@article {pmid36749701,
year = {2023},
author = {Girolamini, L and Pascale, MR and Salaris, S and Mazzotta, M and Orsini, M and Grottola, A and Zini, N and Cristino, S},
title = {Corrigendum: Legionella bononiensis sp. nov., isolated from a hotel water distribution system in northern Italy.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.005710},
pmid = {36749701},
issn = {1466-5034},
}

@article {pmid36749697,
year = {2023},
author = {Pradel, N and Fardeau, ML and Bunk, B and Spröer, C and Boedeker, C and Wolf, J and Neumann-Schaal, M and Pester, M and Spring, S},
title = {Aminithiophilus ramosus gen. nov., sp. nov., a sulphur-reducing bacterium isolated from a pyrite-forming enrichment culture, and taxonomic revision of the family Synergistaceae.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.005691},
pmid = {36749697},
issn = {1466-5034},
abstract = {A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2[T] could be affiliated with the phylum Synergistota. Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2[T] (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2[T] (=DSM 107166[T]=NBRC 114655[T]) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.},
}

@article {pmid36748549,
year = {2023},
author = {Soares, A and Edwards, A and An, D and Bagnoud, A and Bradley, J and Barnhart, E and Bomberg, M and Budwill, K and Caffrey, SM and Fields, M and Gralnick, J and Kadnikov, V and Momper, L and Osburn, M and Mu, A and Moreau, JW and Moser, D and Purkamo, L and Rassner, SM and Sheik, CS and Sherwood Lollar, B and Toner, BM and Voordouw, G and Wouters, K and Mitchell, AC},
title = {A global perspective on bacterial diversity in the terrestrial deep subsurface.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {1},
pages = {},
doi = {10.1099/mic.0.001172},
pmid = {36748549},
issn = {1465-2080},
abstract = {While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.},
}

@article {pmid36747985,
year = {2023},
author = {Green, GBH and DePaola, A and Linville, JG and Morrow, CD and Bej, AK},
title = {High-throughput amplicon sequencing datasets of coastal sediments from three locations of the Gulf of Mexico, USA.},
journal = {Data in brief},
volume = {47},
number = {},
pages = {108895},
pmid = {36747985},
issn = {2352-3409},
abstract = {We present high-throughput amplicon sequence (HTS) datasets of the purified microbial metacommunity DNA of coastal surface sediments from Portersville Bay (PVB) (n = 3), Bayou La Batre (BLB) (n = 3), and Mobile Bay (MOB) (n = 3) of the U.S. Gulf of Mexico (U.S. Gulf Coast). The PVB samples were collected from the oyster aquaculture Shellevator™ system; the BLB samples were from locations on the shoreline adjacent to wild oysters attached to rocks and likely polluted from sewage and possibly chemical contamination from boats, shipyards, and seafood processing facilities; and MOB samples were adjacent to aquaculture oysters in bottom cages. The amplicons of the V4 hypervariable segment of the 16S rRNA gene from each sample were sequenced on an Illumina MiSeq to generate these HTS datasets. The raw sequences were quality-checked, demultiplexed into FASTQ files, denoised using DADA2, and subsampled. Then, the FASTA formatted sequences were assigned the taxonomic ids to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier using the Quantitative Insights Into Microbial Ecology (QIIME2 v2022.2). The applicability of the HTS datasets was confirmed by microbial taxa analysis at the phylum level using the "qiime taxa collapse" command. All HTS datasets are available through the BioSample Submission Portal under the BioProject ID PRJNA876773 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA876773).},
}

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

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

@article {pmid36746236,
year = {2023},
author = {Zhang, L and Hu, C and Zhang, Z and Liu, R and Liu, G and Xue, D and Wang, Z and Wu, C and Wu, X and She, J and Shi, F},
title = {Association Between Prior Appendectomy and The Risk and Course of Crohn's Disease: A Systematic Review and Meta-analysis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102090},
doi = {10.1016/j.clinre.2023.102090},
pmid = {36746236},
issn = {2210-741X},
abstract = {BACKGROUND AND AIMS: The appendix has an important immune function in both health and disease, and appendectomy may influence microbial ecology and immune function. This meta-analysis aims to assess the association between appendectomy and the risk and course of Crohn's disease (CD).

METHODS: PubMed, EMBASE, and the Cochrane Library were used to identify all studies published until June 2022. Data from studies evaluating the association between appendectomy and CD were reviewed.

RESULTS: A total of 28 studies were included in the final analysis, comprising 22 case-control and 6 cohort studies. A positive relationship between prior appendectomy and the risk of developing CD was observed in both case-control studies (odds ratio [OR]: 1.59, 95% confidence interval [CI]: 1.22-2.08) and cohort studies (relative risk [RR]: 2.28, 95% CI: 1.66-3.14). The elevated risk of CD persisted 5 years post-appendectomy (RR = 1.24, 95% CI: 1.12-1.36). The risk of developing CD was similarly elevated regardless of the presence (RR = 1.64, 95% CI: 1.17-2.31) or absence (RR = 2.77, 95% CI: 1.84-4.16) of appendicitis in patients. Moreover, significant differences were found in the proportion of terminal ileum lesions (OR = 1.63; 95% CI: 1.38-1.93) and colon lesions (OR = 0.70; 95% CI: 0.5-0.84) between CD patients with appendectomy and those without appendectomy.

CONCLUSIONS: The risk of developing CD following an appendectomy is significant and persists 5 years postoperatively. Moreover, the elevated risk of CD may mainly occur in the terminal ileum.},
}

@article {pmid36744882,
year = {2023},
author = {Liu, X and Lyu, L and Li, J and Sen, B and Bai, M and Stajich, JE and Collier, JL and Wang, G},
title = {Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0424722},
doi = {10.1128/spectrum.04247-22},
pmid = {36744882},
issn = {2165-0497},
abstract = {Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as "leftover scavengers" and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes. IMPORTANCE Unicellular heterotrophic eukaryotes are an important component of marine ecosystems. However, their ecological functions and modes of nutrition remain largely unknown. Our current understanding of marine microbial ecology is incomplete without integrating these heterotrophic microeukaryotes into the food web models. This study focuses on the unicellular fungus-like protists Labyrinthulomycetes and provides two high-quality genomes of cellulase-producing Labyrinthulomycetes. Our study uncovers the basis of their cellulase production by deciphering the results of genomic, biochemical, and phylogenetic analyses. This study instigates a further investigation of the molecular mechanism of organic matter utilization by Labyrinthulomycetes in the world's oceans.},
}

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

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

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

@article {pmid36741554,
year = {2022},
author = {Lombard, L and van Doorn, R and Groenewald, JZ and Tessema, T and Kuramae, EE and Etolo, DW and Raaijmakers, JM and Crous, PW},
title = {Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia.},
journal = {Fungal systematics and evolution},
volume = {10},
number = {},
pages = {177-215},
pmid = {36741554},
issn = {2589-3831},
abstract = {Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp. strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future. Citation: Lombard L, van Doorn R, Groenewald JZ, Tessema T, Kuramae EE, Etolo DW, Raaijmakers JM, Crous PW (2022). Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia. Fungal Systematics and Evolution 10: 177-215. doi: 10.3114/fuse.2022.10.08.},
}

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

@article {pmid36739716,
year = {2023},
author = {Doni, L and Oliveri, C and Lasa, A and Di Cesare, A and Petrin, S and Martinez-Urtaza, J and Coman, F and Richardson, A and Vezzulli, L},
title = {Large-scale impact of the 2016 Marine Heatwave on the plankton-associated microbial communities of the Great Barrier Reef (Australia).},
journal = {Marine pollution bulletin},
volume = {188},
number = {},
pages = {114685},
doi = {10.1016/j.marpolbul.2023.114685},
pmid = {36739716},
issn = {1879-3363},
abstract = {The Great Barrier Reef (GBR) is the world's largest coral ecosystem and is threatened by climate change. This study investigated the impact of the 2016 Marine Heatwave (MHW) on plankton associated microbial communities along a ∼800 km transect in the GBR. 16S rRNA gene metabarcoding of archived plankton samples collected from November 2014 to August 2016 in this region showed a significant increase in Planctomycetes and bacteria belonging to the genus Vibrio and Synechococcus during and after the heatwave. Notably, Droplet Digital PCR and targeted metagenomic analysis applied on samples collected four months after the MHW event revealed the presence of several potential pathogenic Vibrio species previously associated with diseases in aquatic animals. Overall, the 2016 MHW significantly impacted the surface picoplankton community and fostered the spread of potentially pathogenic bacteria across the GBR providing an additional threat for marine biodiversity in this area.},
}

@article {pmid36737902,
year = {2023},
author = {Cabezas-Terán, K and Grootaert, C and Ortiz, J and Donoso, S and Ruales, J and Van Bockstaele, F and Van Camp, J and Van de Wiele, T},
title = {In vitro bioaccessibility and uptake of β-carotene from encapsulated carotenoids from mango by-products in a coupled gastrointestinal digestion/Caco-2 cell model.},
journal = {Food research international (Ottawa, Ont.)},
volume = {164},
number = {},
pages = {112301},
doi = {10.1016/j.foodres.2022.112301},
pmid = {36737902},
issn = {1873-7145},
abstract = {β-carotene is a carotenoid with provitamin A activity and other health benefits, which needs to become bioavailable upon oral intake to exert its biological activity. A better understanding of its behaviour and stability in the gastrointestinal tract and means to increase its bioavailability are highly needed. Using an in vitro gastrointestinal digestion method coupled to an intestinal cell model, we explored the stability, gastrointestinal bioaccessibility and cellular uptake of β-carotene from microparticles containing carotenoid extracts derived from mango by-products. Three types of microparticles were tested: one with the carotenoid extract as such, one with added inulin and one with added fructooligosaccharides. Overall, β-carotene was relatively stable during the in vitro digestion, as total recoveries were above 68 %. Prebiotics in the encapsulating material, especially inulin, enhanced the bioaccessibility of β-carotene almost 2-fold compared to microparticles without prebiotics. Likewise, β-carotene bioaccessibility increased proportionally with bile salt concentrations during digestion. Yet, a bile salts level above 10 mM did not contribute markedly to β-carotene bioaccessibility of prebiotic containing microparticles. Cellular uptake experiments with non-filtered gastrointestinal digests yielded higher absolute levels of β-carotene taken up in the epithelial cells as compared to uptake assays with filtered digests. However, the proportional uptake of β-carotene was higher for filtered digests (24 - 31 %) than for non-filtered digests (2 - 8 %). Matrix-dependent carotenoid uptake was only visible in the unfiltered medium, thereby pointing to possible other cellular transport mechanisms of non-micellarized carotenoids, besides the concentration effect. Regardless of a filtration step, inulin-amended microparticles consistently resulted in a higher β-carotene uptake than regular microparticles or FOS-amended microparticles. In conclusion, encapsulation of carotenoid extracts from mango by-products displayed chemical stability and release of a bioaccessible β-carotene fraction upon gastrointestinal digestion. This indicates the potential of the microparticles to be incorporated into functional foods with provitamin A activity.},
}

@article {pmid36737826,
year = {2023},
author = {Forgie, AJ and Pepin, DM and Ju, T and Tollenaar, S and Sergi, CM and Gruenheid, S and Willing, BP},
title = {Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {21},
pmid = {36737826},
issn = {2049-2618},
abstract = {BACKGROUND: Vitamin B12 supplements typically contain doses that far exceed the recommended daily amount, and high exposures are generally considered safe. Competitive and syntrophic interactions for B12 exist between microbes in the gut. Yet, to what extent excessive levels contribute to the activities of the gut microbiota remains unclear. The objective of this study was to evaluate the effect of B12 on microbial ecology using a B12 supplemented mouse model with Citrobacter rodentium, a mouse-specific pathogen. Mice were fed a standard chow diet and received either water or water supplemented with B12 (cyanocobalamin: ~120 μg/day), which equates to approximately 25 mg in humans. Infection severity was determined by body weight, pathogen load, and histopathologic scoring. Host biomarkers of inflammation were assessed in the colon before and after the pathogen challenge.

RESULTS: Cyanocobalamin supplementation enhanced pathogen colonization at day 1 (P < 0.05) and day 3 (P < 0.01) postinfection. The impact of B12 on gut microbial communities, although minor, was distinct and attributed to the changes in the Lachnospiraceae populations and reduced alpha diversity. Cyanocobalamin treatment disrupted the activity of the low-abundance community members of the gut microbiota. It enhanced the amount of interleukin-12 p40 subunit protein (IL12/23p40; P < 0.001) and interleukin-17a (IL-17A; P < 0.05) in the colon of naïve mice. This immune phenotype was microbe dependent, and the response varied based on the baseline microbiota. The cecal metatranscriptome revealed that excessive cyanocobalamin decreased the expression of glucose utilizing genes by C. rodentium, a metabolic attribute previously associated with pathogen virulence.

CONCLUSIONS: Oral vitamin B12 supplementation promoted C. rodentium colonization in mice by altering the activities of the Lachnospiraceae populations in the gut. A lower abundance of select Lachnospiraceae species correlated to higher p40 subunit levels, while the detection of Parasutterella exacerbated inflammatory markers in the colon of naïve mice. The B12-induced change in gut ecology enhanced the ability of C. rodentium colonization by impacting key microbe-host interactions that help with pathogen exclusion. This research provides insight into how B12 impacts the gut microbiota and highlights potential consequences of disrupting microbial B12 competition/sharing through over-supplementation. Video Abstract.},
}

@article {pmid36736839,
year = {2023},
author = {Zhao, L and Dou, Q and Chen, S and Wang, Y and Yang, Q and Chen, W and Zhang, H and Du, Y and Xie, M},
title = {Adsorption abilities and mechanisms of Lactobacillus on various nanoplastics.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {138038},
doi = {10.1016/j.chemosphere.2023.138038},
pmid = {36736839},
issn = {1879-1298},
abstract = {As a new type of pollutants, nanoplastics (NPs), which are easily ingested by humans from food wraps, salt, drinking water, have been widely detected in various water environments, and are a threat to human health. It is therefore urgent to develop an efficient method to remove NPs from the diet or relief its harm. In the present study, the possibility of a well-known human probiotic, lactic acid bacteria (LAB), was evaluated to remove NPs from food as an absorbent. The results indicated that LAB from infant feces could efficiently absorb three types NPs, i.e. polypropylene (PP), polyethylene (PE), and polyvinyl chloride (PVC) with the adsorption rates of PP > PE > PVC (PP 78.57%, PE 71.59%, PVC 66.57%) and the Nile red-stained NPs being aggregated on the surfaces of Lactobacillus cells. The smaller the particle size, the stronger the ability of NP adsorption on the cell surface. The hydrophobicity of NPs and bacterial cells affected the adsorption process. The measurement of adsorption rates of different cell components indicated that the overall adsorption effect of cell was better than that of individual cell component. The results of molecular dynamics analysis revealed that adsorption was mainly caused by electrostatic interactions, van der Waals forces, and hydrogen bonds. The hydrophobic interaction was also involved in adsorption process. Overall, this research may provide new information for developing new strategies for NPs removal in intestinal environment.},
}

@article {pmid36735066,
year = {2023},
author = {Modenutti, B and Martyniuk, N and Bastidas Navarro, M and Balseiro, E},
title = {Glacial Influence Affects Modularity in Bacterial Community Structure in Three Deep Andean North-Patagonian Lakes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36735066},
issn = {1432-184X},
abstract = {We analyze the bacteria community composition and the ecological processes structuring these communities in three deep lakes that receive meltwater from the glaciers of Mount Tronador (North-Patagonia, Argentina). Lakes differ in their glacial connectivity and in their turbidity due to glacial particles. Lake Ventisquero Negro is a recently formed proglacial lake and it is still in contact with the glacier. Lakes Mascardi and Frías lost their glacial connectivity during the Pleistocene-Holocene transition. Total dissolved solid concentration has a significant contribution to the environmental gradient determining the segregation of the three lakes. The newly formed lake Ventisquero Negro conformed a particular bacterial community that seemed to be more related to the microorganisms coming from glacier melting than to the other lakes of the basin. The net relatedness index (NRI) showed that the bacterial community of lake Ventisquero Negro is determined by environmental filtering, while in the other lakes, species interaction would be a more important driver. The co-occurrence network analysis showed an increase in modularity and in the number of modules when comparing Lake Ventisquero Negro with the two large glacier-fed lakes suggesting an increase in heterogeneity. At the same time, the presence of modules with phototrophic bacteria (Cyanobium strains) in lakes Frías and Mascardi would reflect the increase of this functional photosynthetic association. Overall, our results showed that the reduction in ice masses in Patagonia will affect downstream large deep Piedmont lakes losing the glacial influence in their bacterial communities.},
}

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

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

@article {pmid36734313,
year = {2023},
author = {Hassan, MM and van Vliet, AHM and Higgins, O and Burke, LP and Chueiri, A and O'Connor, L and Morris, D and Smith, TJ and La Ragione, RM},
title = {Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.14227},
pmid = {36734313},
issn = {1751-7915},
abstract = {Environmental water is considered one of the main vehicles for the transmission of antimicrobial resistance (AMR), posing an increasing threat to humans and animals health. Continuous efforts are being made to eliminate AMR; however, the detection of AMR pathogens from water samples often requires at least one culture step, which is time-consuming and can limit sensitivity. In this study, we employed comparative genomics to identify the prevalence of AMR genes within among: Escherichia coli, Klebsiella, Salmonella enterica and Acinetobacter, using publicly available genomes. The mcr-1, blaKPC (KPC-1 to KPC-4 alleles), blaOXA-48, blaOXA-23 and blaVIM (VIM-1 and VIM-2 alleles) genes are of great medical and veterinary significance, thus were selected as targets for the development of isothermal loop-mediated amplification (LAMP) detection assays. We also developed a rapid and sensitive sample preparation method for an integrated culture-independent LAMP-based detection from water samples. The developed assays successfully detected the five AMR gene markers from pond water within 1 h and were 100% sensitive and specific with a detection limit of 0.0625 μg/mL and 10 cfu/mL for genomic DNA and spiked bacterial cells, respectively. The integrated detection can be easily implemented in resource-limited areas to enhance One Health AMR surveillances and improve diagnostics.},
}

@article {pmid36728429,
year = {2023},
author = {Graffius, S and Garzón, JFG and Zehl, M and Pjevac, P and Kirkegaard, R and Flieder, M and Loy, A and Rattei, T and Ostrovsky, A and Zotchev, SB},
title = {Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0435322},
doi = {10.1128/spectrum.04353-22},
pmid = {36728429},
issn = {2165-0497},
abstract = {Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.},
}

@article {pmid36725750,
year = {2023},
author = {Tessler, M and David, FJ and Cunningham, SW and Herstoff, EM},
title = {Rewilding in Miniature: Suburban Meadows Can Improve Soil Microbial Biodiversity and Soil Health.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36725750},
issn = {1432-184X},
abstract = {Lawns are a ubiquitous, human-made environment created for human enjoyment, leisure, and aesthetics. While net positive for carbon storage, lawns can have negative environmental impacts. Lawns require frequent mowing, which produces high levels of CO2 pollution and kills off native plants. Lawn fertilizing creates its own environmental pollution. One (presumed) ecologically-friendly alternative to lawns is restoration, or rewilding, of these spaces as meadows, which need less maintenance (e.g., infrequent mowing). However, little work has compared lawns against small-scale meadows for biodiversity outside of pollinator studies. Here, we tested the hypotheses that compared to lawns, meadows have (1) unique and higher levels of soil microbial biodiversity and (2) different soil physical and chemical characteristics. We conducted bacterial (16S) and fungal (ITS2) metabarcoding, and found that both bacteria and fungi are indeed more diverse in meadows (significantly so for bacteria). Species composition between meadows and lawns was significantly different for both types of microbes, including higher levels of mycorrhizal fungi in meadows. We also found that chemistry (e.g., potassium and metrics relating to pH) differed significantly between lawns and meadows and was more optimal for plant growth in the meadows. We believe these differences are caused by the different organisms dwelling in these habitats. In summary, these findings point to notable-positive-shifts in microbial and chemical compositions within meadows, further indicating that meadow restoration benefits biodiversity and soil health.},
}

@article {pmid36725749,
year = {2023},
author = {Sullivan, TJ and Roberts, H and Bultman, TL},
title = {Genetic Covariation Between the Vertically Transmitted Endophyte Epichloë canadensis and Its Host Canada Wildrye.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36725749},
issn = {1432-184X},
abstract = {Symbiotic mutualisms are thought to be stabilized by correlations between the interacting genotypes which may be strengthened via vertical transmission and/or reduced genetic variability within each species. Vertical transmission, however, may weaken interactions over time as the endosymbionts would acquire mutations that could not be purged. Additionally, temporal variation in a conditional mutualism could create genetic variation and increased variation in the interaction outcome. In this study, we assessed genetic variation in both members of a symbiosis, the endosymbiotic fungal endophyte Epichloë canadensis and its grass host Canada wildrye (Elymus canadensis). Both species exhibited comparable levels of diversity, mostly within populations rather than between. There were significant differences between populations, although not in the same pattern for the two species, and the differences were not correlated with geographic distance for either species. Interindividual genetic distance matrices for the two species were significantly correlated, although all combinations of discriminant analysis of principle components (DAPC) defined multilocus genotype groups were found suggesting that strict genotype matching is not necessary. Variation in interaction outcome is common in grass/endophyte interactions, and our results suggest that the accumulation of mutations overtime combined with temporal variation in selection pressures increasing genetic variation in the symbiosis may be the cause.},
}

@article {pmid36725211,
year = {2023},
author = {Hernández-Gómez, O and Hua, J},
title = {From the organismal to biosphere levels: environmental impacts on the amphibian microbiota.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuad002},
pmid = {36725211},
issn = {1574-6976},
abstract = {This review summarizes the role of environmental factors on amphibian microbiotas at the organismal, population, community, ecosystem, and biosphere levels. At the organismal-level, tissue source, disease status, and experimental manipulations were the strongest predictors of variation in amphibian microbiotas. At the population-level, habitat quality, disease status, and ancestry were commonly documented as drivers of microbiota turnover. At the community-level, studies focused on how species' niche influence microbiota structure and function. At the ecosystem-level, abiotic and biotic reservoirs were important contributors to microbiota structure. At the biosphere-level, databases, sample banks, and semi-natural experiments were commonly used to describe microbiota assembly mechanisms among temperate and tropical amphibians. Collectively, our review demonstrates that environmental factors can influence microbiotas through diverse mechanisms at all biological scales. Importantly, while environmental mechanisms occurring at each of the different scales can interact to shape microbiotas, the past ten years of research have mostly been characterized by targeted approaches at individual scales. Looking forward, efforts considering how environmental factors at multiple organizational levels interact to shape microbiota diversity and function are paramount. Generating opportunities for meaningful cross-disciplinary interactions and supporting infrastructure for research that spans biological scales are imperative to addressing this gap.},
}

@article {pmid36723682,
year = {2023},
author = {Bulannga, RB and Schmidt, S},
title = {Two Predators, One Prey - the Interaction Between Bacteriophage, Bacterivorous Ciliates, and Escherichia coli.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36723682},
issn = {1432-184X},
abstract = {Bacterivorous ciliates and lytic bacteriophages are two major predators in aquatic environments, competing for the same type of prey. This study investigated the possible interaction of these different microorganisms and their influence on the activity of each other. Therefore, two bacterivorous ciliates, Paramecium sp. RB1 and Tetrahymena sp. RB2, were used as representative ciliates; a T4-like Escherichia coli targeting lytic bacteriophage as a model virus; and E. coli ATCC 25922 as a susceptible bacterial host and prey. The growth of the two ciliates with E. coli ATCC 25922 as prey was affected by the presence of phage particles. The grazing activity of the two ciliates resulted in more than a 99% reduction of the phage titer and bacterial cell numbers. However, viable phage particles were recovered from individual washed cells of the two ciliates after membrane filtration. Therefore, ciliates such as Paramecium sp. RB1 and Tetrahymena sp. RB2 can remove bacteriophages present in natural and artificial waters by ingesting the viral particles and eliminating bacterial host cells required for viral replication. The ingestion of phage particles may marginally contribute to the nutrient supply of the ciliates. However, the interaction of phage particles with ciliate cells may contribute to the transmission of bacteriophages in aquatic environments.},
}

@article {pmid36723077,
year = {2023},
author = {Lennon, JT and Frost, SDW and Nguyen, NK and Peralta, AL and Place, AR and Treseder, KK},
title = {Microbiology and Climate Change: a Transdisciplinary Imperative.},
journal = {mBio},
volume = {},
number = {},
pages = {e0333522},
doi = {10.1128/mbio.03335-22},
pmid = {36723077},
issn = {2150-7511},
abstract = {Climate change is a complex problem involving nonlinearities and feedback that operate across scales. No single discipline or way of thinking can effectively address the climate crisis. Teams of natural scientists, social scientists, engineers, economists, and policymakers must work together to understand, predict, and mitigate the rapidly accelerating impacts of climate change. Transdisciplinary approaches are urgently needed to address the role that microorganisms play in climate change. Here, we demonstrate with case studies how diverse teams and perspectives provide climate-change insight related to the range expansion of emerging fungal pathogens, technological solutions for harmful cyanobacterial blooms, and the prediction of disease-causing microorganisms and their vector populations using massive networks of monitoring stations. To serve as valuable members of a transdisciplinary climate research team, microbiologists must reach beyond the boundaries of their immediate areas of scientific expertise and engage in efforts to build open-minded teams aimed at scalable technologies and adoptable policies.},
}

@article {pmid36722970,
year = {2023},
author = {Melnik, AV and Callewaert, C and Dorrestein, K and Broadhead, R and Minich, JJ and Ernst, M and Humphrey, G and Ackermann, G and Gathercole, R and Aksenov, AA and Knight, R and Dorrestein, PC},
title = {The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0092222},
doi = {10.1128/msystems.00922-22},
pmid = {36722970},
issn = {2379-5077},
abstract = {With growing awareness that what we put in and on our bodies affects our health and wellbeing, little is still known about the impact of textiles on the human skin. Athletic wear often uses silver threading to improve hygiene, but little is known about its effect on the body's largest organ. In this study, we investigated the impact of such clothing on the skin's chemistry and microbiome. Samples were collected from different body sites of a dozen volunteers over the course of 12 weeks. The changes induced by the antibacterial clothing were specific for individuals, but more so defined by gender and body site. Unexpectedly, the microbial biomass on skin increased in the majority of the volunteers when wearing silver-threaded T-shirts. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. Both effects were mainly observed for women. The hallmark of the induced changes was an increase in the abundance of various monounsaturated fatty acids (MUFAs), especially in the upper back. Several microbe-metabolite associations were uncovered, including Cutibacterium, detected in the upper back area, which was correlated with the distribution of MUFAs, and Anaerococcus spp. found in the underarms, which were associated with a series of different bile acids. Overall, these findings point to a notable impact of the silver-threaded material on the skin microbiome and chemistry. We observed that relatively subtle changes in the microbiome result in pronounced shifts in molecular composition. IMPORTANCE The impact of silver-threaded material on human skin chemistry and microbiome is largely unknown. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. The major change was an increase in the abundance of various monounsaturated fatty acids that were also correlated with Cutibacterium. Additionally, Anaerococcus spp., found in the underarms, were associated with different bile acids in the armpit samples. Overall, the impact of the silver-threaded clothing was gender and body site specific.},
}

@article {pmid36721064,
year = {2023},
author = {van Kasteren, S and Rozen, DE},
title = {Using click chemistry to study microbial ecology and evolution.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {9},
pmid = {36721064},
issn = {2730-6151},
abstract = {Technological advances have largely driven the revolution in our understanding of the structure and function of microbial communities. Culturing, long the primary tool to probe microbial life, was supplanted by sequencing and other -omics approaches, which allowed detailed quantitative insights into species composition, metabolic potential, transcriptional activity, secretory responses and more. Although the ability to characterize "who's there" has never been easier or cheaper, it remains technically challenging and expensive to understand what the diverse species and strains that comprise microbial communities are doing in situ, and how these behaviors change through time. Our aim in this brief review is to introduce a developing toolkit based on click chemistry that can accelerate and reduce the expense of functional analyses of the ecology and evolution of microbial communities. After first outlining the history of technological development in this field, we will discuss key applications to date using diverse labels, including BONCAT, and then end with a selective (biased) view of areas where click-chemistry and BONCAT-based approaches stand to have a significant impact on our understanding of microbial communities.},
}

@article {pmid36720878,
year = {2023},
author = {Vincent, F and Gralka, M and Schleyer, G and Schatz, D and Cabrera-Brufau, M and Kuhlisch, C and Sichert, A and Vidal-Melgosa, S and Mayers, K and Barak-Gavish, N and Flores, JM and Masdeu-Navarro, M and Egge, JK and Larsen, A and Hehemann, JH and Marrasé, C and Simó, R and Cordero, OX and Vardi, A},
title = {Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {510},
doi = {10.1038/s41467-023-36049-3},
pmid = {36720878},
issn = {2041-1723},
abstract = {Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.},
}

@article {pmid36719456,
year = {2023},
author = {Lin, Z and Zheng, X and Chen, J},
title = {Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-023-02183-0},
pmid = {36719456},
issn = {1432-184X},
abstract = {How the coral microbiome responds to oceanic pH changes due to anthropogenic climate change, including ocean acidification and deliberate artificial alkalization, remains an open question. Here, we applied a 16S profile and GeoChip approach to microbial taxonomic and gene functional landscapes in the coral Galaxea fascicularis under three pH levels (7.85, 8.15, and 8.45) and tested the influence of pH changes on the cell growth of several coral-associated strains and bacterial populations. Statistical analysis of GeoChip-based data suggested that both ocean acidification and alkalization destabilized functional cores related to aromatic degradation, carbon degradation, carbon fixation, stress response, and antibiotic biosynthesis in the microbiome, which are related to holobiont carbon cycling and health. The taxonomic analysis revealed that bacterial species richness was not significantly different among the three pH treatments, but the community compositions were significantly distinct. Acute seawater alkalization leads to an increase in pathogens as well as a stronger taxonomic shift than acidification, which is worth considering when using artificial ocean alkalization to protect coral ecosystems from ocean acidification. In addition, our co-occurrence network analysis reflected microbial community and functional shifts in response to pH change cues, which will further help to understand the functional ecological role of the microbiome in coral resilience.},
}

@article {pmid36717392,
year = {2023},
author = {Pavlova, ON and Tupikin, AE and Chernitsyna, SM and Bukin, YS and Lomakina, AV and Pogodaeva, TV and Nikonova, AA and Bukin, SV and Zemskaya, TI and Kabilov, MR},
title = {Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36717392},
issn = {1432-184X},
abstract = {Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151[T]), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.},
}

@article {pmid36717391,
year = {2023},
author = {Ma, W and Lin, L and Peng, Q},
title = {Origin, Selection, and Succession of Coastal Intertidal Zone-Derived Bacterial Communities Associated with the Degradation of Various Lignocellulose Substrates.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36717391},
issn = {1432-184X},
abstract = {Terrestrial microbial consortia were reported to play fundamental roles in the global carbon cycle and renewable energy production through the breakdown of complex organic carbon. However, we have a poor understanding of how biotic/abiotic factors combine to influence consortia assembly and lignocellulose degradation in aquatic ecosystems. In this study, we used 96 in situ lignocellulose enriched, coastal intertidal zone-derived bacterial consortia as the initial inoculating consortia and developed 384 cultured consortia under different lignocellulose substrates (aspen, pine, rice straw, and purified Norway spruce lignin) with gradients of salinity and temperature. As coastal consortia, salinity was the strongest driver for assembly, followed by Norway spruce lignin, temperature, and aspen. Moreover, a conceptual model was proposed to demonstrate different succession dynamics between consortia under herbaceous and woody lignocelluloses. The succession of consortium under Norway spruce lignin is greatly related with abiotic factors, while its substrate degradation is mostly correlated with biotic factors. A discrepant pattern was observed in the consortium under rice straw. Finally, we developed four groups of versatile, yet specific consortia. Our study not only reveals that coastal intertidal wetlands are important natural resources to enrich lignocellulolytic degrading consortia but also provides insights into the succession and ecological function of coastal consortium.},
}

@article {pmid36716515,
year = {2023},
author = {Pateraki, C and Magdalinou, E and Skliros, D and Flemetakis, E and Rabaey, K and Koutinas, A},
title = {Transcriptional regulation in key metabolic pathways of Actinobacillus succinogenes in the presence of electricity.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {151},
number = {},
pages = {108376},
doi = {10.1016/j.bioelechem.2023.108376},
pmid = {36716515},
issn = {1878-562X},
abstract = {The potential of renewable energy application via direct electrode interaction for the production of bio-based chemicals is a promising technology. The utilization of extracellular energy in pure culture fermentations aims in intracellular redox balance regulation in order to improve fermentation efficiency. This work evaluates the impact of a bioelectrochemical system in succinic acid fermentation and the metabolic response of Actinobacillus succinogenes. The metabolic pathway regulation of A. succinogenes was evaluated via RNA expression of the key enzymes that participate in TCA cycle, pyruvate metabolism and oxidative phosphorylation. The genes that were significantly overexpressed in BES compared to non-BES were phosphoenolpyruvate carboxykinase (0.4-fold change), inorganic pyrophosphatase (2.3-fold change) and hydrogenase (2.2-fold change) and the genes that were significantly underexpressed were fumarase (-0.94-fold change), pyruvate kinase (-6.9-fold change), all subunits of fumarate reductase (-2.1 to -1.17-fold change), cytochromes I and II (-1.25 and -1.02-fold change, respectively) and two C4-carboxylic acid transporters.},
}

@article {pmid36713329,
year = {2022},
author = {Gusareva, ES and Gaultier, NE and Uchida, A and Premkrishnan, BNV and Heinle, CE and Phung, WJ and Wong, A and Lau, KJX and Yap, ZH and Koh, Y and Ang, PN and Putra, A and Panicker, D and Lee, JGH and Neves, LC and Drautz-Moses, DI and Schuster, SC},
title = {Short-range contributions of local sources to ambient air.},
journal = {PNAS nexus},
volume = {1},
number = {2},
pages = {pgac043},
pmid = {36713329},
issn = {2752-6542},
abstract = {Recent developments in aerobiology have enabled the investigation of airborne biomass with high temporal and taxonomic resolution. In this study, we assess the contributions of local sources to ambient air within a 160,000 m[2] tropical avian park (AP). We sequenced and analyzed 120 air samples from seven locations situated 160 to 400 m apart, representing distinct microhabitats. Each microhabitat contained a characteristic air microbiome, defined by the abundance and richness of its airborne microbial community members, supported by both, PCoA and Random Forest analysis. Each outdoor microhabitat contained 1% to 18.6% location-specific taxa, while a core microbiome of 27.1% of the total taxa was shared. To identify and assess local sources, we compared the AP dataset with a DVE reference dataset from a location 2 km away, collected during a year-round sampling campaign. Intersection of data from the two sites demonstrated 61.6% of airborne species originated from local sources of the AP, 34.5% from ambient air background, and only 3.9% of species were specific to the DVE reference site. In-depth taxonomic analysis demonstrated association of bacteria-dominated air microbiomes with indoor spaces, while fungi-dominated airborne microbial biomass was predominant in outdoor settings with ample vegetation. The approach presented here demonstrates an ability to identify local source contributions against an ambient air background, despite the prevailing mixing of air masses caused by atmospheric turbulences.},
}

@article {pmid36713171,
year = {2022},
author = {Zhang, X and Wang, Y and Xu, Y and Babalola, BJ and Xiang, S and Ma, J and Su, Y and Fan, Y},
title = {Stochastic processes dominate community assembly of ectomycorrhizal fungi associated with Picea crassifolia in the Helan Mountains, China.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1061819},
pmid = {36713171},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding the underlying mechanisms of microbial community assembly is a fundamental topic in microbial ecology. As an integral part of soil organisms, ectomycorrhizal (EM) fungi play vital roles in ecosystems. Picea crassifolia is an important pine species in the Helan Mountains in Inner Mongolia, China, with high ecological and economic values. However, studies of EM fungal diversity and mechanisms underlying community assembly on this pine species are limited.

METHODS: In this study, we investigated EM fungal communities associated with P. crassifolia from 45 root samples across three sites in the Helan Mountains using Illumina Miseq sequencing of the fungal rDNA ITS2 region.

RESULTS: A total of 166 EM fungal OTUs belonging to 24 lineages were identified, of which Sebacina and Tomentella-Thelephora were the most dominant lineages. Ordination analysis revealed that EM fungal communities were significantly different among the three sites. Site/fungus preference analysis showed that some abundant EM fungal OTUs preferred specific sites. Ecological process analysis implied that dispersal limitation and ecological drift in stochastic processes dominantly determined the community assembly of EM fungi.

DISCUSSION: Our study indicates that P. crassifolia harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with a single plant species in a semi-arid forest in northwest China.},
}

@article {pmid36713170,
year = {2022},
author = {Lin, J and Li, G and Sun, L and Wang, S and Meng, X and Sun, L and Yuan, L and Xu, L},
title = {Varieties and ensiling: Impact on chemical composition, fermentation quality and bacterial community of alfalfa.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1091491},
pmid = {36713170},
issn = {1664-302X},
abstract = {INTRODUCTION: Six species of alfalfa commonly found in northern China were collected in the present study.

METHODS: The chemical composition and epiphytic microbial communities during the ensiling were analyzed; and their effects on fermentation quality and silage bacterial communities were assessed. The effects of physicochemical characteristics of alfalfa on the bacterial community were also investigated in terms of nutritional sources of microbial growth and reproduction.

RESULTS AND DISCUSSION: The results showed that the chemical composition was significantly different in various alfalfa varieties, yet, the dominant genera attached to each variety of alfalfa was similar, except for pantoea (p<0.05). After ensiling, both the fermentation quality and microbial community changed obviously (p<0.05). Specifically, ZM2 had lower pH and ammonia nitrogen (NH3-N) content but higher LA content than other varieties of alfalfa silage. Beneficial bacteria such as Lentilactobacillus and Lactiplantibacillus were predominant in ZM2, which accounted for the higher fermentation quality. Significant correlations between the chemical composition of silage, fermentation quality and bacterial communities composition were observed. Moreover, variations in bacteria community structure during the fermentation of alfalfa were mainly influenced by water-soluble carbohydrates (36.79%) and dry matter (21.77%).

CONCLUSION: In conclusion, this study revealed the influence of chemical composition on microbial community and fermentation quality, laying the groundwork for future studies on high-quality silage.},
}

@article {pmid36709487,
year = {2023},
author = {Stahl, LM and Olson, JB},
title = {Investigating the interactive effects of temperature, pH, and salinity on Naegleria fowleri persistence.},
journal = {The Journal of eukaryotic microbiology},
volume = {},
number = {},
pages = {e12964},
doi = {10.1111/jeu.12964},
pmid = {36709487},
issn = {1550-7408},
abstract = {Naegleria fowleri causes primary amoebic meningoencephalitis, a deadly infection that occurs when free-living amoebae enter the nose via freshwater and travel to the brain. N. fowleri naturally thrives in freshwater and soil and is thought to be associated with elevated water temperatures. While environmental and laboratory studies have sought to identify what environmental factors influence its presence, many questions remain. This study investigated the interactive effects of temperature, pH, and salinity on N. fowleri in deionized and environmental waters. Three temperatures (15, 25, 35°C), pH values (6.5, 7.5, 8.5) and salinity concentrations (0.5%, 1.5%, 2.5% NaCl) were used to evaluate the growth of N. fowleri via ATP luminescent assays. Results indicated N. fowleri grew best at 25°C, and multiple interactive effects occurred between abiotic factors. Interactions varied slightly by water type but were largely driven by temperature and salinity. Lower temperature increased N. fowleri persistence at higher salinity levels, while low salinity (0.5% NaCl) supported N. fowleri growth at all temperatures. This research provided an experimental approach to assess interactive effects influencing the persistence of N. fowleri. As climate change impacts water temperatures and conditions, understanding the microbial ecology of N. fowleri will be needed minimize pathogen exposure.},
}

@article {pmid36709366,
year = {2023},
author = {Song, W and Qin, Z and Hu, X and Han, H and Li, A and Zhou, X and Li, Y and Li, R},
title = {Using Bayesian networks with Tabu-search algorithm to explore risk factors for hyperhomocysteinemia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {1610},
pmid = {36709366},
issn = {2045-2322},
abstract = {Hyperhomocysteinemia (HHcy) is a condition closely associated with cardiovascular and cerebrovascular diseases. Detecting its risk factors and taking some relevant interventions still represent the top priority to lower its prevalence. Yet, in discussing risk factors, Logistic regression model is usually adopted but accompanied by some defects. In this study, a Tabu Search-based BNs was first constructed for HHcy and its risk factors, and the conditional probability between nodes was calculated using Maximum Likelihood Estimation. Besides, we tried to compare its performance with Hill Climbing-based BNs and Logistic regression model in risk factor detection and discuss its prospect in clinical practice. Our study found that Age, sex, α1-microgloblobumin to creatinine ratio, fasting plasma glucose, diet and systolic blood pressure represent direct risk factors for HHcy, and smoking, glycosylated hemoglobin and BMI constitute indirect risk factors for HHcy. Besides, the performance of Tabu Search-based BNs is better than Hill Climbing-based BNs. Accordingly, BNs with Tabu Search algorithm could be a supplement for Logistic regression, allowing for exploring the complex network relationship and the overall linkage between HHcy and its risk factors. Besides, Bayesian reasoning allows for risk prediction of HHcy, which is more reasonable in clinical practice and thus should be promoted.},
}

@article {pmid36708393,
year = {2023},
author = {Kļaviņa, D and Lione, G and Kenigsvalde, K and Pellicciaro, M and Muižnieks, I and Silbauma, L and Jansons, J and Gaitnieks, T and Gonthier, P},
title = {Host-associated Intraspecific Phenotypic Variation in the Saprobic Fungus Phlebiopsis gigantea.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36708393},
issn = {1432-184X},
abstract = {Whether intraspecific phenotypic variation in saprobic fungi may be driven by the host of origin has received little attention. We addressed this issue by testing hypotheses using the model system Phlebiopsis gigantea, a wood destroying fungus associated with Picea abies and Pinus sylvestris, among others, and widely employed in practical forestry as a biological control agent. By examining approximately 60 sympatric P. gigantea isolates from both P. abies and P. sylvestris, we showed that the former grew in vitro significantly (P < 0.05) slower than the latter (average 5.56 mm/day vs. 6.84) while producing 1.8-fold significantly higher number of mitospores. An overall significant trade-off between these two phenotypic traits was detected, in particular for isolates originating from P. abies. Comparative inoculation experiments of a subsample of isolates and the assessment of mycelial growth in logs of both hosts allowed to reject the hypothesis that isolates are equally fit in terms of growth rate in wood of both hosts regardless of the host of origin. Tree models revealed that the growth rate of isolates was associated not only with the wood species in which the isolates were inoculated (P < 0.001), P. sylvestris being more rapidly colonized than P. abies, but also with the host of origin of isolates (P < 0.001). Results showed that P. gigantea isolates originating from different hosts differ phenotypically in terms of some key phenotypic traits demonstrating that a host-driven intraspecific phenotypic variation may occur in saprobic fungi.},
}

@article {pmid36708392,
year = {2023},
author = {Figueiredo, MA and da Silva, TH and Pinto, OHB and Leite, MGP and de Oliveira, FS and Messias, MCTB and Rosa, LH and Câmara, PEAS and Lopes, FAC and Kozovits, AR},
title = {Metabarcoding of Soil Fungal Communities in Rupestrian Grassland Areas Preserved and Degraded by Mining: Implications for Restoration.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36708392},
issn = {1432-184X},
abstract = {Rupestrian grasslands are vegetation complexes of the Cerrado biome (Brazilian savanna), exhibiting simultaneously great biodiversity and important open-pit mining areas. There is a strong demand for the conservation of remaining areas and restoration of degraded. This study evaluated, using next-generation sequencing, the diversity and ecological aspects of soil fungal communities in ferruginous rupestrian grassland areas preserved and degraded by bauxite mining in Brazil. In the preserved and degraded area, respectively, 565 and 478 amplicon sequence variants (ASVs) were detected. Basidiomycota and Ascomycota comprised nearly 72% of the DNA, but Ascomycota showed greater abundance than Basidiomycota in the degraded area (64% and 10%, respectively). In the preserved area, taxa of different hierarchical levels (Agaromycetes, Agaricales, Mortierelaceae, and Mortierella) associated with symbiosis and decomposition were predominant. However, taxa that colonize environments under extreme conditions and pathogens (Dothideomycetes, Pleoporales, Pleosporaceae, and Curvularia) prevailed in the degraded area. The degradation reduced the diversity, and modified the composition of taxa and predominant ecological functions in the community. The lack of fungi that facilitate plant establishment and development in the degraded area suggests the importance of seeking the restoration of this community to ensure the success of the ecological restoration of the environment. The topsoil of preserved area can be a source of inocula of several groups of fungi important for the restoration process but which occur in low abundance or are absent in the degraded area.},
}

@article {pmid36707764,
year = {2023},
author = {Pantoja-Feliciano, IG and Karl, JP and Perisin, M and Doherty, LA and McClung, HL and Armstrong, NJ and Renberg, R and Racicot, K and Branck, T and Arcidiacono, S and Soares, JW},
title = {In vitro gut microbiome response to carbohydrate supplementation is acutely affected by a sudden change in diet.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {32},
doi = {10.1186/s12866-023-02776-2},
pmid = {36707764},
issn = {1471-2180},
abstract = {BACKGROUND: Interactions between diet, stress and the gut microbiome are of interest as a means to modulate health and performance. Here, in vitro fermentation was used to explore the effects of a sudden change in diet, 21 days sole sustenance on the Meal, Ready-to-Eat (MRE) U.S. military combat ration, on inter-species competition and functional potential of the human gut microbiota. Human fecal samples collected before and after MRE intervention or consuming a habitual diet (HAB) were introduced to nutrient-rich media supplemented with starch for in vitro fermentation under ascending colon conditions. 16S rRNA amplicon and Whole-metagenome sequencing (WMS) were used to measure community composition and functional potential. Specific statistical analyses were implemented to detect changes in relative abundance from taxa, genes and pathways.

RESULTS: Differential changes in relative abundance of 11 taxa, Dorea, Lachnospira, Bacteroides fragilis, Akkermansia muciniphila, Bifidobacterium adolescentis, Betaproteobacteria, Enterobacteriaceae, Bacteroides egerthii, Ruminococcus bromii, Prevotella, and Slackia, and nine Carbohydrate-Active Enzymes, specifically GH13_14, over the 24 h fermentation were observed as a function of the diet intervention and correlated to specific taxa of interest.

CONCLUSIONS: These findings suggest that consuming MRE for 21 days acutely effects changes in gut microbiota structure in response to carbohydrate but may induce alterations in metabolic capacity. Additionally, these findings demonstrate the potential of starch as a candidate supplemental strategy to functionally modulate specific gut commensals during stress-induced states.},
}

@article {pmid36706488,
year = {2023},
author = {Veloso, S and Amouroux, D and Lanceleur, L and Cagnon, C and Monperrus, M and Deborde, J and Laureau, CC and Duran, R},
title = {Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments.},
journal = {Journal of hazardous materials},
volume = {448},
number = {},
pages = {130858},
doi = {10.1016/j.jhazmat.2023.130858},
pmid = {36706488},
issn = {1873-3336},
abstract = {The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (Corg/Norg and δ[13]C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.},
}

@article {pmid36705425,
year = {2023},
author = {Birzle, C and Schrader, H and Blutke, A and Ferling, H and Scholz-Göppel, K and Wanke, R and Schwaiger, J},
title = {Detection of diclofenac-induced alterations in rainbow trout (Oncorhynchus mykiss) using quantitative-stereological methods.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/etc.5573},
pmid = {36705425},
issn = {1552-8618},
abstract = {In 2013, the non-steroidal anti-inflammatory drug diclofenac (DCF) was included in the watch list for emerging pollutants under the EU Water Framework Directive. Frequently, monitoring data revealed DCF concentrations in surface waters exceeding the proposed environmental quality standards of 0.04 µgL[-1] and 0.126 µgL[-1] . In recent literature, the possible effects of DCF on fish are discussed controversially. To contribute to a realistic risk assessment of DCF, a 28-day exposure experiment was carried on rainbow trout (Oncorhynchus mykiss). To warrant reliability of data, experiments were conducted considering CRED criteria. The test concentrations of DCF used (0.1/0.5/1/5/25/100 µgL[-1]) also included environmentally relevant concentrations. The lowest observed effect concentration (LOEC) for a significant decrease in the plasma concentrations of the DCF-biomarker prostaglandin E2 was 0.5 µgL[-1] (male fish). For objective evaluation of relevant histomorphological parameters of gills and trunk kidneys unbiased quantitative-stereological methods were applied. In the gills, a significant increase of the thickness of the secondary lamella and of the true harmonic mean of barrier thickness in secondary lamellae was present at diclofenac concentrations of 25 µgL[-1] and 100 µgL[-1] . In the trunk kidneys, the absolute and relative volumes of nephrons were significantly decreased, paralleled by a significant increase of the volume of the interstitial renal tissue. With regard to quantitative histomorphological alterations in the trunk kidney, the observed LOEC was 0.5 µgL[-1] . The conducted quantitative histomorphological analyses allow identification and objective quantification of even subtle but significant morphological effects and thus provide an important contribution for the comparability of study results for the determination of NOECs. This article is protected by copyright. All rights reserved. Environ Toxicol Chem 2023;00:0-0. © 2023 SETAC.},
}

@article {pmid36702929,
year = {2023},
author = {Li, T and Wang, X and Wang, X and Huang, J and Shen, L},
title = {Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36702929},
issn = {1432-184X},
abstract = {The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4[+] content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.},
}

@article {pmid36701921,
year = {2023},
author = {Onyango, SO and Beerens, K and Li, Q and Van Camp, J and Desmet, T and Van de Wiele, T},
title = {Glycosidic linkage of rare and new-to-nature disaccharides reshapes gut microbiota in vitro.},
journal = {Food chemistry},
volume = {411},
number = {},
pages = {135440},
doi = {10.1016/j.foodchem.2023.135440},
pmid = {36701921},
issn = {1873-7072},
abstract = {The impact of glycosidic linkage of seven rare and new-to-nature disaccharides on gut bacteria was assessed in vitro. The community shift of the inocula from four donors in response to 1 % (w/v) disaccharide supplementation was captured by sequencing the 16S rRNA gene. A significant loss of bacterial alpha diversity, short lag time, low pH, and high total short-chain fatty acid displayed a faster fermentation of trehalose(Glc-α1,1α-Glc) and fibrulose(fructan, DP2-10). Bacteroides reduced in relative abundance under disaccharide supplementation suggesting a loss in complex carbohydrates metabolizing capacity. Fibrulose and l-arabinose glucoside(Glc-α1,3-l-Ara) significantly stimulated bifidobacteria but was suppressed with trehalose, ribose glucoside(Glc-α1,2-Rib), and 4'-epitrehalose(Glc-α1,1α-Gal) supplementation. Albeit insignificant, bifidobacteria increased with 4'-epikojibiose(Glc-α1,2-Gal), nigerose(Glc-α1,3-Glc), and kojibiose(Glc-α1,2-Glc). Prior conditioning of inoculum in kojibiose medium profoundly induced bifidobacteria by 44 % and 55 % upon reinoculation into kojibiose and fibrulose-supplemented media respectively. This study has demonstrated the importance of the disaccharide structure-function relationship in driving the gut bacterial community.},
}

@article {pmid36700533,
year = {2023},
author = {Palau, J and Trueba-Santiso, A and Yu, R and Mortan, SH and Shouakar-Stash, O and Freedman, DL and Wasmund, K and Hunkeler, D and Marco-Urrea, E and Rosell, M},
title = {Dual C-Br Isotope Fractionation Indicates Distinct Reductive Dehalogenation Mechanisms of 1,2-Dibromoethane in Dehalococcoides- and Dehalogenimonas-Containing Cultures.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.2c07137},
pmid = {36700533},
issn = {1520-5851},
abstract = {Brominated organic compounds such as 1,2-dibromoethane (1,2-DBA) are highly toxic groundwater contaminants. Multi-element compound-specific isotope analysis bears the potential to elucidate the biodegradation pathways of 1,2-DBA in the environment, which is crucial information to assess its fate in contaminated sites. This study investigates for the first time dual C-Br isotope fractionation during in vivo biodegradation of 1,2-DBA by two anaerobic enrichment cultures containing organohalide-respiring bacteria (i.e., either Dehalococcoides or Dehalogenimonas). Different εbulk[C] values (-1.8 ± 0.2 and -19.2 ± 3.5‰, respectively) were obtained, whereas their respective εbulk[Br] values were lower and similar to each other (-1.22 ± 0.08 and -1.2 ± 0.5‰), leading to distinctly different trends (ΛC-Br = Δδ[13]C/Δδ[81]Br ≈ εbulk[C]/εbulk[Br]) in a dual C-Br isotope plot (1.4 ± 0.2 and 12 ± 4, respectively). These results suggest the occurrence of different underlying reaction mechanisms during enzymatic 1,2-DBA transformation, that is, concerted dihaloelimination and nucleophilic substitution (SN2-reaction). The strongly pathway-dependent ΛC-Br values illustrate the potential of this approach to elucidate the reaction mechanism of 1,2-DBA in the field and to select appropriate εbulk[C] values for quantification of biodegradation. The results of this study provide valuable information for future biodegradation studies of 1,2-DBA in contaminated sites.},
}

@article {pmid36700061,
year = {2023},
author = {Sathiananthamoorthy, S and Florman, K and Richard, D and Cheng, KK and Torri, V and McCaig, F and Harber, M and Rohn, JL},
title = {Application of Various Techniques to Gain Insights Into the Complex Urinary Tract Microbial Communities of Renal Transplant Recipients.},
journal = {Transplantation direct},
volume = {9},
number = {2},
pages = {e1418},
pmid = {36700061},
issn = {2373-8731},
abstract = {UNLABELLED: Urinary tract infections (UTIs) are prevalent in renal transplant (RTX) recipients and associated with worse outcomes. Early detection by sensitive diagnostic tests and appropriate treatment strategies in this cohort is therefore crucial, but evidence has shown that current methods may miss genuine infections. Research has shed light on the urinary tract microbial ecology of healthy individuals and nontransplant patients with UTI, but information on the RTx cohort is scant. We conducted a cross-sectional study to (i) compare the gold standard diagnostic culture with alternative techniques and (ii) characterize RTx patient urinary microbial communities.

METHODS: Midstream urine specimens were collected from 51 RTx patients attending a renal transplant clinic and 27 asymptomatic controls. Urinary microscopy, dipstick, and routine culture were performed. To improve sensitivity of microbial detection, we cultured the urinary cell sediment and performed 16S rRNA gene sequencing on urine. Uroplakin-positive urothelial cells shed in urine were analyzed by immunofluorescence staining for any bacterial association.

RESULTS: Sediment culture and 16S rRNA sequencing confirmed detection deficiencies of diagnostic culture and revealed differences in the urobiomes of RTx patients and controls. Specifically, Gardnerella, Escherichia, and Lactobacillus were most abundant in patients, whereas Lactobacillus, Streptococcus, and Gardnerella were most abundant in controls. The application of both culture and sequencing provided a more nuanced view of the urinary microbial communities.

CONCLUSIONS: This study provides insight into the potential problems of diagnostic culture within RTx patients and sheds light on their urinary microbial inhabitants. Further work may identify key microbial signatures and facilitate the development of better tools for UTI detection within this cohort, which could allow targeted intervention before an infection leads to serious consequences. http://links.lww.com/TXD/A479.},
}

@article {pmid36699726,
year = {2022},
author = {Shen, Y and Yu, F and Qiu, L and Gao, M and Xu, P and Zhang, L and Liao, X and Wang, M and Hu, X and Sun, Y and Pan, Y},
title = {Ecological influence by colonization of fluoride-resistant Streptococcus mutans in oral biofilm.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1106392},
pmid = {36699726},
issn = {2235-2988},
abstract = {BACKGROUND: Dental caries is one of the oldest and most common infections in humans. Improved oral hygiene practices and the presence of fluoride in dentifrices and mouth rinses have greatly reduced the prevalence of dental caries. However, increased fluoride resistance in microbial communities is concerning. Here, we studied the effect of fluoride-resistant Streptococcus mutans (S. mutans) on oral microbial ecology and compare it with wild-type S. mutans in vitro.

METHODS: Biofilm was evaluated for its polysaccharide content, scanning electron microscopy (SEM) imaging, acid-producing ability, and related lactic dehydrogenase (LDH), arginine deiminase (ADS), and urease enzymatic activity determination. Fluorescence in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qRT-PCR) were used to evaluate the S. mutans ratio within the biofilm. It was followed by 16S rRNA sequencing to define the oral microbial community.

RESULTS: Fluoride-resistant S. mutans produced increased polysaccharides in presence of NaF (P < 0.05). The enzymatic activities related to both acid and base generation were less affected by the fluoride. In presence of 275 ppm NaF, the pH in the fluoride-resistant strain sample was lower than the wild type. We observed that with the biofilm development and accumulative fluoride concentration, the fluoride-resistant strain had positive relationships with other bacteria within the oral microbial community, which enhanced its colonization and survival. Compared to the wild type, fluoride-resistant strain significantly increased the diversity and difference of oral microbial community at the initial stage of biofilm formation (4 and 24 h) and at a low fluoride environment (0 and 275 ppm NaF) (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that fluoride-resistant strain enhanced the metabolic pathways and glucose transfer.

CONCLUSIONS: Fluoride-resistant S. mutans affected the microecological balance of oral biofilm and its cariogenic properties in vitro, indicating its negative impact on fluoride's caries prevention effect.},
}

@article {pmid36699674,
year = {2022},
author = {Siddiqui, JA and Fan, R and Naz, H and Bamisile, BS and Hafeez, M and Ghani, MI and Wei, Y and Xu, Y and Chen, X},
title = {Insights into insecticide-resistance mechanisms in invasive species: Challenges and control strategies.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1112278},
pmid = {36699674},
issn = {1664-042X},
abstract = {Threatening the global community is a wide variety of potential threats, most notably invasive pest species. Invasive pest species are non-native organisms that humans have either accidentally or intentionally spread to new regions. One of the most effective and first lines of control strategies for controlling pests is the application of insecticides. These toxic chemicals are employed to get rid of pests, but they pose great risks to people, animals, and plants. Pesticides are heavily used in managing invasive pests in the current era. Due to the overuse of synthetic chemicals, numerous invasive species have already developed resistance. The resistance development is the main reason for the failure to manage the invasive species. Developing pesticide resistance management techniques necessitates a thorough understanding of the mechanisms through which insects acquire insecticide resistance. Insects use a variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes. An overabundance of enzymes causes metabolic resistance, detoxifying pesticides and rendering them ineffective against pests. A key factor in the development of metabolic resistance is the amplification of certain metabolic enzymes, specifically esterases, Glutathione S-transferase, Cytochromes p450 monooxygenase, and hydrolyses. Additionally, insect guts offer unique habitats for microbial colonization, and gut bacteria may serve their hosts a variety of useful services. Most importantly, the detoxification of insecticides leads to resistance development. The complete knowledge of invasive pest species and their mechanisms of resistance development could be very helpful in coping with the challenges and effectively developing effective strategies for the control of invasive species. Integrated Pest Management is particularly effective at lowering the risk of chemical and environmental contaminants and the resulting health issues, and it may also offer the most effective ways to control insect pests.},
}

@article {pmid36698845,
year = {2022},
author = {Song, W and Liu, Y and Qiu, L and Qing, J and Li, A and Zhao, Y and Li, Y and Li, R and Zhou, X},
title = {Machine learning-based warning model for chronic kidney disease in individuals over 40 years old in underprivileged areas, Shanxi Province.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {930541},
pmid = {36698845},
issn = {2296-858X},
abstract = {INTRODUCTION: Chronic kidney disease (CKD) is a progressive disease with high incidence but early imperceptible symptoms. Since China's rural areas are subject to inadequate medical check-ups and single disease screening programme, it could easily translate into end-stage renal failure. This study aimed to construct an early warning model for CKD tailored to impoverished areas by employing machine learning (ML) algorithms with easily accessible parameters from ten rural areas in Shanxi Province, thereby, promoting a forward shift of treatment time and improving patients' quality of life.

METHODS: From April to November 2019, CKD opportunistic screening was carried out in 10 rural areas in Shanxi Province. First, general information, physical examination data, blood and urine specimens were collected from 13,550 subjects. Afterward, feature selection of explanatory variables was performed using LASSO regression, and target datasets were balanced using the SMOTE (synthetic minority over-sampling technique) algorithm, i.e., albuminuria-to-creatinine ratio (ACR) and α1-microglobulin-to-creatinine ratio (MCR). Next, Bagging, Random Forest (RF) and eXtreme Gradient Boosting (XGBoost) were employed for classification of ACR outcomes and MCR outcomes, respectively.

RESULTS: 12,330 rural residents were included in this study, with 20 explanatory variables. The cases with increased ACR and increased MCR represented 1,587 (12.8%) and 1,456 (11.8%), respectively. After conducting LASSO, 14 and 15 explanatory variables remained in these two datasets, respectively. Bagging, RF, and XGBoost performed well in classification, with the AUC reaching 0.74, 0.87, 0.87, 0.89 for ACR outcomes and 0.75, 0.88, 0.89, 0.90 for MCR outcomes. The five variables contributing most to the classification of ACR outcomes and MCR outcomes constituted SBP, TG, TC, and Hcy, DBP and age, TG, SBP, Hcy and FPG, respectively. Overall, the machine learning algorithms could emerge as a warning model for CKD.

CONCLUSION: ML algorithms in conjunction with rural accessible indexes boast good performance in classification, which allows for an early warning model for CKD. This model could help achieve large-scale population screening for CKD in poverty-stricken areas and should be promoted to improve the quality of life and reduce the mortality rate.},
}

@article {pmid36697862,
year = {2023},
author = {Kennedy, KM and de Goffau, MC and Perez-Muñoz, ME and Arrieta, MC and Bäckhed, F and Bork, P and Braun, T and Bushman, FD and Dore, J and de Vos, WM and Earl, AM and Eisen, JA and Elovitz, MA and Ganal-Vonarburg, SC and Gänzle, MG and Garrett, WS and Hall, LJ and Hornef, MW and Huttenhower, C and Konnikova, L and Lebeer, S and Macpherson, AJ and Massey, RC and McHardy, AC and Koren, O and Lawley, TD and Ley, RE and O'Mahony, L and O'Toole, PW and Pamer, EG and Parkhill, J and Raes, J and Rattei, T and Salonen, A and Segal, E and Segata, N and Shanahan, F and Sloboda, DM and Smith, GCS and Sokol, H and Spector, TD and Surette, MG and Tannock, GW and Walker, AW and Yassour, M and Walter, J},
title = {Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.},
journal = {Nature},
volume = {613},
number = {7945},
pages = {639-649},
pmid = {36697862},
issn = {1476-4687},
abstract = {Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.},
}

@article {pmid36697746,
year = {2023},
author = {Yan, Y and Lin, T and Xie, W and Zhang, D and Jiang, Z and Han, Q and Zhu, X and Zhang, H},
title = {Contrasting Mechanisms Determine the Microeukaryotic and Syndiniales Community Assembly in a Eutrophic bay.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36697746},
issn = {1432-184X},
abstract = {Syndiniales is a diverse parasitic group, increasingly gaining attention owing to its high taxonomic diversity in marine ecosystems and inhibitory effects on the dinoflagellate blooms. However, their seasonal dynamics, host interactions, and mechanisms of community assembly are largely unknown, particularly in eutrophic waters. Here, using 18S rRNA gene amplicon sequencing, we intended to elucidate the interactions between Syndiniales and microeukaryotes, as well as community assembly processes in a eutrophic bay. The results showed that Syndiniales group II was dominating throughout the year, with substantially higher abundance in the winter and spring, whereas Syndiniales group I was more abundant in the summer and autumn. Temperature and Dinoflagellata were the most important abiotic and biotic factors driving variations of the Syndiniales community, respectively. The assembly processes of microeukaryotes and Syndiniales were completely different, with the former being controlled by a balance between homogeneous selection and drift and the latter being solely governed by drift. Network analysis revealed that Syndiniales group II had the largest number of interactions with microeukaryotes, and they primarily associated with Dinoflagellata in the winter, while interactions with Chlorophyta and Bacillariophyta increased dramatically in summer and autumn. These findings provide significant insights in understanding the interactions and assembly processes of Syndiniales throughout the year, which is critical in revealing the roles of single-celled parasites in driving protist dynamics in eutrophic waters.},
}

@article {pmid36697704,
year = {2023},
author = {Jentzsch, L and Grossart, HP and Plewe, S and Schulze-Makuch, D and Goldhammer, T},
title = {Response of cyanobacterial mats to ambient phosphate fluctuations: phosphorus cycling, polyphosphate accumulation and stoichiometric flexibility.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {6},
pmid = {36697704},
issn = {2730-6151},
abstract = {Cyanobacterial mats inhabit a variety of aquatic habitats, including the most extreme environments on Earth. They can thrive in a wide range of phosphorus (P) levels and are thus important players for ecosystem primary production and P cycling at the sediment-water interface. Polyphosphate (polyP), the major microbial P storage molecule, is assigned a critical role in compensating for phosphate fluctuations in planktonic cyanobacteria, but little is known about potentially analogous mechanisms of mat-forming cyanobacteria. To investigate acclimation strategies of cyanobacterial mats to fluctuating phosphate concentrations, laboratory batch experiments were conducted, in which the cosmopolitan mat-forming, marine cyanobacterium Sodalinema stali was exposed to low dissolved P concentrations, followed by a P pulse. Our results show that the cyanobacteria dynamically adjusted cellular P content to ambient phosphate concentrations and that they had accumulated polyP during periods of high phosphate availability, which was subsequently recycled to sustain growth during phosphate scarcity. However, following the depletion of dispensable cellular P sources, including polyP, we observed a reallocation of P contained in DNA into polyP, accompanied by increasing alkaline phosphatase activity. This suggests a change of the metabolic focus from growth towards maintenance and the attempt to acquire organic P, which would be naturally contained in the sediment. P overplus uptake following a simulated P pulse further suggests that Sodalinema-dominated mats exhibit elaborated mechanisms to cope with severe P fluctuations to overcome unfavourable environmental conditions, and potentially modulate critical P fluxes in the aquatic cycle.},
}

@article {pmid36696803,
year = {2023},
author = {Huang, X and Chen, Q and Fan, Y and Yang, R and Gong, G and Yan, C and Song, Y and Zhang, B and Xi, S and Huang, Y and Xu, H},
title = {Fructooligosaccharides attenuate non-alcoholic fatty liver disease by remodeling gut microbiota and association with lipid metabolism.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {159},
number = {},
pages = {114300},
doi = {10.1016/j.biopha.2023.114300},
pmid = {36696803},
issn = {1950-6007},
abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a common liver disease highly associated with metabolic diseases and gut dysbiosis. Several clinical trials have confirmed that fructooligosaccharides (FOSs) are a viable alternative treatment for NAFLD. However, the mechanisms underlying the activities of FOSs remain unclear.

METHODS: In this study, the effects of FOSs were investigated with the use of two C57BL/6 J mouse models of NAFLD induced by a high-fat, high-cholesterol (HFHC) diet and a methionine- and choline-deficient (MCD) diet, respectively. The measured metabolic parameters included body, fat, and liver weights; and blood glucose, glucose tolerance, and serum levels of glutamate transaminase, aspartate transaminase, and triglycerides. Liver tissues were collected for histological analysis. In addition, 16 S rRNA sequencing was conducted to investigate the effects of FOSs on the composition of the gut microbiota of mice in the HFHC and MCD groups and treated with FOSs.

RESULTS: FOS treatment attenuated severe metabolic changes and hepatic steatosis caused by the HFHC and MCD diets. In addition, FOSs remodeled the structure of gut microbiota in mice fed the HFHC and MCD diets, as demonstrated by increased abundances of Bacteroidetes (phylum level), Klebsiella variicola, Lactobacillus gasseri, and Clostridium perfringens (species level); and decreased abundances of Verrucomicrobia (phylum level) and the Fissicatena group (genus level). Moreover, the expression levels of genes associated with lipid metabolism and inflammation (i.e., ACC1, PPARγ, CD36, MTTP, APOC3, IL-6, and IL-1β) were down-regulated after FOS treatment.

CONCLUSION: FOSs alleviated the pathological phenotype of NAFLD via remodeling of the gut microbiota composition and decreasing hepatic lipid metabolism, suggesting that FOSs as functional dietary supplements can potentially reduce the risk of NAFLD.},
}

@article {pmid36695828,
year = {2023},
author = {Hilderbrand, RH and Bambakidis, T and Crump, BC},
title = {The Roles of Microbes in Stream Restorations.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36695828},
issn = {1432-184X},
abstract = {The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.},
}

@article {pmid36695592,
year = {2023},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Site Specialization of Human Oral Veillonella Species.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0404222},
doi = {10.1128/spectrum.04042-22},
pmid = {36695592},
issn = {2165-0497},
abstract = {Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.},
}

@article {pmid36694586,
year = {2022},
author = {Thirumala, M and Sai Krishna, E and Sindhu Priya, P and Vishnuvardhan Reddy, S},
title = {Characterization of a novel Fluoride resistant bacterial isolate and its capability of Fluoride bioremediation.},
journal = {AIMS microbiology},
volume = {8},
number = {4},
pages = {470-483},
pmid = {36694586},
issn = {2471-1888},
abstract = {A Gram positive rod shaped bacterium designated as isolate H1 with Fluoride resistance up to 4 g/L sodium fluoride (NaF) in LB (Luria-Bertani) agar was isolated from a ground water sample of Narketpally area, Nalgonda district, Telangana, India. The colonies of isolate H1 were off white in color. Growth patterns of isolate H1 were observed at two different concentrations, 100 and 250 ppm, of NaF and also without NaF in the medium. In cases where NaF was present in the media, the lag phases of the growth curves were extended when compared to the absence of NaF. Optimum pH required for the organism's growth was 8. Isolate H1 required a temperature of 37 °C with 150 rpm and 2% NaCl for its optimal growth in the medium without NaF. Meanwhile, isolate H1 could thrive in a diverse pH range, i.e., pH 5-10, and at an NaCl concentration of up to 11% in the medium with NaF. Based on morphological, biochemical and molecular characterization, isolate H1 was identified as belonging to the genus Bacillus. It showed 98.47% 16S rDNA gene sequence similarity with Bacillus australimaris NH71_1[T]. Isolate H1 showed high fluoride removals of 22.5% and 38.2% with 100 and 250 mg/L of NaF in the LB broth when incubated at pH 8 and a temperature of 37 °C with 150 rpm for 3 day. Hence, this organism could be a promising isolate to apply for defluoridation of ground water in fluoride contaminthe ated areas.},
}

@article {pmid36694253,
year = {2023},
author = {Uiterwijk, M and Vojta, L and Šprem, N and Beck, A and Jurković, D and Kik, M and Duscher, GG and Hodžić, A and Reljić, S and Sprong, H and Beck, R},
title = {Diversity of Hepatozoon species in wild mammals and ticks in Europe.},
journal = {Parasites & vectors},
volume = {16},
number = {1},
pages = {27},
pmid = {36694253},
issn = {1756-3305},
abstract = {BACKGROUND: Hepatozoon spp. are tick-borne parasites causing subclinical to clinical disease in wild and domestic animals. Aim of this study was to determine Hepatozoon prevalence and species distribution among wild mammals and ticks in Europe.

METHODS: Samples of wild mammals and ticks, originating from Austria, Bosnia and Herzegovina, Croatia, Belgium and the Netherlands, were tested with PCR to amplify a ~ 670-bp fragment of the small subunit ribosomal RNA gene.

RESULTS: Of the 2801 mammal samples that were used for this study, 370 (13.2%) tested positive. Hepatozoon canis was detected in samples of 178 animals (3 Artiodactyla, 173 Carnivora, 1 Eulipotyphia, 1 Lagomorpha), H. martis in 125 (3 Artiodactyla, 122 Carnivora), H. sciuri in 13 (all Rodentia), Hepatozoon sp. in 47 (among which Hepatozoon sp. Vole isolate, all Rodentia) and H. ayorgbor in 4 (all Rodentia). Regarding origin, 2.9% (6/208) tested positive from Austria, 2.8% (1/36) from Bosnia and Herzegovina, 14.6% (173/1186) from Croatia and 13.9% (190/1371) from Belgium/the Netherlands. Of the 754 ticks collected, 0.0% (0/35) Hyalomma sp., 16.0% (4/25) Dermacentor spp., 0.0% (0/23) Haemaphysalis spp., 5.3% (24/50) Ixodes and 1.4% (3/221) Rhipicephalus spp. tested positive for Hepatozoon (4.2%; 32/754), most often H. canis (n = 22).

CONCLUSIONS: Hepatozoon canis is most present in mammals (especially in Carnivora such as gray wolves and golden jackals) and ticks, followed by H. martis, which was found merely in stone martens and pine martens. None of the rodent-associated Hepatozoon spp. were detected in the ticks, suggesting the possible implication of other arthropod species or non-vectorial routes in the transmission cycle of the hemoprotozoans in rodents. Our findings of H. canis in ticks other than R. sanguineus add to the observation that other ticks are also involved in the life cycle of Hepatozoon. Now that presence of Hepatozoon has been demonstrated in red foxes, gray wolves, mustelids and rodents from the Netherlands and/or Belgium, veterinary clinicians should be aware of the possibility of spill-over to domestic animals, such as dogs.},
}

@article {pmid36694053,
year = {2023},
author = {Arroyo, MC and Laurie, I and Rotsaert, C and Marzorati, M and Risso, D and Karnik, K},
title = {Age-Dependent Prebiotic Effects of Soluble Corn Fiber in M-SHIME[®] Gut Microbial Ecosystems.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {},
number = {},
pages = {},
pmid = {36694053},
issn = {1573-9104},
abstract = {Soluble corn fiber (SCF) has demonstrated prebiotic effects in clinical studies. Using an in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME[®]) model, the effects of SCF treatment on colonic microbiota composition and metabolic activity and on host-microbiome interactions were evaluated using fecal samples from healthy donors of different ages (baby [≤ 2 years], n = 4; adult [18-45 years], n = 2; elderly [70 years], n = 1). During the 3-week treatment period, M-SHIME[®] systems were supplemented with SCF daily (baby, 1.5, 3, or 4.5 g/d; adult, 3 or 8.5 g/d; and elderly, 8.5 g/d). M-SHIME[®] supernatants were evaluated for their effect on the intestinal epithelial cell barrier and inflammatory responses in lipopolysaccharide. (LPS)-stimulated cells. Additionally, short-chain fatty acid (SCFA) production and microbial community composition were assessed. In the baby and adult models, M-SHIME[®] supernatants from SCF treated vessels protected Caco-2 membrane integrity from LPS-induced damage. SCF treatment resulted in the expansion of Bacteroidetes, Firmicutes, and Bifidobacterial, as well as increased SCFA production in all age groups. SCF tended to have the greatest effect on propionate production. These findings demonstrate the prebiotic potential of SCF in babies, adults, and the elderly and provide insight into the mechanisms behind the observed prebiotic effects.},
}

@article {pmid36687598,
year = {2022},
author = {Midani, FS and David, LA},
title = {Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {910390},
pmid = {36687598},
issn = {1664-302X},
abstract = {Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interactions and their impact on ecosystem properties. However, quantifying abundance of more than two microbes in a community in a high throughput fashion requires rapid, inexpensive assays. Here, we show that multicolor flow cytometry combined with a machine learning-based classifier can rapidly quantify species abundances in simple, synthetic microbial communities. Our approach measures community structure over time and detects the exchange of metabolites in a four-member community of fluorescent Bacteroides species. Notably, we quantified species abundances in co-cultures and detected evidence of cooperation in polysaccharide processing and competition for monosaccharide utilization. We also observed that co-culturing on simple sugars, but not complex sugars, reduced microbial productivity, although less productive communities maintained higher community diversity. In summary, our multicolor flow cytometric approach presents an economical, tractable model system for microbial ecology using well-studied human bacteria. It can be extended to include additional species, evaluate more complex environments, and assay response of communities to a variety of disturbances.},
}

@article {pmid36684671,
year = {2023},
author = {Huang, F and Zhu, C and Huang, M and Song, X and Peng, A},
title = {The root enrichment of bacteria is consistent across different stress-resistant plant species.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14683},
pmid = {36684671},
issn = {2167-8359},
abstract = {Bacteria, inhabiting around and in plant roots, confer many beneficial traits to promote plant growth and health. The secretion of root exudates modulates the nutritional state of the rhizosphere and root area, further selecting specific bacteria taxa and shaping the bacteria communities. Many studies of the rhizosphere effects have demonstrated that selection by the plant rhizosphere consistently enriches a set of bacteria taxa, and this is conserved across different plant species. Root selection effects are considered to be stronger than the rhizosphere selection effects, yet studies are limited. Here, we focus on the root selection effects across a group of 11 stress-resistant plant species. We found that the root selection consistently reduced the alpha diversity (represented by total number of observed species, Shannon's diversity, and phylogenetic diversity) and altered the structure and composition of bacteria communities. Furthermore, root selection tended to enrich for clusters of bacteria genera including Pantoea, Akkermansia, Blautia, Acinetobacter, Burkholderia-Paraburkholderia, Novosphingobium, Massilia, Pseudomonas, Chryseobacterium, and Stenotrophomonas. Our study offers some basic knowledge for understanding the microbial ecology of the plant root, and suggests that several bacteria genera are of interest for future studies.},
}

@article {pmid36683960,
year = {2023},
author = {Li, Y and Deng, X and Zhang, N and Shen, Z and Li, R and Shen, Q and Salles, JF},
title = {Rhizosphere suppression hinders antibiotic resistance gene (ARG) spread under bacterial invasion.},
journal = {One health (Amsterdam, Netherlands)},
volume = {16},
number = {},
pages = {100481},
pmid = {36683960},
issn = {2352-7714},
abstract = {The rhizosphere is an extremely important component of the "one health" scenario by linking the soil microbiome and plants, in which the potential enrichment of antibiotic resistance genes (ARGs) might ultimately flow into the human food chain. Despite the increased occurrence of soil-borne diseases, which can lead to increased use of pesticides and antibiotic-producing biocontrol agents, the understanding of the dynamics of ARG spread in the rhizosphere is largely overlooked. Here, tomato seedlings grown in soils conducive and suppressive to the pathogen Ralstonia solanacearum were selected as a model to investigate ARG spread in the rhizosphere with and without pathogen invasion. Metagenomics data revealed that R. solanacearum invasion increased the density of ARGs and mobile genetic elements (MGEs). Although we found ARGs originating from human pathogenic bacteria in both soils, the enrichment was alleviated in the suppressive soil. In summary, the suppressive soil hindered ARG spread through pathogen suppression and had a lower number of taxa carrying antibiotic resistance.},
}

@article {pmid36683707,
year = {2022},
author = {Chen, Q and Fan, Y and Zhang, B and Yan, C and Chen, Z and Wang, L and Hu, Y and Huang, Q and Su, J and Ren, J and Xu, H},
title = {Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1086885},
pmid = {36683707},
issn = {2235-2988},
abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) is a novel microbial treatment for patients with ulcerative colitis (UC). In this study, we performed a clinical trial of capsulized FMT in UC patients to determine the association between the gut fungal community and capsulized FMT outcomes.

DESIGN: This study recruited patients with active UC (N = 22) and healthy individuals (donor, N = 9) according to the criteria. The patients received capsulized FMT three times a week. Patient stool samples were collected before (week 0) and after FMT follow-up visits at weeks 1, 4, and 12. Fungal communities were analysed using shotgun metagenomic sequencing.

RESULTS: According to metagenomic analysis, fungal community evenness index was greater in samples collected from patients, and the overall fungal community was clustered among the samples collected from donors. The dominant fungi in fecal samples collected from donors and patients were Ascomycota and Basidiomycota. However, capsulized FMT ameliorated microbial fungal diversity and altered fungal composition, based on metagenomic analysis of fecal samples collected before and during follow-up visits after capsulized FMT. Fungal diversity decreased in samples collected from patients who achieved remission after capsulized FMT, similar to samples collected from donors. Patients achieving remission after capsulized FMT had specific enrichment of Kazachstania naganishii, Pyricularia grisea, Lachancea thermotolerans, and Schizosaccharomyces pombe compared with patients who did not achieve remission. In addition, the relative abundance of P. grisea was higher in remission fecal samples during the follow-up visit. Meanwhile, decreased levels of pathobionts, such as Candida and Debaryomyces hansenii, were associated with remission in patients receiving capsulized FMT.

CONCLUSION: In the metagenomic analysis of fecal samples from donors and patients with UC receiving capsulized FMT, shifts in gut fungal diversity and composition were associated with capsulized FMT and validated in patients with active UC. We also identified the specific fungi associated with the induction of remission. ClinicalTrails.gov (NCT03426683).},
}

@article {pmid36683444,
year = {2023},
author = {Gegenbauer, C and Bellaire, A and Schintlmeister, A and Schmid, MC and Kubicek, M and Voglmayr, H and Zotz, G and Richter, A and Mayer, VE},
title = {Exo- and endophytic fungi enable rapid transfer of nutrients from ant waste to orchid tissue.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18761},
pmid = {36683444},
issn = {1469-8137},
abstract = {The epiphytic orchid Caularthron bilamellatum sacrifices its water storage tissue for nutrients from the waste of ants lodging inside its hollow pseudobulb. Here, we investigate whether fungi are involved in the rapid translocation of nutrients. Uptake was analysed with a [15] N labelling experiment, subsequent isotope-ratio mass spectrometry (IRMS) and secondary ion mass spectrometry (ToF-SIMS and NanoSIMS). We encountered two hyphae types: a thick melanized type assigned to "black fungi" (Chaetothyriales, Cladosporiales, Mycosphaerellales) in ant waste, and a thin endophytic type belonging to Hypocreales. In few cell layers both hyphae types co-occurred. [15] N accumulation in both hyphae types was conspicuous, while for translocation to the vessels only Hypocreales were involved. There is evidence that the occurrence of the two hyphae types result in a synergism in terms of nutrient uptake. Our study provides the first evidence that a pseudobulb (=stem)-born endophytic network of Hypocreales is involved in the rapid translocation of nitrogen from insect derived waste to the vegetative and reproductive tissue of the host orchid. For C. bilamellatum that has no contact with the soil, ant waste in the hollow pseudobulbs serves as equivalent to soil in terms of nutrient sources.},
}

@article {pmid36683151,
year = {2023},
author = {Vallier, M and Suwandi, A and Ehrhardt, K and Belheouane, M and Berry, D and Čepić, A and Galeev, A and Johnsen, JM and Grassl, GA and Baines, JF},
title = {Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2164448},
doi = {10.1080/19490976.2022.2164448},
pmid = {36683151},
issn = {1949-0984},
abstract = {Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.},
}

@article {pmid36681674,
year = {2023},
author = {Van Holm, W and Carvalho, R and Delanghe, L and Eilers, T and Zayed, N and Mermans, F and Bernaerts, K and Boon, N and Claes, I and Lebeer, S and Teughels, W},
title = {Antimicrobial potential of known and novel probiotics on in vitro periodontitis biofilms.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {3},
pmid = {36681674},
issn = {2055-5008},
abstract = {Several oral diseases are characterized by a shift within the oral microbiome towards a pathogenic, dysbiotic composition. Broad-spectrum antimicrobials are often part of patient care. However, because of the rising antibiotic resistance, alternatives are increasingly desirable. Alternatively, supplying beneficial species through probiotics is increasingly showing favorable results. Unfortunately, these probiotics are rarely evaluated comparatively. In this study, the in vitro effects of three known and three novel Lactobacillus strains, together with four novel Streptococcus salivarius strains were comparatively evaluated for antagonistic effects on proximal agar growth, antimicrobial properties of probiotic supernatant and the probiotic's effects on in vitro periodontal biofilms. Strain-specific effects were observed as differences in efficacy between genera and differences within genera. While some of the Lactobacillus candidates were able to reduce the periodontal pathobiont A. actinomycetemcomitans, the S. salivarius strains were not. However, the S. salivarius strains were more effective against periodontal pathobionts P. intermedia, P. gingivalis, and F. nucleatum. Vexingly, most of the Lactobacillus strains also negatively affected the prevalence of commensal species within the biofilms, while this was lower for S. salivarius strains. Both within lactobacilli and streptococci, some strains showed significantly more inhibition of the pathobionts, indicating the importance of proper strain selection. Additionally, some species showed reductions in non-target species, which can result in unexpected and unexplored effects on the whole microbiome.},
}

@article {pmid36677477,
year = {2023},
author = {Neidhöfer, C and Sib, E and Benhsain, AH and Mutschnik-Raab, C and Schwabe, A and Wollkopf, A and Wetzig, N and Sieber, MA and Thiele, R and Döhla, M and Engelhart, S and Mutters, NT and Parčina, M},
title = {Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/microorganisms11010185},
pmid = {36677477},
issn = {2076-2607},
abstract = {Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals-from three wards and one hospital laboratory-using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1-V2 and V3-V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1-V2 and V3-V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials.},
}

@article {pmid36677425,
year = {2023},
author = {Shedleur-Bourguignon, F and Duchemin, T and P Thériault, W and Longpré, J and Thibodeau, A and Hocine, MN and Fravalo, P},
title = {Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/microorganisms11010133},
pmid = {36677425},
issn = {2076-2607},
abstract = {The microorganisms found on fresh, raw meat cuts at a slaughterhouse can influence the meat's safety and spoilage patterns along further stages of processing. However, little is known about the general microbial ecology of the production environment of slaughterhouses. We used 16s rRNA sequencing and diversity analysis to characterize the microbiota heterogeneity on conveyor belt surfaces in the cutting room of a swine slaughterhouse from different production lines (each associated with a particular piece/cut of meat). Variation of the microbiota over a period of time (six visits) was also evaluated. Significant differences of alpha and beta diversity were found between the different visits and between the different production lines. Bacterial genera indicative of each visit and production line were also identified. We then created random forest models that, based on the microbiota of each sample, allowed us to predict with 94% accuracy to which visit a sample belonged and to predict with 88% accuracy from which production line it was taken. Our results suggest a possible influence of meat cut on processing surface microbiotas, which could lead to better prevention, surveillance, and control of microbial contamination of meat during processing.},
}

@article {pmid36671807,
year = {2023},
author = {Kropochev, AI and Lashin, SA and Matushkin, YG and Klimenko, AI},
title = {Trait-Based Method of Quantitative Assessment of Ecological Functional Groups in the Human Intestinal Microbiome.},
journal = {Biology},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/biology12010115},
pmid = {36671807},
issn = {2079-7737},
abstract = {We propose the trait-based method for quantifying the activity of functional groups in the human gut microbiome based on metatranscriptomic data. It allows one to assess structural changes in the microbial community comprised of the following functional groups: butyrate-producers, acetogens, sulfate-reducers, and mucin-decomposing bacteria. It is another way to perform a functional analysis of metatranscriptomic data by focusing on the ecological level of the community under study. To develop the method, we used published data obtained in a carefully controlled environment and from a synthetic microbial community, where the problem of ambiguity between functionality and taxonomy is absent. The developed method was validated using RNA-seq data and sequencing data of the 16S rRNA amplicon on a simplified community. Consequently, the successful verification provides prospects for the application of this method for analyzing natural communities of the human intestinal microbiota.},
}

@article {pmid36662284,
year = {2023},
author = {He, T and Zhang, X and Du, J and Gilliam, FS and Yang, S and Tian, M and Zhang, C and Zhou, Y},
title = {Arbuscular Mycorrhizal Fungi Shift Soil Bacterial Community Composition and Reduce Soil Ammonia Volatilization and Nitrous Oxide Emissions.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36662284},
issn = {1432-184X},
abstract = {Arbuscular mycorrhizal fungi (AMF) establish mutualistic relationships with the majority of terrestrial plants, increasing plant uptake of soil nitrogen (N) in exchange for photosynthates. And may influence soil ammonia (NH3) volatilization and nitrous oxide (N2O) emissions directly by improving plant N uptake, and/or indirectly by modifying soil bacterial community composition for the soil C availability increasing. However, the effects of AMF on soil NH3 volatilization and N2O emissions and their underlying mechanisms remain unclear. We carried out two independent experiments using contrasting methods, one with a compartmental box device (in 2016) and the other with growth pot experiment (in 2020) to examine functional relationships between AMF and soil NH3 volatilization and N2O emissions under varying N input. The presence of AMF significantly reduced soil NH3 volatilization and N2O emissions while enhancing plant biomass and plant N acquisition, and reducing soil NH4[+] and NO3[-], even with high N input. The presence of AMF also significantly reduced the relative abundance within the bacterial orders Sphingomonadales and Rhizobiales. Sphingomonadales correlated significantly and positively with soil NH3 volatilization in 2016 and N2O emissions, whereas Rhizobiales correlated positively with soil N2O emissions. High N input significantly increased soil NH3 volatilization and N2O emissions with increasing relative abundance of Sphingomonadales and Rhizobiales. These findings demonstrate the contribution of AMF in regulating NH3 and N2O emission by improving plant N uptake and altering soil bacterial communities. They also suggest that altering the rhizosphere microbiome might offer additional potential for restoration of N-enriched agroecosystems.},
}

@article {pmid36656658,
year = {2023},
author = {Zhang, S and Van Haesebroeck, J and Yang, Q and Defoirdt, T},
title = {Indole-3-acetic acid increases the survival of brine shrimp challenged with vibrios belonging to the Harveyi clade.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfd.13759},
pmid = {36656658},
issn = {1365-2761},
abstract = {Vibrios belonging to the Harveyi clade (including closely related species such as Vibrio campbellii, Vibrio harveyi and Vibrio parahaemolyticus) are important pathogens of aquatic organisms. In this study, we investigated the use of indole-3-acetic acid to control disease caused by Harveyi clade vibrios. Indole-3-acetic acid, which can be produced by various seaweeds and microalgae, was added to the rearing water of brine shrimp larvae challenged with 12 different Harveyi clade Vibrio strains. Indole-3-acetic acid significantly decreased the virulence of 10 of the strains without any effect on their growth. The latter is important as it will minimize the selective pressure for resistance development. The survival rate of brine shrimp larvae increased from 1.2-fold to 4.8-fold upon treatment with 400 μM indole-3-acetic acid. Additionally, indole-3-acetic acid significantly decreased the swimming motility in 10 of the strains and biofilm formation in eight of the strains. The mRNA levels of the pirA and pirB toxin genes were decreased to 46% and 42% by indole-3-acetic acid in the AHPND-causing strain V. parahaemolyticus M0904. Hence, our data demonstrate that indole-3-acetic acid has the potential to be an effective virulence inhibitor to control infections in aquaculture.},
}

@article {pmid36654062,
year = {2022},
author = {Song, W and Qiu, L and Qing, J and Zhi, W and Zha, Z and Hu, X and Qin, Z and Gong, H and Li, Y},
title = {Using Bayesian network model with MMHC algorithm to detect risk factors for stroke.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {19},
number = {12},
pages = {13660-13674},
doi = {10.3934/mbe.2022637},
pmid = {36654062},
issn = {1551-0018},
mesh = {Humans ; Bayes Theorem ; *Algorithms ; *Stroke/epidemiology ; Risk Factors ; Logistic Models ; },
abstract = {Stroke is a major chronic non-communicable disease with high incidence, high mortality, and high recurrence. To comprehensively digest its risk factors and take some relevant measures to lower its prevalence is of great significance. This study aimed to employ Bayesian Network (BN) model with Max-Min Hill-Climbing (MMHC) algorithm to explore the risk factors for stroke. From April 2019 to November 2019, Shanxi Provincial People's Hospital conducted opportunistic screening for stroke in ten rural areas in Shanxi Province. First, we employed propensity score matching (PSM) for class balancing for stroke. Afterwards, we used Chi-square testing and Logistic regression model to conduct a preliminary analysis of risk factors for stroke. Statistically significant variables were incorporated into BN model construction. BN structure learning was achieved using MMHC algorithm, and its parameter learning was achieved with Maximum Likelihood Estimation. After PSM, 748 non-stroke cases and 748 stroke cases were included in this study. BN was built with 10 nodes and 12 directed edges. The results suggested that age, fasting plasma glucose, systolic blood pressure, and family history of stroke constitute direct risk factors for stroke, whereas sex, educational levels, high density lipoprotein cholesterol, diastolic blood pressure, and urinary albumin-to-creatinine ratio represent indirect risk factors for stroke. BN model with MMHC algorithm not only allows for a complicated network relationship between risk factors and stroke, but also could achieve stroke risk prediction through Bayesian reasoning, outshining traditional Logistic regression model. This study suggests that BN model boasts great prospects in risk factor detection for stroke.},
}

Humans
Bayes Theorem
*Algorithms
*Stroke/epidemiology
Risk Factors
Logistic Models

@article {pmid36659680,
year = {2019},
author = {Zheng, BX and Zhao, Y and Bi, QF and Zhou, GW and Wang, HJ and Hao, XL and Ding, K},
title = {How to disentangle microbially functional complexity: an insight from the network analysis of C, N, P and S cycling genes.},
journal = {Science bulletin},
volume = {64},
number = {16},
pages = {1129-1131},
doi = {10.1016/j.scib.2019.06.011},
pmid = {36659680},
issn = {2095-9281},
}

@article {pmid36652878,
year = {2023},
author = {Lin, Q and De Vrieze, J and Li, L and Fang, X and Li, X},
title = {Interconnected versus unconnected microorganisms: Does it matter in anaerobic digestion functioning.},
journal = {Journal of environmental management},
volume = {331},
number = {},
pages = {117307},
doi = {10.1016/j.jenvman.2023.117307},
pmid = {36652878},
issn = {1095-8630},
abstract = {Microorganisms in anaerobic digestion (AD) are essential for wastes/pollutants treatment and energy recovery. Due to microbial enormous diversity, developing effective perspectives to understand microbial roles therein is urgent. This study conducted AD of swine manure, used an ensemble-based network analysis to distinguish interconnected, unconnected, copresence (positively interconnected) and mutual-exclusion (negatively interconnected) microorganisms within microbial communities, and explored their importance towards AD performances, using amplicon sequencing of 16S rRNA and 16S rRNA gene. Our analyses revealed greater importance of interconnected than unconnected microorganisms towards CH4 production and AD multifunctionality, which was attributed to higher niche breadth, deterministic community assembly, community stability and phylogenetic conservatism. The diversity was higher in unconnected than interconnected microorganisms, but was not linked to AD performances. Compared to copresence microorganisms, mutual-exclusion microorganisms showed greater and equal importance towards CH4 production and AD multifunctionality, which was attributed to their roles in stabilizing microbial communities. The increased feedstock biodegradability, by replacing part of manure with fructose or apple waste, hardly affected the relative importance of interconnected versus unconnected microorganisms towards CH4 production or AD multifunctionality. Our findings develop a new framework to understand microbial roles, and have important implications in targeted manipulation of critical microorganisms in waste-treatment systems.},
}

@article {pmid36651641,
year = {2023},
author = {Daebeler, A and Güell-Bujons, Q and Mooshammer, M and Zechmeister, T and Herbold, CW and Richter, A and Wagner, M and Daims, H},
title = {Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16337},
pmid = {36651641},
issn = {1462-2920},
abstract = {Nitrite-oxidizing bacteria (NOB) catalyze the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite-oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira, and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.},
}

@article {pmid36648219,
year = {2023},
author = {Jiang, C and Zeng, H},
title = {Unique Habitat of Karst Tiankengs Changes the Taxonomy and Potential Metabolism of Soil Microbial Communities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0231622},
doi = {10.1128/spectrum.02316-22},
pmid = {36648219},
issn = {2165-0497},
abstract = {Microbial communities in karst ecosystems have been extensively studied. However, in a class of deep-lying habitats with unique climates (karst tiankeng), the structure and ecological functions of microorganisms receive little attention, which is essential for understanding the biogeochemistry of karst tiankeng. Herein, microorganisms from inside (ITK) and outside (OTK) karst tiankengs were analyzed by high-throughput sequencing and multivariate statistical analysis. The results showed that the structure and function of soil bacterial communities inside and outside karst tiankengs were significantly different. The ITK microbial communities presented significantly higher Shannon diversity due to the abundant nutrients in karst tiankeng soil. Random molecular ecological network analysis revealed that the ITK network was simpler and more vulnerable and may be susceptible to environmental changes. More positive links within the network indicate that microorganisms adapt to the karst tiankeng through synergies. The keystones in karst tiankeng were mainly involved in the decomposition of soil organic matter and carbon/nitrogen cycles. Although soil total phosphorus and available potassium regulate microbial community structure variation, dispersal limitation is the predominant ecological process within the microbial community in karst tiankeng. In addition, the functional profiles of the microbial communities reveal that some human diseases (such as infectious diseases) exist in OTK. Collectively, these findings have enhanced our understanding of microbial interactions, ecological functions, and community composition processes in karst tiankeng ecosystems. IMPORTANCE Constrained by the trapped terrain, a unique ecosystem has formed in karst tiankeng. Soil microorganisms are essential for the formation and maintenance of ecosystems, but soil microbial ecology research in karst tiankeng is still lacking. In this study, representative habitats inside and outside karst tiankeng were selected to study the taxonomy and potential metabolism of soil microbial communities. The results show that the unique habitat of karst tiankeng reshapes the composition, structure, and function of soil microbial communities. Our results contribute to enhancing our understanding of sustainable recovery strategies in fragile ecosystems and understanding the biodiversity value of karst tiankeng under climate change.},
}

@article {pmid36646914,
year = {2023},
author = {Gruppuso, L and Receveur, JP and Fenoglio, S and Bona, F and Benbow, ME},
title = {Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36646914},
issn = {1432-184X},
abstract = {The frequency of flow intermittency and drying events in Alpine rivers is expected to increase due to climate change. These events can have significant consequences for stream ecological communities, though the effects of reduced flow conditions on microbial communities of decomposing allochthonous leaf material require additional research. In this study, we investigated the bacterial and fungal communities associated with the decomposition of two common species of leaf litter, chestnut (Castanea sativa), and oak (Quercus robur). A sampling of experimentally placed leaf bags occurred over six collection dates (up to 126 days after placement) at seven stream sites in the Western Italian Alps with historically different flow conditions. Leaf-associated bacterial and fungal communities were identified using amplicon-based, high-throughput sequencing. Chestnut and oak leaf material harbored distinct bacterial and fungal communities, with a number of taxonomic groups differing in abundance, though bacterial community structure converged later in decomposition. Historical flow conditions (intermittent vs perennial rivers) and observed conditions (normal flow, low flow, ongoing drying event) had weaker effects on bacterial and fungal communities compared to leaf type and collection date (i.e., length of decomposition). Our findings highlight the importance of leaf characteristics (e.g., C:N ratios, recalcitrance) to the in-stream conditioning of leaf litter and a need for additional investigations of drying events in Alpine streams. This study provides new information on the microbial role in leaf litter decomposition with expected flow changes associated with a global change scenario.},
}

@article {pmid36646913,
year = {2023},
author = {Maucourt, F and Cébron, A and Budzinski, H and Le Menach, K and Peluhet, L and Czarnes, S and Melayah, D and Chapulliot, D and Vallon, L and Plassart, G and Hugoni, M and Fraissinet-Tachet, L},
title = {Prokaryotic, Microeukaryotic, and Fungal Composition in a Long-Term Polychlorinated Biphenyl-Contaminated Brownfield.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36646913},
issn = {1432-184X},
abstract = {Polychlorinated biphenyls (PCBs) are recognized as persistent organic pollutants and accumulate in organisms, soils, waters, and sediments, causing major health and ecological perturbations. Literature reported PCB bio-transformation by fungi and bacteria in vitro, but data about the in situ impact of those compounds on microbial communities remained scarce while being useful to guide biotransformation assays. The present work investigated for the first time microbial diversity from the three-domains-of-life in a long-term contaminated brownfield (a former factory land). Soil samples were ranked according to their PCB concentrations, and a significant increase in abundance was shown according to increased concentrations. Microbial communities structure showed a segregation from the least to the most PCB-polluted samples. Among the identified microorganisms, Bacteria belonging to Gammaproteobacteria class, as well as Fungi affiliated to Saccharomycetes class or Pleurotaceae family, including some species known to transform some PCBs were abundantly retrieved in the highly polluted soil samples.},
}

@article {pmid36645380,
year = {2023},
author = {Mynard, P and Algar, A and Lancaster, L and Bocedi, G and Fahri, F and Gubry-Rangin, C and Lupiyaningdyah, P and Nangoy, M and Osborne, O and Papadopulos, A and Sudiana, IM and Juliandi, B and Travis, J and Herrera-Alsina, L},
title = {Impact of Phylogenetic Tree Completeness and Misspecification of Sampling Fractions on Trait Dependent Diversification Models.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syad001},
pmid = {36645380},
issn = {1076-836X},
abstract = {Understanding the origins of diversity and the factors that drive some clades to be more diverse than others are important issues in evolutionary biology. Sophisticated SSE (state-dependent speciation and extinction) models provide insights into the association between diversification rates and the evolution of a trait. The empirical data used in SSE models and other methods is normally imperfect, yet little is known about how this can affect these models. Here, we evaluate the impact of common phylogenetic issues on inferences drawn from SSE models. Using simulated phylogenetic trees and trait information, we fitted SSE models to determine the effects of sampling fraction (phylogenetic tree completeness) and sampling fraction misspecification on model selection and parameter estimation (speciation, extinction, and transition rates) under two sampling regimes (random and taxonomically biased). As expected, we found that both model selection and parameter estimate accuracies are reduced at lower sampling fractions (i.e., low tree completeness). Furthermore, when sampling of the tree is imbalanced across subclades and tree completeness is ≤ 60%, rates of false positives increase and parameter estimates are less accurate, compared to when sampling is random. Thus, when applying SSE methods to empirical datasets, there are increased risks of false inferences of trait dependent diversification when some sub-clades are heavily under-sampled. Mis-specifying the sampling fraction severely affected the accuracy of parameter estimates: parameter values were over-estimated when the sampling fraction was specified as lower than its true value, and under-estimated when the sampling fraction was specified as higher than its true value. Our results suggest that it is better to cautiously under-estimate sampling efforts, as false positives increased when the sampling fraction was over-estimated. We encourage SSE studies where the sampling fraction can be reasonably estimated and provide recommended best practices for SSE modelling.},
}

@article {pmid36644938,
year = {2023},
author = {van Neerbos, FAC and Dewitte, P and Wäckers, F and Wenseleers, T and Jacquemyn, H and Lievens, B},
title = {Bacterial volatiles elicit differential olfactory responses in insect species from the same and different trophic levels.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.13176},
pmid = {36644938},
issn = {1744-7917},
abstract = {Insect communities consist of species from several trophic levels that have to forage for suitable resources among and within larger patches of non-resources. To locate their resources, insects use diverse stimuli, including olfactory, visual, acoustic, tactile and gustatory cues. While most research has focused on cues derived from plants and other insects, there is mounting evidence that insects also respond to volatile organic compounds (VOCs) emitted by microorganisms. However, to date little is known about how the olfactory response of insects within and across different trophic levels is affected by bacterial VOCs. In this study, we used Y-tube bioassays and chemical analysis of VOCs to assess how VOCs emitted by bacteria affect the olfactory response of insects of the same and different trophic levels. Experiments were performed using two aphid species (Amphorophora idaei Börner and Myzus persicae var. nicotianae Blackman), three primary parasitoid species (Aphidius colemani Viereck, A. ervi Haliday, and A. matricariae Viereck), and two hyperparasitoid species (Asaphes suspensus Nees and Dendrocerus aphidum Rondani). Olfactory responses were evaluated for three bacterial strains (Bacillus pumilus ST18.16/133, Curtobacterium sp. ST18.16/085 and Staphylococcus saprophyticus ST18.16/160) that were isolated from the habitat of the insects. Results revealed that insects from all trophic levels responded to bacterial volatiles, but olfactory responses varied between and within trophic levels. All bacteria produced the same set of volatile compounds, but often in different relative concentrations. For eleven of these volatiles we found contrasting correlations between their concentration and the behaviour of the primary parasitoids and hyperparasitoids. Further, olfactometer experiments on three of these compounds confirmed the contrasting olfactory responses of primary parasitoids and hyperparasitoids. The potential of these findings for the development of novel semiochemical-based strategies to improve biological aphid control has been discussed. This article is protected by copyright. All rights reserved.},
}

@article {pmid36644338,
year = {2022},
author = {Romano, F and Symiakaki, K and Pitta, P},
title = {Sex in the wild: repeated observations of planktonic ciliate conjugation from field samples.},
journal = {Journal of plankton research},
volume = {44},
number = {2},
pages = {333-336},
pmid = {36644338},
issn = {0142-7873},
abstract = {Ciliate conjugation is considered a rare event to encounter in the field and it is mostly reported from cultures. In this work, we describe a synchronized conjugation event of planktonic ciliates that was discovered twice; in September 2019, at two different locations in the Cretan Sea, Eastern Mediterranean, and in October 2020. In 2019, first, at 2 m depth of the coastal station POSEIDON-HCB, in samples fixed with acid Lugol and formaldehyde, we found 340 and 200 mating pairs L[-1]of different ciliate species, respectively; and second, at the Heraklion port, we found 220 mating pairs L[-1] of Strombidinopsis sp. and 1960 mating pairs L[-1] of Strombidium sp. At the Heraklion port visited again in 2020, we found 800 mating pairs L[-1] of Strombidinopsis sp. and 200 mating pairs L[-1] of Strombidium sp. Since detailed descriptions of conjugation in pelagic oligotrich ciliates are missing, our observations indicate that ciliate conjugation could be a frequent and periodic phenomenon, under specific conditions.},
}

@article {pmid36643595,
year = {2023},
author = {Villa, F and Wu, YL and Zerboni, A and Cappitelli, F},
title = {Corrigendum: In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface.},
journal = {Bioscience},
volume = {73},
number = {1},
pages = {69},
doi = {10.1093/biosci/biac109},
pmid = {36643595},
issn = {0006-3568},
abstract = {[This corrects the article DOI: 10.1093/biosci/biac091.].},
}

@article {pmid36640506,
year = {2023},
author = {Lamprea Pineda, PA and Demeestere, K and Toledo, M and Boon, N and Van Langenhove, H and Walgraeve, C},
title = {Long-term biofiltration of gaseous N,N-dimethylformamide: Operational performance and microbial diversity analysis at different conditions.},
journal = {Journal of hazardous materials},
volume = {447},
number = {},
pages = {130767},
doi = {10.1016/j.jhazmat.2023.130767},
pmid = {36640506},
issn = {1873-3336},
abstract = {N,N-Dimethylformamide (DMF) is an organic solvent produced in large quantities worldwide. It is considered as a hazardous air pollutant and its emission should be controlled. However, only a limited number of studies have been performed on the removal of gaseous DMF by biological technologies. In this paper, we evaluate the removal of DMF under mesophilic and thermophilic conditions in a lab-scale biofilter for 472 days. The results show that, at ambient temperature, the biofilter achieved an average removal efficiency (RE) of 99.7 ± 0.3 % at Inlet Loads (ILs) up to 297 ± 52 g DFM m[-3] h[-1] (Empty Bed Residence Time (EBRTs) of 10.7 s). However, a decrease in EBRT (6.4 s) led to an unstable outlet concentration and, thus, to a drop in the biofilter performance (average RE: 90 ± 9 %). Moreover, an increase in temperature up to 65 °C led to a gradual decrease in RE (till 91 ± 7 %). Microbial analysis indicates that once the microorganisms encountered DMF, Rhizobiaceae dominated followed by Alcaligenaceae. Afterwards, a strong decrease in Rhizobiaceae was observed at every increase in temperature, and at 65 °C, the taxa were more heterogeneous. Overall, our experimental results indicate that biofiltration is a promising technique to remove DMF from waste gas streams.},
}

@article {pmid36639537,
year = {2023},
author = {Osvatic, JT and Yuen, B and Kunert, M and Wilkins, L and Hausmann, B and Girguis, P and Lundin, K and Taylor, J and Jospin, G and Petersen, JM},
title = {Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36639537},
issn = {1751-7370},
abstract = {Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.},
}

@article {pmid36202391,
year = {2023},
author = {Haskell-Ramsay, CF and Dodd, FL and Smith, D and Cuthbertson, L and Nelson, A and Lodge, JK and Jackson, PA},
title = {Mixed Tree Nuts, Cognition, and Gut Microbiota: A 4-Week, Placebo-Controlled, Randomized Crossover Trial in Healthy Nonelderly Adults.},
journal = {The Journal of nutrition},
volume = {152},
number = {12},
pages = {2778-2788},
doi = {10.1093/jn/nxac228},
pmid = {36202391},
issn = {1541-6100},
abstract = {BACKGROUND: Beneficial effects of nut supplementation on cognitive function have previously been demonstrated in young and older adults. Alterations to gut microbiota have also been shown following tree nut consumption. However, no data exists on the effects of nuts on cognition and intestinal microbial communities assessed within the same study.

OBJECTIVES: The study aimed to examine the effects of daily consumption of tree nuts for 4 wk on cognitive function (primary outcome), mood, metabolomics, and gut microbial species (secondary outcomes) in healthy, nonelderly adults.

METHODS: This randomized, placebo-controlled, double-blind, counterbalanced crossover study assessed the effects of 4 wk of supplementation with 30 g/d mixed tree nuts versus placebo on cognition and mood in 79 healthy adults aged 18-49 y. Metabolic responses, gut bacterial community structure, and the potential for these to impact cognition were explored using a multi-omic approach. Bacterial community analysis was conducted in Quantitative Insights Into Microbial Ecology 2 (QIIME2).

RESULTS: Mixed model analysis indicated that nut consumption led to significant improvements to accuracy (placebo M = 92.2% compared with NUTS M = 94.5%; P = 0.019) and speed of response (placebo M = 788 ms compared with NUTS M = 757 ms; P = 0.004) on a picture recognition task. No significant changes to bacterial community α or β diversity were observed when comparing nut consumption to the placebo arm. However, an unclassified Lachnospiraceae amplicon sequence variant (ASV) was significantly enriched in participants when supplemented with nuts (P = 0.015). No correlations were observed between the changes to picture recognition and the changes to the unclassified Lachnospiraceae ASV. There were no significant changes to the urinary metabolome.

CONCLUSIONS: These findings indicate a positive effect of nut on cognition following only 4 wk of consumption in a healthy nonelderly sample, as well as upregulation of a microbial taxa associated with gut health. The effects appear to be independent of one another, but further exploration is required in those experiencing cognitive decline and/or gut dysbiosis.},
}

@article {pmid36635570,
year = {2023},
author = {Strachan, CR and Yu, XA and Neubauer, V and Mueller, AJ and Wagner, M and Zebeli, Q and Selberherr, E and Polz, MF},
title = {Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {36635570},
issn = {2058-5276},
abstract = {The activities of different microbes in the cow rumen have been shown to modulate the host's ability to utilize plant biomass, while the host-rumen interface has received little attention. As datasets collected worldwide have pointed to Campylobacteraceae as particularly abundant members of the rumen epithelial microbiome, we targeted this group in a subset of seven cows with meta- and isolate genome analysis. We show that the dominant Campylobacteraceae lineage has recently speciated into two populations that were structured by genome-wide selective sweeps followed by population-specific gene import and recombination. These processes led to differences in gene expression and enzyme domain composition that correspond to the ability to utilize acetate, the main carbon source for the host, at the cost of inhibition by propionate. This trade-off in competitive ability further manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture-independent analyses, our results highlight how recent evolutionary dynamics can shape key functional roles in the rumen microbiome.},
}

@article {pmid36635489,
year = {2023},
author = {Wang, J and Raza, W and Jiang, G and Yi, Z and Fields, B and Greenrod, S and Friman, VP and Jousset, A and Shen, Q and Wei, Z},
title = {Bacterial volatile organic compounds attenuate pathogen virulence via evolutionary trade-offs.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36635489},
issn = {1751-7370},
abstract = {Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plant-pathogenic Ralstonia solanacearum bacterium adapts to VOC-mixture produced by a biocontrol Bacillus amyloliquefaciens T-5 bacterium and how these adaptations might affect its virulence. We found that VOC selection led to a clear increase in VOC-tolerance, which was accompanied with cross-tolerance to several antibiotics commonly produced by soil bacteria. The increasing VOC-tolerance led to trade-offs with R. solanacearum virulence, resulting in almost complete loss of pathogenicity in planta. At the genetic level, these phenotypic changes were associated with parallel mutations in genes encoding lipopolysaccharide O-antigen (wecA) and type-4 pilus biosynthesis (pilM), which both have been linked with outer membrane permeability to antimicrobials and plant pathogen virulence. Reverse genetic engineering revealed that both mutations were important, with pilM having a relatively larger negative effect on the virulence, while wecA having a relatively larger effect on increased antimicrobial tolerance. Together, our results suggest that microbial VOCs are important drivers of bacterial evolution and could potentially be used in biocontrol to select for less virulent pathogens via evolutionary trade-offs.},
}

@article {pmid36631688,
year = {2023},
author = {Rasmussen, TS and Koefoed, AK and Deng, L and Muhammed, MK and Rousseau, GM and Kot, W and Sprotte, S and Neve, H and Franz, CMAP and Hansen, AK and Vogensen, FK and Moineau, S and Nielsen, DS},
title = {CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36631688},
issn = {1751-7370},
abstract = {Many bacteria and archaea harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, few of these systems have been confirmed experimentally to be active in gut bacteria. Here, we demonstrate experimentally that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage assays in vitro but also in vivo using gnotobiotic (GB) mice. Both high phage titer and an increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Fewer new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able to co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.},
}

@article {pmid36631293,
year = {2023},
author = {Mason, AR and Taylor, LS and DeBruyn, JM},
title = {Microbial ecology of vertebrate decomposition in terrestrial ecosystems.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad006},
pmid = {36631293},
issn = {1574-6941},
abstract = {Vertebrate decomposition results in an ephemeral disturbance of the surrounding environment. Microbial decomposers are recognized as key players in the breakdown of complex organic compounds, controlling carbon and nutrient fate in the ecosystem and potentially serving as indicators of time since death for forensic applications. As a result, there has been increasing attention on documenting the microbial communities associated with vertebrate decomposition, or the 'necrobiome'. These necrobiome studies differ in the vertebrate species, microhabitats (e.g. skin vs. soil), and geographic locations studied, but many are narrowly focused on the forensic application of microbial data, missing the larger opportunity to understand the ecology of these communities. To further our understanding of microbial dynamics during vertebrate decomposition and identify knowledge gaps, there is a need to assess the current works from an ecological systems perspective. In this review, we examine recent work pertaining to microbial community dynamics and succession during vertebrate (human and other mammals) decomposition in terrestrial ecosystems, through the lens of a microbial succession ecological framework. From this perspective, we describe three major microbial microhabitats (internal, external, and soil) in terms of their unique successional trajectories and identify three major knowledge gaps that remain to be addressed.},
}

@article {pmid36629441,
year = {2023},
author = {Šigutová, H and Šigut, M and Pyszko, P and Kostovčík, M and Kolařík, M and Drozd, P},
title = {Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0316022},
doi = {10.1128/spectrum.03160-22},
pmid = {36629441},
issn = {2165-0497},
abstract = {Microorganisms are key mediators of interactions between insect herbivores and their host plants. Despite a substantial interest in studying various aspects of these interactions, temporal variations in microbiomes of woody plants and their consumers remain understudied. In this study, we investigated shifts in the microbiomes of leaf-mining larvae (Insecta: Lepidoptera) and their host trees over one growing season in a deciduous temperate forest. We used 16S and ITS2 rRNA gene metabarcoding to profile the bacterial and fungal microbiomes of leaves and larvae. We found pronounced shifts in the leaf and larval microbiota composition and richness as the season progressed, and bacteria and fungi showed consistent patterns. The quantitative similarity between leaf and larval microbiota was very low for bacteria (~9%) and decreased throughout the season, whereas fungal similarity increased and was relatively high (~27%). In both leaves and larvae, seasonality, along with host taxonomy, was the most important factor shaping microbial communities. We identified frequently occurring microbial taxa with significant seasonal trends, including those more prevalent in larvae (Streptococcus, Candida sake, Debaryomyces prosopidis, and Neoascochyta europaea), more prevalent in leaves (Erwinia, Seimatosporium quercinum, Curvibasidium cygneicollum, Curtobacterium, Ceramothyrium carniolicum, and Mycosphaerelloides madeirae), and frequent in both leaves and larvae (bacterial strain P3OB-42, Methylobacterium/Methylorubrum, Bacillus, Acinetobacter, Cutibacterium, and Botrytis cinerea). Our results highlight the importance of considering seasonality when studying the interactions between plants, herbivorous insects, and their respective microbiomes, and illustrate a range of microbial taxa persistent in larvae, regardless of their occurrence in the diet. IMPORTANCE Leaf miners are endophagous insect herbivores that feed on plant tissues and develop and live enclosed between the epidermis layers of a single leaf for their entire life cycle. Such close association is a precondition for the evolution of more intimate host-microbe relationships than those found in free-feeding herbivores. Simultaneous comparison of bacterial and fungal microbiomes of leaves and their tightly linked consumers over time represents an interesting study system that could fundamentally contribute to the ongoing debate on the microbial residence of insect gut. Furthermore, leaf miners are ideal model organisms for interpreting the ecological and evolutionary roles of microbiota in host plant specialization. In this study, the larvae harbored specific microbial communities consisting of core microbiome members. Observed patterns suggest that microbes, especially bacteria, may play more important roles in the caterpillar holobiont than generally presumed.},
}

@article {pmid36629429,
year = {2023},
author = {Dragone, NB and Whittaker, K and Lord, OM and Burke, EA and Dufel, H and Hite, E and Miller, F and Page, G and Slayback, D and Fierer, N},
title = {The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga.},
journal = {mBio},
volume = {},
number = {},
pages = {e0331322},
doi = {10.1128/mbio.03313-22},
pmid = {36629429},
issn = {2150-7511},
abstract = {The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.},
}

@article {pmid36623784,
year = {2023},
author = {Anedda, E and Farrell, ML and Morris, D and Burgess, CM},
title = {Evaluating the impact of heavy metals on antimicrobial resistance in the primary food production environment: A scoping review.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {121035},
doi = {10.1016/j.envpol.2023.121035},
pmid = {36623784},
issn = {1873-6424},
abstract = {Heavy metals are naturally occurring environmental compounds, which can influence antimicrobial resistance (AMR) dissemination. However, there is limited information on how heavy metals may act as a selective pressure on AMR in the primary food production environment. This review aims to examine the literature on this topic in order to identify knowledge gaps. A total of 73 studies, which met pre-established criteria, were included. These investigations were undertaken between 2008 and 2021, with a significant increase in the last three years. The majority of studies included were undertaken in China. Soil, water and manure were the most common samples analysed, and the sampling locations varied from areas with a natural presence of heavy metals, areas intentionally amended with heavy metals or manure, to areas close to industrial activity or mines. Fifty-four per cent of the investigations focused on the analysis of four or more heavy metals, and copper and zinc were the metals most frequently analysed (n = 59, n = 49, respectively). The findings of this review highlight a link between heavy metals and AMR in the primary food production environment. Heavy metals impacted the abundance and dissemination of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), with MGEs also observed as playing a key role in the spread of ARGs and metal resistance genes (MRGs). Harmonization of methodologies used in future studies would increase the opportunity for comparison between studies. Further research is also required to broaden the availability of data at a global level.},
}

@article {pmid36516408,
year = {2022},
author = {Kasanke, CP and Zhao, Q and Alfaro, T and Walter, CA and Hobbie, SE and Cheeke, TE and Hofmockel, KS},
title = {Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16823},
pmid = {36516408},
issn = {1365-294X},
abstract = {Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. To evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.},
}

@article {pmid36621691,
year = {2023},
author = {Cui, H and Xu, R and Yu, Z and Meng, F},
title = {Phylogenetic group-based assembly and co-occurrence pattern of the microbial community in full-scale wastewater treatment plants during the Chinese spring festival.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {137775},
doi = {10.1016/j.chemosphere.2023.137775},
pmid = {36621691},
issn = {1879-1298},
abstract = {The quality and quantity of domestic sewage discharge vary significantly during the Chinese Spring Festival due to the huge population shift. The dynamics of microbial community traits during the Spring Festival, particularly the phylogenetic group-based assembly and co-occurrence patterns, are however little understood. Here, influent and activated sludge samples from 2 full-scale wastewater treatment plants were collected bi-daily throughout a 20-day Spring Festival period and subjected to high-throughput Illumina-MiSeq sequencing. The findings revealed that whereas the microbial communities in the activated sludge displayed a comparatively stable pattern, and the influent communities experienced significant temporal fluctuations in terms of diversity and composition. The characterization by "Infer Community Assembly Mechanisms by Phylogenetic-bin based null model" demonstrated that for Competibacter glycogen-accumulating organisms, the assembly mechanism shifted from deterministic process (HoS = 69.5%) before the Spring Festival to stochastic process (DR = 65.9%) after the Spring Festival. The network analysis revealed that the network structure of sludge communities was more stable before the Spring Festival than that after the Spring Festival. Additionally, sludge communities had no keystone species in common with the influent before the Spring Festival, while the sludge and influent communities shared two keystone taxa after the Spring Festival (Sebaldella and Candidatus Competibacter). This study would deepen our understanding of the microbial ecology in biological wastewater treatment systems, which also aids in managing wastewater treatment plants.},
}

@article {pmid36615993,
year = {2022},
author = {Mosquera-Romero, S and Anaya-Garzon, J and Garcia-Timermans, C and Van Dorpe, J and Hoorens, A and Commenges-Bernole, N and Verbeken, K and Rabaey, K and Varia, J},
title = {Combined Gold Recovery and Nanoparticle Synthesis in Microbial Systems Using Fractional Factorial Design.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/nano13010083},
pmid = {36615993},
issn = {2079-4991},
abstract = {Green synthesis of gold nanoparticles (AuNPs) using microorganisms has been generally studied aiming for high-yield production and morphologies appropriated for various applications, such as bioremediation, (bio)sensors, and (bio)catalysis. Numerous approaches showed the individual effect of factors influencing the synthesis of AuNPs with limited analysis of the governing factors enhancing the production and desired quality of the precipitates. This study proposes a fractional-factorial design to investigate the simultaneous influence of seven environmental factors (cell concentration, temperature, anoxic/oxic conditions, pH, gold concentration, electron donor type, and bacterial species) on the recovery yield and synthesis of targeted AuNPs. Various sizes and morphologies of the AuNPs were obtained by varying the environmental factors studied. The factors with significant effects (i.e., 0.2 mM Au and pH 5) were selected according to statistical analysis for optimal removal of 88.2 ± 3.5% of gold and with the production of valuable 50 nm AuNPs, which are known for their enhanced sensitivity. Implications of the cytochrome-C on the bacterial mechanisms and the provision of electron donors via an electrochemical system are further discussed. This study helps develop gold recovery and nanoparticle synthesis methods, focusing on the determining factor(s) for efficient, low-cost, green synthesis of valuable materials.},
}

@article {pmid36611775,
year = {2022},
author = {Imperatore, R and Fronte, B and Scicchitano, D and Orso, G and Marchese, M and Mero, S and Licitra, R and Coccia, E and Candela, M and Paolucci, M},
title = {Dietary Supplementation with a Blend of Hydrolyzable and Condensed Tannins Ameliorates Diet-Induced Intestinal Inflammation in Zebrafish (Danio rerio).},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/ani13010167},
pmid = {36611775},
issn = {2076-2615},
abstract = {The current study evaluated the effects of hydrolyzable and condensed tannins from chestnut and quebracho wood, respectively (TSP, Silvafeed[®]), on zebrafish with intestinal inflammation induced by a plant-based diet (basal diet). Four experimental diets were prepared as follows: the basal diet + 0 TSP, the basal diet + TSP at 0.9 g/kg of feed, the basal diet + TSP at 1.7 g/kg of feed, and the basal diet + TSP at 3.4 g/kg of feed. Eighty-four zebrafish (Danio rerio) were fed for 12 days with the experimental diets. In zebrafish fed the basal diet, intestine integrity appeared to be altered, with damaged intestinal villi, high immunoexpression of tumor necrosis factor-α (TNFα) and cyclooxygenase 2 (COX2), and high expression of the cox2, interleukin 1 (il-1b), interleukin 8 (cxcl8-l1), and tnfα genes. The tannin treatment partially restored intestinal morphology and downregulated the expression of cytokines. The best activity was detected with 1.7 and 3.4 g/kg of feed. In the guts of all groups, Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes were the most represented phyla. The most represented genera were Plesiomonas and Sphingomonas, belonging to the Proteobacteria phylum; Cetobacterium, belonging to the Fusobacteria phylum; and Lactobacillus, belonging to the Firmicutes phylum. No significant differences were detected among groups, except for a slight decrease in the Fusobacteria phylum and slight increases in the Shewanella and Bacteroides genera with TSP. In conclusion, these results suggest that tannins can improve the zebrafish intestinal inflammation caused by a terrestrial-plant-based diet in a dose-dependent manner.},
}

@article {pmid36610634,
year = {2023},
author = {Li, C and Liu, C and Liu, J and Feng, C},
title = {Insight into the temporal dynamics of microbial succession and ecology mechanisms in biological activated carbon tanks.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {161366},
doi = {10.1016/j.scitotenv.2022.161366},
pmid = {36610634},
issn = {1879-1026},
abstract = {Biological activated carbon (BAC) has long been applied in China to guarantee water quality and to achieve drinking water regulations. However, a knowledge gap remains regarding the temporal dynamics of microbial communities, particularly microbe-based assembly and co-occurrence patterns. Accordingly, this study investigated the evolution of BAC microbial communities using a pilot-scale system and examined by multivariate ecological combined with high-throughput Illumina sequencing and statistical methods. The results showed that BAC microbial diversity reached its peak in 2 years and declined thereafter. Microbial communities composition was accompanied by significant temporal evolution in the BAC biofilm. Deterministic processes gained in importance along with time, especially homogeneous selection which contributed 59.09 %-75.63 % to the community assembly in 8-yr, 9-yr, and 10-yr BAC (relative contribution: 59.09 %-75.63 %). According to co-occurrence network analysis, microbial networks have more unstable structures over time, as evidenced by higher modularity, heightened connectivity, and fewer keystones. Moreover, the interaction between microbial taxa tended to have a higher proportion of competitive relationships during the operation of the BAC tank, ranging from 13.51 % to 76.35 %. Based on these dynamic ecological processes, microbial community succession in BAC biofilm might undergo four phases: community establishment (Years 0-2); community stability (Years 2-5); community quasi-degradation (Years 5-8); community degradation (Years 8-10). The performance of BAC was greatly influenced by community development, and contaminant removal gradually decreased as community succession proceeded. These results add to our knowledge of microbial ecology and provide the basis for further research into microbial communities' regulation strategies in BAC tanks.},
}

@article {pmid36602317,
year = {2023},
author = {An, XL and Xu, JX and Xu, MR and Zhao, CX and Li, H and Zhu, YG and Su, JQ},
title = {Dynamics of Microbial Community and Potential Microbial Pollutants in Shopping Malls.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057622},
doi = {10.1128/msystems.00576-22},
pmid = {36602317},
issn = {2379-5077},
abstract = {Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.},
}

@article {pmid36596939,
year = {2023},
author = {Lemberger, U and Pjevac, P and Hausmann, B and Berry, D and Moser, D and Jahrreis, V and Özsoy, M and Shariat, SF and Veser, J},
title = {The microbiome of kidney stones and urine of patients with nephrolithiasis.},
journal = {Urolithiasis},
volume = {51},
number = {1},
pages = {27},
pmid = {36596939},
issn = {2194-7236},
mesh = {Humans ; *Metabolic Syndrome ; RNA, Ribosomal, 16S/genetics ; *Kidney Calculi/diagnosis ; *Nephrolithiasis/urine ; *Microbiota ; Bacteria ; },
abstract = {The incidence of nephrolithiasis is rising worldwide. Although it is a multifactorial disease, lifestyle plays a major role in its etiology. Another considerable factor could be an aberrant microbiome. In our observational single-center study, we aimed to investigate the composition of bacteria in kidney stones and urine focusing on patients with features of metabolic syndrome. Catheterized urine and kidney stones were collected prospectively from 100 consecutive patients undergoing endoscopic nephrolithotomy between 2020 and 2021 at our clinic. Microbiome composition was analyzed via 16S rRNA gene amplicon sequencing. Detection of bacteria was successful in 24% of the analyzed kidney stones. These patients had a prolonged length of stay compared to patients without verifiable bacteria in their stones (2.9 vs 1.5 days). Patients with features of metabolic syndrome were characterized by kidney stones colonized with classical gastrointestinal bacteria and displayed a significant enrichment of Enterococcaceae and Enterobacteriaceae. Stones of patients without features of metabolic syndrome characterized by Ureaplasma and Staphylococcaceae. Patients with bacteria in their kidney stones exhibit a longer length of stay, possibly due to more complex care. Patients presenting with features of metabolic syndrome displayed a distinct stone microbiome compared to metabolically fit patients. Understanding the role of bacteria in stone formation could enable targeted therapy, prevention of post-operative complications and new therapeutic strategies.},
}

Humans
*Metabolic Syndrome
RNA, Ribosomal, 16S/genetics
*Kidney Calculi/diagnosis
*Nephrolithiasis/urine
*Microbiota
Bacteria

@article {pmid36592956,
year = {2023},
author = {Martiniuk, JT and Hamilton, J and Dodsworth, T and Measday, V},
title = {Grape-associated fungal community patterns persist from berry to wine on a fine geographical scale.},
journal = {FEMS yeast research},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsyr/foac067},
pmid = {36592956},
issn = {1567-1364},
abstract = {Wine grape fungal community composition is influenced by abiotic factors including geography and vintage. Compositional differences may correlate with different wine metabolite composition and sensory profiles, suggesting a microbial role in the shaping of a wine's terroir, or regional character. While grape and wine-associated fungal community composition has been studied extensively at a regional and sub-regional scale, it has not been explored in detail on fine geographical scales over multiple harvests. Over two years, we examined the fungal communities on Vitis Vinifera cv. Pinot noir grape berry surfaces, in crushed grapes, and in lab spontaneous fermentations from three vineyards within a <1km radius in Canada's Okanagan Valley wine region. We also evaluated the effect of winery environment exposure on fungal community composition by sampling grapes crushed and fermented in the winery at commercial scale. Spatiotemporal community structure was evident among grape berry surface, crushed grape and fermentation samples, with each vineyard exhibiting a distinct fungal community signature. Crushed grape fungal populations were richer in fermentative yeast species compared to grape berry surface fungal populations. Our study suggests that, as on a regional level, fungal populations may contribute to fine-scale -terroir," with significant implications for single-vineyard wines.},
}

@article {pmid36592918,
year = {2022},
author = {Burke, LP and Chique, C and Fitzhenry, K and Chueiri, A and O'Connor, L and Hooban, B and Cahill, N and Brosnan, E and Olaore, L and Sullivan, E and Reilly, L and Morris, D and Hynds, P and O'Dwyer, J},
title = {Characterization of Shiga toxin-producing Escherichia coli presence, serogroups and risk factors from private groundwater sources in western Ireland.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {161302},
doi = {10.1016/j.scitotenv.2022.161302},
pmid = {36592918},
issn = {1879-1026},
abstract = {Over recent years, Ireland has reported the highest crude incidence rates of Shiga toxin-producing Escherichia coli (STEC) enteritis in Europe. Unregulated private groundwater sources have emerged as an important potential transmission route for STEC, with up to 750,000 Irish residents reliant on these sources for domestic waters. This study aimed to investigate the prevalence and serogroup profile of STEC contamination from domestic private wells in western Ireland. Fifty-two groundwater sources were analysed during two sampling campaigns in the autumn (September/October) of 2019 (n = 21) and 2021 (n = 31). Untreated groundwater samples (30 L) were collected and analysed using the "CapE" (capture, amplify, extract) method. Extracted DNA was tested using multiplex real-time PCR for Shiga toxin stx1 and/or stx2 and eae genes. STEC positive DNA samples were tested for clinically relevant serogroups by real-time PCR. Data relating to 27 potential groundwater contamination risk factors were geospatially linked to each well and assessed for association with E. coli, stx1 and/or stx2 and eae presence/absence. Overall, 20/52 wells (38.4 %) were positive for E. coli (median concentration 8.5 MPN/100 mL as assessed by Colilert-18 method). Stx1 and/or stx2 was detected in 10/52 (19.2 %) wells overall and 8/20 E. coli positive wells, equating to a STEC to "generic" E. coli detection ratio of 40 %. Six of these wells (30 %) were also positive for eae. One or more serogroup-specific gene targets were identified in all but one stx1 and/or stx2 positive sample, with O145 (n = 6), O157 (n = 5) and O103 (n = 4) most prevalent. STEC presence was significantly associated with decreasing well depth (U = -2.243; p = 0.024) and increasing 30-day mean antecedent rainfall (U = 2.126; p = 0.034). Serogroup O104 was associated with increased sheep density (U = 2.089; p = 0.044) and detection of stx1 and/or stx2 + eae with increased septic tank density (U = 2.246 p = 0.023). Findings indicate high detection rates of clinically relevant STEC in E. coli contaminated groundwater sources in Ireland.},
}

@article {pmid36590596,
year = {2022},
author = {Hu, X and Fan, R and Song, W and Qing, J and Yan, X and Li, Y and Duan, Q and Li, Y},
title = {Landscape of intestinal microbiota in patients with IgA nephropathy, IgA vasculitis and Kawasaki disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1061629},
pmid = {36590596},
issn = {2235-2988},
abstract = {OBJECTIVE: To explore the common differential flora of IgAN, Kawasaki disease and IgA vasculitis by screening and analyzing the differential intestinal flora between the three disease groups of IgAN, Kawasaki disease and IgA vasculitis and their healthy controls.

METHODS: Papers on 16srRNA sequencing-related intestinal flora of IgAN, Kawasaki disease and IgA vasculitis were searched in databases, the literature was systematically collated and analysed, the original data was download from the relevant databases, and then the operational taxonomic unit and species classification analysis were performed. Besides, Alpha diversity analysis and Beta diversity analysis were performed to screen for IgAN, Kawasaki disease and I1gA vasculitis groups and finally compare the common intestinal differential flora among the three groups.

RESULTS: Among the common differential flora screened, Lachnospiracea_incertae_sedis was lower in both the IgAN and Kawasaki disease groups than in the respective healthy controls; Coprococcus was low in the IgAN group but high in the IgA vasculitis group. Fusicatenibacter was lower in both the Kawasaki disease and IgA vasculitis groups than in their respective healthy controls, and Intestinibacter was low in the Kawasaki disease group, but its expression was high in the IgA vasculitis group.

CONCLUSION: The dysbiosis of the intestinal flora in the three groups of patients with IgAN, Kawasaki disease and IgA vasculitis, its effect on the immunity of the organism and its role in the development of each disease group remain unclear, and the presence of their common differential flora may further provide new ideas for the association of the pathogenesis of the three diseases.},
}