmid35040752,
year = {2022},
author = {Chen, Y and Wang, H and Lu, W and Wu, T and Yuan, W and Zhu, J and Lee, YK and Zhao, J and Zhang, H and Chen, W},
title = {Human gut microbiome aging clocks based on taxonomic and functional signatures through multi-view learning.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2025016},
doi = {10.1080/19490976.2021.2025016},
pmid = {35040752},
issn = {1949-0984},
abstract = {The human gut microbiome is a complex ecosystem that is closely related to the aging process. However, there is currently no reliable method to make full use of the metagenomics data of the gut microbiome to determine the age of the host. In this study, we considered the influence of geographical factors on the gut microbiome, and a total of 2604 filtered metagenomics data from the gut microbiome were used to construct an age prediction model. Then, we developed an ensemble model with multiple heterogeneous algorithms and combined species and pathway profiles for multi-view learning. By integrating gut microbiome metagenomics data and adjusting host confounding factors, the model showed high accuracy (R2 = 0.599, mean absolute error = 8.33 years). Besides, we further interpreted the model and identify potential biomarkers for the aging process. Among these identified biomarkers, we found that Finegoldia magna, Bifidobacterium dentium, and Clostridium clostridioforme had increased abundance in the elderly. Moreover, the utilization of amino acids by the gut microbiome undergoes substantial changes with increasing age which have been reported as the risk factors for age-associated malnutrition and inflammation. This model will be helpful for the comprehensive utilization of multiple omics data, and will allow greater understanding of the interaction between microorganisms and age to realize the targeted intervention of aging.},
}

@article {pmid35040746,
year = {2022},
author = {Koutoukidis, DA and Jebb, SA and Zimmerman, M and Otunla, A and Henry, JA and Ferrey, A and Schofield, E and Kinton, J and Aveyard, P and Marchesi, JR},
title = {The association of weight loss with changes in the gut microbiota diversity, composition, and intestinal permeability: a systematic review and meta-analysis.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2020068},
doi = {10.1080/19490976.2021.2020068},
pmid = {35040746},
issn = {1949-0984},
abstract = {The gut microbiome may be a mediator between obesity and health outcomes. However, it is unclear how intentional weight loss changes the gut microbiota and intestinal permeability. We aimed to systematically review and quantify this association. We searched Medline, Embase, CINAHL, Cochrane databases, and trial registries until June 2020 (PROSPERO: CRD42020205292). We included trials of weight loss interventions (energy-restricted diets, pharmacotherapy, bariatric surgery) reporting on the microbiome. Two reviewers independently completed screening, extraction, and risk assessment with the ROBINS-I tool. Pooled standardized mean differences (SMDs) were obtained from random-effects meta-analyses. Forty-seven trials with 1,916 participants (81% female) and a median follow-up of 6 months (range: 2-24) were included. Based on imprecise evidence but with fairly consistent direction of effect, weight loss was associated with a statistically significant increase in α-diversity [SMD: 0.4 (95% CI: 0.2, 0.6], p < .0001, I2 = 70%, n = 30 studies) and a statistically significant reduction in intestinal permeability [SMD: -0.7 (95% CI: -0.9, -0.4), p < .0001, I2 = 83%, n = 17 studies]. Each kg of weight loss was associated with a 0.012 (95% CI: 0.0003, 0.024, p = .045) increase in α-diversity and a -0.017 (95% CI: -0.034, -0.001, p = .038) reduction in intestinal permeability. There was clear evidence of increases in the relative abundance of Akkermansia, but no clear evidence of changes in individual phyla, species, or fecal short-chain fatty acids. Restricting the analyses to the studies with lower risk of bias did not materially alter the estimates. Increasing weight loss is positively associated with increases in gut microbiota α-diversity and reductions in intestinal permeability.},
}

@article {pmid35040740,
year = {2022},
author = {Liu, Y and Qiu, C and Li, X and McClements, DJ and Wang, C and Zhang, Z and Jiao, A and Long, J and Zhu, K and Wang, J and Jin, Z},
title = {Application of starch-based nanoparticles and cyclodextrin for prebiotics delivery and controlled glucose release in the human gut: a review.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/10408398.2022.2028127},
pmid = {35040740},
issn = {1549-7852},
abstract = {Starches are a major constituent of staple foods and are the main source of energy in the human diet (55-70%). In the gastrointestinal tract, starches are hydrolyzed into glucose by α-amylase and α-glucosidase, which leads to a postprandial glucose elevation. High levels of blood glucose levels over sustained periods may promote type 2 diabetes mellitus (T2DM) and obesity. Increasing consumption of starchy foods with a lower glycemic index may therefore contribute to improved health. In this paper, the preparation and properties of several starch-based nanoparticles (SNPs) and cyclodextrins (CDs) derivatives are reviewed. In particular, we focus on the various mechanisms responsible for the ability of these edible nanomaterials to modulate glucose release and the gut microbiome in the gastrointestinal tract. The probiotic functions are achieved through encapsulation and protection of prebiotics or bioactive components in foods or the human gut. This review therefore provides valuable information that could be used to design functional foods for improving human health and wellbeing.},
}

@article {pmid35040699,
year = {2022},
author = {David, MM and Tataru, C and Pope, Q and Baker, LJ and English, MK and Epstein, HE and Hammer, A and Kent, M and Sieler, MJ and Mueller, RS and Sharpton, TJ and Tomas, F and Vega Thurber, R and Fern, XZ},
title = {Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0105821},
doi = {10.1128/msystems.01058-21},
pmid = {35040699},
issn = {2379-5077},
abstract = {A growing body of research has established that the microbiome can mediate the dynamics and functional capacities of diverse biological systems. Yet, we understand little about what governs the response of these microbial communities to host or environmental changes. Most efforts to model microbiomes focus on defining the relationships between the microbiome, host, and environmental features within a specified study system and therefore fail to capture those that may be evident across multiple systems. In parallel with these developments in microbiome research, computer scientists have developed a variety of machine learning tools that can identify subtle, but informative, patterns from complex data. Here, we recommend using deep transfer learning to resolve microbiome patterns that transcend study systems. By leveraging diverse public data sets in an unsupervised way, such models can learn contextual relationships between features and build on those patterns to perform subsequent tasks (e.g., classification) within specific biological contexts.},
}

@article {pmid35040272,
year = {2022},
author = {Jin, YY and Guo, Y and Zheng, CT and Liu, WC},
title = {Effect of heat stress on ileal microbial community of indigenous yellow-feather broilers based on 16S rRNA gene sequencing.},
journal = {Veterinary medicine and science},
volume = {},
number = {},
pages = {},
doi = {10.1002/vms3.734},
pmid = {35040272},
issn = {2053-1095},
support = {32002196//National Nature Science Foundation of China/ ; 2018A030307023//Natural Science Foundation of Guangdong Province/ ; 2017KQNCX090//Innovative Strong School Engineering Project of Guangdong Provincial Department of Education/ ; Q2018302//Innovative Strong School Engineering Project of Guangdong Provincial Department of Education/ ; R18007//Talent Research Start-up Project of Guangdong Ocean University/ ; 573118025//South China Sea Scholar of Guangdong Ocean University/ ; },
abstract = {OBJECTIVES: The broiler chickens are susceptible to heat stress (HS), including the indigenous broilers raised in tropical and subtropical regions. HS caused intestinal dysfunction and disrupted the gut microbiota. However, the researches about the effects of HS on ileal microbiome of indigenous broilers are limited. Therefore, this experiment used 16S rRNA sequencing to analyse the ileal microbial community in indigenous yellow-feather broilers under HS.

MATERIAL AND METHODS: The single factor completely random design was used in the present study, and forty 8-week-old Chinese indigenous yellow-feather broilers (Huaixiang chickens) were randomly divided into two treatments: normal temperature (NT) group and HS group. There are five replications with four broilers per replicate in each group. The broilers in NT group were raised at 21.3 ± 1.2°C during the whole experimental period, the broilers in HS group were exposed to 32.5 ± 1.4°C for 8 h/day from 9:00 am to 17:00 pm and the temperature of rest time is consistent with NT group. The experiment lasted for 4 weeks.

RESULTS: The results showed that HS exposure had no significant effects on the alpha diversity index of ileal microflora of broilers, including the Shannon, Simpson, Chao1 and ACE indexes (p > 0.05). At the genus level, HS significantly reduced the relative abundance of Campylobacter (p < 0.05), and increased the abundance of Delftia (p < 0.05). In addition, prediction of microbial community function indicated that HS significantly enhanced the abundance of the microflora related to lipid metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism and reduced the abundance of the microflora related to nucleotide metabolism and amino acid metabolism.

CONCLUSIONS: Taken together, the present study revealed that chronic HS (4 weeks) exposure changes the abundance of the ileal microflora of broilers. These findings provided new insights into the role of HS in influencing ileal microbial community in indigenous broilers.},
}

@article {pmid35040024,
year = {2022},
author = {Mulpuru, V and Mishra, N},
title = {Antimicrobial Peptides from Human Microbiome Against Multidrug Efflux Pump of Pseudomonas aeruginosa: a Computational Study.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {35040024},
issn = {1867-1314},
abstract = {The excess use of antibiotics has led to the evolution of multidrug-resistant pathogenic strains causing worldwide havoc. These multidrug-resistant strains require potent inhibitors. Pseudomonas aeruginosa is a lead cause of nosocomial infections and also feature in the critical priority list of the world health organization (WHO) for the development of new antibiotics against their antimicrobial resistance. Antimicrobial peptides (AMPs) found in almost every life form from microorganisms to humans are known to defend their hosts against various pathogens. Owing to the diversity of the human microbiome, in this study, we have identified the cell-penetrating AMPs from the human microbiome and studied their inhibitory activity against the outer membrane protein OprM of the MexAB-OprM, a constitutively expressed multidrug efflux pump of the Ps. aeruginosa. Screening of the AMPs from the human microbiome resulted in the identification of 147 cell-penetrating AMPs (CPAMPs). The virtual screening of these CPAMPs against the OprM protein showed significant inhibitory results with the top docked AMP showing binding affinity exceeding -30 kcal/mol. The molecular dynamic simulation determined the interaction stabilities between the AMPs and the OprM at the binding site. Further, the residue interaction networks (RINs) are analyses to identify the inhibitory patterns. Later, these patterns were confirmed by MM-PBSA analysis suggesting that the AMPs are majorly stabilized by electrostatic interactions at the binding site. Thus, the high binding affinity and insights from the molecular interaction signify that the identified CPAMPs from the human microbiome can be further explored as inhibitory agents against multidrug-resistant Ps. aeruginosa.},
}

@article {pmid35040004,
year = {2022},
author = {Wang, CZ and Wan, C and Luo, Y and Zhang, CF and Zhang, QH and Chen, L and Liu, Z and Wang, DH and Lager, M and Li, CH and Jiang, TL and Hou, L and Yuan, CS},
title = {Effects of dihydroartemisinin, a metabolite of artemisinin, on colon cancer chemoprevention and adaptive immune regulation.},
journal = {Molecular biology reports},
volume = {},
number = {},
pages = {},
pmid = {35040004},
issn = {1573-4978},
support = {AT004418//National Center for Complementary and Alternative Medicine/ ; AT005362//National Center for Complementary and Alternative Medicine/ ; 5P30DK042086/DK/NIDDK NIH HHS/United States ; },
abstract = {BACKGROUND: Artemisinin (ART) is an anti-malaria natural compound with a moderate anticancer action. As a metabolite of ART, dihydroartemisinin (DHA) may have stronger anti-colorectal cancer (CRC) bioactivities. However, the effects of DHA and ART on CRC chemoprevention, including adaptive immune regulation, have not been systematically evaluated and compared.

METHODS: Coupled with a newly-established HPLC analytical method, enteric microbiome biotransformation was conducted to identify if the DHA is a gut microbial metabolite of ART. The anti-CRC potential of these compounds was compared using two different human CRC cell lines for cell cycle arrest, apoptotic induction, and anti-inflammation activities. Naive CD4+ T cells were also obtained for testing the compounds on the differentiation of Treg, Th1 and Th17.

RESULTS: Using compound extraction and analytical methods, we observed for the first time that ART completely converted into its metabolites by gut microbiome within 24 h, but no DHA was detected. Although ART did not obviously influence cancer cell growth in the concentration tested, DHA very significantly inhibited the cancer cell growth at relatively low concentrations. DHA included G2/M cell cycle arrest via upregulation of cyclin A and apoptosis. Both ART and DHA downregulated the pro-inflammatory cytokine expression. The DHA significantly promoted Treg cell proliferation, while both ART and DHA inhibited Th1 and Th17 cell differentiation.

CONCLUSIONS: As a metabolite of ART, DHA possessed stronger anti-CRC activities. The DHA significantly inhibited cell growth via cell cycle arrest, apoptosis induction and anti-inflammation actions. The adaptive immune regulation is a related mechanism of actions for the observed effects.},
}

@article {pmid35039906,
year = {2022},
author = {Liu, H and Lin, G and Gao, D and Chen, H and He, M and Lu, J},
title = {Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35039906},
issn = {1432-184X},
support = {91858208//National Natural Science Foundation of China/ ; 311020005//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 2019M663209//China Postdoctoral Science Foundation/ ; },
abstract = {Determinism and stochasticity in microbial community composition decisions have attracted wide attention. However, there is no consensus on their interrelationships and relative importance, and the mechanism controlling the interaction between the two ecological processes remains to be revealed. The interaction of the two ecological processes on the continental shelf of the South China Sea was studied by performing 16S rRNA gene amplicon sequencing on 90 sediments at multiple depths in five sites. Three nearshore sites have higher microbial diversity than those two close to the shelf margin. Different microbial composition was observed between sites and microbial composition of nearshore sites was positively correlated with total nitrogen, total sulfur, total organic carbon, and dissolved oxygen, while that of offshore was positively correlated with total carbon, salinity, and photosynthetically active radiation. The null model test showed that the community composition among layers of the same site and between nearby sites was mainly dominated by the homogeneous selection, while that between distant sites was mainly affected by dispersal limitation, which indicates that geographic scale influences the interactivities of determinism and stochasticity. Our research indicates that the balance of these two ecological processes along the geographic scale is mainly determined by the dispersal ability of microbes and environmental heterogeneity between areas. The study provides new insights into how deterministic and stochastic processes shape microbial community composition on the continental shelf.},
}

@article {pmid35039849,
year = {2022},
author = {Wei, N and Whyle, RL and Ashman, TL and Jamieson, MA},
title = {Genotypic variation in floral volatiles influences floral microbiome more strongly than interactions with herbivores and mycorrhizae in strawberries.},
journal = {Horticulture research},
volume = {},
number = {},
pages = {},
doi = {10.1093/hr/uhab005},
pmid = {35039849},
issn = {2662-6810},
abstract = {The floral microbiome is of significant relevance to plant reproduction and crop productivity. While plant genotype is key to floral microbiome assembly, whether and how genotypic variation in floral traits and plant-level mutualistic and antagonistic interactions at the rhizosphere and phyllosphere influence the microbiome in the anthosphere remain little known. Using a factorial field experiment that manipulated biotic interactions belowground (mycorrhizae treatments) and aboveground (herbivory treatments) in three strawberry genotypes, we assessed how genotypic variation in flower abundance and size and plant-level biotic interactions influence the bidirectional relationships between floral volatile organic compounds (VOCs) and the floral microbiome using structural equation modeling. We found that plant genotype played a stronger role, overall, in shaping the floral microbiome than biotic interactions with mycorrhizae and herbivores. Genotypic variation in flower abundance and size influenced the emission of floral VOCs, especially terpenes (e.g. α- and β-pinene, ocimene isomers) and benzenoids (e.g. p-anisaldehyde, benzaldehyde), which in turn affected floral bacterial and fungal communities. While the effects of biotic interactions on floral traits including VOCs were weak, mycorrhizae treatments (mycorrhizae and herbivory + mycorrhizae) affected the fungal community composition in flowers. These findings improve our understanding of the mechanisms by which plant genotype influences floral microbiome assembly and provide the first evidence that biotic interactions at the rhizosphere and phyllosphere can influence the floral microbiome, and offer important insights into agricultural microbiomes.},
}

@article {pmid35039534,
year = {2022},
author = {Lee, SJ and Rho, M},
title = {Multimodal deep learning applied to classify healthy and disease states of human microbiome.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {824},
pmid = {35039534},
issn = {2045-2322},
support = {2017M3A9F3041232//National Research Foundation of Korea/ ; 2020-0-01373//Institute of Information & Communications Technology Planning & Evaluation (IITP)/ ; },
abstract = {Metagenomic sequencing methods provide considerable genomic information regarding human microbiomes, enabling us to discover and understand microbial diseases. Compositional differences have been reported between patients and healthy people, which could be used in the diagnosis of patients. Despite significant progress in this regard, the accuracy of these tools needs to be improved for applications in diagnostics and therapeutics. MDL4Microbiome, the method developed herein, demonstrated high accuracy in predicting disease status by using various features from metagenome sequences and a multimodal deep learning model. We propose combining three different features, i.e., conventional taxonomic profiles, genome-level relative abundance, and metabolic functional characteristics, to enhance classification accuracy. This deep learning model enabled the construction of a classifier that combines these various modalities encoded in the human microbiome. We achieved accuracies of 0.98, 0.76, 0.84, and 0.97 for predicting patients with inflammatory bowel disease, type 2 diabetes, liver cirrhosis, and colorectal cancer, respectively; these are comparable or higher than classical machine learning methods. A deeper analysis was also performed on the resulting sets of selected features to understand the contribution of their different characteristics. MDL4Microbiome is a classifier with higher or comparable accuracy compared with other machine learning methods, which offers perspectives on feature generation with metagenome sequences in deep learning models and their advantages in the classification of host disease status.},
}

@article {pmid35039521,
year = {2022},
author = {Nearing, JT and Douglas, GM and Hayes, MG and MacDonald, J and Desai, DK and Allward, N and Jones, CMA and Wright, RJ and Dhanani, AS and Comeau, AM and Langille, MGI},
title = {Microbiome differential abundance methods produce different results across 38 datasets.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {342},
pmid = {35039521},
issn = {2041-1723},
abstract = {Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. Here, we compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups. We test for differences in amplicon sequence variants and operational taxonomic units (ASVs) between these groups. Our findings confirm that these tools identified drastically different numbers and sets of significant ASVs, and that results depend on data pre-processing. For many tools the number of features identified correlate with aspects of the data, such as sample size, sequencing depth, and effect size of community differences. ALDEx2 and ANCOM-II produce the most consistent results across studies and agree best with the intersect of results from different approaches. Nevertheless, we recommend that researchers should use a consensus approach based on multiple differential abundance methods to help ensure robust biological interpretations.},
}

@article {pmid35039079,
year = {2022},
author = {Adu-Oppong, B and Thänert, R and Wallace, MA and Burnham, CD and Dantas, G},
title = {Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {6},
pmid = {35039079},
issn = {2049-2618},
abstract = {BACKGROUND: The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic patients in routine standard-of-care urine tests. Here, we used shotgun metagenomic sequencing to characterize the microbial composition of asymptomatic volunteers in a set of 30 longitudinally collected urine specimens. Using permutation tests, we established a range of asymptomatic microbiota states, and use these to contextualize the microbiota of 122 urine specimens collected from patients with suspected UTIs diagnostically categorized by standard-of-care urinalysis within that range. Finally, we used a standard-of-care culture protocol to evaluate the efficiency of culture-based recovery of the urinary microbiota.

RESULTS: The majority of genitourinary microbiota in individals suspected to have UTI overlapped with the spectrum of asymptomatic microbiota states. Longitudinal characterization of the genitourinary microbiome in urine specimens collected from asymptomatic volunteers revealed fluctuations of microbial functions and taxonomy over time. White blood cell counts from urinalysis suggested that urine specimens categorized as 'insignificant', 'contaminated', or 'no-growth' by conventional culture methods frequently showed signs of urinary tract inflammation, but this inflammation is not associated with genitourinary microbiota dysbiosis. Comparison of directly sequenced urine specimens with standard-of-care culturing confirmed that culture-based diagnosis biases genitourinary microbiota recovery towards the traditional uropathogens Escherichia coli and Klebsiella pneumoniae.

CONCLUSION: Here, we utilize shotgun metagenomic sequencing to establish a baseline of asymptomatic genitourinary microbiota states. Using this baseline we establish substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Our results establish that bacterial presence alone does not explain the onset of clinical symptoms. Video Abstract.},
}

@article {pmid35038883,
year = {2021},
author = {Hornová, Markéta and Pařízek, Antonín and Koucký, Michal},
title = {The role of the microbiome in pregnancy.},
journal = {Ceska gynekologie},
volume = {86},
number = {6},
pages = {422-427},
doi = {10.48095/cccg2021422},
pmid = {35038883},
issn = {1210-7832},
abstract = {OBJECTIVE: To provide a comprehensive overview of the available information on the maternal microbio-me and its effect on pregnancy and preterm birth.

METHODS: Systematic review of available literature on the topic was done using the PubMed database.

CONCLUSION: Etiology of preterm labor is multifactorial. Individual setting of humoral and cellular immune response is key; however, lately the focus has shifted to the role of the microbio-me, especially the vaginal one. The role of additional microbio-mes and the relationship between different compartments are the focus of intensive research. Mainly the differences in the maternal and neonatal microbio-me depend on the method of delivery and administration of different antibio-tics during pregnancy and labor. The uterine cavity is no longer thought to be without colonization and the formation of the fetal microbio-me begins early in pregnancy.},
}

@article {pmid35038733,
year = {2022},
author = {Zhang, Y and D'Souza, G and Fakhry, C and Bigelow, EO and Usyk, M and Burk, RD and Zhao, N},
title = {Oral HPV associated with differences in oral microbiota beta diversity and microbiota abundance.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiac010},
pmid = {35038733},
issn = {1537-6613},
abstract = {BACKGROUND: While cervicovaginal microbiome has been associated with cervical human papillomavirus (HPV) infection, little is known regarding the association of oral microbiome with oral HPV, a cause of oropharyngeal cancer.

METHODS: A cross-sectional analysis of 495 participants from the Men and Women Offering Understanding of Throat HPV study was conducted. 16S rRNA gene amplicon sequencing was performed on saliva samples. HPV DNA in oral rinse samples was tested. Associations of oral microbiome diversity, taxon abundance and predicted functional pathways with oral HPV were assessed, adjusting for age, race/ethnicity, education, HIV, current smoking, and sequencing batch.

RESULTS: Participants with oral HPV (n=68) compared to those without HPV had similar oral microbiome alpha-diversity yet different beta-diversity (Bray-Curtis distance for bacterial taxa: p=0.009; functional pathways: p=0.02). Participants with oral HPV had higher abundance of Actinomycetaceae, Prevotellaceae, Veillonellaceae, Campylobacteraceae, Bacteroidetes, and lower abundance of Gemellaceae (false discovery rate<0.10). We also found differential functional potential of oral microbiome by oral HPV status: xenobiotic biodegradation-related pathways were less abundant among participants with oral HPV, suggesting potential xenobiotic-induced toxic effects with implications for HPV susceptibility.

CONCLUSIONS: Our findings suggest a shift in oral microbiome community structure, composition and functional potential between individuals with and without oral HPV.},
}

@article {pmid35038644,
year = {2022},
author = {van der Houwen, TB and van Hagen, PM and van Laar, JAM},
title = {Immunopathogenesis of Behçet's disease and treatment modalities.},
journal = {Seminars in arthritis and rheumatism},
volume = {52},
number = {},
pages = {151956},
doi = {10.1016/j.semarthrit.2022.151956},
pmid = {35038644},
issn = {1532-866X},
abstract = {INTRODUCTION: Behçet's disease (BD) is an auto-inflammatory disease, primarily characterized by recurrent painful mucocutaneous ulcerations.

METHODS: A literature search was performed to write a narrative review into the pathogenesis and current treatment options of BD.

RESULTS: The pathogenesis of BD remains to be elucidated, but is considered a genetically primed disease in which an external trigger causes immune activation resulting in inflammatory symptoms. GWAS data show an association between multiple genetic polymorphisms (HLA-B51, ERAP1, IL10 and IL23R-IL12RB2) and increased susceptibility to BD. Bacteria as streptococci, an unbalanced microbiome or molecular mimicry trigger the inflammation in BD. Increased production or responsiveness of pro-inflammatory components of the innate immune response (TLR, neutrophils, NK-cells or γδ T-cells) to these triggers may be a crucial step in the pathogenesis of BD. Additionally to an increased autoinflammatory response there is evidence of a dysregulated adaptive immune system, with a disturbed Th1/Th2 balance, expansion of Th17 cells and possibly a decrease in regulatory T cells, resulting in a surplus in pro-inflammatory cytokines. The inflammation causes a typical clinical phenotype including orogenital ulcerations, uveitis and skin lesions. Treatment is aimed at the aberrations found in the innate (neutrophils and γδ-T cells) and adaptive immune system (TNF-α, INF-γ, IL-1), directed at organ involvement and individualized based on patient characteristics.

CONCLUSION: We presented an extensive review into the pathogenesis and treatment options of BD.},
}

@article {pmid35038617,
year = {2021},
author = {Ruegg, PL},
title = {The bovine milk microbiome - an evolving science.},
journal = {Domestic animal endocrinology},
volume = {79},
number = {},
pages = {106708},
doi = {10.1016/j.domaniend.2021.106708},
pmid = {35038617},
issn = {1879-0054},
abstract = {Improved access to genome based, culture independent methods has generated great interest in defining the bovine milk microbiome. Several comprehensive reviews of this subject have recently been published and the purpose of this short review is to consolidate current understanding of the relevance and biological significance of this emerging topic. In contrast to mucosal organs that contain rich and well-characterized culturable and nonculturable microbial communities, milk obtained from the healthy bovine mammary gland usually contains few or no viable bacteria. The low bacterial biomass of milk has created methodological challenges that have resulted in considerable variability in results of studies that have used genomic methods to define the microbiota of milk obtained from healthy or diseased mammary glands. While genomes from several bacterial genera are routinely identified from samples of milk, teat skin and the teat canal, the viability, origin, and function of these organisms is uncertain as environmental factors have been shown to strongly influence the composition of these bacterial populations. Possible sources of microbial DNA include bacteria introduced from skin or the environment, bacteria trapped in teat canal keratin or bacteria engulfed by phagocytes. Researchers have not achieved consensus about key concepts such as the presence of a core commensal milk microbiome or dysbiosis as part of a causal pathway disrupting udder health. Understanding of the bovine milk microbiome has been greatly impeded by a lack of standardized methods used to collect, process, and assess bovine milk samples. Sample collection is a critical first step that will determine the validity of results. To minimize contamination with external sources of bacterial DNA, teat sanitation methods used for collection of milk samples that will be subjected to extraction and amplification of bacteria DNA should far exceed aseptic techniques used for collection of milk samples that will be submitted for microbiological culture. A number of laboratory issues have yet to be resolved. Contamination of low biomass samples with bacterial DNA from laboratory reagents is a well-known issue that has affected results of studies using bovine milk samples and results of sequencing of negative controls should always be reported. Replication of experiments has rarely been performed and consistency in results are lacking. While progress has been made, standardization of methods and replication using samples originating from differing farm conditions are critically needed to solidify knowledge of this emerging topic.},
}

@article {pmid35038526,
year = {2022},
author = {Chakraborty, A and Suchy, M and Hubert, CRJ and Ryan, MC},
title = {Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {153092},
doi = {10.1016/j.scitotenv.2022.153092},
pmid = {35038526},
issn = {1879-1026},
abstract = {Nitrate pollution is a major threat to groundwater quality in agricultural areas. Natural attenuation of nitrate in contaminated aquifers is mediated by denitrifying microbial populations in anoxic environments. Vertical distribution of denitrifying microbial communities in aquifers is greatly influenced by groundwater redox conditions, local hydrogeological parameters, and seasonal variability in groundwater flow and recharge. In this study, we investigated groundwater geochemistry and the composition of bacterial and archaeal communities with increasing depth in a shallow nitrate-contaminated aquifer in British Columbia, Canada. High-resolution passive diffusion sampling was conducted to collect groundwater at 10-cm intervals from 4 to 20 m below ground surface (mbgs) in the aquifer. Geochemical analyses of major ions indicated a general shift in the groundwater chemistry below 16 mbgs including decreasing chloride concentrations that suggest two-end member mixing of shallow and deep groundwater with different chemistries. A redoxcline was further observed within a 2 m transition zone at 18-20 mbgs characterized by sharp declines in nitrate concentrations and increases in sulfate and total inorganic carbon. Excursions in δ15N-NO3- and δ18O-NO3- in the same depth interval are consistent with denitrification, and a concomitant decrease in δ34S-SO42- suggested that denitrification was coupled to sulfide or sulfur oxidation. Microbial communities within this depth interval were significantly dissimilar to those above and below, featuring putative lithotrophic denitrifying bacteria belonging to the genera Sulfurifustis, Sulfuritalea and Sulfuricella. These lineages were detected in greatest abundance at 19 mbgs while the abundances of putative heterotrophic sulfate-reducing bacteria belonging to the genus Desulfosporosinus were greatest at 20 mbgs. In addition to help distinguish denitrification from mixing-induced changes in groundwater chemistry, the above observed vertical stratification of the microbial key players connects nitrate removal to the locations of the aquifer sampled.},
}

@article {pmid35038517,
year = {2022},
author = {Yin, B and Tan, S and Wang, J and Pan, K and Wang, WX and Wang, X},
title = {Antibiotic application may raise the potential of methylmercury accumulation in fish.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {152946},
doi = {10.1016/j.scitotenv.2022.152946},
pmid = {35038517},
issn = {1879-1026},
abstract = {Mercury (Hg) biotransformation can significantly affect the Hg speciation and bioaccumulation in fish, where gut microbiota play an important role in this process. Antibiotics have been extensively used in aquaculture and can affect gut microbial structure. However, the influence of antibiotics on Hg biotransformation in fish has not been thoroughly understood. The present study investigated the effects of antibiotic (florfenicol) application on gut microbiota and subsequent impacts on Hg biotransformation and bioaccumulation in tilapia (Oreochromis mossambicus). The results showed that the florfenicol treatment did not affect IHg accumulation in the IHg-exposed fish or the MeHg accumulation in the MeHg-exposed fish. However, methylation was significantly weakened (from 0.015% d-1 to 0.005% d-1) and demethylation was completely terminated (from 0.046% d-1 to non-observable level) in the florfenicol-treated fish as compared to the control fish. This can be ascribed to the major shift in the richness of microbial methylators/demethylators in fish gut. Furthermore, florfenicol disturbed the homeostasis of gut microbiome and enhanced the growth of opportunistic pathogens. Our results strongly suggested that antibiotic application significantly altered the gut microbial community, thereby increasing the potential of MeHg accumulation by fish. This study highlights the importance of appropriate use of antibiotics in aquaculture as well as decreasing the environmental risks of Hg contamination in fish.},
}