@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.<br><br>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).<br><br>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.<br><br>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&#x202f;=&#x202f;1.24, 95% CI: 1.12-1.36). The risk of developing CD was similarly elevated regardless of the presence (RR&#x202f;=&#x202f;1.64, 95% CI: 1.17-2.31) or absence (RR&#x202f;=&#x202f;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&#x202f;=&#x202f;1.63; 95% CI: 1.38-1.93) and colon lesions (OR&#x202f;=&#x202f;0.70; 95% CI: 0.5-0.84) between CD patients with appendectomy and those without appendectomy.<br><br>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.<br><br>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.<br><br>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.<br><br>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 na&#xef;ve 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.<br><br>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 na&#xef;ve 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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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%).<br><br>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.<br><br>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&#xa0;h fermentation were observed as a function of the diet intervention and correlated to specific taxa of interest.<br><br>CONCLUSIONS: These findings suggest that consuming MRE for 21&#xa0;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 &amp; 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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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 &#x3b1;1-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.<br><br>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.<br><br>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 &amp; pharmacotherapy = Biomedecine &amp; 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.<br><br>METHODS: In this study, the effects of FOSs were investigated with the use of two C57BL/6&#xa0;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&#xa0;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.<br><br>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, PPAR&#x3b3;, CD36, MTTP, APOC3, IL-6, and IL-1&#x3b2;) were down-regulated after FOS treatment.<br><br>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 &amp; 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.<br><br>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&#x2009;~&#x2009;670-bp fragment of the small subunit ribosomal RNA gene.<br><br>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&#x2009;=&#x2009;22).<br><br>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.<br><br>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.<br><br>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.<br><br>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.}, }
@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.<br><br>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.<br><br>METHODS: This randomized, placebo-controlled, double-blind, counterbalanced crossover study assessed the effects of 4 wk of supplementation with 30&#xa0;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).<br><br>RESULTS: Mixed model analysis indicated that nut consumption led to significant improvements to accuracy (placebo M&#xa0;=&#xa0;92.2%&#xa0;compared with NUTS M&#xa0;=&#xa0;94.5%; P&#xa0;=&#xa0;0.019) and speed of response (placebo M&#xa0;=&#xa0;788&#xa0;ms compared with NUTS M&#xa0;=&#xa0;757&#xa0;ms; P&#xa0;=&#xa0;0.004) on a picture recognition task. No significant changes to bacterial community &#x3b1; or &#x3b2; 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&#xa0;=&#xa0;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.<br><br>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.}, }
@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.<br><br>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.<br><br>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.<br><br>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.}, }
@article {pmid36590430, year = {2022}, author = {Krohn, C and Khudur, L and Dias, DA and van den Akker, B and Rees, CA and Crosbie, ND and Surapaneni, A and O'Carroll, DM and Stuetz, RM and Batstone, DJ and Ball, AS}, title = {The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1079136}, pmid = {36590430}, issn = {1664-302X}, abstract = {The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.}, }
@article {pmid36587901, year = {2022}, author = {Lietaer, L and Pascottini, OB and Lacoere, T and Kerckhof, FM and Martens, A and Van de Wiele, T and Opsomer, G}, title = {Studying the pre-implantation uterine microbiota in cattle using transabdominal laparoscopic low-volume lavage: Aiming for zero-contamination.}, journal = {Journal of microbiological methods}, volume = {205}, number = {}, pages = {106664}, doi = {10.1016/j.mimet.2022.106664}, pmid = {36587901}, issn = {1872-8359}, abstract = {Recent studies have suggested that bacteria associated with the female reproductive tract - the uterine microbiota - may be important for reproductive health and pregnancy success. Therefore, uterine microbiome research gained much interest in the last few years. However, it is challenging to study late postpartum uterine samples, since they hold a low microbial biomass. Next-generation sequencing techniques are very sensitive for microbial identification, but they cannot make a distinction between actual microbiota and contaminant bacteria or their DNA. Our aim was to test a new method to sample the bovine uterine lumen in vivo, while minimizing the risk of cross-contamination. In order to evaluate this method, we performed a descriptive assessment of the microbial composition of the obtained samples. Transabdominal, laparoscopic sampling of the uterine lumen was conducted in five Holstein-Friesian cows. Uterine fluid from the uterine horns was collected by low-volume lavage. DNA from the samples was extracted using two different DNA extraction methods, and negative controls (sampling blank controls and DNA extraction blank controls) were included. Bacteria were identified using 16S rRNA gene amplicon sequencing. In this proof-of-concept study, no evidence for authentically present uterine microbiota could be found. During laparoscopic sampling, some practical challenges were encountered, and the reliability of low-volume-lavage for the collection of a low microbial biomass could be questioned. By comparing two DNA extraction methods, a significant contamination background could be noticed originating from the DNA extraction kits.}, }
@article {pmid36590333, year = {2021}, author = {Koshy-Chenthittayil, S and Mendes, P and Laubenbacher, R}, title = {Optimization of Agent-Based Models Through Coarse-Graining: A Case Study in Microbial Ecology.}, journal = {Letters in biomathematics}, volume = {8}, number = {1}, pages = {167-178}, pmid = {36590333}, issn = {2373-7867}, abstract = {Optimization and control are important objectives across biology and biomedicine, and mathematical models are a key enabling technology. This paper reports a computational study of model-based multi-objective optimization in the setting of microbial ecology, using agent-based models. This modeling framework is well-suited to the field, but is not amenable to standard control-theoretic approaches. Furthermore, due to computational complexity, simulation-based optimization approaches are often challenging to implement. This paper presents the results of an approach that combines control-dependent coarse-graining with Pareto optimization, applied to two models of multi-species bacterial biofilms. It shows that this approach can be successful for models whose computational complexity prevents effective simulation-based optimization.}, }
@article {pmid36586465, year = {2022}, author = {McDonagh, F and Singh, NK and Venkateswaran, K and Lonappan, AM and Hallahan, B and Tuohy, A and Burke, L and Kovarova, A and Miliotis, G}, title = {First complete genome of a multidrug resistant strain of the novel human pathogen Kalamiella piersonii (GABEKP28) identified in human saliva.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2022.12.003}, pmid = {36586465}, issn = {2213-7173}, abstract = {OBJECTIVES: Kalamiella piersonii is a newly identified bacterial species, firstly isolated from surfaces of the International Space Station (ISS). It also appears as a novel human pathogen reported to be implicated in bacteremia and kidney stone disease. Here, we report the first complete genome of a multidrug resistant (MDR) strain of K.piersonii (GABEKP28) isolated from the saliva of a patient with treatment resistant schizophrenia, in order to determine the mobile genetic elements, antibiotic resistance genes (ARGs) and virulence factors (VFs) harbored by such a strain of this novel species.<br><br>METHODS: Whole-genome sequencing (WGS) was performed using DNABSEQ (PE150) and Nanopore MinION platforms. Hybrid assembly was conducted using Unicycler v0.5.0. Genome assembly quality was verified using QUAST v5.0.2. The assembly was annotated using PROKKA v1.14.5. ARGs and VFs were identifies using Abricate v1.0.0 RESULTS: : K.piersonii GABEKP28 was classified as MDR while also carrying plasmidic genetic determinants associated with a hypervirulent phenotype. The complete genome size is 3 881 479 bp and has GC content of 57.76% while it encodes for 3 525 CDS. The strain was also identified to carry three plasmids of 513 647 bp, 261 771 bp, 106 029 bp respectively.<br><br>CONCLUSION: K.piersonii GABEKP28 is the first complete genome of this species to be submitted to GenBank, and only the second from a human host to be sequenced. The WGS data with multiple plasmids, ARGs and VFs will aid in understanding the pathogenicity, evolution and phylogeny of this novel opportunistic pathogen.}, }
@article {pmid36585490, year = {2022}, author = {Zhao, J and Wang, Z and Li, C and Shi, T and Liang, Y and Jiao, N and Zhang, Y}, title = {Significant Differences in Planktonic Virus Communities Between "Cellular Fraction" (0.22 ~ 3.0 µm) and "Viral Fraction" (&lt; 0.22 μm) in the Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36585490}, issn = {1432-184X}, abstract = {Compared to free-living viruses (< 0.22 m) in the ocean, planktonic viruses in the "cellular fraction" (0.22 ~ 3.0 μm) are now far less well understood, and the differences between them remain largely unexplored. Here, we revealed that even in the same seawater samples, the "cellular fraction" comprised significantly distinct virus communities from the free virioplankton, with only 13.87% overlap in viral contigs at the species level. Compared to the viral genomes deposited in NCBI RefSeq database, 99% of the assembled viral genomes in the "cellular fraction" represented novel genera. Notably, the assembled (near-) complete viral genomes within the "cellular fraction" were significantly larger than that in the "viral fraction," and the "cellular fraction" contained three times more species of giant viruses or jumbo phages with genomes > 200 kb than the "viral fraction." The longest complete genomes of jumbo phage (~ 252 kb) and giant virus (~ 716 kb) were both detected only in the "cellular fraction." Moreover, a relatively higher proportion of proviruses were predicted within the "cellular fraction" than "viral fraction." Besides the substantial divergence in viral community structure, the different fractions also contained their unique viral auxiliary metabolic genes; e.g., those potentially participating in inorganic carbon fixation in deep sea were detected only in the "cellular-fraction" viromes. In addition, there was a considerable divergence in the community structure of both "cellular fraction" and "viral fraction" viromes between the surface and deep-sea habitats, suggesting that they might have similar environmental adaptation properties. The findings deepen our understanding of the complexity of viral community structure and function in the ocean.}, }
@article {pmid36585489, year = {2022}, author = {Zhang, Y and Liu, F and Liang, H and Gao, D}, title = {Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36585489}, issn = {1432-184X}, abstract = {Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m[2]‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m[2]‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m[2]‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.}, }
@article {pmid36584949, year = {2022}, author = {Fraser, MW and Martin, BC and Wong, HL and Burns, BP and Kendrick, GA}, title = {Sulfide intrusion in a habitat forming seagrass can be predicted from relative abundance of sulfur cycling genes in sediments.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161144}, doi = {10.1016/j.scitotenv.2022.161144}, pmid = {36584949}, issn = {1879-1026}, abstract = {Sulfide intrusion from sediments is an increasingly recognized contributor to seagrass declines globally, yet the relationship between sediment microorganisms and sulfide intrusion has received little attention. Here, we use metagenomic sequencing and stable isotope ([34]S) analysis to examine this relationship in Cockburn Sound, Australia, a seagrass-dominated embayment with a gradient of sulfide stress and seagrass declines. There was a significant positive relationship between sulfide intrusion into seagrasses and sulfate reduction genes in sediment microbial communities, which was greatest at sites with long term seagrass declines. This is the first demonstration of a significant link between sulfur cycling genes present in seagrass sediments and sulfide intrusion in a habitat-forming seagrass that is experiencing long-term shoot density decline. Given that microorganisms respond rapidly to environmental change, the quantitative links established in this study can be used as a potential management tool to enable the prediction of sulfide stress on large habitat forming seagrasses; a global issue expected to worsen with climate change. Originality-significance statement In this study, we combine metagenomic analysis, stable isotope ecology and seagrass physiology to show a significant, positive relationship between sulfate reducing genes in sediment microbial communities and sulfide intrusion in overlying seagrasses. Our study represents the first demonstration of a significant link between the genomics of seagrass-associated microbes and sulfide intrusion in a habitat-forming seagrass experiencing long-term declines. This is important from a global change perspective as sulfide intrusion is increasingly being recorded as a driver of seagrass declines across the globe, and will worsen with climate change given the increase in sulfate reduction rates under higher temperatures.}, }
@article {pmid36584719, year = {2022}, author = {Andrzejak, T and Raje, H and LaFleur, G and Willis, J and Boopathy, R}, title = {Water quality and antibiotic resistance in the recreational waters.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128546}, doi = {10.1016/j.biortech.2022.128546}, pmid = {36584719}, issn = {1873-2976}, abstract = {The overuse and improper disposal of antibiotics results in antibiotic resistance. This raises concern over the presence of antibiotic resistant bacteria (ARB) in waterways and pose health risks of antibiotic resistant infections to water recreationists. The purpose of this study was to monitor water quality, microbial ecology, and antibiotic resistance in water and biofilm on submerged plastics at two public boat launches in southeastern Louisiana. Water and biofilm samples were collected once a month, in triplicate, from two public boat launches in Louisiana, USA for a year. Water quality metrics included nitrate, ammonia, sulfate, phosphate, and organic carbon. Water samples were tested for total and fecal coliform abundance and the presence of ARB. Out of 131 bacterial isolates studied from these two sites, 86% of them tested positive for antibiotic resistance with multi-drug resistance. Antibiotic resistance genes (ARGs) for sulfonamide (sul2), bacitracin (bacA) and ampicillin (ampA) were identified in bacterial isolates from water and biofilm samples at both sites. Molecular genetic diversity analysis identified distinct taxonomic diversity differences in biofilm bacteria compared to the planktonic bacteria in the surrounding water. Biofilm samples showed increased diversity at the phylum, genus, and species levels.}, }
@article {pmid36583056, year = {2022}, author = {Doster, E and Pinnell, LJ and Noyes, NR and Parker, JK and Anderson, CA and Booker, CW and Hannon, SJ and McAllister, TA and Gow, SP and Belk, KE and Morley, PS}, title = {Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {970358}, pmid = {36583056}, issn = {1664-302X}, abstract = {INTRODUCTION: Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle.<br><br>METHODS: This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics.<br><br>RESULTS: Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively).<br><br>DISCUSSION: Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.}, }
@article {pmid36583045, year = {2022}, author = {Puig, S and Bañeras, L and Heijne, AT and Paquete, CM}, title = {Editorial: Latest breakthroughs in microbial electrochemistry research.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1100272}, doi = {10.3389/fmicb.2022.1100272}, pmid = {36583045}, issn = {1664-302X}, }
@article {pmid36579161, year = {2022}, author = {Metcalf, CJE and Tepekule, B and Bruijning, M and Koskella, B}, title = {Hosts, microbiomes, and the evolution of critical windows.}, journal = {Evolution letters}, volume = {6}, number = {6}, pages = {412-425}, pmid = {36579161}, issn = {2056-3744}, abstract = {The absence of microbial exposure early in life leaves individuals vulnerable to immune overreaction later in life, manifesting as immunopathology, autoimmunity, or allergies. A key factor is thought to be a "critical window" during which the host's immune system can "learn" tolerance, and beyond which learning is no longer possible. Animal models indicate that many mechanisms have evolved to enable critical windows, and that their time limits are distinct and consistent. Such a variety of mechanisms, and precision in their manifestation suggest the outcome of strong evolutionary selection. To strengthen our understanding of critical windows, we explore their underlying evolutionary ecology using models encompassing demographic and epidemiological transitions, identifying the length of the critical window that would maximize fitness in different environments. We characterize how direct effects of microbes on host mortality, but also indirect effects via microbial ecology, will drive the optimal length of the critical window. We find that indirect effects such as magnitude of transmission, duration of infection, rates of reinfection, vertical transmission, host demography, and seasonality in transmission all have the effect of redistributing the timing and/or likelihood of encounters with microbial taxa across age, and thus increasing or decreasing the optimal length of the critical window. Declining microbial population abundance and diversity are predicted to result in increases in immune dysfunction later in life. We also make predictions for the length of the critical window across different taxa and environments. Overall, our modeling efforts demonstrate how critical windows will be impacted over evolution as a function of both host-microbiome/pathogen interactions and dispersal, raising central questions about potential mismatches between these evolved systems and the current loss of microbial diversity and/or increases in infectious disease.}, }
@article {pmid36203239, year = {2023}, author = {Munley, JA and Kelly, LS and Pons, EE and Kannan, KB and Coldwell, PS and Whitley, EM and Gillies, GS and Efron, PA and Nagpal, R and Mohr, AM}, title = {Multicompartmental traumatic injury and the microbiome: Shift to a pathobiome.}, journal = {The journal of trauma and acute care surgery}, volume = {94}, number = {1}, pages = {15-22}, pmid = {36203239}, issn = {2163-0763}, support = {T32 GM008721/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Previous animal models have demonstrated altered gut microbiome after mild traumatic injury; however, the impact of injury severity and critical illness is unknown. We hypothesized that a rodent model of severe multicompartmental injuries and chronic stress would demonstrate microbiome alterations toward a "pathobiome" characterized by an overabundance of pathogenic organisms, which would persist 1 week after injury.<br><br>METHODS: Male Sprague-Dawley rats (n = 8 per group) were subjected to either multiple injuries (PT) (lung contusion, hemorrhagic shock, cecectomy, and bifemoral pseudofractures), PT plus daily chronic restraint stress for 2 hours (PT/CS), or naive controls. Fecal microbiome was measured on days 0, 3, and 7 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analysis. Microbial &#x3b1; diversity was assessed using Chao1 and Shannon indices, and &#x3b2; diversity with principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin; ileum and descending colon tissues were reviewed for injury. Analyses were performed in GraphPad (GraphPad Software, La Jolla, CA) and R (R Foundation for Statistical Computing, Vienna, Austria), with significance defined as p < 0.05.<br><br>RESULTS: There were significant alterations in &#x3b2; diversity at day 3 and between all groups. By day 3, both PT and PT/CS demonstrated significantly depleted bacterial diversity (Chao1) (p = 0.01 and p = 0.001, respectively) versus naive, which persisted up to day 7 in PT/CS only (p = 0.001). Anaerostipes and Rothia dominated PT and Lactobacillus bloomed in PT/CS cohorts by day 7. Plasma occludin was significantly elevated in PT/CS compared with naive (p = 0.04), and descending colon of both PT and PT/CS showed significantly higher injury compared with naive (p = 0.005, p = 0.006).<br><br>CONCLUSIONS: Multiple injuries with and without chronic stress induces significant alterations in microbiome diversity and composition within 3 days; these changes are more prominent and persist for 1 week postinjury with stress. This rapid and persistent transition to a "pathobiome" phenotype represents a critical phenomenon that may influence outcomes after severe trauma and critical illness.}, }
@article {pmid36578577, year = {2022}, author = {Hsu, PL and Di, HJ and Cameron, K and Podolyan, A and Chau, H and Luo, J and Miller, B and Carrick, S and Johnstone, P and Ferguson, S and Wei, W and Shen, J and Zhang, L and Liu, H and Zhao, T and Wei, W and Ding, W and Pan, H and Liu, Y and Li, B}, title = {Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1048735}, pmid = {36578577}, issn = {1664-302X}, abstract = {The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha[-1]) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.}, }
@article {pmid36578575, year = {2022}, author = {Coutinho, TA and Jacques, MA and Jones, J}, title = {Editorial: Emergence and re-emergence of plant diseases caused by Xanthomonas species.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1081601}, pmid = {36578575}, issn = {1664-302X}, }
@article {pmid36578568, year = {2022}, author = {Dirren-Pitsch, G and Bühler, D and Salcher, MM and Bassin, B and Le Moigne, A and Schuler, M and Pernthaler, J and Posch, T}, title = {FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1070232}, pmid = {36578568}, issn = {1664-302X}, abstract = {Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.}, }
@article {pmid36578531, year = {2023}, author = {Lasa, AV and Guevara, M&#xc1; and Villadas, PJ and Fernández-González, AJ and Cervera, MT and Fernández-López, M}, title = {Bacteriome dataset from the rhizosphere of trees in a Pinus pinaster and Pinus halepensis dominated forest subjected to drought conditions.}, journal = {Data in brief}, volume = {46}, number = {}, pages = {108805}, pmid = {36578531}, issn = {2352-3409}, abstract = {The Mediterranean basin is drastically affected by intense and frequent droughts, which jeopardize the diversity and survival of its forest, for example, Pinus pinaster forests. The dynamics of the bacterial communities inhabiting the rhizosphere of Pinus pinaster and other plants from a pine dominated forest under contrasting hydric conditions was monitored. The forest was located in Sierra de Oria (southeast Spain), and it was mainly composed by P. pinaster, P. halepensis, woody shrub species and herbaceous plants. 18 trees visually belonging to P. pinaster located along the perimeter and across the forest were selected for the analysis. All the trees were separated at least 50 m each other. Although all of them belonged to P. pinaster morphologically according to visual identification, the genotyping of the roots confirmed that they corresponded to P. pinaster, P. halepensis, and other plant species different from genus Pinus, although in the last case it was not possible to identify the plant species. At a distance less than 50 cm from the trunk, the litter and topsoil were removed, and the soil closely attached to non-suberified roots (rhizosphere soil) was collected (depth of 5-25 cm). Sampling was carried out in two seasons with contrasting temperature and rainfall patterns: on July 18, 2017 (summer) and April 24, 2018 (spring). After rhizosphere soil DNA and RNA extraction (and cDNA synthesis), a metabarcoding approach was followed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene and its derived transcripts by Illumina MiSeq platform. Sequencing reads were bioinformatically processed; specifically, they were filtered, trimmed, clustered into ASV (Amplicon Sequence Variants), and taxonomically identified. As a result, a total of 1,123,209 and 1,089,359 quality sequences were obtained from DNA and RNA-derived libraries, which resulted in 5,241 and 5,231 ASVs, respectively. Total communities (DNA) were mainly dominated by phyla Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Bacteroidetes in summer and spring, while potentially active populations (RNA libraries) were rich in Proteobacteria, Acidobacteria, Candidate division WPS-1, Actinobacteria and Verrucomicrobia both in summer and spring. On the other hand, DNA libraries were mainly dominated by genera Sphingomonas and acidobacterial groups Gp4 and Gp6, while potentially active bacteria (RNA) were rich in acidobacterial Gp3, Gp4, Gp6 and Phenylobacterium, although their relative abundance depended on the considered season. This dataset can provide valuable information about bacterial candidates which could be used as bioindicators of drought conditions. In addition to shifts in the bacterial relative abundance due to seasonal changes, the ratio RNA-based cDNA:DNA could be calculated as proxy of the potential activity of bacterial taxa. Moreover, these data could aid in developing bioformulations based on microorganisms which could be resistant to desiccation and involved in the drought resistance mechanisms of the host plant.}, }
@article {pmid36577993, year = {2022}, author = {Qi, Q and Wang, L and Gebremedhin, MA and Li, S and Wang, X and Shen, J and Zhu, Y and Andegiorgish, AK and Cheng, Y and Shi, L and Zhou, J and Yang, Y and Kang, Y and Yang, W and Zhu, Z and Zeng, L}, title = {The impact of early-life antibiotics and probiotics on gut microbial ecology and infant health outcomes: a Pregnancy and Birth Cohort in Northwest China (PBCC) study protocol.}, journal = {BMC pediatrics}, volume = {22}, number = {1}, pages = {738}, pmid = {36577993}, issn = {1471-2431}, abstract = {BACKGROUND: Unreasonable use of antibiotics and probiotics can alter the gut ecology, leading to antibiotic resistance and suboptimal health outcomes during early life. Our study aims are to clarify the association among antibiotic and probiotic exposure in early life, the microecology of the gut microbiota, and the development of antibiotic resistance; to investigate the long-term impact of antibiotics and probiotics on the health outcomes of infants and young children; and to provide a theoretical basis for the rational use of antibiotics and probiotics from a life course perspective.<br><br>METHODS: The study is a prospective, longitudinal birth cohort study conducted in Shaanxi Province, China from 2018 to 2024. A total of 3,000 eligible mother-child pairs will be enrolled from rural, suburban, and urban areas. The recruitment of the participants begins at pregnancy, and the newborns will be followed up for 2&#xa0;years at successive timepoints: within 3&#xa0;days after birth, 42&#xa0;days after birth, and at 3, 6, 12, 18, and 24&#xa0;months of age. Sociodemographic data, environmental exposures, dietary patterns, psychological conditions, and medical and drug histories are collected. Cognitive and behavioural development among infants and young children and questionnaires on antibiotic knowledge and behaviour among caregivers will be collected at 12 and 24&#xa0;months of age. The faecal samples are collected and analysed by 16S rRNA high-throughput sequencing and quantitative PCR (qPCR) for antibiotic resistance genes.<br><br>DISCUSSION: The findings will inform antibiotic and probiotic use for pregnant women and infants and contribute to establishing rational use strategies of antibiotics and probiotics for paediatricians, health practitioners, and drug administration policy-makers.<br><br>TRIAL REGISTRATION: The study was registered on the Chinese Clinical Trial Registry (ChiCTR) platform, http://www.chictr.org.cn (Record ID: ChiCTR2100047531, June 20, 2021).}, }
@article {pmid36576521, year = {2022}, author = {Westreich, LR and Westreich, ST and Tobin, PC}, title = {Bacterial and Fungal Symbionts in Pollen Provisions of a Native Solitary Bee in Urban and Rural Environments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36576521}, issn = {1432-184X}, abstract = {Among insects, symbionts such as bacteria and fungi can be linked to their physiology and immature development, and in some cases are part of a defense system against parasites and diseases. Current bacterial and fungal symbiont associations in solitary bees are understudied, especially in the Pacific Northwest region of the USA. We collected pollen provisions from the native spring-foraging solitary bee, Osmia lignaria Say, across two distinct foraging periods over 2 years at 22 sites along an urban-to-rural gradient in western Washington. We then used next-generation sequencing to identify bacterial and fungi within pollen provisions and assessed the effect of their richness and diversity on O. lignaria larval development success and adult emergence. We detected a significantly positive relationship between bacterial diversity in pollen with O. lignaria larval developmental success, and higher bacterial richness and diversity during the later foraging period. Fungal generic richness and diversity decreased with increasing plant richness. Although neither was associated with O. lignaria developmental success, we did detect Ascosphaera spp. known to be pathogenic to O. lignaria and other bee species. Neither bacterial or fungal richness or diversity was affected by site type when classified as urban or rural. This study provides new information on bacterial and fungal symbionts present in pollen provisions of a native solitary bee when foraging across urban and rural areas of the Pacific Northwest.}, }
@article {pmid36575570, year = {2022}, author = {Zhou, J and Song, W and Tu, Q}, title = {To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbac594}, pmid = {36575570}, issn = {1477-4054}, abstract = {High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.}, }
@article {pmid36480133, year = {2022}, author = {Eck, M and Schwab, ST and Nelson, TF and Wurst, K and Iberl, S and Schleheck, D and Link, C and Battagliarin, G and Mecking, S}, title = {Biodegradable High-Density Polyethylene-like Material.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202213438}, doi = {10.1002/anie.202213438}, pmid = {36480133}, issn = {1521-3773}, support = {832480/ERC_/European Research Council/International ; }, abstract = {We report a novel polyester material generated from readily available biobased 1,18-octadecanedicarboxylic acid and ethylene glycol possesses a polyethylene-like solid-state structure and also tensile properties similar to high density polyethylene (HDPE). Despite its crystallinity, high melting point (Tm =96 °C) and hydrophobic nature, polyester-2,18 is subject to rapid and complete hydrolytic degradation in in vitro assays with isolated naturally occurring enzymes. Under industrial composting conditions (ISO standard 14855-1) the material is biodegraded with mineralization above 95 % within two months. Reference studies with polyester-18,18 (Tm =99 °C) reveal a strong impact of the nature of the diol repeating unit on degradation rates, possibly related to the density of ester groups in the amorphous phase. Depolymerization by methanolysis indicates suitability for closed-loop recycling.}, }
@article {pmid36575453, year = {2022}, author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S}, title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {500}, pmid = {36575453}, issn = {1741-7015}, abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.<br><br>METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.<br><br>RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.<br><br>CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.}, }
@article {pmid36574886, year = {2022}, author = {Lee, M and Yoo, K and Kim, H and Song, KG and Kim, D and Tiedje, JM and Lee, PH and Park, J}, title = {Metatranscriptional characterization of metabolic dynamics in anaerobic membrane bioreactor producing methane from low-strength wastewater.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128532}, doi = {10.1016/j.biortech.2022.128532}, pmid = {36574886}, issn = {1873-2976}, abstract = {An anaerobic membrane bioreactor (AnMBR) with media is an emerging carbon-neutral biotechnology for low-strength wastewater (LSWW) treatment and methane recovery. Understanding metabolic dynamics among methanogens and syntrophic bacteria is important in optimizing the design and operation of AnMBR. However, little is known about it, especially in media-attached microbial communities. This study explored metabolic dynamics to compare media-attached and suspended conditions. Accordingly, metagenomes and metatranscriptomes from AnMBRs with polymeric media and fed with different influent concentrations (350 and 700 mg-COD/L) were analyzed. Metabolic dynamics were profoundly influenced by the different growth habitats and influent conditions, although the applied influent concentrations are within the range of typical LSWW. Metabolic dynamics prediction results suggest that media-attached-growth habitats may have provided a more favorable microenvironment for methanogens to grow and produce methane, especially under low influent conditions. These findings provide significant implications for optimizing floating media design and operation of AnMBR-producing methane from LSWW.}, }
@article {pmid36574041, year = {2022}, author = {Lozano, IL and González-Olalla, JM and Medina-Sánchez, JM}, title = {New Insights for the Renewed Phytoplankton-Bacteria Coupling Concept: the Role of the Trophic Web.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36574041}, issn = {1432-184X}, abstract = {It is widely accepted that in many aquatic ecosystems bacterioplankton is dependent on and regulated by organic carbon supplied by phytoplankton, leading to coupled algae-bacteria relationship. In this study, an in-depth analysis of this relationship has been carried out by combining two approaches: (i) a correlation analyses between heterotrophic bacterial production (BP) vs. primary production (PP) or algal excretion of organic carbon (EOC), (ii) the balance between bacterial carbon demands (BCD) and the supply of C as EOC, measured as BCD:EOC ratio. During the study period (2013-2016), the algae-bacteria relationship was constantly changing from a coupling in 2013, uncoupling in 2014 and 2015, and an incipient return to coupling (in 2016). Our results show that top-down control (bacterivory) by algal mixotrophy acts as a decoupling force since it provides a fresh C source different to algal EOC to satisfy bacterial carbon demands. Notably, a relationship between the BCD:EOC ratio and the ecosystem metabolic balance (Primary production (PP): respiration (R)) was found, suggesting that PP:R may be a good predictor of the algae-bacteria coupling. This analysis, including the comparison between basal and potential ecosystem metabolic balance, can be a tool to improve knowledge on the interaction between both biotics compartments, which the traditional analyses on coupling may not capture.}, }
@article {pmid36571608, year = {2022}, author = {la Rosa, GM and García-Oliva, F and Ovando-Vázquez, C and Celis-García, LB and López-Reyes, L and López-Lozano, NE}, title = {Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36571608}, issn = {1432-184X}, abstract = {Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability.}, }
@article {pmid36569156, year = {2022}, author = {Meller, S and Al Khatri, MSA and Alhammadi, HK and Álvarez, G and Alvergnat, G and Alves, LC and Callewaert, C and Caraguel, CGB and Carancci, P and Chaber, AL and Charalambous, M and Desquilbet, L and Ebbers, H and Ebbers, J and Grandjean, D and Guest, C and Guyot, H and Hielm-Björkman, A and Hopkins, A and Kreienbrock, L and Logan, JG and Lorenzo, H and Maia, RCC and Mancilla-Tapia, JM and Mardones, FO and Mutesa, L and Nsanzimana, S and Otto, CM and Salgado-Caxito, M and de Los Santos, F and da Silva, JES and Schalke, E and Schoneberg, C and Soares, AF and Twele, F and Vidal-Martínez, VM and Zapata, A and Zimin-Veselkoff, N and Volk, HA}, title = {Expert considerations and consensus for using dogs to detect human SARS-CoV-2-infections.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1015620}, pmid = {36569156}, issn = {2296-858X}, }
@article {pmid36565551, year = {2022}, author = {Li, Q and Stautemas, J and Omondi Onyango, S and De Mey, M and Duchi, D and Tuenter, E and Hermans, N and Calders, P and Van de Wiele, T}, title = {Human gut microbiota stratified by (+)-catechin metabolism dynamics reveals colon region-dependent metabolic profile.}, journal = {Food chemistry}, volume = {408}, number = {}, pages = {135203}, doi = {10.1016/j.foodchem.2022.135203}, pmid = {36565551}, issn = {1873-7072}, abstract = {Catechins have proven to have several health benefits, yet a huge interindividual variability occurs. The metabolic potency of the colonic microbiota towards catechin is a key determinant of this variability. Microbiota from two donors - previously characterized as a fast and a slow converter- were incubated with (+)-catechin in vitro. The robustness of in vitro metabolic profiles was verified by well-fitted human trials. The colon region-dependent and donor-dependent patterns were reflected in both metabolic features and colonic microbiota composition. Upstream and downstream metabolites were mainly detected in the proximal and distal colons, respectively, and were considered important explanatory variables for microbiota clustering in the corresponding colon regions. Higher abundances of two catechin-metabolizing bacteria, Eggerthella and Flavonifractor were found in the distal colon compared to the proximal colon and in slow converter than fast converter. Additionally, these two bacteria were enriched in treatment samples compared to sham treatment samples.}, }
@article {pmid36563760, year = {2022}, author = {Xie, L and Li, W and Pang, X and Liu, Q and Yin, C}, title = {Soil properties and root traits are important factors driving rhizosphere soil bacterial and fungal community variations in alpine Rhododendron nitidulum shrub ecosystems along an altitudinal gradient.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161048}, doi = {10.1016/j.scitotenv.2022.161048}, pmid = {36563760}, issn = {1879-1026}, abstract = {Both soil properties and plant root traits are pivotal factors affecting microbial communities. However, there is still limited information about their importance in shaping rhizosphere soil microbial communities, particularly in less-studied alpine shrub ecosystems. To investigate the effects of altitude (3300, 3600, 3900, and 4200 m) on the diversity and composition of rhizosphere soil bacterial and fungal communities, as well as the factors shaping rhizosphere soil microbial communities, we conducted this study in alpine Rhododendron nitidulum shrub ecosystems from the Zheduo mountain of the eastern Tibetan Plateau. Results demonstrated that bacterial community diversity and richness decreased to the lowest value at 3600 m and then increased at higher altitudes compared with 3300 m; whereas fungal richness at 3300 m was much lower than at other altitudes, and was closely related to soil properties and root traits. The composition of rhizosphere soil bacterial and fungal communities at the low altitude (3300 m) was different from that at high altitudes. Permutational multivariate analysis of variance and redundancy analysis indicated that soil properties (soil water content, pH, NO3[-]-N, and available phosphorus) and root traits (surface area, and maximum depth) were the major factors explaining the variations of rhizosphere soil bacterial and fungal communities. Specific bacterial and fungal taxa along altitudes were identified. The bacterial taxa Planctomycetota was dominant at 3300 and 3600 m with low soil nutrient availability and high root surface area, whereas the fungal taxa Mortierellomycota was abundant at 3900 and 4200 m with high soil nutrient availability and low root surface area. These results suggested that different soil microbes can respond differently to altitude. This study provides a novel insight into factors driving rhizosphere soil bacterial and fungal community variations, which could improve our understanding of microbial ecology in alpine R. nitidulum shrub ecosystems along altitude.}, }
@article {pmid36562630, year = {2022}, author = {Larrouy, JL and Dhami, MK and Jones, EE and Ridgway, HJ}, title = {Physiological stage drives fungal community dynamics and diversity in Leptospermum scoparium (mānuka) flowers.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16324}, pmid = {36562630}, issn = {1462-2920}, abstract = {Flowers are an important niche for microbes, and microbes in turn influence plant fitness. As flower morphology and biology change rapidly over time, dynamic niches for microbes are formed and lost. Floral physiology at each life stage can therefore influence arrival, persistence and loss of microbial species; however, this remains little understood despite its potential consequences for host reproductive success. Through internal transcribed spacer 1 (ITS1) community profiling, we characterised the effect of transitioning through five floral stages of mānuka (Leptospermum scoparium), from immature bud to spent flower, and subsequent allocation to seed, on the flower-inhabiting fungal community. We found nectar-consuming yeasts from Aureobasidium and Vishniacozyma genera, and functionally diverse filamentous fungi from the Cladosporium genus dominated the anthosphere. The candidate core microbiota persisted across this dynamic niche despite high microbial turnover, as observed in shifts in community composition and diversity as flowers matured and senesced. The results demonstrated that floral stages are strong drivers of anthosphere fungal community assembly and dynamics. This study represents the first detailed exploration of fungi through floral development, building on fundamental knowledge in microbial ecology of healthy flowers. This article is protected by copyright. All rights reserved.}, }
@article {pmid36560818, year = {2022}, author = {Budzyńska, D and Zwart, MP and Hasiów-Jaroszewska, B}, title = {Defective RNA Particles of Plant Viruses-Origin, Structure and Role in Pathogenesis.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/v14122814}, pmid = {36560818}, issn = {1999-4915}, abstract = {The genomes of RNA viruses may be monopartite or multipartite, and sub-genomic particles such as defective RNAs (D RNAs) or satellite RNAs (satRNAs) can be associated with some of them. D RNAs are small, deletion mutants of a virus that have lost essential functions for independent replication, encapsidation and/or movement. D RNAs are common elements associated with human and animal viruses, and they have been described for numerous plant viruses so far. Over 30 years of studies on D RNAs allow for some general conclusions to be drawn. First, the essential condition for D RNA formation is prolonged passaging of the virus at a high cellular multiplicity of infection (MOI) in one host. Second, recombination plays crucial roles in D RNA formation. Moreover, during virus propagation, D RNAs evolve, and the composition of the particle depends on, e.g., host plant, virus isolate or number of passages. Defective RNAs are often engaged in transient interactions with full-length viruses-they can modulate accumulation, infection dynamics and virulence, and are widely used, i.e., as a tool for research on cis-acting elements crucial for viral replication. Nevertheless, many questions regarding the generation and role of D RNAs in pathogenesis remain open. In this review, we summarise the knowledge about D RNAs of plant viruses obtained so far.}, }
@article {pmid36557627, year = {2022}, author = {Tao, L and Chai, J and Liu, H and Huang, W and Zou, Y and Wu, M and Peng, B and Wang, Q and Tang, K}, title = {Characterization and Dynamics of the Gut Microbiota in Rice Fishes at Different Developmental Stages in Rice-Fish Coculture Systems.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/microorganisms10122373}, pmid = {36557627}, issn = {2076-2607}, abstract = {The rice-fish system (RFS), a traditional coculture farming model, was selected as a "globally important agricultural heritage system." Host-associated microbiota play important roles in development, metabolism, physiology, and immune function. However, studies on the gut microbiota of aquatic animals in the RFS are scarce, especially the lack of baseline knowledge of the dynamics of gut microbial communities in rice fish during different developmental stages. In this study, we characterized the microbial composition, community structure, and functions of several sympatric aquatic animals (common carp (Cyprinus carpio), crucian carp (Carassius carassius), and black-spotted frogs (Pelophylax nigromaculatus)), and the environment (water) in the RFS using 16S rRNA gene sequencing. Moreover, we investigated stage-specific signatures in the gut microbiota of common carp throughout the three developmental stages (juvenile, sub-adult, and adult). Our results indicated that the Fusobacteriota, Proteobacteria, and Firmicutes were dominant gut microbial phyla in rice fish. The differences in gut microbial compositions and community structure between the three aquatic species were observed. Although no significant differences in alpha diversity were observed across the three developmental stages, the microbial composition and community structure varied with development in common carp in the RFS, with an increase in the relative abundance of Firmicutes in sub-adults and a shift in the functional features of the community. This study sheds light on the gut microbiota of aquatic animals in the RFS. It deepens our understanding of the dynamics of gut microflora during common carp development, which may help improve aquaculture strategies in the RFS.}, }
@article {pmid36557593, year = {2022}, author = {Delgadillo-Ordoñez, N and Raimundo, I and Barno, AR and Osman, EO and Villela, H and Bennett-Smith, M and Voolstra, CR and Benzoni, F and Peixoto, RS}, title = {Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/microorganisms10122340}, pmid = {36557593}, issn = {2076-2607}, abstract = {The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.}, }
@article {pmid36554499, year = {2022}, author = {Dania, MI and Faraji, B and Wachira, J}, title = {Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, doi = {10.3390/ijerph192416621}, pmid = {36554499}, issn = {1660-4601}, support = {5UL1GM118973/GM/NIGMS NIH HHS/United States ; 5U54MD013376/NH/NIH HHS/United States ; }, abstract = {Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely Lactobacillaceae, Burkholderiaceae, Streptococcaceae, Leuconostocaceae, and Acetobacteraceae. Clostridiaceae was the dominant family in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.}, }
@article {pmid36549925, year = {2022}, author = {Hodžić, A and Alić, A}, title = {Hepatozoon silvestris: an emerging feline vector-borne pathogen in Europe?.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2022.12.001}, pmid = {36549925}, issn = {1471-5007}, abstract = {Hepatozoon silvestris (Adeleorina: Hepatozoidae) is a recently described agent of feline hepatozoonosis. Although possibly emerging in Europe, this apicomplexan parasite is still largely unknown. Here, we provide insight into our current knowledge of the parasite's distribution, biology, and pathogenesis of the associated disease.}, }
@article {pmid36549441, year = {2022}, author = {Bilbija, B and Spitzweg, C and Papoušek, I and Fritz, U and Földvári, G and Mullett, M and Ihlow, F and Sprong, H and Civáňová Křížová, K and Anisimov, N and Belova, OA and Bonnet, SI and Bychkova, E and Czułowska, A and Duscher, GG and Fonville, M and Kahl, O and Karbowiak, G and Kholodilov, IS and Kiewra, D and Krčmar, S and Kumisbek, G and Livanova, N and Majláth, I and Teresa Manfredi, M and Mihalca, AD and Miró, G and Moutailler, S and Nebogatkin, IV and Tomanović, S and Vatansever, Z and Yakovich, M and Zanzani, S and Široký, P}, title = {Dermacentor reticulatus - a tick on its way from glacial refugia to a panmictic Eurasian population.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2022.11.002}, pmid = {36549441}, issn = {1879-0135}, abstract = {The ornate dog tick (Dermacentor reticulatus) shows a recently expanding geographic distribution. Knowledge on its intraspecific variability, population structure, rate of genetic diversity and divergence, including its evolution and geographic distribution, is crucial to understand its dispersal capacity. All such information would help to evaluate the potential risk of future spread of associated pathogens of medical and veterinary concern. A set of 865 D. reticulatus ticks was collected from 65 localities across 21 countries, from Portugal in the west to Kazakhstan and southern Russia in the east. Cluster analyses of 16 microsatellite loci were combined with nuclear (ITS2, 18S) and mitochondrial (12S, 16S, COI) sequence data to uncover the ticks' population structures and geographical patterns. Approximate Bayesian computation was applied to model evolutionary relationships among the found clusters. Low variability and a weak phylogenetic signal showing an east-west cline were detected both for mitochondrial and nuclear sequence markers. Microsatellite analyses revealed three genetic clusters, where the eastern and western cluster gradient was supplemented by a third, northern cluster. Alternative scenarios could explain such a tripartite population structure by independent formation of clusters in separate refugia, limited gene flow connected with isolation by distance causing a "bipolar pattern", and the northern cluster deriving from admixture between the eastern and western populations. The best supported demographic scenario of this tick species indicates that the northern cluster derived from admixture between the eastern and western populations 441 (median) to 224 (mode) generations ago, suggesting a possible link with the end of the Little Ice Age in Europe.}, }
@article {pmid36548240, year = {2022}, author = {Lee, JR and Terauds, A and Carwardine, J and Shaw, JD and Fuller, RA and Possingham, HP and Chown, SL and Convey, P and Gilbert, N and Hughes, KA and McIvor, E and Robinson, SA and Ropert-Coudert, Y and Bergstrom, DM and Biersma, EM and Christian, C and Cowan, DA and Frenot, Y and Jenouvrier, S and Kelley, L and Lee, MJ and Lynch, HJ and Njåstad, B and Quesada, A and Roura, RM and Shaw, EA and Stanwell-Smith, D and Tsujimoto, M and Wall, DH and Wilmotte, A and Chadès, I}, title = {Threat management priorities for conserving Antarctic biodiversity.}, journal = {PLoS biology}, volume = {20}, number = {12}, pages = {e3001921}, doi = {10.1371/journal.pbio.3001921}, pmid = {36548240}, issn = {1545-7885}, abstract = {Antarctic terrestrial biodiversity faces multiple threats, from invasive species to climate change. Yet no large-scale assessments of threat management strategies exist. Applying a structured participatory approach, we demonstrate that existing conservation efforts are insufficient in a changing world, estimating that 65% (at best 37%, at worst 97%) of native terrestrial taxa and land-associated seabirds are likely to decline by 2100 under current trajectories. Emperor penguins are identified as the most vulnerable taxon, followed by other seabirds and dry soil nematodes. We find that implementing 10 key threat management strategies in parallel, at an estimated present-day equivalent annual cost of US$23 million, could benefit up to 84% of Antarctic taxa. Climate change is identified as the most pervasive threat to Antarctic biodiversity and influencing global policy to effectively limit climate change is the most beneficial conservation strategy. However, minimising impacts of human activities and improved planning and management of new infrastructure projects are cost-effective and will help to minimise regional threats. Simultaneous global and regional efforts are critical to secure Antarctic biodiversity for future generations.}, }
@article {pmid36545206, year = {2022}, author = {Molina, V and Lavergne, C and Eissler, Y and Junier, P}, title = {Editorial: Microbial ecology and ecosystems from a Southern perspective.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1098400}, pmid = {36545206}, issn = {1664-302X}, }
@article {pmid36542127, year = {2022}, author = {Davis, TS and Stewart, JE and Clark, C and Van Buiten, C}, title = {Nutritional Profile and Ecological Interactions of Yeast Symbionts Associated with North American Spruce Beetle (Dendroctonus rufipennis).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36542127}, issn = {1432-184X}, abstract = {To better understand functional ecology of bark beetle-microbial symbioses, we characterized yeast associates of North American spruce beetle (Dendroctous rufipennis Kirby) across populations. Seven yeast species were detected; Wickerhamomyces canadensis (Wickerham) Kurtzman et al. (Sachharomycetales: Saccharomycetaceae) was the most common (74% of isolates) and found in all populations. Isolates of W. canadensis were subsequently tested for competitive interactions with symbiotic (Leptographium abietinum, = Grosmannia abietina) and pathogenic (Beauvaria bassiana) filamentous fungi, and isolates were nutritionally profiled (protein and P content). Exposure to yeast headspace emissions had isolate-dependent effects on colony growth of symbiotic and pathogenic fungi; most isolates of W. canadensis slightly inhibited growth rates of symbiotic (L. abietinum, mean effect: - 4%) and entomopathogenic (B. bassiana, mean effect: - 6%) fungi. However, overall variation was high (range: - 35.4 to + 88.6%) and some yeasts enhanced growth of filamentous fungi whereas others were consistently inhibitory. The volatile 2-phenylethanol was produced by W. canadensis and synthetic 2-phenylethanol reduced growth rates of both L. abietinum and B. bassiana by 36% on average. Mean protein and P content of Wickerhamomyces canadensis cultures were 0.8% and 7.2%, respectively, but isolates varied in nutritional content and protein content was similar to that of host tree phloem. We conclude that W. canadensis is a primary yeast symbiont of D. rufipennis in the Rocky Mountains and emits volatiles that can affect growth of associated microbes. Wickerhamomyces canadensis isolates vary substantially in limiting nutrients (protein and P), but concentrations are less than reported for the symbiotic filamentous fungus L. abietinum.}, }
@article {pmid36542126, year = {2022}, author = {Wicaksono, WA and Buko, A and Kusstatscher, P and Cernava, T and Sinkkonen, A and Laitinen, OH and Virtanen, SM and Hyöty, H and Berg, G}, title = {Impact of Cultivation and Origin on the Fruit Microbiome of Apples and Blueberries and Implications for the Exposome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36542126}, issn = {1432-184X}, abstract = {Vegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland), and two fruit production methods (naturally grown and horticultural). Microbial abundance, diversity, and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (naturally grown or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e., for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered an important but relatively unexplored external exposomic factor.}, }
@article {pmid36539202, year = {2022}, author = {Almeida-Silva, F and Zhao, T and Ullrich, KK and Schranz, ME and Van de Peer, Y}, title = {Syntenet: an R/Bioconductor package for the inference and analysis of synteny networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btac806}, pmid = {36539202}, issn = {1367-4811}, abstract = {SUMMARY: Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate.<br><br>AVAILABILITY: syntenet is available on Bioconductor (https://bioconductor.org/packages/syntenet), and the source code is available on a GitHub repository (https://github.com/almeidasilvaf/syntenet).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36538089, year = {2022}, author = {Moukarzel, R and Ridgway, HJ and Waller, L and Guerin-Laguette, A and Cripps-Guazzone, N and Jones, EE}, title = {Soil Arbuscular Mycorrhizal Fungal Communities Differentially Affect Growth and Nutrient Uptake by Grapevine Rootstocks.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36538089}, issn = {1432-184X}, abstract = {Arbuscular mycorrhizal fungi (AMF) deliver potentially significant services in sustainable agricultural ecosystems, yet we still lack evidence showing how AMF abundance and/or community composition can benefit crops. In this study, we manipulated AMF communities in grapevine rootstock and measured plant growth and physiological responses. Glasshouse experiments were set up to determine the interaction between rootstock variety and different AMF communities, using AMF communities originating under their own (i.e., "home") soil and other rootstocks' (i.e., "away") soil. The results revealed that specific AMF communities had differential effects on grapevine rootstock growth and nutrient uptake. It was demonstrated that a rootstock generally performed better in the presence of its own AMF community. This study also showed that AMF spore diversity and the relative abundance of certain species is an important factor as, when present in equal abundance, competition between species was indicated to occur, resulting in a reduction in the positive growth outcomes. Moreover, there was a significant difference between the communities with some AMF communities increasing plant growth and nutrient uptake compared with others. The outcomes also demonstrated that some AMF communities indirectly influenced the chlorophyll content in grapevine leaves through the increase of specific nutrients such as K, Mn, and Zn. The findings also indicated that some AMF species may deliver particular benefits to grapevine plants. This work has provided an improved understanding of community level AMF-grapevine interaction and delivered an increased knowledge of the ecosystem services they provide which will benefit the wine growers and the viticulture industry.}, }
@article {pmid36537799, year = {2022}, author = {Tyc, O and Kulkarni, P and Ossowicki, A and Tracanna, V and Medema, MH and van Baarlen, P and van IJcken, WFJ and Verhoeven, KJF and Garbeva, P}, title = {Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0057422}, doi = {10.1128/msystems.00574-22}, pmid = {36537799}, issn = {2379-5077}, abstract = {Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.}, }
@article {pmid36534053, year = {2022}, author = {Amaneesh, C and Anna Balan, S and Silpa, PS and Kim, JW and Greeshma, K and Aswathi Mohan, A and Robert Antony, A and Grossart, HP and Kim, HS and Ramanan, R}, title = {Gross Negligence: Impacts of Microplastics and Plastic Leachates on Phytoplankton Community and Ecosystem Dynamics.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c05817}, pmid = {36534053}, issn = {1520-5851}, abstract = {Plastic debris is an established environmental menace affecting aquatic systems globally. Recently, microplastics (MP) and plastic leachates (PL) have been detected in vital human organs, the vascular system, and in vitro animal studies positing severe health hazards. MP and PL have been found in every conceivable aquatic ecosystem─from open oceans and deep sea floors to supposedly pristine glacier lakes and snow covered mountain catchment sites. Many studies have documented the MP and PL impacts on a variety of aquatic organisms, whereby some exclusively focus on aquatic microorganisms. Yet, the specific MP and PL impacts on primary producers have not been systematically analyzed. Therefore, this review focuses on the threats posed by MP, PL, and associated chemicals on phytoplankton, their comprehensive impacts at organismal, community, and ecosystem scales, and their endogenous amelioration. Studies on MP- and PL-impacted individual phytoplankton species reveal the production of reactive oxygen species, lipid peroxidation, physical damage of thylakoids, and other physiological and metabolic changes, followed by homo- and heteroaggregations, ultimately eventuating in decreased photosynthesis and primary productivity. Likewise, analyses of the microbial community in the plastisphere show a radically different profile compared to the surrounding planktonic diversity. The plastisphere also enriches multidrug-resistant bacteria, cyanotoxins, and pollutants, accelerating microbial succession, changing the microbiome, and thus, affecting phytoplankton diversity and evolution. These impacts on cellular and community scales manifest in changed ecosystem dynamics with widespread bottom-up and top-down effects on aquatic biodiversity and food web interactions. These adverse effects─through altered nutrient cycling─have "knock-on" impacts on biogeochemical cycles and greenhouse gases. Consequently, these impacts affect provisioning and regulating ecosystem services. Our citation network analyses (CNA) further demonstrate dire effects of MP and PL on all trophic levels, thereby unsettling ecosystem stability and services. CNA points to several emerging nodes indicating combined toxicity of MP, PL, and their associated hazards on phytoplankton. Taken together, our study shows that ecotoxicity of plastic particles and their leachates have placed primary producers and some aquatic ecosystems in peril.}, }
@article {pmid36533929, year = {2022}, author = {Rojas, CA and Holekamp, KE and Viladomat Jasso, M and Souza, V and Eisen, JA and Theis, KR}, title = {Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0096522}, doi = {10.1128/msystems.00965-22}, pmid = {36533929}, issn = {2379-5077}, abstract = {The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas' guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host's life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.}, }
@article {pmid36533921, year = {2022}, author = {Graf, F and Zehentner, B and Fellner, L and Scherer, S and Neuhaus, K}, title = {Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0235122}, doi = {10.1128/spectrum.02351-22}, pmid = {36533921}, issn = {2165-0497}, abstract = {The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes. IMPORTANCE The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated, since such genes are not allowed in genome annotations. However, ribosome profiling catches mRNA in the moment of being template for protein production. Using this technique and subsequent experiments, we verified 3 novel overlapping genes encoded in antisense of known genes. This adds more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes.}, }
@article {pmid36533904, year = {2022}, author = {Timmis, K and Berry, D and Bonfante, P and Cunliffe, M and Danchin, A and Galperin, M and Lopez, P and Stewart, F and Wood, T}, title = {Juan Luis Ramos: an exceptional Editor of Environmental Microbiology.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16315}, pmid = {36533904}, issn = {1462-2920}, }
@article {pmid36530964, year = {2022}, author = {Inomura, K and Deutsch, C and Jahn, O and Dutkiewicz, S and Follows, MJ}, title = {Global patterns in marine organic matter stoichiometry driven by phytoplankton ecophysiology.}, journal = {Nature geoscience}, volume = {15}, number = {12}, pages = {1034-1040}, pmid = {36530964}, issn = {1752-0894}, abstract = {The proportion of major elements in marine organic matter links cellular processes to global nutrient, oxygen and carbon cycles. Differences in the C:N:P ratios of organic matter have been observed between ocean biomes, but these patterns have yet to be quantified from the underlying small-scale physiological and ecological processes. Here we use an ecosystem model that includes adaptive resource allocation within and between ecologically distinct plankton size classes to attribute the causes of global patterns in the C:N:P ratios. We find that patterns of N:C variation are largely driven by common physiological adjustment strategies across all phytoplankton, while patterns of N:P are driven by ecological selection for taxonomic groups with different phosphorus storage capacities. Although N:C varies widely due to cellular adjustment to light and nutrients, its latitudinal gradient is modest because of depth-dependent trade-offs between nutrient and light availability. Strong latitudinal variation in N:P reflects an ecological balance favouring small plankton with lower P storage capacity in the subtropics, and larger eukaryotes with a higher cellular P storage capacity in nutrient-rich high latitudes. A weaker N:P difference between southern and northern hemispheres, and between the Atlantic and Pacific oceans, reflects differences in phosphate available for cellular storage. Despite simulating only two phytoplankton size classes, the emergent global variability of elemental ratios resembles that of all measured species, suggesting that the range of growth conditions and ecological selection sustain the observed diversity of stoichiometry among phytoplankton.}, }
@article {pmid36530180, year = {2022}, author = {Messadi, N and Mechmeche, M and Setti, K and Tizemmour, Z and Hamdi, M and Kachouri, F}, title = {Optimization of Extraction Parameters and Characterization of Tunisian Date Extract: A Scientific Approach Toward Their Utilization.}, journal = {Sugar tech : an international journal of sugar crops &amp; related industries}, volume = {}, number = {}, pages = {1-13}, pmid = {36530180}, issn = {0972-1525}, abstract = {UNLABELLED: The response surface methodology (RSM) was used in order to select the extraction conditions of extract from Kentichi date powder; a by-product of the date-processing process. Powder/solvent ratio, extraction temperature, and extraction time all had an impact on sugar yield, and these model factors have quadratic effects influencing sugar yield. Optimal extraction was obtained with 300 g/L powder/solvent ratio, 32.7 °C extraction temperature, and 2.1 h extraction time. Under these conditions, Kentichi date powder's (KDP) sugar yield was 77.1%, which was close to the predicted value of the model (80.50%). The results of Kentichi date powder extract (KDPE) showed that the total sugar content is 160.09 g/L. However, the protein content is 10.31 g/L with a majority of the essential amino acids (essentially glutamic acid (28.39 mg/L) and aspartic acid (9.65 mg/L)). The determination of antioxidant activity of KDPE showed a high activity (DPPH IC50 = 4.8 mg/mL, ABTS IC50 = 3 mg/mL, FRAP = 4.70 μmol AAE/mL and, TAA = 18.04 μmol Fe(II)/mL). The results show also that the freeze-drying technique has a lot of potential for producing powder from KDPE with many desirable properties. The findings indicate that KDPE with a high nutritional value could be used as a component for the formulation of functional foods.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12355-022-01223-2.}, }
@article {pmid36529834, year = {2022}, author = {Kormas, K and Nikouli, E and Kousteni, V and Damalas, D}, title = {Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36529834}, issn = {1432-184X}, abstract = {Fish microbiome science is progressing fast, but it is biased toward farmed or laboratory fish species against natural fish populations, which remain considerably underinvestigated. We analyzed the midgut bacterial microbiota of 45 specimens of 12 fish species collected from the Gyaros Island marine protected area (Aegean Sea, Greece). The species belong to seven taxonomic families and are either herbivores or omnivores. Mucosa midgut bacterial diversity was assessed by amplicon metabarcoding of the 16S rRNA V3-V4 gene region. A total of 854 operational taxonomic units (OTUs) were identified. In each fish species, between 2 and 18 OTUs dominated with cumulative relative abundance ≥ 70%. Most of the dominating bacterial taxa have been reported to occur both in wild and farmed fish populations. The midgut bacterial communities were different among the 12 fish species, except for Pagrus pagrus and Pagellus erythrinus, which belong to the Sparidae family. No differentiation of the midgut bacterial microbiota was found based on feeding habits, i.e., omnivorous vs. carnivorous. Comparing wild and farmed P. pagrus midgut bacterial microbiota revealed considerable variation between them. Our results expand the gut microbiota of wild fish and support the host species effect as the more likely factor shaping intestinal bacterial microbiota.}, }
@article {pmid36528730, year = {2022}, author = {Bizic, M and Brad, T and Ionescu, D and Barbu-Tudoran, L and Zoccarato, L and Aerts, JW and Contarini, PE and Gros, O and Volland, JM and Popa, R and Ody, J and Vellone, D and Flot, JF and Tighe, S and Sarbu, SM}, title = {Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36528730}, issn = {1751-7370}, abstract = {Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2 (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3[-] as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.}, }
@article {pmid36528203, year = {2022}, author = {Jaiswal, S and Singh, DK and Shukla, P}, title = {Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {120867}, doi = {10.1016/j.envpol.2022.120867}, pmid = {36528203}, issn = {1873-6424}, abstract = {Contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due toits persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential Lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-[1], 3300-2800 cm-[1] and 785-540 cm-[1]. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.}, }
@article {pmid36524228, year = {2022}, author = {Othieno, J and Njagi, O and Masika, S and Apamaku, M and Tenge, E and Mwasa, B and Kimondo, P and Gardner, E and Von Dobschuetz, S and Muriira, J and Adul, B and Mwongela, L and Hambe, HA and Nyariki, T and Fasina, FO}, title = {Knowledge, attitudes, and practices on camel respiratory diseases and conditions in Garissa and Isiolo, Kenya.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {1022146}, pmid = {36524228}, issn = {2297-1769}, abstract = {BACKGROUND: Livestock farmers' attitudes, practices, and behaviors are major factors in infection prevention and control of animal diseases. Kenya has the fourth largest global camel population, and the industry has grown over the last two decades, transforming beyond the traditional camel-keeping areas to include peri-urban camel trade and value chain growth. The dromedary camel is resilient, and it is a preferred species in the arid and semi-arid areas (ASALs) of Kenya. However, it still faces many health and production challenges; to identify infection drivers and risky behaviors for camel respiratory illnesses and conditions in Kenya, we conducted a knowledge, attitudes, and practices (KAP) survey.<br><br>METHOD: Using a set of tools (questionnaires, key informant interviews, and focus group discussions), we interviewed camel owners, herders, agro-veterinary outlets, and other relevant value chain stakeholders in Garissa and Isiolo counties (n = 85). Data were analyzed using descriptive and analytic statistics.<br><br>RESULTS: Most camel owners/herders are male and most are relatively uneducated (85.5%). The camels were used primarily for milk and meat production, income generation, and transport. Larger herd sizes (>30 camels) and owner/herder's lack of formal education are risk factors for owner-reported respiratory illnesses in camels. Major clinical signs of respiratory conditions were coughing (85.7%), nasal discharge (59.7%), and fever (23.4%). Diseases, lack of feeds, theft, and marketing challenges are the major constraints to camel production in Kenya. Owners-herders use drugs indiscriminately and this may contribute to antimicrobial resistance challenges.<br><br>CONCLUSION: Practitioners in the camel value chain want more commitment from the government and animal health officials on support services and access to veterinary services. Watering points, grazing areas, and marketing points are the primary areas for congregating camels and have a significant potential for disease spread. Kenya camels have a massive capacity for rural and ASALs' livelihoods transformation but the identified health challenges, and other issues must be addressed. Further studies on the Kenyan camels' respiratory microbial ecology are important to understand microbial risks and reduce the burden of zoonotic infections. Intensification of risk communication and community engagement, and messaging targeted at behavior change interventions should be directed at camel value chain actors.}, }
@article {pmid36523823, year = {2022}, author = {Bernasconi, R and Lund, MA and Blanchette, ML}, title = {Non-charismatic waterbodies and ecosystem disservices: Mine pit lakes are underrepresented in the literature.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1063594}, pmid = {36523823}, issn = {1664-302X}, abstract = {Pit lakes are one of the greatest legacies of open-cut mining. Despite the potential hazards of these lakes, they represent newly formed ecosystems with great scientific and ecological potential. Although thousands of pit lakes occur on every inhabited continent, with more being created, the microbial ecology of pit lakes is relatively under-researched. We evaluated the current state of microbial research in pit lakes by performing a Web of Science search and creating a literature database. Study lakes were categorized according to location and water quality (pH and conductivity) which is a key community and environmental concern. Research technology employed in the study was also categorized. We compared research effort in lakes, rivers, and streams which are the more "charismatic" inland aquatic ecosystems. Pit lake publications on microbes from 1987 to 2022 (n = 128) were underrepresented in the literature relative to rivers and streams (n = 321) and natural lakes (n = 948). Of the 128 pit lake publications, 28 were within the field of geochemistry using indirect measures of microbial activity. Most pit lake microbial research was conducted in a few acidic lakes in Germany due to social pressure for remediation and government initiative. Relatively few studies have capitalized on emerging technology. Pit lake microbial research likely lags other more charismatic ecosystems given that they are viewed as performing "ecosystem disservices," but this is socially complex and requires further research. Improving understanding of microbial dynamics in pit lakes will allow scientists to deliver safer pit lakes to communities.}, }
@article {pmid36523636, year = {2022}, author = {Morales, C and Rojas, G and Rebolledo, C and Rojas-Herrera, M and Arias-Carrasco, R and Cuadros-Orellana, S and Maracaja-Coutinho, V and Saavedra, K and Leal, P and Lanas, F and Salazar, LA and Saavedra, N}, title = {Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {943609}, pmid = {36523636}, issn = {2235-2988}, abstract = {INTRODUCTION: In recent years, several studies have evidenced the importance of the microbiome to host physiology as metabolism regulator, along with its potential role in triggering various diseases. In this study, we analyzed the gut microbiota in hypercholesterolemic (cases) and normocholesterolemic (controls) individuals to identify characteristic microbial signature for each condition.<br><br>METHODS: Stool samples were obtained from 57 adult volunteers (27 hypercholesterolemic and 30 controls). The taxonomic profiling of microbial communities was performed using high-throughput sequencing of 16S rRNA V3-V4 amplicons, followed by data analysis using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and linear discriminant analysis (LDA) effect size (LEfSe).<br><br>RESULTS: Significant differences were observed in weight, height, body mass index (BMI) and serum levels of triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-C) between the groups (p<0.05). LEfSe showed differentially abundant prokaryotic taxa (&#x3b1;=0.05, LDA score > 2.0) in the group of hypercholesterolemic individuals (Methanosphaera, Rothia, Chromatiales, Clostridiales, Bacillaceae and Coriobacteriaceae) and controls (Faecalibacterium, Victivallis and Selenomonas) at various taxonomic levels. In addition, through the application of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2), the predominance of pathways related to biosynthesis in hypercholesterolemic patients was established, compared to controls in which degradation pathways were predominant. Finally, in the analysis of co-occurrence networks, it was possible to identify associations between the microorganisms present in both studied groups.<br><br>CONCLUSION: Our results point out to unique microbial signatures, which likely play a role on the cholesterol metabolism in the studied population.}, }
@article {pmid36523515, year = {2022}, author = {Thongthaisong, P and Kasada, M and Grossart, HP and Wollrab, S}, title = {Critical role of parasite-mediated energy pathway on community response to nutrient enrichment.}, journal = {Ecology and evolution}, volume = {12}, number = {12}, pages = {e9622}, pmid = {36523515}, issn = {2045-7758}, abstract = {Parasites form an integral part of food webs, however, they are often ignored in classic food web theory or limited to the investigation of trophic transmission pathways. Specifically, direct consumption of parasites by nonhost predators is rarely considered, while it can contribute substantially to energy flow in food webs. In aquatic systems, chytrids constitute a major group of fungal parasites whose free-living infective stages (zoospores) form a highly nutritional food source to zooplankton. Thereby, the consumption of zoospores can create an energy pathway from otherwise inedible phytoplankton to zooplankton ("mycoloop"). This parasite-mediated energy pathway might be of special importance during phytoplankton blooms dominated by inedible or toxic primary producers like cyanobacteria, which are on the rise with eutrophication and global warming. We theoretically investigated community dynamics and energy transfer in a food web consisting of an edible nonhost and an inedible host phytoplankton species, a parasitic fungus, and a zooplankton species grazing on edible phytoplankton and fungi. Food web dynamics were investigated along a nutrient gradient contrasting nonadaptive zooplankton species representative for filter feeders like cladocerans and zooplankton with the ability to actively adapt their feeding preferences like many copepod species. Overall, the importance of the mycoloop for zooplankton increases with nutrient availability. This increase is smooth for nonadaptive consumers. For adaptive consumers, we observe an abrupt shift from an almost exclusive preference for edible phytoplankton at low nutrient levels to a strong preference for parasitic fungi at high nutrient levels. The model predicts that parasitic fungi could contribute up to 50% of the zooplankton diet in nutrient-rich environments, which agrees with empirical observations on zooplankton gut content from eutrophic systems during blooms of inedible diatoms or cyanobacteria. Our findings highlight the role of parasite-mediated energy pathways for predictions of energy flow and community composition under current and future environmental change.}, }
@article {pmid36523400, year = {2022}, author = {Upadhyay, V and Suryawanshi, R and Tasoff, P and McCavitt-Malvido, M and Kumar, GR and Murray, VW and Noecker, C and Bisanz, JE and Hswen, Y and Ha, C and Sreekumar, B and Chen, IP and Lynch, SV and Ott, M and Lee, S and Turnbaugh, PJ}, title = {Mild SARS-CoV-2 infection results in long-lasting microbiota instability.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2022.12.07.519508}, pmid = {36523400}, abstract = {UNLABELLED: Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila . Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology.<br><br>IMPORTANCE: Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.}, }
@article {pmid36521745, year = {2022}, author = {Araujo, ASF and Jia, X and Miranda, ARL and de Araujo Pereira, AP and Melo, VMM and Rocha, SMB and Costa, RM and da Silva Saraiva, TC and Mendes, LW and Salles, JF}, title = {Changes in the bacterial rare biosphere after permanent application of composted tannery sludge in a tropical soil.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {137487}, doi = {10.1016/j.chemosphere.2022.137487}, pmid = {36521745}, issn = {1879-1298}, abstract = {Composted tannery sludge (CTS) promotes shifts in soil chemical properties, affecting microbial communities. Although the effect of CTS application on the bacterial community has been studied, it is unclear whether this impact discriminates between the dominant and rare species. This present study investigated how the dominant and rare bacterial communities respond over time to different concentrations of CTS application (0, 2.5, 5, 10, and 20 tons/ha) for 180 days. The richness of operational taxonomic units (OTU) was 30-fold higher in the rare than in the dominant biosphere. While some phyla shifted their relative abundance differently in the dominant and rare biosphere, some genera increased their relative abundance under higher CTS concentrations, such as Nocardioides (∼100%), Rubrobacter (∼300%), and Nordella (∼400%). Undominated processes largely governed the dominant biosphere (76.97%), followed by homogeneous (12.51%) and variable (8.03%) selection, and to a lesser extent, the dispersal limitation (2.48%). The rare biosphere was driven by the CTS application as evidenced by the exclusively homogeneous selection (100%). This study showed that the rare biosphere was more sensitive to changes in soil chemical parameters due to CTS application, which evidences the importance explore this portion of the bacterial community for its biotechnological use in contaminated soils.}, }
@article {pmid36520668, year = {2022}, author = {Ibberson, CB and Barraza, JP and Holmes, AL and Cao, P and Whiteley, M}, title = {Precise spatial structure impacts antimicrobial susceptibility of S. aureus in polymicrobial wound infections.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {51}, pages = {e2212340119}, doi = {10.1073/pnas.2212340119}, pmid = {36520668}, issn = {1091-6490}, abstract = {A hallmark of microbial ecology is that interactions between members of a community shape community function. This includes microbial communities in human infections, such as chronic wounds, where interactions can result in more severe diseases. Staphylococcus aureus is the most common organism isolated from human chronic wound infections and has been shown to have both cooperative and competitive interactions with Pseudomonas aeruginosa. Still, despite considerable study, most interactions between these microbes have been characterized using in vitro well-mixed systems, which do not recapitulate the infection environment. Here, we characterized interactions between S. aureus and P. aeruginosa in chronic murine wounds, focusing on the role that both macro- and micro-scale spatial structures play in disease. We discovered that S. aureus and P. aeruginosa coexist at high cell densities in murine wounds. High-resolution imaging revealed that these microbes establish a patchy distribution, only occupying 5 to 25% of the wound volume. Using a quantitative framework, we identified a precise spatial structure at both the macro (mm)- and micro (µm)-scales, which was largely mediated by P. aeruginosa production of the antimicrobial 2-heptyl-4-hydroxyquinoline N-oxide, while the antimicrobial pyocyanin had no impact. Finally, we discovered that this precise spatial structure enhances S. aureus tolerance to aminoglycoside antibiotics but not vancomycin. Our results provide mechanistic insights into the biogeography of S. aureus and P. aeruginosa coinfected wounds and implicate spatial structure as a key determinant of antimicrobial tolerance in wound infections.}, }
@article {pmid36520387, year = {2023}, author = {Melayah, D and Bontemps, Z and Bruto, M and Nguyen, A and Oger, P and Hugoni, M}, title = {Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {17-35}, pmid = {36520387}, issn = {1940-6029}, abstract = {High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.}, }
@article {pmid36520176, year = {2022}, author = {Martínez-Yáñez, MG and Silva-Ortega, CO and Hernández-Aranda, VA and Vallejo-Pérez, MR and Alcalá-Briseño, R and Vega-Manriquez, DX and Aguilar-Benítez, G and Jarquin-Gálvez, R and Lara-Ávila, JP}, title = {Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36520176}, issn = {1432-184X}, abstract = {Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of agroecological and circular economy approaches.}, }
@article {pmid36519160, year = {2022}, author = {Frąc, M and Hannula, ES and Bełka, M and Salles, JF and Jedryczka, M}, title = {Soil mycobiome in sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1033824}, doi = {10.3389/fmicb.2022.1033824}, pmid = {36519160}, issn = {1664-302X}, abstract = {The soil microbiome contributes to several ecosystem processes. It plays a key role in sustainable agriculture, horticulture and forestry. In contrast to the vast number of studies focusing on soil bacteria, the amount of research concerning soil fungal communities is limited. This is despite the fact that fungi play a crucial role in the cycling of matter and energy on Earth. Fungi constitute a significant part of the pathobiome of plants. Moreover, many of them are indispensable to plant health. This group includes mycorrhizal fungi, superparasites of pathogens, and generalists; they stabilize the soil mycobiome and play a key role in biogeochemical cycles. Several fungal species also contribute to soil bioremediation through their uptake of high amounts of contaminants from the environment. Moreover, fungal mycelia stretch below the ground like blood vessels in the human body, transferring water and nutrients to and from various plants. Recent advances in high-throughput sequencing combined with bioinformatic tools have facilitated detailed studies of the soil mycobiome. This review discusses the beneficial effects of soil mycobiomes and their interactions with other microbes and hosts in both healthy and unhealthy ecosystems. It may be argued that studying the soil mycobiome in such a fashion is an essential step in promoting sustainable and regenerative agriculture.}, }
@article {pmid36518175, year = {2022}, author = {Tang, Q and Huang, J and Zhang, S and Qin, H and Dong, Y and Wang, C and Li, D and Zhou, R}, title = {Characterizing the correlation between species/strain-specific starter with community assembly and metabolic regulation in Xiaoqu Pei.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100170}, doi = {10.1016/j.crmicr.2022.100170}, pmid = {36518175}, issn = {2666-5174}, abstract = {Studying the correlation between microbiome metabolism and flavor of fermented foods has garnered significant attention recently. Understanding the contribution of metabolic regulation and environmental stress to microecosystems is essential for exploring the mechanisms of action of traditional fermented foods. Here, the interaction between microbial communities was investigated using a Xiaoqu fermentation system, processed as "simulative microecosystems," in which starters were composed of Rhizopus-specific species/strains, Meyerozyma guilliermondii, and Bacillus licheniformis. The differences between community succession and metabolites were also explored. The results indicated that Rhizopus species/strain specificity affected starch hydrolyzation, resulting in a remarkable difference in the type and content of organic acids. This further suggested that the differences in nutrient abundance and organic acids influenced the colonization of microorganisms in the fermentation system, thereby influencing the succession of their communities. The fungi in the community predominantly originated from starters, whereas the bacteria were derived from both the environment and starter. Environmentally colonized microbes were the major contributors to the co-occurrence network and were strongly correlated with network. Regional characteristics of fermented foods were closely related to environmental microbes. These results contribute to the understanding of microbial assembly and flavor metabolism in fermented foods and provide strategies for quality regulation.}, }
@article {pmid36516248, year = {2022}, author = {Diaz-Tang, G and Meneses, EM and Patel, K and Mirkin, S and García-Diéguez, L and Pajon, C and Barraza, I and Patel, V and Ghali, H and Tracey, AP and Blanar, CA and Lopatkin, AJ and Smith, RP}, title = {Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics.}, journal = {Science advances}, volume = {8}, number = {50}, pages = {eadd0924}, doi = {10.1126/sciadv.add0924}, pmid = {36516248}, issn = {2375-2548}, abstract = {Understanding the mechanisms by which populations of bacteria resist antibiotics has implications in evolution, microbial ecology, and public health. The inoculum effect (IE), where antibiotic efficacy declines as the density of a bacterial population increases, has been observed for multiple bacterial species and antibiotics. Several mechanisms to account for IE have been proposed, but most lack experimental evidence or cannot explain IE for multiple antibiotics. We show that growth productivity, the combined effect of growth and metabolism, can account for IE for multiple bactericidal antibiotics and bacterial species. Guided by flux balance analysis and whole-genome modeling, we show that the carbon source supplied in the growth medium determines growth productivity. If growth productivity is sufficiently high, IE is eliminated. Our results may lead to approaches to reduce IE in the clinic, help standardize the analysis of antibiotics, and further our understanding of how bacteria evolve resistance.}, }
@article {pmid36516075, year = {2022}, author = {Hu, A and Meng, F and Tanentzap, AJ and Jang, KS and Wang, J}, title = {Dark Matter Enhances Interactions within Both Microbes and Dissolved Organic Matter under Global Change.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c05052}, pmid = {36516075}, issn = {1520-5851}, abstract = {There are vast but uncharacterized microbial taxa and chemical metabolites (that is, dark matter) across the Earth's ecosystems. A lack of knowledge about dark matter hinders a complete understanding of microbial ecology and biogeochemical cycles. Here, we examine sediment bacteria and dissolved organic matter (DOM) in 300 microcosms along experimental global change gradients in subtropical and subarctic climate zones of China and Norway, respectively. We develop an indicator to quantify the importance of dark matter by comparing co-occurrence network patterns with and without dark matter in bacterial or DOM assemblages. In both climate zones, dark matter constitutes approximately 30-56% of bacterial taxa and DOM metabolites and changes connectivity within bacterial and DOM assemblages by between -15.5 and +61.8%. Dark matter is generally more important for changing network connectivity within DOM assemblages than those of microbes, especially in the subtropical zone. However, the importance of dark matter along global change gradients is strongly correlated between bacteria and DOM and consistently increased toward higher primary productivity because of increasing temperatures and nutrient enrichment. Our findings highlight the importance of microbial and chemical dark matter for changing biogeochemical interactions under global change.}, }
@article {pmid36511762, year = {2022}, author = {Leite, MFA and Liu, B and Cardozo, EG and E Silva, HR and Luz, RL and Muchavisoy, KHM and Moraes, FHR and Rousseau, GX and Kowalchuk, G and Gehring, C and Kuramae, EE}, title = {Microbiome resilience of Amazonian forests: agroforest divergence to bacteria and secondary forest succession convergence to fungi.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16556}, pmid = {36511762}, issn = {1365-2486}, abstract = {An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant-soil interactions of the natural mature forest. However, the role of microbial community in tropical AFS remains largely unknown. This knowledge is crucial for evaluating the sustainability of AFS and practices given the key role of microbes in the aboveground-belowground interactions. The current study, by comparing different AFS and successions of secondary and mature forests, showed that AFS fostered distinct groups of bacterial community, diverging from the mature forests, likely a result of management practices while secondary forests converged to the same soil microbiome found in the mature forest, by favoring the same groups of fungi. Model simulations reveal that AFS would require profound changes in aboveground biomass and in soil factors to reach the same microbiome found in mature forests. In summary AFS practices did not result in ecosystems mimicking natural forest plant-soil interactions but rather reshaped the ecosystem to a completely different relation between aboveground biomass, soil abiotic properties, and the soil microbiome.}, }
@article {pmid36511717, year = {2022}, author = {Chen, Y and Lyu, Y and Zhang, J and Li, Q and Lyu, L and Zhou, Y and Kong, J and Zeng, X and Zhang, S and Li, J}, title = {Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0333822}, doi = {10.1128/spectrum.03338-22}, pmid = {36511717}, issn = {2165-0497}, abstract = {Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.}, }
@article {pmid36511696, year = {2022}, author = {Higgins, O and Chueiri, A and O'Connor, L and Lahiff, S and Burke, L and Morris, D and Pfeifer, NM and Santamarina, BG and Berens, C and Menge, C and Caniça, M and Manageiro, V and Kisand, V and Hassan, MM and Gardner, B and van Vliet, AHM and La Ragione, RM and Gonzalez-Zorn, B and Smith, TJ}, title = {Portable Differential Detection of CTX-M ESBL Gene Variants, blaCTX-M-1 and blaCTX-M-15, from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0331622}, doi = {10.1128/spectrum.03316-22}, pmid = {36511696}, issn = {2165-0497}, abstract = {Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an increasing AMR public health issue with the transmission between animals and humans via zoonotic pathogens now a major area of interest. Accurate and timely identification of ESBL-expressing E. coli CTX-M variants is essential for disease monitoring, targeted antibiotic treatment and infection control. This study details the first report of portable diagnostics technology for the rapid differential detection of CTX-M AMR markers blaCTX-M-1 and blaCTX-M-15, facilitating improved identification and surveillance of these closely related variants. Further application of this portable internally controlled multiplex CTX-M-1/15 LEC-LAMP assay will provide new information on the transmission and prevalence of these CTX-M ESBL alleles. Furthermore, this transferable diagnostic technology can be applied to other new and emerging relevant AMR markers of interest providing more efficient and specific portable pathogen detection for improved epidemiological surveillance.}, }
@article {pmid36511682, year = {2022}, author = {Teng, W and Liao, B and Chen, M and Shu, W}, title = {Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0214522}, doi = {10.1128/spectrum.02145-22}, pmid = {36511682}, issn = {2165-0497}, abstract = {Bacterial evolution is characterized by strong purifying selection as well as rapid adaptive evolution in changing environments. In this context, the genomic GC content (genomic GC) varies greatly but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses. To illuminate the evolutionary mechanisms of the genomic GC, we analyzed the base composition and functional inventory of 11,083 representative genomes. A phylogenetically constrained bimodal distribution of the genomic GC, which mainly originated from parallel divergences in the early evolution, was demonstrated. Such variation of the genomic GC can be well explained by DNA replication and repair (DRR), in which multiple pathways correlate with the genomic GC. Furthermore, the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes. Our findings support that the mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC. This highlights the importance of indirect effects of natural selection, which indicates a new model for bacterial evolution. IMPORTANCE GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously. Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism. This would imply that, when thinking about the evolution of life, diverse processes of adaptation exist, and combined effects of natural selection should be considered.}, }
@article {pmid36510309, year = {2022}, author = {Boekhorst, J and Venlet, N and Procházková, N and Hansen, ML and Lieberoth, CB and Bahl, MI and Lauritzen, L and Pedersen, O and Licht, TR and Kleerebezem, M and Roager, HM}, title = {Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {223}, pmid = {36510309}, issn = {2049-2618}, abstract = {BACKGROUND: It has been hypothesised that the gut microbiota causally affects obesity via its capacity to extract energy from the diet. Yet, evidence elucidating the role of particular human microbial community structures and determinants of microbiota-dependent energy harvest is lacking.<br><br>RESULTS: Here, we investigated whether energy extraction from the diet in 85 overweight adults, estimated by dry stool energy density, was associated with intestinal transit time and variations in microbial community diversity and overall structure stratified as enterotypes. We hypothesised that a slower intestinal transit would allow for more energy extraction. However, opposite of what we expected, the stool energy density was positively associated with intestinal transit time. Stratifications into enterotypes showed that individuals with a Bacteroides enterotype (B-type) had significantly lower stool energy density, shorter intestinal transit times, and lower alpha-diversity compared to individuals with a Ruminococcaceae enterotype (R-type). The Prevotella (P-type) individuals appeared in between the B- and R-type. The differences in stool energy density between enterotypes were not explained by differences in habitual diet, intake of dietary fibre or faecal bacterial cell counts. However, the R-type individuals showed higher urinary and faecal levels of microbial-derived proteolytic metabolites compared to the B-type, suggesting increased colonic proteolysis in the R-type individuals. This could imply a less effective colonic energy extraction in the R-type individuals compared to the B-type individuals. Notably, the R-type had significantly lower body weight compared to the B-type.<br><br>CONCLUSIONS: Our findings suggest that gut microbial energy harvest is diversified among individuals by intestinal transit time and associated gut microbiome ecosystem variations. A better understanding of these associations could support the development of personalised nutrition and improved weight-loss strategies. Video Abstract.}, }
@article {pmid36509943, year = {2022}, author = {Li, W and Ma, ZS}, title = {The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-022-02148-9}, pmid = {36509943}, issn = {1432-184X}, abstract = {The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies.}, }
@article {pmid36506396, year = {2022}, author = {Daba, G and Berecha, G and Lievens, B and Hundera, K and Helsen, K and Honnay, O}, title = {Contrasting coffee leaf rust epidemics between forest coffee and semi-forest coffee agroforestry systems in SW-Ethiopia.}, journal = {Heliyon}, volume = {8}, number = {12}, pages = {e11892}, pmid = {36506396}, issn = {2405-8440}, abstract = {Ethiopian Arabica coffee is produced in different agroforestry systems which differ in forest management intensity. In forest coffee systems (FC), coffee shrubs grow naturally in the understory of Afromontane forests with little human intervention, whereas in semi-forest coffee systems (SFC) thinning of the canopy and removal of the understory is applied. Coffee leaf rust (CLR) disease is a growing concern for coffee agroforestry, but to what extent infection pressure is affected by management intensity is poorly known. Here we assessed CLR infection through time across FC and SFC systems in SW-Ethiopia. CLR infection was significantly higher for SFC, with a gradual reduction of this difference during the beginning of dry season (November) through main rainy season of (July). Our findings also demonstrated that CLR infections were significantly lower in the FC system as compared to SFC system in both years 2015/16 and 2020/21. The higher CLR infection was partly explained by lower crown cover and higher human impact. We expect that reduced wind speed and droplet penetration under closed canopies and reduced human-facilitated spore dispersal are the dominating mechanisms behind lower CLR infection in FC systems, yet lower coffee density in FC may also play a role. Overall, our results indicate that although higher management intensity still generally results in higher total yields per hectare, proportionally larger losses due to CLR infection can be expected. Therefore, introducing more coffee genetic diversity, screening resistant coffee varieties and increasing canopy cover in the SFC will mitigate the CLR disease pressure and guarantee the sustainability of higher yields of the system in the future. Also, lower yields in the FC will be rewarded through providing price premiums so that farmers instantly get a higher price for their lower yield, guaranteeing livelihoods.}, }
@article {pmid36504693, year = {2022}, author = {Amano, C and Zhao, Z and Sintes, E and Reinthaler, T and Stefanschitz, J and Kisadur, M and Utsumi, M and Herndl, GJ}, title = {Limited carbon cycling due to high-pressure effects on the deep-sea microbiome.}, journal = {Nature geoscience}, volume = {15}, number = {12}, pages = {1041-1047}, pmid = {36504693}, issn = {1752-0894}, abstract = {Deep-sea microbial communities are exposed to high-pressure conditions, which has a variable impact on prokaryotes depending on whether they are piezophilic (that is, pressure-loving), piezotolerant or piezosensitive. While it has been suggested that elevated pressures lead to higher community-level metabolic rates, the response of these deep-sea microbial communities to the high-pressure conditions of the deep sea is poorly understood. Based on microbial activity measurements in the major oceanic basins using an in situ microbial incubator, we show that the bulk heterotrophic activity of prokaryotic communities becomes increasingly inhibited at higher hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was about one-third of that measured in the same community at atmospheric pressure conditions. In the bathypelagic zone-between 1,000 and 4,000 m depth-~85% of the prokaryotic community was piezotolerant and ~5% of the prokaryotic community was piezophilic. Despite piezosensitive-like prokaryotes comprising only ~10% (mainly members of Bacteroidetes, Alteromonas) of the deep-sea prokaryotic community, the more than 100-fold metabolic activity increase of these piezosensitive prokaryotes upon depressurization leads to high apparent bulk metabolic activity. Overall, the heterotrophic prokaryotic activity in the deep sea is likely to be substantially lower than hitherto assumed, with major impacts on the oceanic carbon cycling.}, }
@article {pmid36503688, year = {2022}, author = {Delgado-Baquerizo, M and Hu, HW and Maestre, FT and Guerra, CA and Eisenhauer, N and Eldridge, DJ and Zhu, YG and Chen, QL and Trivedi, P and Du, S and Makhalanyane, TP and Verma, JP and Gozalo, B and Ochoa, V and Asensio, S and Wang, L and Zaady, E and Illán, JG and Siebe, C and Grebenc, T and Zhou, X and Liu, YR and Bamigboye, AR and Blanco-Pastor, JL and Duran, J and Rodríguez, A and Mamet, S and Alfaro, F and Abades, S and Teixido, AL and Peñaloza-Bojacá, GF and Molina-Montenegro, MA and Torres-Díaz, C and Perez, C and Gallardo, A and García-Velázquez, L and Hayes, PE and Neuhauser, S and He, JZ}, title = {The global distribution and environmental drivers of the soil antibiotic resistome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {219}, pmid = {36503688}, issn = {2049-2618}, abstract = {BACKGROUND: Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth's largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs.<br><br>RESULTS: We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs.<br><br>CONCLUSIONS: Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract.}, }
@article {pmid36503639, year = {2022}, author = {Hodžić, A and Dheilly, NM and Cabezas-Cruz, A and Berry, D}, title = {The helminth holobiont: a multidimensional host-parasite-microbiota interaction.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2022.11.012}, pmid = {36503639}, issn = {1471-5007}, abstract = {Gastrointestinal helminths have developed multiple mechanisms by which they manipulate the host microbiome to make a favorable environment for their long-term survival. While the impact of helminth infections on vertebrate host immunity and its gut microbiota is relatively well studied, little is known about the structure and functioning of microbial populations supported by metazoan parasites. Here we argue that an integrated understanding of the helminth-associated microbiome and its role in the host disease pathogenesis may facilitate the discovery of specific microbial and/or genetic patterns critical for parasite biology and subsequently pave the way for the development of alternative control strategies against parasites and parasitic disease.}, }
@article {pmid36502425, year = {2022}, author = {Ye, F and Sun, Z and Moore, SS and Wu, J and Hong, Y and Wang, Y}, title = {Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36502425}, issn = {1432-184X}, abstract = {Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.}, }
@article {pmid36500505, year = {2022}, author = {Ben Rejeb, I and Charfi, I and Baraketi, S and Hached, H and Gargouri, M}, title = {Bread Surplus: A Cumulative Waste or a Staple Material for High-Value Products?.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {23}, pages = {}, doi = {10.3390/molecules27238410}, pmid = {36500505}, issn = {1420-3049}, abstract = {Food waste has been widely valorized in the past years in order to develop eco-friendly materials. Among others, bread waste is currently of increasing interest, as it is considered a huge global issue with serious environmental impacts and significant economic losses that have become even greater in the post-pandemic years due to an increase in cereal prices, which has led to higher production costs and bread prices. Owing to its richness in polysaccharides, bread waste has been previously studied for its physico-chemical characteristics and its numerous biotechnological applications. The present review highlights the re-use of bread waste and its valorization as a valuable resource by making value-added products through numerous technological processes to increase efficiency at all stages. Many research studies reporting several transformation methods of surplus bread into ethanol, lactic acid, succinic acid, biohydrogen, hydroxymethylfurfural, proteins and pigments, glucose-fructose syrup, aroma compounds, and enzymes are widely discussed. The wide variety of suggested applications for recycling bread waste provides significant insights into the role of technology development in potentially maximizing resource recovery and consequently contributing to environmental performance by reducing the amount of bread waste in landfills.}, }
@article {pmid36500302, year = {2022}, author = {Kuttithodi, AM and Nikhitha, D and Jacob, J and Narayanankutty, A and Mathews, M and Olatunji, OJ and Rajagopal, R and Alfarhan, A and Barcelo, D}, title = {Antioxidant, Antimicrobial, Cytotoxicity, and Larvicidal Activities of Selected Synthetic Bis-Chalcones.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {23}, pages = {}, doi = {10.3390/molecules27238209}, pmid = {36500302}, issn = {1420-3049}, abstract = {Plants are known to have numerous phytochemicals and other secondary metabolites with numerous pharmacological and biological properties. Among the various compounds, polyphenols, flavonoids, anthocyanins, alkaloids, and terpenoids are the predominant ones that have been explored for their biological potential. Among these, chalcones and bis-chalcones are less explored for their biological potential under in vitro experiments, cell culture models, and animal studies. In the present study, we evaluated six synthetic bis-chalcones that were different in terms of their aromatic cores, functional group substitution, and position of substitutions. The results indicated a strong antioxidant property in terms of DPPH and ABTS radical-scavenging potentials and ferric-reducing properties. In addition, compounds 1, 2, and 4 exhibited strong antibacterial activities against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella enteritidis. The disc diffusion assay values were indicative of the antibacterial properties of these compounds. Overall, the study indicated the antioxidant and antimicrobial properties of the compounds. Our preliminary studies point to the potential of this class of compounds for further in vivo investigation.}, }
@article {pmid36495359, year = {2022}, author = {Liu, W and Qiu, K and Xie, Y and Huang, Y and Wang, R and Li, H and Meng, W and He, Y and Li, Y and Li, H and Zhao, P and Yang, Y}, title = {High-Throughput Absolute Quantification Sequencing Reveals that a Combination of Leguminous Shrubs Is Effective in Driving Soil Bacterial Diversity During the Process of Desertification Reversal.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36495359}, issn = {1432-184X}, abstract = {Desertification leads to the extreme fragility of ecosystems and seriously threatens ecosystem functioning in desert areas. The planting of xerophytes, especially leguminous shrubs, is an effective and common means to reverse desertification. Soil microorganisms play a crucial role in nutrient cycling and energy flow in ecosystems. However, the effects of introducing leguminous shrubs on soil microbial diversity and the relevant mechanisms are not clear. Here, we employed the high-throughput absolute quantification 16S rRNA sequencing method to analyze the diversity of soil bacteria in sand-fixing areas of mixed shrublands with three combinations of shrubs, i.e., C. korshinskii × Corethrodendron scoparium (CaKCoS), C. korshinskii × Calligonum mongolicum (CaKCaM), and C. scoparium × C. mongolicum (CoSCaM), in the south of the Mu Us Sandy Land, China. This area suffered from moving dunes 20 years ago, but after introducing these shrubs to fix the dunes, the ecosystem was restored. Additionally, the effects of soil physicochemical properties on soil bacterial composition and diversity were analyzed with redundancy analysis (RDA) and structural equation modeling (SEM). It was found that the Shannon index of soil bacteria in CaKCoS was significantly higher than that in CaKCaM and CoSCaM, and the abundance of the dominant phyla, including Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Thaumarchaeota, Armatimonadetes, candidate_division_WPS-1, and Nitrospirae, increased significantly in CaKCoS and CaKCaM compared to that in CoSCaM. RDA showed that the majority of soil properties, such as total nitrogen (TN), available potassium (AK), N:P ratio, soil moisture (SM), and available phosphorus (AP), were important soil environmental factors affecting the abundance of the dominant phyla, and RDA1 and RDA2 accounted for 56.66% and 2.35% of the total variation, respectively. SEM showed that the soil bacterial α-diversity was positively affected by the soil organic carbon (SOC), N:P ratio, and total phosphorus (TP). Moreover, CaKCoS had higher SM, total carbon (TC), total potassium (TK), and AP than CaKCaM and CoSCaM. Collectively, these results highlight a conceptual framework in which the combination of leguminous shrubs can effectively drive soil bacterial diversity by improving soil physicochemical properties and maintaining ecosystem functioning during desertification reversal.}, }
@article {pmid36482478, year = {2022}, author = {Hodžić, A and Alić, A and Spahić, A and Harl, J and Beck, R}, title = {Genetic diversity of Echinococcus granulosus sensu lato from animals and humans in Bosnia and Herzegovina.}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {457}, pmid = {36482478}, issn = {1756-3305}, abstract = {BACKGROUND: Cystic echinococcosis (CE) is recognized as one of the most prevalent zoonotic diseases in Bosnia and Herzegovina. However, no systemic investigation of the genetic diversity of Echinococcus granulosus sensu lato circulating among animals and humans in the country has been performed to date.<br><br>METHODS: In this preliminary study, we analysed one cyst each from 36 sheep, 27 cattle, 27 pigs, 11 wild boars and 16 human patients for amplification and partial sequencing of the adenosine triphosphate 6 (atp6) and cytochrome c oxidase 1 (cox1) genes. The host species, fertility rate and organ cyst location were recorded for each subject involved in the study.<br><br>RESULTS: Overall, the atp6 gene was successfully amplified and sequenced from 110 samples, while 96 of the PCRs for cox1 were positive. Three zoonotic genotypes of E. granulosus sensu stricto (G1 and G3) and Echinococcus canadensis (G7) were identified in our isolates based on analyses of the atp6 gene. These genotypes were represented by 11 different genetic variants (haplotypes), six of which were identified for the first time in the present study.<br><br>CONCLUSIONS: This study demonstrates, for the first time, that CE in Bosnia and Herzegovina is predominantly caused by E. granulosus sensu stricto and E. canadensis clusters, which exhibited a lower genetic diversity compared to isolates from other European countries. Further molecular studies employing other mitochondrial and nuclear genes are required to better understand the transmission cycles of E. granulosus sensu stricto among intermediate and definitive hosts in the country.}, }
@article {pmid36480164, year = {2022}, author = {Engelberts, JP and Robbins, SJ and Herbold, CW and Moeller, FU and Jehmlich, N and Laffy, PW and Wagner, M and Webster, NS}, title = {Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16302}, pmid = {36480164}, issn = {1462-2920}, abstract = {Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterisation of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterised a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provides the framework to adopt I. basta as a model organism for studying host-microbe interactions and provides a basis for in-depth physiological experiments. This article is protected by copyright. All rights reserved.}, }
@article {pmid36479626, year = {2022}, author = {Geerinck, MWJ and Van Hee, S and Gloder, G and Crauwels, S and Colazza, S and Jacquemyn, H and Cusumano, A and Lievens, B}, title = {Diversity and composition of the microbiome associated with eggs of the Southern green stinkbug, Nezara viridula (Hemiptera: Pentatomidae).}, journal = {MicrobiologyOpen}, volume = {11}, number = {6}, pages = {e1337}, doi = {10.1002/mbo3.1337}, pmid = {36479626}, issn = {2045-8827}, abstract = {Although microbial communities of insects from larval to adult stage have been increasingly investigated in recent years, little is still known about the diversity and composition of egg-associated microbiomes. In this study, we used high-throughput amplicon sequencing and quantitative PCR to get a better understanding of the microbiome of insect eggs and how they are established using the Southern green stinkbug Nezara viridula (L.) (Hemiptera: Pentatomidae) as a study object. First, to determine the bacterial community composition, egg masses from two natural populations in Belgium and Italy were examined. Subsequently, microbial community establishment was assessed by studying stinkbug eggs of different ages obtained from laboratory strains (unlaid eggs collected from the ovaries, eggs less than 24 h old, and eggs collected 4 days after oviposition). Both the external and internal egg-associated microbiomes were analyzed by investigating egg washes and surface-sterilized washed eggs, respectively. Eggs from the ovaries were completely devoid of bacteria, indicating that egg-associated bacteria were deposited on the eggs during or after oviposition. The bacterial diversity of deposited eggs was very low, with on average 6.1 zero-radius operational taxonomic units (zOTUs) in the external microbiome and 1.2 zOTUs in internal samples of egg masses collected from the field. Bacterial community composition and density did not change significantly over time, suggesting limited bacterial growth. A Pantoea-like symbiont previously found in the midgut of N. viridula was found in every sample and generally occurred at high relative and absolute densities, especially in the internal egg samples. Additionally, some eggs harbored a Sodalis symbiont, which has previously been found in the abdomen of several insects, but so far not in N. viridula populations. We conclude that the egg-associated bacterial microbiome of N. viridula is species-poor and dominated by a few symbionts, particularly the species-specific obligate Pantoea-like symbiont.}, }
@article {pmid36478428, year = {2022}, author = {Lee, JS and Lee, SM and Son, HS and Yoon, YN and Shin, JE and Sul, WJ and Yu, DA and Choe, YB and Lee, YW}, title = {Analysis of the Microbiome of the Ear Canal in Normal Individuals and Patients with Chronic Otitis Externa.}, journal = {Annals of dermatology}, volume = {34}, number = {6}, pages = {461-471}, doi = {10.5021/ad.22.153}, pmid = {36478428}, issn = {2005-3894}, support = {//Konkuk University/Korea ; }, abstract = {BACKGROUND: Recently, microbiome research has been actively conducted for various skin areas. However, no study has yet compared the microbiome of bacteria and fungi in the ear canal of healthy individuals and patients with chronic otitis externa in Korea.<br><br>OBJECTIVE: This study aimed to investigate the difference in the distribution of fungal and bacterial microbial communities in ear canal samples of healthy individuals and patients with chronic otitis externa.<br><br>METHODS: In 24 patients with bilateral chronic otitis externa and 24 healthy controls, cotton swabs were used to obtain samples from the bilateral ear canal. To characterize the fungal and bacterial communities, we sequenced and analyzed the 16S rRNA V4-V5 and ITS1 regions using Quantitative Insights into Microbial Ecology 2, respectively.<br><br>RESULTS: The alpha diversity analysis for bacteria and fungi confirmed that both richness and evenness decreased in the patient group. The beta diversity analysis for bacteria confirmed that these parameters differed between the control and patient groups. The beta diversity analysis for fungi showed no difference between the groups.<br><br>CONCLUSION: We observed different skin microbiomes in the patients with chronic otitis externa compared with those in the healthy individuals.}, }
@article {pmid36478022, year = {2022}, author = {Watson, M and May, G and Bushley, KE}, title = {Sources of Fungal Symbionts in the Microbiome of a Mobile Insect Host, Spodoptera frugiperda.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36478022}, issn = {1432-184X}, abstract = {The sources of fungal symbionts of insects are not well understood, yet the acquisition and assembly of fungal communities in mobile insect hosts have important implications for the ecology of migratory insects and their plant hosts. To determine potential sources of fungi associated with the fall armyworm (Spodoptera frugiperda), we characterized the fungal communities associated with four different ecological compartments (insects, infested leaves, uninfested leaves, and soil) and estimated the contributions of each of these potential sources to the insect's fungal microbiome. Results show that insect fungal community composition was distinct from and more varied than the composition of fungal communities in the environment of those insects (plants and soil). Among the sources evaluated, on average we found a surprisingly large apparent contribution from other congeneric S. frugiperda insect larvae (ca. 25%) compared to the contribution from soil or plant sources (< 5%). However, a large proportion of the insect microbiome could not be attributed to the sampled sources and was instead attributed to unknown sources (ca. 50%). Surprisingly, we found little evidence for exchange of fungal taxa, with the exception of a Fusarium oxysporum and a Cladosporium sp. OTU, between larvae and the infested leaves on which they fed. Together, our results suggest that mobile insects such as S. frugiperda obtain their fungal symbionts from a variety of sources, not limited to plants and soil, but including conspecific insects and other unsampled environmental sources, and that transmission among insects may play an important role in acquisition of fungal symbionts.}, }
@article {pmid36399337, year = {2022}, author = {Janssen, K and Krasenbrink, J and Strangfeld, S and Kroheck, S and Josten, M and Engeser, M and Bierbaum, G}, title = {Elucidation of the Bridging Pattern of the Lantibiotic Pseudomycoicidin.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {e202200540}, doi = {10.1002/cbic.202200540}, pmid = {36399337}, issn = {1439-7633}, abstract = {Lantibiotics are post-translationally modified antibiotic peptides with lanthionine thioether bridges that represent potential alternatives to conventional antibiotics. The lantibiotic pseudomycoicidin is produced by Bacillus pseudomycoides DSM 12442 and is effective against many Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. While prior work demonstrated that pseudomycoicidin possesses one disulfide bridge and four thioether bridges, the ring topology has so far remained unclear. Here, we analyzed several pseudomycoicidin analogues that are affected in ring formation via MALDI-TOF-MS and tandem mass spectrometry with regard to their dehydration and fragmentation patterns, respectively. As a result, we propose a bridging pattern involving Thr8 and Cys13, Thr10 and Cys16, Ser18 and Cys21, and Ser20 and Cys26, thus, forming two double ring systems. Additionally, we localized the disulfide bridge to connect Cys3 and Cys7 and, therefore, fully elucidated the bridging pattern of pseudomycoicidin.}, }
@article {pmid36475832, year = {2022}, author = {Jens, JN and Breiner, DJ and Neve, RL and Fiebig, MM and Phelan, VV}, title = {MBRA-2: a Modified Chemostat System to Culture Biofilms.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0292822}, doi = {10.1128/spectrum.02928-22}, pmid = {36475832}, issn = {2165-0497}, abstract = {Culture-dependent approaches for investigating microbial ecology aim to model the nutrient content of specific environments by simplifying the system for high-resolution molecular analysis. These in vitro systems are enticing due to their increased throughput compared to animal models, flexibility in modulating nutrient content and community composition, scaling of culture volume to isolate biological molecules, and control of environmental parameters, such as temperature, humidity, and nutrient flow. However, different devices are used to investigate homogenous, planktonic microbial communities and heterogeneous biofilms. Here, we present the minibioreactor array 2 (MBRA-2) with media rails, a benchtop multireactor system derived from the MBRA system that enables researchers to use the same system to grow planktonic and biofilm cultures. We simplified flow through the system and reduced contamination, leakage, and time required for array assembly by designing and implementing a reusable media rail to replace the branched tubing traditionally used to convey media through chemostat arrays. Additionally, we altered the structure of the six-bioreactor strip to incorporate a removable lid to provide easy access to the bioreactor wells, enabling biofilm recovery and thorough cleaning for reuse. Using Pseudomonas aeruginosa, a model biofilm-producing organism, we show that the technical improvements of the MBRA-2 for biofilms growth does not disrupt the function of the bioreactor array. IMPORTANCE The MBRA-2 with media rails provides an accessible system for investigators to culture heterogenous, suspended biofilms under constant flow.}, }
@article {pmid36475750, year = {2022}, author = {Wollein Waldetoft, K and Sundius, S and Kuske, R and Brown, SP}, title = {Defining the Benefits of Antibiotic Resistance in Commensals and the Scope for Resistance Optimization.}, journal = {mBio}, volume = {}, number = {}, pages = {e0134922}, doi = {10.1128/mbio.01349-22}, pmid = {36475750}, issn = {2150-7511}, abstract = {Antibiotic resistance is a major medical and public health challenge, characterized by global increases in the prevalence of resistant strains. The conventional view is that all antibiotic resistance is problematic, even when not in pathogens. Resistance in commensal bacteria poses risks, as resistant organisms can provide a reservoir of resistance genes that can be horizontally transferred to pathogens or may themselves cause opportunistic infections in the future. While these risks are real, we propose that commensal resistance can also generate benefits during antibiotic treatment of human infection, by promoting continued ecological suppression of pathogens. To define and illustrate this alternative conceptual perspective, we use a two-species mathematical model to identify the necessary and sufficient ecological conditions for beneficial resistance. We show that the benefits are limited to species (or strain) interactions where commensals suppress pathogen growth and are maximized when commensals compete with, rather than prey on or otherwise exploit pathogens. By identifying benefits of commensal resistance, we propose that rather than strictly minimizing all resistance, resistance management may be better viewed as an optimization problem. We discuss implications in two applied contexts: bystander (nontarget) selection within commensal microbiomes and pathogen treatment given polymicrobial infections. IMPORTANCE Antibiotic resistance is commonly viewed as universally costly, regardless of which bacterial cells express resistance. Here, we derive an opposing logic, where resistance in commensal bacteria can lead to reductions in pathogen density and improved outcomes on both the patient and public health scales. We use a mathematical model of commensal-pathogen interactions to define the necessary and sufficient conditions for beneficial resistance, highlighting the importance of reciprocal ecological inhibition to maximize the benefits of resistance. More broadly, we argue that determining the benefits as well as the costs of resistances in human microbiomes can transform resistance management from a minimization to an optimization problem. We discuss applied contexts and close with a review of key resistance optimization dimensions, including the magnitude, spectrum, and mechanism of resistance.}, }
@article {pmid36472419, year = {2022}, author = {Coker, J and Zhalnina, K and Marotz, C and Thiruppathy, D and Tjuanta, M and D'Elia, G and Hailu, R and Mahosky, T and Rowan, M and Northen, TR and Zengler, K}, title = {A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0095122}, doi = {10.1128/msystems.00951-22}, pmid = {36472419}, issn = {2379-5077}, abstract = {Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.}, }
@article {pmid36471016, year = {2022}, author = {Wang, YJ and He, XH and Meng, LL and Zou, YN and Wu, QS}, title = {Extraradical Mycorrhizal Hyphae Promote Soil Carbon Sequestration through Difficultly Extractable Glomalin-Related Soil Protein in Response to Soil Water Stress.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36471016}, issn = {1432-184X}, abstract = {Soil water stress (WS) affects the decomposition of soil organic carbon (SOC) and carbon (C) emissions. Glomalin, released by arbuscular mycorrhizal fungi into soil that has been defined as glomalin-related soil protein (GRSP), is an important pool of SOC, with hydrophobic characteristics. We hypothesized that mycorrhizal fungi have a positive effect on SOC pools under soil WS for C sequestration in GRSP secreted by extraradical mycorrhizal hyphae. A microsystem was used to establish a root chamber (co-existence of roots and extraradical mycorrhizal hyphae) and a hyphal chamber (the presence of extraradical mycorrhizal hyphae) to study changes in plant growth, leaf water potential, soil aggregate stability, SOC, GRSP, C concentrations in GRSP (CGRSP), and the contribution of CGRSP to SOC after inoculating Rhizophagus intraradices with trifoliate orange (Poncirus trifoliata) in the root chamber under adequate water (AW) and WS. Inoculation with R. intraradices alleviated negative effects on leaf water potential and plant growth after 7 weeks of WS. Soil WS decreased SOC and mean weight diameter (MWD), while AMF inoculation led to an increase in SOC and MWD in both chambers, with the most prominent increase in the hyphal chamber under WS. The C concentration in easily extractable GRSP (EE-GRSP) and difficultly extractable GRSP (DE-GRSP) was 7.32 - 12.57 and 24.90 - 32.60 mg C/g GRSP, respectively. WS reduced CGRSP, while AMF mitigated the reduction. Extraradical mycorrhizal hyphae increased GRSP production and CGRSP, along with a more prominent increase in DE-GRSP under WS than under AW. Extraradical mycorrhizal hyphae increased the contribution of CDE-GRSP to SOC only under WS. CEE-GRSP and CDE-GRSP were significantly positively correlated with SOC and MWD. It is concluded that extraradical mycorrhizal hyphae prominently promoted C sequestration of recalcitrant DE-GRSP under soil WS, thus contributing more organic C accumulation and preservation in aggregates and soil C pool.}, }
@article {pmid36468868, year = {2022}, author = {Zeng, L and Walker, AR and Burne, RA and Taylor, ZA}, title = {Glucose Phosphotransferase System Modulates Pyruvate Metabolism, Bacterial Fitness, and Microbial Ecology in Oral Streptococci.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0035222}, doi = {10.1128/jb.00352-22}, pmid = {36468868}, issn = {1098-5530}, abstract = {Spontaneous mutants with defects in the primary glucose phosphotransferase permease (manLMNO) of Streptococcus sanguinis SK36 showed enhanced fitness at low pH. Transcriptomics and metabolomics with a manL deletion mutant (SK36/manL) revealed redirection of pyruvate to production of acetate and formate, rather than lactate. These observations were consistent with measurements of decreased lactic acid accumulation and increased excretion of acetate, formate, pyruvate, and H2O2. Genes showing increased expression in SK36/manL included those encoding carbohydrate transporters, extracellular glycosidases, intracellular polysaccharide metabolism, and arginine deiminase and pathways for metabolism of acetoin, ethanolamine, ascorbate, and formate, along with genes required for membrane biosynthesis and adhesion. Streptococcus mutans UA159 persisted much better in biofilm cocultures with SK36/manL than with SK36, an effect that was further enhanced by culturing the biofilms anaerobically but dampened by adding arginine to the medium. We posited that the enhanced persistence of S. mutans with SK36/manL was in part due to excess excretion of pyruvate by the latter, as addition of pyruvate to S. mutans-S. sanguinis cocultures increased the proportions of UA159 in the biofilms. Reducing the buffer capacity or increasing the concentration of glucose benefited UA159 when cocultured with SK36, but not with SK36/manL, likely due to the altered metabolism and enhanced acid tolerance of the mutant. When manL was deleted in S. mutans or Streptococcus gordonii, the mutants presented altered fitness characteristics. Our study demonstrated that phosphotransferase system (PTS)-dependent modulation of central metabolism can profoundly affect streptococcal fitness and metabolic interactions, revealing another dimension in commensal-pathogen relationships influencing dental caries development. IMPORTANCE Dental caries is underpinned by a dysbiotic microbiome and increased acid production. As beneficial bacteria that can antagonize oral pathobionts, oral streptococci such as S. sanguinis and S. gordonii can ferment many carbohydrates, despite their relative sensitivity to low pH. We characterized the molecular basis for why mutants of glucose transporter ManLMNO of S. sanguinis showed enhanced production of hydrogen peroxide and ammonia and improved persistence under acidic conditions. A metabolic shift involving more than 300 genes required for carbohydrate transport, energy production, and envelope biogenesis was observed. Significantly, manL mutants engineered in three different oral streptococci displayed altered capacities for acid production and interspecies antagonism, highlighting the potential for targeting the glucose-PTS to modulate the pathogenicity of oral biofilms.}, }
@article {pmid36468853, year = {2022}, author = {Zhang, B and Zhao, C and Zhang, X and Li, X and Zhang, Y and Liu, X and Yin, J and Li, X and Wang, J and Wang, S}, title = {An Elemental Diet Enriched in Amino Acids Alters the Gut Microbial Community and Prevents Colonic Mucus Degradation in Mice with Colitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0088322}, doi = {10.1128/msystems.00883-22}, pmid = {36468853}, issn = {2379-5077}, abstract = {The role of dietary amino acids or intact proteins in the progression of colitis remains controversial, and the mechanism involving gut microbes is unclear. Here, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of dextran sulfate sodium (DSS)-induced colitis in mice. Our results showed that the ED induced remission of colitis in mice. Notably, ED treatment reduced the abundance of the mucolytic bacteria Akkermansia and Bacteroides, which was attributed to decreased colonic protein fermentation. Consistently, the activities of mucolytic enzymes were decreased, leading to protection against mucus layer degradation and microbial invasion. Fecal microbiota transplantation from ED-fed mice reshaped microbial ecology and alleviated intestinal inflammation in recipient mice. The ED failed to induce remission of colitis in pseudogermfree mice. Together, our results demonstrate the critical role of the gut microbiota in the prevention of colitis by an ED. IMPORTANCE The prevalence of inflammatory bowel disease is rapidly increasing and has become a global burden. Several specific amino acids have been shown to benefit mucosal healing and colitis remission. However, the role of amino acids or intact proteins in diets and enteral nutrition formulas is controversial, and the mechanisms involving gut microbes remain unclear. In this study, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of colitis in mice. The underlying mechanisms were explored by utilizing fecal microbiota transplantation and pseudogermfree mice. ED treatment reduced the abundance of mucolytic bacteria, thereby protecting the mucus layer from microbial invasion and degradation. For the first time, we convincingly demonstrated the critical role of gut microbiota in the effects of the ED. This study may provide new insights into the gut microbiota-diet interaction and its role in human health.}, }
@article {pmid36466646, year = {2022}, author = {Twing, KI and Ward, LM and Kane, ZK and Sanders, A and Price, RE and Pendleton, HL and Giovannelli, D and Brazelton, WJ and McGlynn, SE}, title = {Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {960335}, pmid = {36466646}, issn = {1664-302X}, abstract = {Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.}, }
@article {pmid36465136, year = {2022}, author = {Simmonds, EG and Adjei, KP and Andersen, CW and Hetle Aspheim, JC and Battistin, C and Bulso, N and Christensen, HM and Cretois, B and Cubero, R and Davidovich, IA and Dickel, L and Dunn, B and Dunn-Sigouin, E and Dyrstad, K and Einum, S and Giglio, D and Gjerløw, H and Godefroidt, A and González-Gil, R and Gonzalo Cogno, S and Große, F and Halloran, P and Jensen, MF and Kennedy, JJ and Langsæther, PE and Laverick, JH and Lederberger, D and Li, C and Mandeville, EG and Mandeville, C and Moe, E and Navarro Schröder, T and Nunan, D and Sicacha-Parada, J and Simpson, MR and Skarstein, ES and Spensberger, C and Stevens, R and Subramanian, AC and Svendsen, L and Theisen, OM and Watret, C and O'Hara, RB}, title = {Insights into the quantification and reporting of model-related uncertainty across different disciplines.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105512}, pmid = {36465136}, issn = {2589-0042}, abstract = {Quantifying uncertainty associated with our models is the only way we can express how much we know about any phenomenon. Incomplete consideration of model-based uncertainties can lead to overstated conclusions with real-world impacts in diverse spheres, including conservation, epidemiology, climate science, and policy. Despite these potentially damaging consequences, we still know little about how different fields quantify and report uncertainty. We introduce the "sources of uncertainty" framework, using it to conduct a systematic audit of model-related uncertainty quantification from seven scientific fields, spanning the biological, physical, and political sciences. Our interdisciplinary audit shows no field fully considers all possible sources of uncertainty, but each has its own best practices alongside shared outstanding challenges. We make ten easy-to-implement recommendations to improve the consistency, completeness, and clarity of reporting on model-related uncertainty. These recommendations serve as a guide to best practices across scientific fields and expand our toolbox for high-quality research.}, }
@article {pmid36463738, year = {2022}, author = {Li, J and Yu, S and Liu, Q and Wang, D and Yang, L and Wang, J and Zuo, R}, title = {Screening of hazardous groundwater pollutants responsible for microbial ecological consequences by integrated nontargeted analysis and high-throughput sequencing technologies.}, journal = {Journal of hazardous materials}, volume = {445}, number = {}, pages = {130516}, doi = {10.1016/j.jhazmat.2022.130516}, pmid = {36463738}, issn = {1873-3336}, abstract = {Organic contaminants, especially hydrophobic organic contaminants (HOCs), pose potential ecological threats even at environmental concentrations. Characterization of HOC profiles and identification of key environmental stressors are vital but still challenging in groundwater quality management. In this study, a strategy for identifying the key environmental stressors among HOCs in groundwater based on integrated chemical monitoring technologies and microbial ecology analysis methods was proposed and applied to typical groundwater samples. Specifically, the characteristics of HOCs were systematically analyzed based on nontargeted and targeted approaches, and microbial community assembly and specific biomarker analysis were combined to determine the major ecological processes and key environmental stressors. The results showed that a total of 234 HOCs were detected in groundwater collected from Tongzhou, Beijing; among them, phthalate esters (PAEs) were screened out as key environmental stressors, considering that they made relatively higher microbial ecology contributions. Furthermore, their influences on the structure and function of the groundwater microbial community were evaluated by adopting high-throughput sequencing and bioinformatics analysis technologies. These findings confirmed PAEs as vital determinants driving microbial assembly, shifting community structure, and regulating community function in groundwater; in addition, the findings validated the feasibility and suitability of the proposed strategy.}, }
@article {pmid36460563, year = {2022}, author = {Sutherland, WJ and Bennett, C and Brotherton, PNM and Butterworth, HM and Clout, MN and Côté, IM and Dinsdale, J and Esmail, N and Fleishman, E and Gaston, KJ and Herbert-Read, JE and Hughes, A and Kaartokallio, H and Le Roux, X and Lickorish, FA and Matcham, W and Noor, N and Palardy, JE and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Scobey, R and Spalding, MD and Tonneijck, FH and Tubbs, N and Watson, JEM and Wentworth, JE and Wilson, JD and Thornton, A}, title = {A global biological conservation horizon scan of issues for 2023.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2022.10.005}, pmid = {36460563}, issn = {1872-8383}, abstract = {We present the results of our 14th horizon scan of issues we expect to influence biological conservation in the future. From an initial set of 102 topics, our global panel of 30 scientists and practitioners identified 15 issues we consider most urgent for societies worldwide to address. Issues are novel within biological conservation or represent a substantial positive or negative step change at global or regional scales. Issues such as submerged artificial light fisheries and accelerating upper ocean currents could have profound negative impacts on marine or coastal ecosystems. We also identified potentially positive technological advances, including energy production and storage, improved fertilisation methods, and expansion of biodegradable materials. If effectively managed, these technologies could realise future benefits for biological diversity.}, }
@article {pmid36460187, year = {2022}, author = {Liu, X and Zhang, J and Si, J and Li, P and Gao, H and Li, W and Chen, Y}, title = {What happens to gut microorganisms and potential repair mechanisms when meet heavy metal(loid)s.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120780}, doi = {10.1016/j.envpol.2022.120780}, pmid = {36460187}, issn = {1873-6424}, abstract = {Heavy metal (loid) pollution is a significant threat to human health, as the intake of heavy metal (loid)s can cause disturbances in intestinal microbial ecology and metabolic disorders, leading to intestinal and systemic diseases. Therefore, it is important to understand the effects of heavy metal (loid)s on intestinal microorganisms and the necessary approaches to restore them after damage. This review provides a summary of the effects of common toxic elements, such as lead (Pb), cadmium (Cd), chromium (Cr), and metalloid arsenic (As), on the microbial community and structure, metabolic pathways and metabolites, and intestinal morphology and structure. The effects of heavy metal (loid)s on metabolism are focused on energy, nitrogen, and short-chain fatty acid metabolism. We also discussed the main solutions for recovery of intestinal microorganisms from the effects of heavy metal (loid)s, namely the supplementation of probiotics, recombinant bacteria with metal resistance, and the non-toxic transformation of heavy metal (loid) ions by their own intestinal flora. This article provides insight into the toxic effects of heavy metals and As on gut microorganisms and hosts and provides additional therapeutic options to mitigate the damage caused by these toxic elements.}, }
@article {pmid36460149, year = {2022}, author = {Araujo, ASF and Miranda, ARL and Pereira, APA and de Melo, WJ and Melo, VMM and Ventura, SH and Brito Junior, ES and de Medeiros, EV and Araujo, FF and Mendes, LW}, title = {Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137417}, doi = {10.1016/j.chemosphere.2022.137417}, pmid = {36460149}, issn = {1879-1298}, abstract = {Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg[-1] Cr) and Cr-contaminated soils (∼250 mg kg[-1] Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.}, }
@article {pmid36455460, year = {2022}, author = {Rothman, JA and Saghir, A and Chung, SA and Boyajian, N and Dinh, T and Kim, J and Oval, J and Sharavanan, V and York, C and Zimmer-Faust, AG and Langlois, K and Steele, JA and Griffith, JF and Whiteson, KL}, title = {Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes.}, journal = {Water research}, volume = {229}, number = {}, pages = {119421}, doi = {10.1016/j.watres.2022.119421}, pmid = {36455460}, issn = {1879-2448}, abstract = {Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs (as measured through PERMANOVA, P < 0.001) and that the relative abundance of many individual AMR genes/variants increased over time (as measured with MaAsLin2, Padj < 0.05). Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.}, }
@article {pmid36452921, year = {2022}, author = {Xu, H and Wu, N and Na, N and Sun, L and Zhao, Y and Ding, H and Fang, Y and Wang, T and Xue, Y and Zhong, J}, title = {Fermentation weight loss, fermentation quality, and bacterial community of ensiling of sweet sorghum with lactic acid bacteria at different silo densities.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1013913}, pmid = {36452921}, issn = {1664-302X}, abstract = {Sweet sorghum is an important forage in arid and semi-arid climatic regions. This study aimed to reveal the fermentation weight loss (FWL), fermentation quality, and bacterial community of ensiling of sweet sorghum with lactic acid bacteria LAB; (Lactiplantibacillus plantarum and Lentilactobacillus buchneri) at different silo densities. For this study, sweet sorghum was harvested at the first spikelet of inflorescence stage and ensiled without or with LAB (CK or L) in polyethylene laboratory-scale silos (diameter, 20 cm; height, 30 cm) at densities of 650 (CK_650 and L_650), 700 (CK_700 and L_700), and 750 kg/m[3] (CK_750 and L_750), respectively. The FWL, fermentation quality, microbial counts, and bacterial community of the silage were assessed after 100 days of ensiling. L_750 had a lower FWL than CK_650, _700, and _750 after 100 days of ensiling (P < 0.005), and the FWL was affected by silo density and inoculating LAB (P < 0.005). All silages had low pH (<4.0) and ammonia nitrogen content (<50 g/kg total nitrogen) and did not contain propionic and butyric acids; moreover, inoculating LAB increased lactic and acetic acids (P < 0.005). Bacterial communities in inoculated and uninoculated silages were clustered together, respectively, and clearly separated from each other. The total abundance of Lactiplantibacillus and Lentilactobacillus in fresh forage was <1%. Lactiplantibacillus had the highest abundance in all silages (from 71.39 to 93.27%), followed by Lentilactobacillus (from 3.59 to 27.63%). Inoculating LAB increased the abundance of Lentilactobacillus in each silo density (P < 0.005) and decreased Lactiplantibacillus in the silage in densities of 700 and 750 kg/m[3] (P < 0.005); moreover, increasing silo density decreased Lactiplantibacillus abundance and increased Lentilactobacillus abundance in inoculated silages (P < 0.005). Overall, sweet sorghum silage showed satisfactory fermentation quality, with a density of no <650 kg/m[3], and inoculating LAB improved fermentation quality and reduced FWL. Lactiplantibacillus and Lentilactobacillus presented as minor taxa in fresh sweet sorghum and dominated the bacterial community of all silages. Inoculating LAB was the main factor affecting the bacterial community of sweet sorghum silage. Moreover, inoculating LAB and increasing silo density can contribute to the decreasing Lactiplantibacillus abundance and increasing Lentilactobacillus abundance.}, }
@article {pmid36451971, year = {2022}, author = {Villa, F and Wu, YL and Zerboni, A and Cappitelli, F}, title = {In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface.}, journal = {Bioscience}, volume = {72}, number = {12}, pages = {1156-1175}, pmid = {36451971}, issn = {0006-3568}, abstract = {Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.}, }
@article {pmid36449026, year = {2022}, author = {Badger Hanson, E and Docherty, KM}, title = {Mini-review: Current and Future Perspectives on Microbially Focused Restoration Strategies in Tallgrass Prairies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36449026}, issn = {1432-184X}, abstract = {Ecosystem restoration is a critical conservation strategy, especially for increasing resilience and resistance to climate change. Current restoration efforts that convert reclaimed agricultural land to native tallgrass prairies typically focus on aboveground communities, but it can take decades to restore soil microbial biodiversity and function using these strategies, if they recover at all. This incomplete restoration can have detrimental impacts on longer-term restoration goals, such as supporting late-successional plant species and facilitating soil carbon sequestration. Soil microorganisms are key components in determining the fate of organic material that enters the soil. They mediate decomposition rates and contribute to plant-microbe-soil interactions, produce microbial biomass, necromass, and metabolic products, and physically protect soil carbon through aggregation. Interactions with plants and controls over soil carbon vary widely depending on the specific microbial taxa present, their physiology, their functional capabilities, and their responses to environmental stressors. Thus, the ability for new restorations, prairie conservation corridors, and prairies planted in marginal lands to act as carbon sinks and help balance greenhouse gas emissions can depend on the success of microbial restoration. Next-generation sequencing approaches can support novel methods for evaluating existing restoration practices and developing microbially focused management strategies. This review summarizes the growing body of literature describing microbially focused tallgrass prairie restoration and considers when and how integrating next-generation sequencing approaches into management efforts can be beneficial. We provide a roadmap for future restoration efforts where microbial ecologists, restoration ecologists, and land managers can work together to meet their goals to promote climate-ready restored ecosystems.}, }
@article {pmid36445401, year = {2022}, author = {Bates, KA and Friesen, J and Loyau, A and Butler, H and Vredenburg, VT and Laufer, J and Chatzinotas, A and Schmeller, DS}, title = {Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36445401}, issn = {1432-184X}, abstract = {The amphibian skin microbiome is important in maintaining host health, but is vulnerable to perturbation from changes in biotic and abiotic conditions. Anthropogenic habitat disturbance and emerging infectious diseases are both potential disrupters of the skin microbiome, in addition to being major drivers of amphibian decline globally. We investigated how host environment (hydrology, habitat disturbance), pathogen presence, and host biology (life stage) impact the skin microbiome of wild Dhofar toads (Duttaphrynus dhufarensis) in Oman. We detected ranavirus (but not Batrachochytrium dendrobatidis) across all sampling sites, constituting the first report of this pathogen in Oman, with reduced prevalence in disturbed sites. We show that skin microbiome beta diversity is driven by host life stage, water source, and habitat disturbance, but not ranavirus infection. Finally, although trends in bacterial diversity and differential abundance were evident in disturbed versus undisturbed sites, bacterial co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for amphibian skin microbiome diversity and taxa abundance being associated with habitat disturbance, with bacterial co-occurrence (and likely broader aspects of microbial community ecology) being largely site specific.}, }
@article {pmid36445161, year = {2022}, author = {Sylvain, F&#xc9; and Leroux, N and Normandeau, &#xc9; and Holland, A and Bouslama, S and Mercier, PL and Luis Val, A and Derome, N}, title = {Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0206422}, doi = {10.1128/spectrum.02064-22}, pmid = {36445161}, issn = {2165-0497}, abstract = {Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.}, }
@article {pmid36445112, year = {2022}, author = {Sánchez-Navarro, R and Nuhamunada, M and Mohite, OS and Wasmund, K and Albertsen, M and Gram, L and Nielsen, PH and Weber, T and Singleton, CM}, title = {Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0063222}, doi = {10.1128/msystems.00632-22}, pmid = {36445112}, issn = {2379-5077}, abstract = {Microorganisms produce a wide variety of secondary/specialized metabolites (SMs), the majority of which are yet to be discovered. These natural products play multiple roles in microbiomes and are important for microbial competition, communication, and success in the environment. SMs have been our major source of antibiotics and are used in a range of biotechnological applications. In silico mining for biosynthetic gene clusters (BGCs) encoding the production of SMs is commonly used to assess the genetic potential of organisms. However, as BGCs span tens to over 200 kb, identifying complete BGCs requires genome data that has minimal assembly gaps within the BGCs, a prerequisite that was previously only met by individually sequenced genomes. Here, we assess the performance of the currently available genome mining platform antiSMASH on 1,080 high-quality metagenome-assembled bacterial genomes (HQ MAGs) previously produced from wastewater treatment plants (WWTPs) using a combination of long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies. More than 4,200 different BGCs were identified, with 88% of these being complete. Sequence similarity clustering of the BGCs implies that the majority of this biosynthetic potential likely encodes novel compounds, and few BGCs are shared between genera. We identify BGCs in abundant and functionally relevant genera in WWTPs, suggesting a role of secondary metabolism in this ecosystem. We find that the assembly of HQ MAGs using long-read sequencing is vital to explore the genetic potential for SM production among the uncultured members of microbial communities. IMPORTANCE Cataloguing secondary metabolite (SM) potential using genome mining of metagenomic data has become the method of choice in bioprospecting for novel compounds. However, accurate biosynthetic gene cluster (BGC) detection requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until very recently with new long-read technologies. Here, we determined the biosynthetic potential of activated sludge (AS), the microbial community used in resource recovery and wastewater treatment, by mining high-quality metagenome-assembled genomes generated from long-read data. We found over 4,000 BGCs, including BGCs in abundant process-critical bacteria, with no similarity to the BGCs of characterized products. We show how long-read MAGs are required to confidently assemble complete BGCs, and we determined that the AS BGCs from different studies have very little overlap, suggesting that AS is a rich source of biosynthetic potential and new bioactive compounds.}, }
@article {pmid36444830, year = {2022}, author = {Russo, V and Ancora, M and Gatta, V and Orsini, M and Prencipe, G and Peserico, A and Colosimo, A and El Khatib, M and Mauro, A and Di Berardino, C and Scialabba, S and Tiboni, GM and Marcacci, M and Cammà, C and Barboni, B}, title = {Profiling of mitochondrial heteroplasmy in single human oocytes by next-generation sequencing.}, journal = {Molecular reproduction and development}, volume = {}, number = {}, pages = {}, doi = {10.1002/mrd.23655}, pmid = {36444830}, issn = {1098-2795}, abstract = {Mitochondrial DNA (mtDNA) plays a crucial role in the development of a competent oocyte. Indeed, mtDNA alterations may predispose to chromosome nondisjunction, resulting in infertility due to a reduced vitality and quality of oocytes and embryos. In this methods paper, the multiple displacement amplification approach was applied in combination with next-generation sequencing (NGS) to amplify and sequence, in single-end, the entire mtDNA of single human oocytes to directly construct genomic NGS libraries, and subsequently, to highlight and quantify the mutations they presented. The bioinformatic workflow was carried out with a specific ad hoc developed in-house software. This approach proved to be sensitive and specific, also highlighting the mutations present in heteroplasmy, showing deletion, insertion or substitution mutations in the genes involved in the respiratory chain, even if the found variants were benign or of uncertain meaning. The analysis of mtDNA mutations in the oocyte could provide a better understanding of specific genetic abnormalities and of their possible effect on oocyte developmental competence. This study shows how this approach, based on a massive parallel sequencing of clonally amplified DNA molecules, allows to sequence the entire mitochondrial genome of single oocytes in a short time and with a single analytical run and to verify mtDNA mutations.}, }
@article {pmid36443470, year = {2022}, author = {Jang, H and Koh, H and Gu, W and Kang, B}, title = {Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20465}, pmid = {36443470}, issn = {2045-2322}, mesh = {Humans ; Cloud Computing ; *Microbiota ; *Gastrointestinal Microbiome ; Mouth ; Skin ; }, abstract = {Pairing (or blocking) is a design technique that is widely used in comparative microbiome studies to efficiently control for the effects of potential confounders (e.g., genetic, environmental, or behavioral factors). Some typical paired (block) designs for human microbiome studies are repeated measures designs that profile each subject's microbiome twice (or more than twice) (1) for pre and post treatments to see the effects of a treatment on microbiome, or (2) for different organs of the body (e.g., gut, mouth, skin) to see the disparity in microbiome between (or across) body sites. Researchers have developed a sheer number of web-based tools for user-friendly microbiome data processing and analytics, though there is no web-based tool currently available for such paired microbiome studies. In this paper, we thus introduce an integrative web-based tool, named MiPair, for design-based comparative analysis with paired microbiome data. MiPair is a user-friendly web cloud service that is built with step-by-step data processing and analytic procedures for comparative analysis between (or across) groups or between baseline and other groups. MiPair employs parametric and non-parametric tests for complete or incomplete block designs to perform comparative analyses with respect to microbial ecology (alpha- and beta-diversity) and taxonomy (e.g., phylum, class, order, family, genus, species). We demonstrate its usage through an example clinical trial on the effects of antibiotics on gut microbiome. MiPair is an open-source software that can be run on our web server (http://mipair.micloud.kr) or on user's computer (https://github.com/yj7599/mipairgit).}, }
@article {pmid36442715, year = {2022}, author = {Islam, T and Albracht-Schulte, K and Ramalingam, L and Schlabritz-Lutsevich, N and Park, OH and Zabet-Moghaddam, M and Kalupahana, NS and Moustaid-Moussa, N}, title = {Anti-inflammatory mechanisms of polyphenols in adipose tissue inflammation: Role of gut microbiota, intestinal barrier integrity and zinc homeostasis.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {109242}, doi = {10.1016/j.jnutbio.2022.109242}, pmid = {36442715}, issn = {1873-4847}, abstract = {Obesity is associated with an imbalance of micro-and macro-nutrients, dysbiosis, and a "leaky" gut phenomenon. Polyphenols, such as curcumin, resveratrol, and anthocyanin may alleviate the systemic effects of obesity, potentially by improving gut microbiota, intestinal barrier integrity (IBI), and zinc homeostasis. The essential micronutrient zinc plays a crucial role in the regulation of enzymatic processes, including inflammation, maintenance of the microbial ecology, and intestinal barrier integrity. In this review, we focus on IBI- which prevents intestinal lipopolysaccharide (LPS) leakage - as a critical player in polyphenol-mediated protective effects against obesity-associated white adipose tissue (WAT) inflammation. This occurs through mechanisms that block the movement of the bacterial endotoxin LPS across the gut barrier. Available research suggests that polyphenols reduce WAT and systemic inflammation via crosstalk with inflammatory NF-κB, the mammalian target of rapamycin (mTOR) signaling and zinc homeostasis.}, }
@article {pmid36442312, year = {2022}, author = {Zhong, X and Yu, S and Xu, H}, title = {Colonization dynamics in body-size spectrum of protozoan periphytons for marine bioassessment using two modified sampling systems.}, journal = {Marine pollution bulletin}, volume = {186}, number = {}, pages = {114382}, doi = {10.1016/j.marpolbul.2022.114382}, pmid = {36442312}, issn = {1879-3363}, abstract = {The body-size spectrum of microperiphytons has been proved to be a powerful tool for bioassessment. To explore colonization dynamics in body-size spectrum of periphytic protozoa in two modified sampling systems of both glass slide (mGS) and polyurethane foam unit (mPFU), a 28-day colonization survey was conducted in coastal waters of the Yellow Sea, China. A total of 7 body-size ranks were identified from 62 species, with 7 ranks (60 species) in the mGS and 6 ranks (37 species) in the mPFU system. The stable pattern with similar body-size spectra was found earlier in the mGS system than mPFU system during the colonization period. Both the trajectory and bootstrapped average analyses revealed that the colonization dynamics were significantly different in the body-size spectrum between the two methods. Based on our data, it suggests that the mGS system might be a better choice than the mPFU system for bioassessment in marine ecosystems.}, }
@article {pmid36441249, year = {2022}, author = {Scherer, BP and Mast, A}, title = {Red Mangrove Propagule Bacterial Communities Vary With Geographic, But Not Genetic Distance.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36441249}, issn = {1432-184X}, abstract = {Bacterial communities associated with plant propagules remain understudied, despite the opportunities that propagules represent as dispersal vectors for bacteria to new sites. These communities may be the product of a combination of environmental influence and inheritance from parent to offspring. The relative role of these mechanisms could have significant implications for our understanding of plant-microbe interactions. We studied the correlates of microbiome community similarities across an invasion front of red mangroves (Rhizophora mangle L.) in Florida, where the species is expanding northward. We collected georeferenced propagule samples from 110 individuals of red mangroves across 11 populations in Florida and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. We found no core community of bacterial amplicon sequence variants (ASVs) across the Florida range of red mangroves, though there were some ASVs shared among individuals within most populations. Populations differed significantly as measured by Bray-Curtis dissimilarity, but not Unifrac distance. We generated data from 6 microsatellite loci from 60 individuals across 9 of the 11 populations. Geographic distance was correlated with beta diversity, but genetic distance was not. We conclude that red mangrove propagule bacterial communities are likely influenced more by local environmental acquisition than by inheritance.}, }
@article {pmid36440485, year = {2022}, author = {Alsayed, AR and Al-Dulaimi, A and Alkhatib, M and Al Maqbali, M and Al-Najjar, MAA and Al-Rshaidat, MMD}, title = {A comprehensive clinical guide for Pneumocystis jirovecii pneumonia: a missing therapeutic target in HIV-uninfected patients.}, journal = {Expert review of respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1080/17476348.2022.2152332}, pmid = {36440485}, issn = {1747-6356}, abstract = {INTRODUCTION: Pneumocystis jirovecii is an opportunistic, human-specific fungus that causes Pneumocystis pneumonia (PCP). PCP symptoms are non-specific. A patient with P. jirovecii and another lung infection faces a diagnostic challenge. It may be difficult to determine which of these agents is responsible for the clinical symptoms, preventing effective treatment. Diagnostic and treatment efforts have been made more difficult by the rising frequency with which coronavirus 2019 (COVID-19) and PCP co-occur.<br><br>AREAS COVERED: Herein, we provide a comprehensive review of clinical and pharmacological recommendations along with a literature review of PCP in immunocompromised patients focusing on HIV-uninfected patients.<br><br>EXPERT OPINION: PCP may be masked by identifying co-existing pathogens that are not necessarily responsible for the observed infection. Patients with severe form COVID-19 should be examined for underlying immunodeficiency, and co-infections must be considered as co-infection with P. jirovecii may worsen COVID-19's severity and fatality. PCP should be investigated in patients with PCP risk factors who come with pneumonia and suggestive radiographic symptoms but have not previously received PCP prophylaxis. PCP prophylaxis should be explored in individuals with various conditions that impair the immune system, depending on their PCP risk.}, }
@article {pmid36439796, year = {2022}, author = {Bandini, F and Vaccari, F and Soldano, M and Piccinini, S and Misci, C and Bellotti, G and Taskin, E and Cocconcelli, PS and Puglisi, E}, title = {Rigid bioplastics shape the microbial communities involved in the treatment of the organic fraction of municipal solid waste.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1035561}, pmid = {36439796}, issn = {1664-302X}, abstract = {While bioplastics are gaining wide interest in replacing conventional plastics, it is necessary to understand whether the treatment of the organic fraction of municipal solid waste (OFMSW) as an end-of-life option is compatible with their biodegradation and their possible role in shaping the microbial communities involved in the processes. In the present work, we assessed the microbiological impact of rigid polylactic acid (PLA) and starch-based bioplastics (SBB) spoons on the thermophilic anaerobic digestion and the aerobic composting of OFMSW under real plant conditions. In order to thoroughly evaluate the effect of PLA and SBB on the bacterial, archaeal, and fungal communities during the process, high-throughput sequencing (HTS) technology was carried out. The results suggest that bioplastics shape the communities' structure, especially in the aerobic phase. Distinctive bacterial and fungal sequences were found for SBB compared to the positive control, which showed a more limited diversity. Mucor racemosus was especially abundant in composts from bioplastics' treatment, whereas Penicillium roqueforti was found only in compost from PLA and Thermomyces lanuginosus in that from SBB. This work shed a light on the microbial communities involved in the OFMSW treatment with and without the presence of bioplastics, using a new approach to evaluate this end-of-life option.}, }
@article {pmid36436634, year = {2022}, author = {Sakarika, M and Regueira, A and Rabaey, K and Ganigué, R}, title = {Thermophilic caproic acid production from grass juice by sugar-based chain elongation.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {160501}, doi = {10.1016/j.scitotenv.2022.160501}, pmid = {36436634}, issn = {1879-1026}, abstract = {Medium chain carboxylic acids (MCCA) such as caproic acid have a plethora of applications, ranging from food additives to bioplastics. MCCA can be produced via microbial chain elongation using waste and side-streams as substrates, a process that can be more sustainable than conventional production routes. Most chain elongation studies have focused on mesophilic conditions, with only two recent studies hinting at the possibility of thermophilic chain elongation, but a systematic study of its mechanisms is lacking. Here, we investigated thermophilic chain elongation from grass juice, to understand the effect of key operational parameters (pH, temperature, substrate) on the process performance and to establish the key microbial genera and their role in the system. The genus Caproiciproducens was identified as responsible for thermophilic chain elongation, and caproic acid production was most favorable at pH 6.0 and 50 °C among the conditions tested, reaching an average concentration of 3.4 g/L. Batch experiments showed that the substrate for caproic acid production were glucose and xylose, while lactic acid led to the production of only butyric acid. Fed-batch experiments showed that substrate availability and the presence of caproic acid in the system play a major role in shaping the profile of thermophilic chain elongation. The increase of the total sugar concentration by glucose addition (without changing the organic load) during continuous operation led to a microbial community dominated (75 %) by Caproiciproducens and increased by 76 % the final average caproic acid concentration to 6.0 g/L (13 gCOD/L) which represented 32 % (g/g) of the total carboxylic acids. The highest concentration achieved was 7.2 g/L (day 197) which is the highest concentration reported under thermophilic conditions thus far. The results of this work pave the way to the potential development of thermophilic systems for upgrading various underexplored abundant and cheap sugar-rich side-streams to caproic acid.}, }
@article {pmid36436244, year = {2023}, author = {Sun, W and Qian, X and Wang, X and Gu, J}, title = {Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion.}, journal = {Journal of environmental management}, volume = {326}, number = {Pt B}, pages = {116864}, doi = {10.1016/j.jenvman.2022.116864}, pmid = {36436244}, issn = {1095-8630}, mesh = {Cattle ; Animals ; *Manure/analysis ; *Anti-Bacterial Agents/pharmacology/metabolism ; Enrofloxacin/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.}, }
@article {pmid36434466, year = {2022}, author = {Hietaranta, E and Juottonen, H and Kytöviita, MM}, title = {Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems.}, journal = {Oecologia}, volume = {}, number = {}, pages = {}, pmid = {36434466}, issn = {1432-1939}, abstract = {Basic knowledge on dispersal of microbes in pollinator networks is essential for plant, insect, and microbial ecology. Thorough understanding of the ecological consequences of honeybee farming on these complex plant-pollinator-microbe interactions is a prerequisite for sustainable honeybee keeping. Most research on plant-pollinator-microbe interactions have focused on temperate agricultural systems. Therefore, information on a wild plant that is a seasonal bottleneck for pollinators in cold climate such as Salix phylicifolia is of specific importance. We investigated how floral visitation by insects influences the community structure of bacteria and fungi in Salix phylicifolia inflorescences under natural conditions. Insect visitors were experimentally excluded with net bags. We analyzed the microbiome and measured pollen removal in open and bagged inflorescences in sites where honeybees were foraging and in sites without honeybees. Site and plant individual explained most of the variation in floral microbial communities. Insect visitation and honeybees had a smaller but significant effect on the community composition of microbes. Honeybees had a specific effect on the inflorescence microbiome and, e.g., increased the relative abundance of operational taxonomic units (OTUs) from the bacterial order Lactobacillales. Site had a significant effect on the amount of pollen removed from inflorescences but this was not due to honeybees. Insect visitors increased bacterial and especially fungal OTU richness in the inflorescences. Pollinator visits explained 38% variation in fungal richness, but only 10% in bacterial richness. Our work shows that honeybee farming affects the floral microbiome in a wild plant in rural boreal ecosystems.}, }
@article {pmid36434303, year = {2022}, author = {Querejeta, M and Hervé, V and Perdereau, E and Marchal, L and Herniou, EA and Boyer, S and Giron, D}, title = {Changes in Bacterial Community Structure Across the Different Life Stages of Black Soldier Fly (Hermetia illucens).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36434303}, issn = {1432-184X}, abstract = {The digestive capacity of organic compounds by the black soldier fly (BSF, Hermetia illucens, Diptera: Stratiomyidae, Linnaeus, 1758) is known to rely on complex larva-microbiota interactions. Although insect development is known to be a driver of changes of bacterial communities, the fluctuations along BSF life cycle in terms of composition and diversity of bacterial communities are still unknown. In this work, we used a metabarcoding approach to explore the differences in bacterial diversity along all four BSF developmental stages: eggs, larvae, pupae, and adult. We detected not only significant differences in bacterial community composition and species richness along the development of BSF, but also nine prevalent amplicon single variants (ASVs) forming the core microbiota. Out of the 2010 ASVs identified, 160 were significantly more abundant in one of the life stages. Moreover, using PICRUSt2, we inferred 27 potential metabolic pathways differentially used among the BSF life cycle. This distribution of metabolic pathways was congruent with the bacterial taxonomic distribution among life stages, demonstrating that the functional requirements of each phase of development are drivers of bacterial composition and diversity. This study provides a better understanding of the different metabolic processes occurring during BSF development and their links to changes in bacterial taxa. This information has important implications for improving bio-waste processing in such an economically important insect species.}, }
@article {pmid36432829, year = {2022}, author = {May-Mutul, CG and López-Garrido, MA and O'Connor-Sánchez, A and Peña-Ramírez, YJ and Labrín-Sotomayor, NY and Estrada-Medina, H and Ferrer, MM}, title = {Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {22}, pages = {}, doi = {10.3390/plants11223098}, pmid = {36432829}, issn = {2223-7747}, abstract = {During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.}, }
@article {pmid36431270, year = {2022}, author = {Cheng, T and Zhi, H and Liu, Y and Zhang, S and Song, Z and Li, Y}, title = {Dual Anti-Glomerular Basement Membrane and Anti-Neutrophil Cytoplasmic Antibodies-Positive Rapidly Progressive Glomerulonephritis with Rheumatoid Arthritis and Sjogren's Syndrome: A Case Report and Literature Review.}, journal = {Journal of clinical medicine}, volume = {11}, number = {22}, pages = {}, doi = {10.3390/jcm11226793}, pmid = {36431270}, issn = {2077-0383}, abstract = {Rapidly progressive glomerulonephritis (RPGN) is a life-threatening disease characterized by rapid progressive deterioration of renal function and extensive formation of crescents. Some antibodies tend to be positive, such as a perinuclear anti-neutrophil cytoplasmic antibody (p-ANCA) and anti-glomerular basement membrane (anti-GBM) antibodies, in most patients with the disease. However, cases of double positivity for the above antibodies are considered to be rare. In addition, both rheumatoid arthritis (RA) and Sjogren's syndrome (SS) are deemed to be independent immune disorders that can cause renal impairment. Nevertheless, the association between RPGN and these two diseases has not been elucidated in previous studies. Here, we provide a case of RPGN with the concurrence of RA and SS characterized by double positivity in anti-GBM antibodies and p-ANCA. After aggressive treatment with cyclophosphamide, glucocorticoids, and plasma exchange, the patient improved significantly. Despite the malignant event of arteriovenous fistula rupture and bleeding during treatment, the patient survived with renal function recovery for the rest of the follow-up period.}, }
@article {pmid36431177, year = {2022}, author = {Zhi, W and Yuan, X and Song, W and Jin, G and Li, Y}, title = {Fecal Microbiota Transplantation May Represent a Good Approach for Patients with Focal Segmental Glomerulosclerosis: A Brief Report.}, journal = {Journal of clinical medicine}, volume = {11}, number = {22}, pages = {}, doi = {10.3390/jcm11226700}, pmid = {36431177}, issn = {2077-0383}, abstract = {This is the first report of fecal microbiota transplantation (FMT) in patients with chronic kidney disease. The patient was subjected to focal segmental glomerulosclerosis (FSGS), with onset in April 2021. The main manifestation featured abnormal renal function and no proteinuria at the level of nephrotic syndrome. In May 2021, she showed biopsy-proven FSGS and was treated with glucocorticoid. However, after glucocorticoid reduction, the patient's serum creatinine increased again, so she adjusted the dosage and continued use until now. In April 2022, the patient was prescribed the FMT capsules. After FMT, the renal function remained stable, urinary protein decreased, reaching the clinical standard of complete remission, and there was no recurrence after glucocorticoid reduction. Furthermore, the patient showed significantly decreased hyperlipidemia, triglyceride (TG) and cholesterol (CHO) after FMT. During FMT, the level of cytokines fluctuated slightly, but returned to the pre-transplantation level after three months. From this, we conclude that FMT is a potential adjuvant therapy for FSGS, and patients can benefit from improving renal function and dyslipidemia.}, }
@article {pmid36430059, year = {2022}, author = {Savadova-Ratkus, K and Mazur-Marzec, H and Karosienė, J and Sivonen, K and Suurnäkki, S and Kasperovičienė, J and Paškauskas, R and Koreivienė, J}, title = {Cyanobacteria and Their Metabolites in Mono- and Polidominant Shallow Eutrophic Temperate Lakes.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {22}, pages = {}, doi = {10.3390/ijerph192215341}, pmid = {36430059}, issn = {1660-4601}, mesh = {*Lakes ; Ecosystem ; *Cyanobacteria ; Biota ; Biomass ; }, abstract = {Monodominant (one species dominates) or polidominant (multiple species dominate) cyanobacterial blooms are pronounced in productive freshwater ecosystems and pose a potential threat to the biota due to the synthesis of toxins. Seasonal changes in cyanobacteria species and cyanometabolites composition were studied in two shallow temperate eutrophic lakes. Data on cyanobacteria biomass and diversity of dominant species in the lakes were combined with chemical and molecular analyses of fifteen potentially toxin-producing cyanobacteria species (248 isolates from the lakes). Anatoxin-a, saxitoxin, microcystins and other non-ribosomal peptides formed the diverse profiles in monodominant (Planktothrix agardhii) and polidominant (Aphanizomenon gracile, Limnothrix spp. and Planktolyngbya limnetica) lakes. However, the harmfulness of the blooms depended on the ability of the dominant species to synthesize cyanometabolites. It was confirmed that P. agardhii produced a greater amount and diverse range of MCs and other NRPs. In the polidominant lake, isolates of the co-dominant A. gracile, L. planctonica and P. limnetica synthesized no or only small amounts of cyanometabolites. In general, the profile of cyanometabolites was greater in cyanobacteria isolates than in environmental samples, indicating a high potential for toxic cyanobacteria bloom.}, }
@article {pmid36427812, year = {2022}, author = {Ramsperger, AFRM and Bergamaschi, E and Panizzolo, M and Fenoglio, I and Barbero, F and Peters, R and Undas, A and Purker, S and Giese, B and Lalyer, CR and Tamargo, A and Moreno-Arribas, MV and Grossart, HP and Kühnel, D and Dietrich, J and Paulsen, F and Afanou, AK and Zienolddiny-Narui, S and Eriksen Hammer, S and Kringlen Ervik, T and Graff, P and Brinchmann, BC and Nordby, KC and Wallin, H and Nassi, M and Benetti, F and Zanella, M and Brehm, J and Kress, H and Löder, MGJ and Laforsch, C}, title = {Nano- and microplastics: a comprehensive review on their exposure routes, translocation, and fate in humans.}, journal = {NanoImpact}, volume = {29}, number = {}, pages = {100441}, doi = {10.1016/j.impact.2022.100441}, pmid = {36427812}, issn = {2452-0748}, abstract = {Contamination of the environment with nano-and microplastic particles (NMPs) and its putative adverse effects on organisms, ecosystems, and human health is gaining increasing scientific and public attention. Various studies show that NMPs occur abundantly within the environment, leading to a high likelihood of human exposure to NMPs. Here, different exposure scenarios can occur. The most notable exposure routes of NMPs into the human body are via the airways and gastrointestinal tract (GIT) through inhalation or ingestion, but also via the skin due to the use of personal care products (PCPs) containing NMPs. Once NMPs have entered the human body, it is possible that they are translocated from the exposed organ to other body compartments. In our review article, we combine the current knowledge on the (1) exposure routes of NMPs to humans with the basic understanding of the potential (2) translocation mechanisms into human tissues and, consequently, their (3) fate within the human body. Regarding the (1) exposure routes, we reviewed the current knowledge on the occurrence of NMPs in food, beverages, personal care products and the air (focusing on indoors and workplaces) and found that the studies suggest an abundant presence of MPs within the exposure scenarios. The overall abundance of MPs in exposure matrices relevant to humans highlights the importance of understanding whether NMPs have the potential for tissue translocation. Therefore, we describe the current knowledge on the potential (2) translocation pathways of NMPs from the skin, GIT and respiratory systems to other body compartments. Here, particular attention was paid to how likely NMPs can translocate from the primary exposed organs to secondary organs due to naturally occurring defence mechanisms against tissue translocation. Based on the current understanding, we conclude that a dermal translocation of NMPs is rather unlikely. In contrast, small MPs and NPs can generally translocate from the GIT and respiratory system to other tissues. Thus, we reviewed the existing literature on the (3) fate of NMPs within the human body. Based on the current knowledge of the contamination of human exposure routes and the potential translocation mechanisms, we critically discuss the size of the detected particles reported in the fate studies. In some cases, the particles detected in human tissue samples exceed the size of a particle to overcome biological barriers allowing particle translocation into tissues. Therefore, we emphasize the importance of critically reading and discussing the presented results of NMP in human tissue samples.}, }
@article {pmid36424853, year = {2022}, author = {Chang, J and Duong, TA and Schoeman, C and Ma, X and Roodt, D and Barker, N and Li, Z and Van de Peer, Y and Mizrachi, E}, title = {The Genome of the King Protea, Protea cynaroides.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.16044}, pmid = {36424853}, issn = {1365-313X}, abstract = {The king protea (Protea cynaroides), an early-diverging eudicot, is the most iconic species from the Megadiverse Cape Floristic Region, and the national flower of South Africa. Perhaps best known for its iconic flower head, Protea is a key genus for the South African horticulture industry and cut-flower market. Ecologically, the genus and the family Proteaceae are important models for radiation and adaptation, particularly to soils with limited phosphorus bio-availability. Here, we present a high-quality chromosome-scale assembly of the P. cynaroides genome as the first representative of the Fynbos biome. We reveal an ancestral Whole-Genome Duplication (WGD) event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family and its extant diversity in all Southern continents. The relatively stable genome structure of P. cynaroides is invaluable for comparative studies and for unveiling paleopolyploidy in other groups, such as the distantly related sister group Ranunculales. Comparative genomics in sequenced genomes of the Proteales shows loss of key arbuscular mycorrhizal symbiosis genes likely ancestral to the Family, and possibly the Order. The P. cynaroides genome empowers new research in plant diversification, horticulture, and adaptation, particularly to nutrient-poor soils.}, }
@article {pmid36423548, year = {2023}, author = {Wu, D and Zhao, J and Su, Y and Yang, M and Dolfing, J and Graham, DW and Yang, K and Xie, B}, title = {Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria.}, journal = {Water research}, volume = {228}, number = {Pt A}, pages = {119359}, doi = {10.1016/j.watres.2022.119359}, pmid = {36423548}, issn = {1879-2448}, mesh = {Humans ; *Drinking Water ; China ; Water Supply ; Bacteria/genetics ; Anti-Bacterial Agents ; }, abstract = {Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 10[6] cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.}, }
@article {pmid36423338, year = {2022}, author = {Abera, S and Shimels, M and Tessema, T and Raaijmakers, JM and Dini-Andreote, F}, title = {Back to the roots: defining the core microbiome of Sorghum bicolor in agricultural field soils from the centre of origin.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, doi = {10.1093/femsec/fiac136}, pmid = {36423338}, issn = {1574-6941}, mesh = {Humans ; *Sorghum ; Soil ; Plant Roots ; *Microbiota/genetics ; Rhizosphere ; Edible Grain ; }, abstract = {Sorghum is a major staple crop in sub-Saharan Africa with yields severely impacted by biotic and abiotic factors. Here, we analysed the taxonomic diversity and biogeographical distribution of bacterial taxa of 48 agricultural fields along a transect of approximately 2000 km across the Ethiopian sorghum belt, the centre of origin of sorghum. The ultimate goal is to identify-yet-unexplored-beneficial plant-microbe associations. Based on bulk soil bacterial communities and DArT-SNP analyses of 59 sorghum accessions, we selected three microbiologically distinct field soils and 12 sorghum genotypes, including commercial varieties, wild relatives, and farmer-preferred landraces. The results showed a core rhizosphere microbiome of 2125 amplicon sequence variants (ASVs), belonging to eight bacterial families consistently found across the three soil types and the 12 sorghum genotypes. Integration of the rhizosphere bacterial community analysis with DArT-SNP sorghum genotyping revealed the association of differentially abundant ASVs with sorghum genotypic traits, including the distinct recruitment of Pseudomonadaceae by the stay-green, drought-tolerant, and wild sorghum genotypes. Collectively, these results provide new insights into the core and accessory bacterial taxa in the sorghum rhizosphere in the centre of origin, setting a baseline for targeted isolation and functional characterization of putative beneficial rhizobacteria.}, }
@article {pmid36422381, year = {2022}, author = {Cantillo-González, A and Anguita, J and Rojas, C and Vargas, IT}, title = {Winogradsky Bioelectrochemical System as a Novel Strategy to Enrich Electrochemically Active Microorganisms from Arsenic-Rich Sediments.}, journal = {Micromachines}, volume = {13}, number = {11}, pages = {}, pmid = {36422381}, issn = {2072-666X}, abstract = {Bioelectrochemical systems (BESs) have been extensively studied for treatment and remediation. However, BESs have the potential to be used for the enrichment of microorganisms that could replace their natural electron donor or acceptor for an electrode. In this study, Winogradsky BES columns with As-rich sediments extracted from an Andean watershed were used as a strategy to enrich lithotrophic electrochemically active microorganisms (EAMs) on electrodes (i.e., cathodes). After 15 months, Winogradsky BESs registered power densities up to 650 μWcm[-2]. Scanning electron microscopy and linear sweep voltammetry confirmed microbial growth and electrochemical activity on cathodes. Pyrosequencing evidenced differences in bacterial composition between sediments from the field and cathodic biofilms. Six EAMs from genera Herbaspirillum, Ancylobacter, Rhodococcus, Methylobacterium, Sphingomonas, and Pseudomonas were isolated from cathodes using a lithoautotrophic As oxidizers culture medium. These results suggest that the tested Winogradsky BES columns result in an enrichment of electrochemically active As-oxidizing microorganisms. A bioelectrochemical boost of centenarian enrichment approaches, such as the Winogradsky column, represents a promising strategy for prospecting new EAMs linked with the biogeochemical cycles of different metals and metalloids.}, }
@article {pmid36421212, year = {2022}, author = {Stoll, ML and Wang, J and Kau, CH and Pierce, MK and Morrow, CD and Geurs, NC}, title = {Pro-Inflammatory Oral Microbiota in Juvenile Spondyloarthritis: A Pilot Study.}, journal = {Children (Basel, Switzerland)}, volume = {9}, number = {11}, pages = {}, pmid = {36421212}, issn = {2227-9067}, support = {P30Ar050948/NH/NIH HHS/United States ; UL1TR000165/NH/NIH HHS/United States ; }, abstract = {The role of the microbiota in the pathogenesis of arthritis is gaining increasing attention. While multiple studies have queried the intestinal microbiota, very few have analyzed the contents of the oral microbiota. In this pilot study, we obtained salivary and sub-gingival specimens from a cohort of six healthy controls and five children with well-controlled spondyloarthritis (SpA) and performed 16S sequencing on bacteria obtained from both habitats. The Quantitative Insight into Microbial Ecology tool suite was used to generate operational taxonomic units, Phyloseq was used for diversity analyses, and DeSeq2 was used to compare abundances while adjusting for multiple comparisons. A repeat specimen was obtained from one subject during a flare. Clustering based upon diagnosis was observed from both habitats, with decreased alpha diversity seen within the plaque obtained from the patients vs. controls. Among the differentially abundant taxa were statistically significantly increased plaque Fusobacterium and salivary Rothia mucilaginosa among the patients compared to the controls. Additionally, the abundance of plaque Fusobacterium increased in one patient at the time of a flare. Our data suggest that the oral cavity may harbor bacteria involved in the pathogenesis of spondyloarthritis; additional studies are warranted.}, }
@article {pmid36419905, year = {2023}, author = {Zhang, X and Arbour, T and Zhang, D and Wei, S and Rabaey, K}, title = {Microbial electrosynthesis of acetate from CO2 under hypersaline conditions.}, journal = {Environmental science and ecotechnology}, volume = {13}, number = {}, pages = {100211}, pmid = {36419905}, issn = {2666-4984}, abstract = {Microbial electrosynthesis (MES) enables the bioproduction of multicarbon compounds from CO2 using electricity as the driver. Although high salinity can improve the energetic performance of bioelectrochemical systems, acetogenic processes under elevated salinity are poorly known. Here MES under 35-60 g L[-1] salinity was evaluated. Acetate production in two-chamber MES systems at 35 g L[-1] salinity (seawater composition) gradually decreased within 60 days, both under -1.2 V cathode potential (vs. Ag/AgCl) and -1.56 A m[-2] reductive current. Carbonate precipitation on cathodes (mostly CaCO3) likely declined the production through inhibiting CO2 supply, the direct electrode contact for acetogens and H2 production. Upon decreasing Ca[2+] and Mg[2+] levels in three-chamber reactors, acetate was stably produced over 137 days along with a low cathode apparent resistance at 1.9 ± 0.6 mΩ m[2] and an average production rate at 3.80 ± 0.21 g m[-2] d[-1]. Increasing the salinity step-wise from 35 to 60 g L[-1] gave the most efficient acetate production at 40 g L[-1] salinity with average rates of acetate production and CO2 consumption at 4.56 ± 3.09 and 7.02 ± 4.75 g m[-2] d[-1], respectively. The instantaneous coulombic efficiency for VFA averaged 55.1 ± 31.4%. Acetate production dropped at higher salinity likely due to the inhibited CO2 dissolution and acetogenic metabolism. Acetobacterium up to 78% was enriched on cathodes as the main acetogen at 35 g L[-1]. Under high-salinity selection, 96.5% Acetobacterium dominated on the cathode along with 34.0% Sphaerochaeta in catholyte. This research provides a first proof of concept that MES starting from CO2 reduction can be achieved at elevated salinity.}, }
@article {pmid36419170, year = {2022}, author = {Chang, J and Tian, L and Leite, MFA and Sun, Y and Shi, S and Xu, S and Wang, J and Chen, H and Chen, D and Zhang, J and Tian, C and Kuramae, EE}, title = {Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {196}, pmid = {36419170}, issn = {2049-2618}, mesh = {*Oryza/microbiology ; Nitrogen ; Carbon ; Manganese ; Iron ; Bacteria/genetics ; Soil ; }, abstract = {BACKGROUND: The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome.<br><br>RESULTS: Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots.<br><br>CONCLUSION: We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract.}, }
@article {pmid36415023, year = {2022}, author = {Baumgartner, M and Zirnbauer, R and Schlager, S and Mertens, D and Gasche, N and Sladek, B and Herbold, C and Bochkareva, O and Emelianenko, V and Vogelsang, H and Lang, M and Klotz, A and Moik, B and Makristathis, A and Berry, D and Dabsch, S and Khare, V and Gasche, C}, title = {Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2143218}, pmid = {36415023}, issn = {1949-0984}, mesh = {Humans ; *Enteropathogenic Escherichia coli/genetics ; *Colitis, Ulcerative ; *Escherichia coli Infections ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; }, abstract = {With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic E. coli (aEPEC) with IBD disease activity. The presence of diarrheagenic E. coli was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins espV and espG2 distinguish aEPEC cultured from UC and Crohn's disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune-microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro.}, }
@article {pmid36413896, year = {2023}, author = {Mijnendonckx, K and Rogiers, T and Giménez Del Rey, FJ and Merroun, ML and Williamson, A and Ali, MM and Charlier, D and Leys, N and Boon, N and Van Houdt, R}, title = {PrsQ2, a small periplasmic protein involved in increased uranium resistance in the bacterium Cupriavidus metallidurans.}, journal = {Journal of hazardous materials}, volume = {444}, number = {Pt A}, pages = {130410}, doi = {10.1016/j.jhazmat.2022.130410}, pmid = {36413896}, issn = {1873-3336}, mesh = {*Uranium/toxicity ; *Cupriavidus/genetics ; Uranyl Nitrate ; Acclimatization ; }, abstract = {Uranium contamination is a widespread problem caused by natural and anthropogenic activities. Although microorganisms thrive in uranium-contaminated environments, little is known about the actual molecular mechanisms mediating uranium resistance. Here, we investigated the resistance mechanisms driving the adaptation of Cupriavidus metallidurans NA4 to toxic uranium concentrations. We selected a spontaneous mutant able to grow in the presence of 1 mM uranyl nitrate compared to 250 µM for the parental strain. The increased uranium resistance was acquired via the formation of periplasmic uranium-phosphate precipitates facilitated by the increased expression of a genus-specific small periplasmic protein, PrsQ2, regulated as non-cognate target of the CzcS2-CzcR2 two-component system. This study shows that bacteria can adapt to toxic uranium concentrations and explicates the complete genetic circuit behind the adaptation.}, }
@article {pmid36413834, year = {2023}, author = {Páez-Watson, T and van Loosdrecht, MCM and Wahl, SA}, title = {Predicting the impact of temperature on metabolic fluxes using resource allocation modelling: Application to polyphosphate accumulating organisms.}, journal = {Water research}, volume = {228}, number = {Pt A}, pages = {119365}, doi = {10.1016/j.watres.2022.119365}, pmid = {36413834}, issn = {1879-2448}, mesh = {Temperature ; *Polyphosphates ; *Resource Allocation ; Biomass ; Sewage ; }, abstract = {The understanding of microbial communities and the biological regulation of its members is crucial for implementation of novel technologies using microbial ecology. One poorly understood metabolic principle of microbial communities is resource allocation and biosynthesis. Resource allocation theory in polyphosphate accumulating organisms (PAOs) is limited as a result of their slow imposed growth rate (typical sludge retention times of at least 4 days) and limitations to quantify changes in biomass components over a 6 hours cycle (less than 10% of their growth). As a result, there is no direct evidence supporting that biosynthesis is an exclusive aerobic process in PAOs that alternate continuously between anaerobic and aerobic phases. Here, we apply resource allocation metabolic flux analysis to study the optimal phenotype of PAOs over a temperature range of 4 °C to 20 °C. The model applied in this research allowed to identify optimal metabolic strategies in a core metabolic model with limited constraints based on biological principles. The addition of a constraint limiting biomass synthesis to be an exclusive aerobic process changed the metabolic behaviour and improved the predictability of the model over the studied temperature range by closing the gap between prediction and experimental findings. The results validate the assumption of limited anaerobic biosynthesis in PAOs, specifically "Candidatus Accumulibacter" related species. Interestingly, the predicted growth yield was lower, suggesting that there are mechanistic barriers for anaerobic growth not yet understood nor reflected in the current models of PAOs. Moreover, we identified strategies of resource allocation applied by PAOs at different temperatures as a result of the decreased catalytic efficiencies of their biochemical reactions. Understanding resource allocation is paramount in the study of PAOs and their currently unknown complex metabolic regulation, and metabolic modelling based on biological first principles provides a useful tool to develop a mechanistic understanding.}, }
@article {pmid36410318, year = {2023}, author = {Kelly, LC and Rivett, DW and Pakostova, E and Creer, S and Cotterell, T and Johnson, DB}, title = {Mineralogy affects prokaryotic community composition in an acidic metal mine.}, journal = {Microbiological research}, volume = {266}, number = {}, pages = {127257}, doi = {10.1016/j.micres.2022.127257}, pmid = {36410318}, issn = {1618-0623}, mesh = {*Archaea ; Acids/metabolism ; Bacteria ; *Microbiota ; Sulfides/metabolism ; Minerals/metabolism ; }, abstract = {The microbial ecology of acidic mine and sulfide cave ecosystems is well characterised with respect to aquatic communities, typically revealing low taxonomic complexity and dominance by a relatively limited number of cosmopolitan acidophilic bacterial and archaeal taxa. Whilst pH, temperature, and geochemistry are recognised drivers of diversity in these ecosystems, the specific question of a possible influence of substratum mineralogy on microbial community composition remains unanswered. Here we address this void, using 81 subterranean mineral samples from a low temperature abandoned, acidic, sulfide ore mine system at Mynydd Parys (Parys Mountain in English), Wales, UK. Four primary and 15 secondary minerals were identified via x-ray diffraction, each sample containing a maximum of five and an average of two minerals. The mineralogy of primary (e.g. pyrite and quartz) and secondary (e.g. melanterite and pisanite) minerals was significantly correlated with prokaryotic community structure at multiple taxonomic levels, implying that the mineralosphere effect reported in less extreme terrestrial environments is also implicated in driving prokaryotic community composition in extremely acidic, base metal-bearing sulfide mineralisation at Mynydd Parys. Twenty phyla were identified, nine of which were abundant (mean relative abundance >1%). While taxa characteristic of acidic mines were detected, for example Leptospirillum (phylum Nitrospirae), Acidithiobacillus (phylum Proteobacteria), Sulfobacillus (phylum Firmicutes) and Ferroplasma (phylum Euryarchaeota), their abundance in individual samples was highly variable. Indeed, in the majority of the 81 samples investigated the abundance of these and other typical acidic mine taxa was low, with 25% of samples devoid of sequences from recognised acidic mine taxa. Most notable amongst the bacterial taxa not previously reported in such environments were the recently cultivated Muribaculaceae family (phylum Bacteroidetes), which often dominated Mynydd Parys samples regardless of their mineralogical content. Our results pose further questions regarding the mechanisms by which taxa not previously reported in such extreme environments appear to survive in Mynydd Parys, opening up research pathways for exploring the biodiversity drivers underlying microbial community composition and function in extremely acidic mine environments.}, }
@article {pmid36409329, year = {2022}, author = {Changey, F and Aissaoui, G and Plain, C and Ranger, J and Legout, A and Zeller, B and Epron, D and Lerch, TZ}, title = {Prolonged Effect of Forest Soil Compaction on Methanogen and Methanotroph Seasonal Dynamics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36409329}, issn = {1432-184X}, abstract = {Methane (CH4) oxidation by methanotrophic bacteria in forest soils is the largest biological sink for this greenhouse gas on earth. However, the compaction of forest soils by logging traffic has previously been shown to reduce the potential rate of CH4 uptake. This change could be due to not only a decrease of methanotrophs but also an increase in methanogen activity. In this study, we investigated whether the decrease in CH4 uptake by forest soils, subjected to compaction by heavy machinery 7 years earlier, can be explained by quantitative and qualitative changes in methanogenic and methanotrophic communities. We measured the functional gene abundance and polymorphism of CH4 microbial oxidizers (pmoA) and producers (mcrA) at different depths and during different seasons. Our results revealed that the soil compaction effect on the abundance of both genes depended on season and soil depth, contrary to the effect on gene polymorphism. Bacterial pmoA abundance was significantly lower in the compacted soil than in the controls across all seasons, except in winter in the 0-10 cm depth interval and in summer in the 10-20 cm depth interval. In contrast, archaeal mcrA abundance was higher in compacted than control soil in winter and autumn in the two soil depths investigated. This study shows the usefulness of using pmoA and mcrA genes simultaneously in order to better understand the spatial and temporal variations of soil CH4 fluxes and the potential effect of physical disturbances.}, }
@article {pmid36407791, year = {2022}, author = {Rawat, D and Sharma, U and Poria, P and Finlan, A and Parker, B and Sharma, RS and Mishra, V}, title = {Iron-dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms the basis for a sustainable bioremediation system.}, journal = {ISME communications}, volume = {2}, number = {}, pages = {83}, pmid = {36407791}, issn = {2730-6151}, abstract = {Phototrophic communities of autotrophic microalgae and heterotrophic bacteria perform complex tasks of nutrient acquisition and tackling environmental stress but remain underexplored as a basis for the bioremediation of emerging pollutants. In industrial monoculture designs, poor iron uptake by microalgae limits their productivity and biotechnological efficacy. Iron supplementation is expensive and ineffective because iron remains insoluble in an aqueous medium and is biologically unavailable. However, microalgae develop complex interkingdom associations with siderophore-producing bacteria that help solubilize iron and increase its bioavailability. Using dye degradation as a model, we combined environmental isolations and synthetic ecology as a workflow to design a simplified microbial community based on iron and carbon exchange. We established a mutualism between the previously non-associated alga Chlorella sorokiniana and siderophore-producing bacterium Ralstonia pickettii. Siderophore-mediated increase in iron bioavailability alleviated Fe stress for algae and increased the reductive iron uptake mechanism and bioremediation potential. In exchange, C. sorokiniana produced galactose, glucose, and mannose as major extracellular monosaccharides, supporting bacterial growth. We propose that extracellular iron reduction by ferrireductase is crucial for azoreductase-mediated dye degradation in microalgae. These results demonstrate that iron bioavailability, often overlooked in cultivation, governs microalgal growth, enzymatic processes, and bioremediation potential. Our results suggest that phototrophic communities with an active association for iron and carbon exchange have the potential to overcome challenges associated with micronutrient availability, while scaling up bioremediation designs.}, }
@article {pmid36406446, year = {2022}, author = {Guo, R and Ma, X and Zhang, J and Liu, C and Thu, CA and Win, TN and Aung, NL and Win, HS and Naing, S and Li, H and Zhou, F and Wang, P}, title = {Microbial community structures and important taxa across oxygen gradients in the Andaman Sea and eastern Bay of Bengal epipelagic waters.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1041521}, pmid = {36406446}, issn = {1664-302X}, abstract = {In oceanic oxygen minimum zones (OMZs), the abundances of aerobic organisms significantly decrease and energy shifts from higher trophic levels to microorganisms, while the microbial communities become critical drivers of marine biogeochemical cycling activities. However, little is known of the microbial ecology of the Andaman Sea and eastern Bay of Bengal (BoB) OMZs. In the present study, a total of 131 samples which from the Andaman Sea and eastern BoB epipelagic waters were analyzed. The microbial community distribution patterns across oxygen gradients, including oxygenic zones (OZs, dissolved oxygen [DO] ≥ 2 mg/L), oxygen limited zones (OLZs, 0.7 mg/L < DO < 2 mg/L), and OMZs (DO ≤ 0.7 mg/L), were investigated. Mantel tests and Spearman's correlation analysis revealed that DO was the most important driver of microbial community structures among several environmental factors. Microbial diversity, richness, and evenness were highest in the OLZs and lowest in the OZs. The microbial community compositions of OZ and OMZ waters were significantly different. Random forest analysis revealed 24 bioindicator taxa that differentiated OZ, OLZ, and OMZ water communities. These bioindicator taxa included Burkholderiaceae, HOC36, SAR11 Clade IV, Thioglobaceae, Nitrospinaceae, SAR86, and UBA10353. Further, co-occurrence network analysis revealed that SAR202, AEGEAN-169, UBA10353, SAR406, and Rhodobacteraceae were keystone taxa among the entire interaction network of the microbial communities. Functional prediction further indicated that the relative abundances of microbial populations involved in nitrogen and sulfur cycling were higher in OMZs. Several microbial taxa, including the Thioglobaceae, Nitrospinaceae, SAR202, SAR406, WPS-2, UBA10353, and Woeseiaceae, may be involved in nitrogen and/or sulfur cycling, while also contributing to oxygen consumption in these waters. This study consequently provides new insights into the microbial community structures and potentially important taxa that contribute to oxygen consumption in the Andaman Sea and eastern BoB OMZ.}, }
@article {pmid36401317, year = {2022}, author = {Nata'ala, MK and Avila Santos, AP and Coelho Kasmanas, J and Bartholomäus, A and Saraiva, JP and Godinho Silva, S and Keller-Costa, T and Costa, R and Gomes, NCM and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Nunes da Rocha, U}, title = {MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {57}, pmid = {36401317}, issn = {2524-6372}, abstract = {BACKGROUND: Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST.<br><br>RESULTS: In total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature&#xa0;and oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most samples were sequenced using Illumina sequencing technology (84.33%). More than 55% of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as 'ocean'. The 'Quick Search' and 'Advanced Search' tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allows easy download of raw sequence data of selected samples from their respective repositories. As a use case, we demonstrated how to use the&#xa0;MarineMetagenomeDB web app to select estuarine metagenomes for&#xa0;potential large-scale microbial biogeography studies.<br><br>CONCLUSION: The MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/ .}, }
@article {pmid36400616, year = {2022}, author = {Secchi, G and Amalfitano, N and Carafa, I and Franciosi, E and Gallo, L and Schiavon, S and Sturaro, E and Tagliapietra, F and Bittante, G}, title = {Milk metagenomics and cheese-making properties as affected by indoor farming and summer highland grazing.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2022-22449}, pmid = {36400616}, issn = {1525-3198}, abstract = {The study of the complex relationships between milk metagenomics and milk composition and cheese-making efficiency as affected by indoor farming and summer highland grazing was the aim of the present work. The experimental design considered monthly sampling (over 5 mo) of the milk produced by 12 Brown Swiss cows divided into 2 groups: the first remained on a lowland indoor farm from June to October, and the second was moved to highland pastures in July and then returned to the lowland farm in September. The resulting 60 milk samples (2 kg each) were used to analyze milk composition, milk coagulation, curd firming, and syneresis processes, and to make individual model cheeses to measure cheese yields and nutrient recoveries in the cheese. After DNA extraction and Illumina Miseq sequencing, milk microbiota amplicons were also processed by means of an open-source pipeline called Quantitative Insights Into Microbial Ecology (Qiime2, version 2018.2; https://qiime2.org). Out of a total of 44 taxa analyzed, 13 bacterial taxa were considered important for the dairy industry (lactic acid bacteria, LAB, 5 taxa; and spoilage bacteria, 4) and for human (other probiotics, 2) and animal health (pathogenic bacteria, 2). The results revealed the transhumant group of cows transferred to summer highland pastures showed an increase in almost all the LAB taxa, bifidobacteria, and propionibacteria, and a reduction in spoilage taxa. All the metagenomic changes disappeared when the transhumant cows were moved back to the permanent indoor farm. The relationships between 17 microbial traits and 30 compositional and technological milk traits were investigated through analysis of correlation and latent explanatory factor analysis. Eight latent factors were identified, explaining 75.3% of the total variance, 2 of which were mainly based on microbial traits: pro-dairy bacteria (14% of total variance, improving during summer pasturing) and pathogenic bacteria (6.0% of total variance). Some bacterial traits contributed to other compositional-technological latent factors (gelation, udder health, and caseins).}, }
@article {pmid36399842, year = {2022}, author = {Li, Y and Ling, J and Xue, J and Huang, J and Zhou, X and Wang, F and Hou, W and Zhao, J and Xu, Y}, title = {Acute stress of the typical disinfectant glutaraldehyde-didecyldimethylammonium bromide (GD) on sludge microecology in livestock wastewater treatment plants: Effect and its mechanisms.}, journal = {Water research}, volume = {227}, number = {}, pages = {119342}, doi = {10.1016/j.watres.2022.119342}, pmid = {36399842}, issn = {1879-2448}, mesh = {Swine ; Animals ; Sewage ; *Disinfectants/pharmacology ; Glutaral/pharmacology ; Livestock ; *African Swine Fever ; Reactive Oxygen Species ; *COVID-19 ; *Water Purification ; Nitrogen ; }, abstract = {Glutaraldehyde and didecyldimethylammonium bromide (GD) is a disinfectant widely used to prevent African swine fever (ASF) in livestock farms. However, the effect of residual GD on the activated sludge microbial ecology of receiving wastewater treatment plants (WWTPs) remains largely unknown. In this study, seven simulated systems were established to research the effects of GD on WWTPs and reveal the underlying mechanisms of microecological responses to GD at different concentrations. Both the nitrogen and carbon removal rates decreased with increasing GD concentrations, and nitrogen metabolism was inhibited more obviously, but the inhibition weakened with increasing stress duration. Microorganisms activated their SoxRS systems to promote ATP synthesis and electron transfer to support the hydrolysis and efflux of GD by producing a small number of ROS when exposed to GD at less than 1 mg/L. The overproduction of ROS led to a decrease of antioxidant and nitrogen removal enzyme activities, and upregulation of the porin gene increased the risk of GD entering the intracellular space upon exposure to GD at concentrations higher than 1 mg/L. Some denitrifiers survived via resistance and their basic capabilities of sugar metabolism and nitrogen assimilation. Notably, low concentrations of disinfectants could promote vertical and horizontal transfer of multiple resistance genes, especially aminoglycosides, among microorganisms, which might increase not only the adaptation capability of denitrifiers but also the risk to ecological systems. Therefore, the risks of disinfectants targeting ASF on ecology and health as well as the effects of disinfectant residuals from the COVID-19 epidemic should receive more attention.}, }
@article {pmid36399746, year = {2022}, author = {Sinclair, P and Brackley, CA and Carballo-Pacheco, M and Allen, RJ}, title = {Model for Quorum-Sensing Mediated Stochastic Biofilm Nucleation.}, journal = {Physical review letters}, volume = {129}, number = {19}, pages = {198102}, doi = {10.1103/PhysRevLett.129.198102}, pmid = {36399746}, issn = {1079-7114}, mesh = {*Quorum Sensing ; *Biofilms ; Bacteria ; }, abstract = {Surface-attached bacterial biofilms cause disease and industrial biofouling, as well as being widespread in the natural environment. Density-dependent quorum sensing is one of the mechanisms implicated in biofilm initiation. Here we present and analyze a model for quorum-sensing triggered biofilm initiation. In our model, individual, planktonic bacteria adhere to a surface, proliferate, and undergo a collective transition to a biofilm phenotype. This model predicts a stochastic transition between a loosely attached, finite layer of bacteria near the surface and a growing biofilm. The transition is governed by two key parameters: the collective transition density relative to the carrying capacity and the immigration rate relative to the detachment rate. Biofilm initiation is complex, but our model suggests that stochastic nucleation phenomena may be relevant.}, }
@article {pmid36399658, year = {2022}, author = {Simmer, RA and Schnoor, JL}, title = {Phytoremediation, Bioaugmentation, and the Plant Microbiome.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {23}, pages = {16602-16610}, doi = {10.1021/acs.est.2c05970}, pmid = {36399658}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; *Soil Pollutants/metabolism ; Plants/metabolism ; Soil ; *Microbiota ; }, abstract = {Understanding plant biology and related microbial ecology as a means to phytoremediate soil and groundwater contamination has broadened and advanced the field of environmental engineering and science over the past 30 years. Using plants to transform and degrade xenobiotic organic pollutants delivers new methods for environmental restoration. Manipulations of the plant microbiome through bioaugmentation, endophytes, adding various growth factors, genetic modification, and/or selecting the microbial community via insertion of probiotics or phages for gene transfer are future areas of research to further expand this green, cost-effective, aesthetically pleasing technology─phytoremediation.}, }
@article {pmid36399496, year = {2022}, author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac1049}, pmid = {36399496}, issn = {1362-4962}, support = {GM134688/NH/NIH HHS/United States ; BBSRC/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.}, }
@article {pmid36396943, year = {2022}, author = {Minich, JJ and Härer, A and Vechinski, J and Frable, BW and Skelton, ZR and Kunselman, E and Shane, MA and Perry, DS and Gonzalez, A and McDonald, D and Knight, R and Michael, TP and Allen, EE}, title = {Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6978}, pmid = {36396943}, issn = {2041-1723}, mesh = {Animals ; Biomass ; *Fishes ; Ecology ; *Microbiota ; Gills ; Vertebrates ; Mammals ; }, abstract = {Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.}, }
@article {pmid36388928, year = {2022}, author = {Plunder, S and Burkard, M and Lauer, UM and Venturelli, S and Marongiu, L}, title = {Determination of phage load and administration time in simulated occurrences of antibacterial treatments.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1040457}, pmid = {36388928}, issn = {2296-858X}, abstract = {The use of phages as antibacterials is becoming more and more common in Western countries. However, a successful phage-derived antibacterial treatment needs to account for additional features such as the loss of infective virions and the multiplication of the hosts. The parameters critical inoculation size (V F) and failure threshold time (T F) have been introduced to assure that the viral dose (V ϕ) and administration time (T ϕ) would lead to the extinction of the targeted bacteria. The problem with the definition of V F and T F is that they are non-linear equations with two unknowns; thus, obtaining their explicit values is cumbersome and not unique. The current study used machine learning to determine V F and T F for an effective antibacterial treatment. Within these ranges, a Pareto optimal solution of a multi-criterial optimization problem (MCOP) provided a pair of V ϕ and T ϕ to facilitate the user's work. The algorithm was tested on a series of in silico microbial consortia that described the outgrowth of a species at high cell density by another species initially present at low concentration. The results demonstrated that the MCOP-derived pairs of V ϕ and T ϕ could effectively wipe out the bacterial target within the context of the simulation. The present study also introduced the concept of mediated phage therapy, where targeting booster bacteria might decrease the virulence of a pathogen immune to phagial infection and highlighted the importance of microbial competition in attaining a successful antibacterial treatment. In summary, the present work developed a novel method for investigating phage/bacteria interactions that can help increase the effectiveness of the application of phages as antibacterials and ease the work of microbiologists.}, }
@article {pmid36386706, year = {2022}, author = {Zhao, M and Zhang, H and Pan, G and Yin, H and Sun, J and Yu, Z and Bai, C and Xue, Y}, title = {Effect of exogenous microorganisms on the fermentation quality, nitrate degradation and bacterial community of sorghum-sudangrass silage.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1052837}, pmid = {36386706}, issn = {1664-302X}, abstract = {This study aims to investigate the effects of adding Lactobacillus buchneri (LB), Lactobacillus brevis (LBR) and Bacillus subtilis (BS) on the fermentation quality, nitrate degradation and bacterial community of sorghum-sudangrass silage. The results showed that the addition of LB significantly increased the pH and acetic acid content (p < 0.05), but high-quality silage was obtained. The addition of LBR and BS improved the fermentation quality of sorghum-sudangrass silage. The use of additives reduced the nitrate content in sorghum-sudangrass silage. The LB group increased the release of N2O at 3-7 days of ensiling (p < 0.05), and LBR and BS increased the release of N2O at 1-40 days of ensiling (p < 0.05). On the first day of ensiling, all silages were dominated by Weisslla, over 3 days of ensiling all silages were dominated by Lactobacillus. Acinetobacter, Serratia, Aquabacterium, and unclassified_f_enterobacteriaceae showed significant negative correlations with nitrate degradation during sorghum-sudangrass ensiling (p < 0.05). The BS and LBR groups increased the metabolic abundance of denitrification, dissimilatory nitrate reduction, and assimilatory nitrate reduction (p < 0.05). Overall, the additive ensures the fermentation quality of sorghum-sudangrass silage and promotes the degradation of nitrate by altering the bacterial community.}, }
@article {pmid36386657, year = {2022}, author = {Liu, J and Wang, X and Liu, J and Liu, X and Zhang, XH and Liu, J}, title = {Comparison of assembly process and co-occurrence pattern between planktonic and benthic microbial communities in the Bohai Sea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1003623}, pmid = {36386657}, issn = {1664-302X}, abstract = {Unraveling the mechanisms structuring microbial community is a central goal in microbial ecology, but a detailed understanding of how community assembly processes relate to living habitats is still lacking. Here, via 16S rRNA gene amplicon sequencing, we investigated the assembly process of microbial communities in different habitats [water verse sediment, free-living (FL) verse particle-associated (PA)] and their impacts on the inter-taxa association patterns in the coastal Bohai Sea, China. The results showed clear differences in the composition and diversity of microbial communities among habitats, with greater dissimilarities between water column and sediment than between FL and PA communities. The microbial community assembly was dominated by dispersal limitation, ecological drift, and homogeneous selection, but their relative importance varied in different habitats. The planktonic communities were mainly shaped by dispersal limitation and ecological drift, whereas homogeneous selection played a more important role in structuring the benthic communities. Furthermore, the assembly mechanisms differed between FL and PA communities, especially in the bottom water with a greater effect of ecological drift and dispersal limitation on the FL and PA fractions, respectively. Linking assembly process to co-occurrence pattern showed that the relative contribution of deterministic processes (mainly homogeneous selection) increased under closer co-occurrence relationships. By contrast, stochastic processes exerted a higher effect when there were less inter-taxa connections. Overall, our findings demonstrate contrasting ecological processes underpinning microbial community distribution in different habitats including different lifestyles, which indicate complex microbial dynamic patterns in coastal systems with high anthropogenic perturbations.}, }
@article {pmid36386638, year = {2022}, author = {Djeni, TN and Keisam, S and Kouame, KH and Assohoun-Djeni, CN and Ake, FDM and Amoikon, LST and Tuikhar, N and Labala, RK and Dje, MK and Jeyaram, K}, title = {Dynamics of microbial populations and metabolites of fermenting saps throughout tapping process of ron and oil palm trees in Côte d'Ivoire.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {954917}, pmid = {36386638}, issn = {1664-302X}, abstract = {Palm wine fermentation is a complex microbial process that evolves with tapping times. The dynamics in microbiota and metabolites throughout palm wine tapping days is still not established, which are critical for the distinctive characteristics of palm wine taste and quality, and thus the mastery of the daily quality fluctuation during tapping. We analyzed the changes in microbial community structure by amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region, and metabolite profile changes using mass spectrometry in palm wine collected over 25-30 days tapping of ron (Borassus aethiopum) and oil palms (Elaeis guineensis) from Côte d'Ivoire. The stage-wise collected palm wine samples showed distinct changes in microbial diversity and pH, supporting microbial community dynamics during palm wine tapping. Results highlighted the dominance of Saccharomyces cerevisiae in early stages and the emergence of non-Saccharomyces yeasts, particularly Hanseniaspora spp. in the later stages of oil palm wine tapping, vice versa in the case of ron palm wine tapping, with a unique presence of Saccharomycodes in the later stages (15-30 days). Fructophilic lactic acid bacteria (FLAB), mainly Fructobacillus and Leuconostoc, encountered in both types of palm wine tapping showed a decline at later stages of oil palm wine tapping. In this type of palm wine, acetic acid bacteria with genera Acetobacter and Glucanoacetobacter, by surpassing Lactobacillus in the last stage become dominant, whereas Lactobacillus remained dominant in ron palm wine throughout tapping days. The decline in the relative abundance of gevotroline and essential amino acids during the later stages of palm wine tapping (15-25 days) supports the difference in the health benefits of the palm wine obtained from different days of tapping, indicating that early stages of tapping is more nutritional and healthy than the later stages. The microbial dynamics may be a potential indicator of metabolite changes during palm sap fermentation, thus contributing to establish particular features of palm wines in different stages of tapping. This understanding of microbial ecology and chemical composition changes during palm wine tapping can be used as biomarkers to assess palm wine's quality and help to design an optimum starter culture.}, }
@article {pmid36385637, year = {2022}, author = {Natalini, JG and Singh, S and Segal, LN}, title = {The dynamic lung microbiome in health and disease.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {1-14}, pmid = {36385637}, issn = {1740-1534}, abstract = {New methods and technologies within the field of lung biology are beginning to shed new light into the microbial world of the respiratory tract. Long considered to be a sterile environment, it is now clear that the human lungs are frequently exposed to live microbes and their by-products. The nature of the lung microbiome is quite distinct from other microbial communities inhabiting our bodies such as those in the gut. Notably, the microbiome of the lung exhibits a low biomass and is dominated by dynamic fluxes of microbial immigration and clearance, resulting in a bacterial burden and microbiome composition that is fluid in nature rather than fixed. As our understanding of the microbial ecology of the lung improves, it is becoming increasingly apparent that certain disease states can disrupt the microbial-host interface and ultimately affect disease pathogenesis. In this Review, we provide an overview of lower airway microbial dynamics in health and disease and discuss future work that is required to uncover novel therapeutic targets to improve lung health.}, }
@article {pmid36384808, year = {2022}, author = {Park, J and Davis, K and Lajoie, G and Parfrey, LW}, title = {Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {55}, pmid = {36384808}, issn = {2524-6372}, abstract = {BACKGROUND: Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites.<br><br>RESULTS: We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (>&#x2009;6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250&#xa0;km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus.<br><br>CONCLUSIONS: Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.}, }
@article {pmid36383236, year = {2022}, author = {Peralta-Maraver, I and Rutere, C and Horn, MA and Reche, I and Behrends, V and Reiss, J and Robertson, AL}, title = {Correction to: Intermediate levels of predation and nutrient enrichment enhance the activity of ibuprofen degrading bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-022-02145-y}, pmid = {36383236}, issn = {1432-184X}, }
@article {pmid36378688, year = {2022}, author = {Bermúdez-Méndez, E and Bronsvoort, KF and Zwart, MP and van de Water, S and Cárdenas-Rey, I and Vloet, RPM and Koenraadt, CJM and Pijlman, GP and Kortekaas, J and Wichgers Schreur, PJ}, title = {Incomplete bunyavirus particles can cooperatively support virus infection and spread.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001870}, pmid = {36378688}, issn = {1545-7885}, mesh = {Animals ; Humans ; *Rift Valley fever virus/genetics ; *Orthobunyavirus ; *Rift Valley Fever/genetics/metabolism ; *Virus Diseases ; Virion/metabolism ; *Culicidae ; *Arboviruses ; Mammals ; }, abstract = {Bunyaviruses lack a specific mechanism to ensure the incorporation of a complete set of genome segments into each virion, explaining the generation of incomplete virus particles lacking one or more genome segments. Such incomplete virus particles, which may represent the majority of particles produced, are generally considered to interfere with virus infection and spread. Using the three-segmented arthropod-borne Rift Valley fever virus as a model bunyavirus, we here show that two distinct incomplete virus particle populations unable to spread autonomously are able to efficiently complement each other in both mammalian and insect cells following co-infection. We further show that complementing incomplete virus particles can co-infect mosquitoes, resulting in the reconstitution of infectious virus that is able to disseminate to the mosquito salivary glands. Computational models of infection dynamics predict that incomplete virus particles can positively impact virus spread over a wide range of conditions, with the strongest effect at intermediate multiplicities of infection. Our findings suggest that incomplete particles may play a significant role in within-host spread and between-host transmission, reminiscent of the infection cycle of multipartite viruses.}, }
@article {pmid36378579, year = {2022}, author = {Matassa, S and Boeckx, P and Boere, J and Erisman, JW and Guo, M and Manzo, R and Meerburg, F and Papirio, S and Pikaar, I and Rabaey, K and Rousseau, D and Schnoor, J and Smith, P and Smolders, E and Wuertz, S and Verstraete, W}, title = {How can we possibly resolve the planet's nitrogen dilemma?.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14159}, pmid = {36378579}, issn = {1751-7915}, abstract = {Nitrogen is the most crucial element in the production of nutritious feeds and foods. The production of reactive nitrogen by means of fossil fuel has thus far been able to guarantee the protein supply for the world population. Yet, the production and massive use of fertilizer nitrogen constitute a major threat in terms of environmental health and sustainability. It is crucial to promote consumer acceptance and awareness towards proteins produced by highly effective microorganisms, and their potential to replace proteins obtained with poor nitrogen efficiencies from plants and animals. The fact that reactive fertilizer nitrogen, produced by the Haber Bosch process, consumes a significant amount of fossil fuel worldwide is of concern. Moreover, recently, the prices of fossil fuels have increased the cost of reactive nitrogen by a factor of 3 to 5 times, while international policies are fostering the transition towards a more sustainable agro-ecology by reducing mineral fertilizers inputs and increasing organic farming. The combination of these pressures and challenges opens opportunities to use the reactive nitrogen nutrient more carefully. Time has come to effectively recover used nitrogen from secondary resources and to upgrade it to a legal status of fertilizer. Organic nitrogen is a slow-release fertilizer, it has a factor of 2.5 or higher economic value per unit nitrogen as fertilizer and thus adequate technologies to produce it, for instance by implementing photobiological processes, are promising. Finally, it appears wise to start the integration in our overall feed and food supply chains of the exceptional potential of biological nitrogen fixation. Nitrogen produced by the nitrogenase enzyme, either in the soil or in novel biotechnology reactor systems, deserves to have a 'renaissance' in the context of planetary governance in general and the increasing number of people who desire to be fed in a sustainable way in particular.}, }
@article {pmid36374338, year = {2022}, author = {Yan, Y and Xie, Y and Zhang, J and Li, R and Ali, A and Cai, Z and Huang, X and Liu, L}, title = {Effects of Reductive Soil Disinfestation Combined with Liquid-Readily Decomposable Compounds and Solid Plant Residues on the Bacterial Community and Functional Composition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36374338}, issn = {1432-184X}, abstract = {Reductive soil disinfestation (RSD) incorporated with sole plant residues or liquid-readily decomposable compounds is an effective management strategy to improve soil health. However, the synthetic effects of RSD incorporated with liquid-readily decomposable compounds and solid plant residues on soil ecosystem services remain unclear. Field experiments were carried out to investigate the effects of untreated soil (CK), RSD incorporated with sawdust (SA), molasses (MO), and their combinations (SA + MO) on the bacterial community and functional composition. The results showed that RSD treatments significantly altered soil bacterial community structure compared to CK treatment. The bacterial community structure and composition in MO and SA + MO treatments were clustered compared to SA treatment. This was mainly attributed to the readily decomposable carbon sources in molasses having a stronger driving force to reshape the soil microbial community during the RSD process. Furthermore, the functional compositions, such as the disinfestation efficiency of F. oxysporum (96.4 - 99.1%), abundances of nitrogen functional genes, soil metabolic activity, and functional diversity, were significantly increased in all of the RSD treatments. The highest disinfestation efficiency and abundances of denitrification (nirS and nrfA) and nitrogen fixation (nifH) genes were observed in SA + MO treatment. Specifically, SA + MO treatment enriched more abundant beneficial genera, e.g., Oxobacter, Paenibacillus, Cohnella, Rummeliibacillus, and Streptomyces, which were significantly and positively linked to disinfestation efficiency, soil metabolic activity, and denitrification processes. Our results indicated that combining RSD practices with liquid-readily decomposable compounds and solid plant residues could effectively improve soil microbial community and functional composition.}, }
@article {pmid36374046, year = {2022}, author = {Agarwal, V and Inomura, K and Mouw, CB}, title = {Quantitative Analysis of the Trade-Offs of Colony Formation for Trichodesmium.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0202522}, doi = {10.1128/spectrum.02025-22}, pmid = {36374046}, issn = {2165-0497}, abstract = {There is considerable debate about the benefits and trade-offs for colony formation in a major marine nitrogen fixer, Trichodesmium. To quantitatively analyze the trade-offs, we developed a metabolic model based on carbon fluxes to compare the performance of Trichodesmium colonies and free trichomes under different scenarios. Despite reported reductions in carbon fixation and nitrogen fixation rates for colonies relative to free trichomes, we found that model colonies can outperform individual cells in several cases. The formation of colonies can be advantageous when respiration rates account for a high proportion of the carbon fixation rate. Negative external influence on vital rates, such as mortality due to predation or micronutrient limitations, can also create a net benefit for colony formation relative to individual cells. In contrast, free trichomes also outcompete colonies in many scenarios, such as when respiration rates are equal for both colonies and individual cells or when there is a net positive external influence on rate processes (i.e., optimal environmental conditions regarding light and temperature or high nutrient availability). For both colonies and free trichomes, an increase in carbon fixation relative to nitrogen fixation rates would increase their relative competitiveness. These findings suggest that the formation of colonies in Trichodesmium might be linked to specific environmental and ecological circumstances. Our results provide a road map for empirical studies and models to evaluate the conditions under which colony formation in marine phytoplankton can be sustained in the natural environment. IMPORTANCE Trichodesmium is a marine filamentous cyanobacterium that fixes nitrogen and is an important contributor to the global nitrogen cycle. In the natural environment, Trichodesmium can exist as individual cells (trichomes) or as colonies (puffs and tufts). In this paper, we try to answer a longstanding question in marine microbial ecology: how does colony formation benefit the survival of Trichodesmium? To answer this question, we developed a carbon flux model that utilizes existing published rates to evaluate whether and when colony formation can be sustained. Enhanced respiration rates, influential external factors such as environmental conditions and ecological interactions, and variable carbon and nitrogen fixation rates can all create scenarios for colony formation to be a viable strategy. Our results show that colony formation is an ecologically beneficial strategy under specific conditions, enabling Trichodesmium to be a globally significant organism.}, }
@article {pmid36373138, year = {2022}, author = {Hillary, LS and Adriaenssens, EM and Jones, DL and McDonald, JE}, title = {RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels.}, journal = {ISME communications}, volume = {2}, number = {}, pages = {34}, pmid = {36373138}, issn = {2730-6151}, support = {BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The distribution and diversity of RNA viruses in soil ecosystems are largely unknown, despite their significant impact on public health, ecosystem functions, and food security. Here, we characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3462 viral contigs in RNA viromes from purified virus-like-particles in five soil-types and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited minimal similarity in viral community composition, but with >10-fold more viral contigs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses predicted soil RNA viral communities are formed from viruses of bacteria, plants, fungi, vertebrates and invertebrates, with only 12% of viral contigs belonging to the bacteria-infecting Leviviricetes class. 11% of viral contigs were found to be most closely related to members of the Ourmiavirus genus, suggesting that members of this clade of plant viruses may be far more widely distributed and diverse than previously thought. These results contrast with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities, therefore, have the potential to exert influence on inter-kingdom interactions across terrestrial biomes.}, }
@article {pmid36372840, year = {2022}, author = {Ye, G and Chen, J and Yang, P and Hu, HW and He, ZY and Wang, D and Cao, D and Zhang, W and Wu, B and Wu, Y and Wei, X and Lin, Y}, title = {Non-native Plant Species Invasion Increases the Importance of Deterministic Processes in Fungal Community Assembly in a Coastal Wetland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36372840}, issn = {1432-184X}, abstract = {Fungal communities are essential to the maintenance of soil multifunctionality. Plant invasion represents a growing challenge for the conservation of soil biodiversity across the globe, but the impact of non-native species invasion on fungal diversity, community structure, and assembly processes remains largely unknown. Here, we examined the diversity, community composition, functional guilds, and assembly process of fungi at three soil depths underneath a native species, three non-native species, and a bare tidal flat from a coastal wetland. Plant species was more important than soil depth in regulating the diversity, community structure, and functional groups of fungi. Non-native species, especially Spartina alterniflora, increased fungal diversity, altered fungal community structure, and increased the relative abundance of saprotrophic and pathogenic fungi in coastal wetland soils. Stochastic processes played a predominant role in driving fungal community assembly, explaining more than 70% of the relative contributions. However, compared to a native species, non-native species, especially S. alterniflora, reduced the relative influence of stochastic processes in fungal community assembly. Collectively, our results provide novel evidence that non-native species can increase fungal diversity, the relative abundance of saprotrophic and pathogenic fungi, and deterministic processes in the assembly of fungi in coastal wetlands, which can expand our knowledge of the dynamics of fungal communities in subtropical coastal wetlands.}, }
@article {pmid36370453, year = {2022}, author = {Alfradique Monteiro, D and Fazolato, CSB and Martins, LF and Tavora Coelho da Costa Rachid, C}, title = {The bacteriome of the halophyte Atriplex nummularia (old man saltbush) in salt-affected soils - an ecological model.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, doi = {10.1093/femsec/fiac135}, pmid = {36370453}, issn = {1574-6941}, mesh = {Humans ; Male ; *Atriplex/genetics ; Salt-Tolerant Plants/microbiology ; Soil ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; Bacteria/genetics ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {Halophytes, plants capable of growing under saline conditions, are an important source of bacteria with biotechnological potential for plant growth under extreme conditions. In this study, we evaluated the halophyte Atriplex nummularia bacteriome assemblage from three different salinized sites in northeastern Brazil with different edaphoclimatic characteristics, understanding the participation of the plant in the assembly of its microbiome. We sampled 30 specimens, from which the leaves, roots, and rhizospheric soil were subjected to 16S rRNA gene sequencing, bringing forth patterns of alpha and beta diversity, taxonomical composition, co-occurrence network, and the core microbiome of each compartment. Overall, this species harbors a very restricted set of endophytic microbes, and communities showed an increasing gradient of complexity (soil > root > leaf), reflecting a change in the main selective pressure being active over the microbial community. Although the leaf bacteriome was influenced basically by host factors, the soil community was modulated by the environment, and the root bacteriome was structured by both factors. These results help us understand how plant-microbe interactions occur in saline environments. As these plants shelter microbes that potentially alleviate abiotic stresses, we discuss how culture-independent methods could contribute to the prospection of plant growth promoting bacteria in plants.}, }
@article {pmid36369598, year = {2022}, author = {Havenga, M and Halleen, F and Baloyi, A and Bester, M and Linde, CC and Mostert, L}, title = {Predominant Clonal Reproduction with Infrequent Genetic Recombination of Phaeoacremonium minimum in Western Cape Vineyards.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36369598}, issn = {1432-184X}, abstract = {Phaeoacremonium minimum is an important esca and Petri disease pathogen that causes dieback of grapevines in South Africa. Little is known regarding the reproductive strategy of the pathogen. Sexual reproduction could lead to a better adaptation of the pathogen to disease management strategies by combining alleles through recombination. The study aimed to investigate the genetic diversity and recombination potential of eight populations in the Western Cape, from six commercial vineyards and two nursery rootstock mother blocks. This was achieved by developing and applying nine polymorphic microsatellites and mating-type-specific markers. Thirty-seven genotypes were identified from 295 isolates. Populations were characterised by the same dominant genotype (MLG20 occurring 65.43%), low genotypic diversity (H) and high numbers of clones (81.36% of dataset). However, genotypes from the same sampling sites were not closely related based on a minimum spanning network and had high molecular variation within populations (94%), suggesting that multiple introductions of different genotypes occurred over time. Significant linkage disequilibrium among loci (r̅d) further indicated a dominant asexual cycle, even though perithecia have been observed in these four populations. The two rootstock mother blocks had unique genotypes and genotypes shared with the vineyard populations. Propagation material obtained from infected rootstock mother blocks could lead to the spread of more genotypes to newly established vineyards. Based on our results, it is important to determine the health status of rootstock mother blocks. Management strategies must focus on reducing aerial inoculum to prevent repeated infections and further spread of P. minimum genotypes.}, }
@article {pmid36368693, year = {2022}, author = {Poppeliers, SWM and Hefting, M and Dorrepaal, E and Weedon, JT}, title = {Functional microbial ecology in arctic soils: the need for a year-round perspective.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, pmid = {36368693}, issn = {1574-6941}, mesh = {*Soil ; Arctic Regions ; Climate Change ; Carbon Cycle ; *Microbiota ; }, abstract = {The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.}, }
@article {pmid36368382, year = {2022}, author = {Monahan, C and Morris, D and Nag, R and Cummins, E}, title = {Risk ranking of macrolide antibiotics - Release levels, resistance formation potential and ecological risk.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 2}, pages = {160022}, doi = {10.1016/j.scitotenv.2022.160022}, pmid = {36368382}, issn = {1879-1026}, abstract = {Antibiotic resistance (AR) development in natural water bodies is a significant source of concern. Macrolide antibiotics in particular have been identified as pollutants of concern for AR development throughout the literature, as well as by state and international authorities. This study utilises a probabilistic model to examine the risk of AR development arising from human-use macrolide residues, utilising administration rates from Ireland as a case study. Stages modelled included level of administration, excretion, degradation in wastewater, removal in wastewater treatment, assuming conventional activated sludge (CAS) treatment, and dilution. Release estimates per day, as well as risk quotient values for antibiotic resistance development and ecological impact, are generated for erythromycin, clarithromycin, and azithromycin. In the modelled scenario in which conventional activated sludge treatment is utilised in wastewater treatment, this model ranks risk of resistance development for each antibiotic in the order clarithromycin > azithromycin > erythromycin, with mean risk quotient values of 0.50, 0.34 and 0.12, respectively. A membrane bioreactor scenario was also modelled, which reduced risk quotient values for all three macrolides by at least 50 %. Risk of ecological impact for each antibiotic was also examined, by comparing environmental concentrations predicted to safety limits based on toxicity data for cyanobacteria and other organisms from the literature, with azithromycin being identified as the macrolide of highest risk. This study compares and quantifies the risk of resistance development and ecological impact for a high-risk antibiotic group in the Irish context, and demonstrates the potential for risk reduction achieved by adoption of alternative (e.g. membrane bioreactor) technology.}, }
@article {pmid36368371, year = {2023}, author = {Kumar, A and Ajay, A and Dasgupta, B and Bhadury, P and Sanyal, P}, title = {Deciphering the nitrate sources and processes in the Ganga river using dual isotopes of nitrate and Bayesian mixing model.}, journal = {Environmental research}, volume = {216}, number = {Pt 4}, pages = {114744}, doi = {10.1016/j.envres.2022.114744}, pmid = {36368371}, issn = {1096-0953}, mesh = {*Rivers ; Nitrates/analysis ; Environmental Monitoring ; Bayes Theorem ; *Water Pollutants, Chemical/analysis ; Nitrogen Isotopes/analysis ; Fertilizers/analysis ; China ; }, abstract = {The dual isotopes of dissolved NO3- (n = 43) has been used to delineate the nitrate sources and N-cycling processes in the Ganga river. The proportional contribution of nitrate from different sources has been estimated using the Bayesian mixing model. The seasonal NO3- concentration in the lower stretch of the river Ganga varied between 4.1 and 64.1 μM with higher concentration during monsoon and post-monsoon season and lower concentration during the pre-monsoon and winter season. The temporal variation in the isotopic values ranged between +0.0 and +9.6‰ for δ[15]NNO3- and -1.2 to +11.0‰ for δ[18]ONO3-. The spatial NO3- concentration during the post-monsoon season varied between 23.2 and 57.7 μM, with higher values from the middle and lower values from the lower stretch of the river Ganga. The isotopic ratio during the post-monsoon season varied between -1.0 and +11.3‰ for δ[15]NNO3- and -4.6 to +5.2‰ for δ[18]ONO3-. The temporal dataset from the lower stretch of the river Ganga showed the dominance of nitrate derived from the nitrification of soil organic matter (SOM) (average ∼53.4%). The nitrate contribution from synthetic fertilizers was observed to be higher during the post-monsoon season (34.7 ± 23.4%) compared to that in the monsoon (25.5 ± 19.5%) and pre-monsoon (22.2 ± 19.6%) season. No significant seasonal variations were observed in the nitrate input from manure/sewage (∼13.9%). Spatial samples collected during the post-monsoon season showed higher contribution of synthetic fertilizer in the lower stretch (34.6 ± 22.7%) compared to the middle stretch (21.1 ± 18.2%), which indicates greater influence of the agricultural activity in the lower stretch. The dual isotope study of dissolved NO3- established that the nitrate in the Ganga river water is mostly derived from the nitrification of incoming organic compounds and is subsequently removed via assimilatory nitrate uptake. The study also emphasises significant nitrification and assimilatory nitrate removal processes operating in the mixing zone of the Ganga river and Hooghly estuary.}, }
@article {pmid36365043, year = {2022}, author = {Han, H and Saed, YA and Song, W and Wang, M and Li, Y}, title = {Prevalence of Non-SARS-CoV-2 Respiratory Pathogens and Co-Infection with SARS-CoV-2 in the Early Stage of COVID-19 Epidemic.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36365043}, issn = {2076-0817}, abstract = {BACKGROUND: This study aims to reflect the prevalence of non-SARS-CoV-2 respiratory pathogens and co-infection with SARS-CoV-2 in the early stage of the COVID-19 epidemic, considering SARS-CoV-2 broke out during influenza season and its symptoms resemble those of influenza.<br><br>METHODS: A total of 685 nucleic acid samples of respiratory pathogens were collected from 1 November 2019 to 20 January 2020 and were detected by the 13 Respiratory Pathogen Multiplex Detection Kit and Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit.<br><br>RESULTS: In Wuhan, human rhinovirus was the most frequent infectious pathogen in November (31.5%) and human respiratory syncytial virus appeared the most in December and January (37.1%, 8.6%, respectively). Detection of SARS-CoV-2 first appeared from January 1 to January 10. Generally, 115 patients of 616 patients (18.7%) from Wuhan were infected with SARS-CoV-2, and only two children were co-infected with other respiratory pathogens. In Taiyuan, influenza A virus was detected most frequently in December and January (30.3%, 12%, respectively) without infection of SARS-CoV-2.<br><br>CONCLUSIONS: Some cases diagnosed with influenza before routine nucleic acid testing of SARS-CoV-2 were attributed to COVID-19. Co-infection between SARS-CoV-2 and other non-SARS-CoV-2 respiratory pathogens existed in the early stage of COVID-19 epidemic.}, }
@article {pmid36364003, year = {2022}, author = {Jivkova, D and Sathiyanarayanan, G and Harir, M and Hertkorn, N and Schmitt-Kopplin, P and Sanhaji, G and Fochesato, S and Berthomieu, C and Heyraud, A and Achouak, W and Santaella, C and Heulin, T}, title = {Production and Characterization of a Novel Exopolysaccharide from Ramlibacter tataouinensis.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {21}, pages = {}, pmid = {36364003}, issn = {1420-3049}, mesh = {Humans ; Gas Chromatography-Mass Spectrometry ; *Comamonadaceae ; Rhamnose ; *Cysts ; Polysaccharides, Bacterial/chemistry ; }, abstract = {The current study examines the desiccation-resistant Ramlibacter tataouinensis TTB310[T] as a model organism for the production of novel exopolysaccharides and their structural features. This bacterium is able to produce dividing forms of cysts which synthesize cell-bound exopolysaccharide. Initial experiments were conducted on the enrichment of cyst biomass for exopolysaccharide production under batch-fed conditions in a pilot-scale bioreactor, with lactate as the source of carbon and energy. The optimized medium produced significant quantities of exopolysaccharide in a single growth phase, since the production of exopolysaccharide took place during the division of the cysts. The exopolysaccharide layer was extracted from the cysts using a modified trichloroacetic acid method. The biochemical characterization of purified exopolysaccharide was performed by gas chromatography, ultrahigh-resolution mass spectrometry, nuclear magnetic resonance, and Fourier-transform infrared spectrometry. The repeating unit of exopolysaccharide was a decasaccharide consisting of ribose, glucose, rhamnose, galactose, mannose, and glucuronic acid with the ratio 3:2:2:1:1:1, and additional substituents such as acetyl, succinyl, and methyl moieties were also observed as a part of the exopolysaccharide structure. This study contributes to a fundamental understanding of the novel structural features of exopolysaccharide from a dividing form of cysts, and, further, results can be used to study its rheological properties for various industrial applications.}, }
@article {pmid36363794, year = {2022}, author = {Zaitseva, S and Badmaev, N and Kozyreva, L and Dambaev, V and Barkhutova, D}, title = {Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia).}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363794}, issn = {2076-2607}, abstract = {Soil microbial communities play key roles in biogeochemical cycles and greenhouse gas formation during the decomposition of the released organic matter in the thawing permafrost. The aim of our research was to assess the taxonomic prokaryotic diversity in soil-ecological niches of the Darkhituy-Khaimisan transect during the initial period of soil thawing. We investigated changes in the microbial communities present in the active layer of four sites representing distinct habitats (larch forest, birch forest, meadow steppe and thermokarst lake). We explore the relationship between the biogeochemical differences among habitats and the active layer microbial community via a spatial (across habitats, and with depth through the active layer) community survey using high-throughput Illumina sequencing. Microbial communities showed significant differences between active and frozen layers and across ecosystem types, including a high relative abundance of Alphaproteobacteria, Firmicutes, Crenarchaeota, Bacteroidota and Gemmatimonadota in the active layer and a high relative abundance of Actinobacteriota and Desulfobacterota in the frozen layer. Soil pH, temperature and moisture were the most significant parameters underlying the variations in the microbial community composition. CCA suggested that the differing environmental conditions between the four soil habitats had strong influences on microbial distribution and diversity and further explained the variability of soil microbial community structures.}, }
@article {pmid36363713, year = {2022}, author = {Hurtado-McCormick, V and Trevathan-Tackett, SM and Bowen, JL and Connolly, RM and Duarte, CM and Macreadie, PI}, title = {Pathways for Understanding Blue Carbon Microbiomes with Amplicon Sequencing.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363713}, issn = {2076-2607}, abstract = {The capacity of Blue Carbon Ecosystems to act as carbon sinks is strongly influenced by the metabolism of soil-associated microbes, which ultimately determine how much carbon is accumulated or returned to the atmosphere. The rapid evolution of sequencing technologies has facilitated the generation of tremendous amounts of data on what taxa comprise belowground microbial assemblages, largely available as isolated datasets, offering an opportunity for synthesis research that informs progress on understanding Blue Carbon microbiomes. We identified questions that can be addressed with a synthesis approach, including the high variability across datasets, space, and time due to differing sampling techniques, ecosystem or vegetation specificity, and the relationship between microbiome community and edaphic properties, particularly soil carbon. To address these questions, we collated 34 16S rRNA amplicon sequencing datasets, including bulk soil or rhizosphere from seagrass, mangroves, and saltmarshes within publicly available repositories. We identified technical and theoretical challenges that precluded a synthesis of multiple studies with currently available data, and opportunities for addressing the knowledge gaps within Blue Carbon microbial ecology going forward. Here, we provide a standardisation toolbox that supports enacting tasks for the acquisition, management, and integration of Blue Carbon-associated sequencing data and metadata to potentially elucidate novel mechanisms behind Blue Carbon dynamics.}, }
@article {pmid36360970, year = {2022}, author = {Sousa, V and Spratt, D and Davrandi, M and Mardas, N and Beltrán, V and Donos, N}, title = {Oral Microcosm Biofilms Grown under Conditions Progressing from Peri-Implant Health, Peri-Implant Mucositis, and Peri-Implantitis.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {21}, pages = {}, pmid = {36360970}, issn = {1660-4601}, mesh = {Humans ; *Peri-Implantitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Mucositis ; Biofilms ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {Peri-implantitis is a disease influenced by dysbiotic microbial communities that play a role in the short- and long-term outcomes of its clinical treatment. The ecological triggers that establish the progression from peri-implant mucositis to peri-implantitis remain unknown. This investigation describes the development of a novel in vitro microcosm biofilm model. Biofilms were grown over 30 days over machined titanium discs in a constant depth film fermentor (CDFF), which was inoculated (I) with pooled human saliva. Following longitudinal biofilm sampling across peri-implant health (PH), peri-implant mucositis (PM), and peri-implantitis (PI) conditions, the characterisation of the biofilms was performed. The biofilm analyses included imaging by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM), selective and non-selective culture media of viable biofilms, and 16S rRNA gene amplification and sequencing. Bacterial qualitative shifts were observed by CLSM and SEM across conditions, which were defined by characteristic phenotypes. A total of 9 phyla, 83 genera, and 156 species were identified throughout the experiment. The phyla Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria showed the highest prevalence in PI conditions. This novel in vitro microcosm model provides a high-throughput alternative for growing microcosm biofilms resembling an in vitro progression from PH-PM-PI conditions.}, }
@article {pmid36358990, year = {2022}, author = {Scott, E and De Paepe, K and Van de Wiele, T}, title = {Postbiotics and Their Health Modulatory Biomolecules.}, journal = {Biomolecules}, volume = {12}, number = {11}, pages = {}, pmid = {36358990}, issn = {2218-273X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; Fatty Acids, Volatile ; Vitamins ; Inflammation ; }, abstract = {Postbiotics are a new category of biotics that have the potential to confer health benefits but, unlike probiotics, do not require living cells to induce health effects and thus are not subject to the food safety requirements that apply to live microorganisms. Postbiotics are defined as a "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Postbiotic components include short-chain fatty acids, exopolysaccharides, vitamins, teichoic acids, bacteriocins, enzymes and peptides in a non-purified inactivated cell preparation. While research into postbiotics is in its infancy, there is increasing evidence that postbiotics have the potential to modulate human health. Specifically, a number of postbiotics have been shown to improve gut health by strengthening the gut barrier, reducing inflammation and promoting antimicrobial activity against gut pathogens. Additionally, research is being conducted into the potential application of postbiotics to other areas of the body, including the skin, vagina and oral cavity. The purpose of this review is to set out the current research on postbiotics, demonstrate how postbiotics are currently used in commercial products and identify a number of knowledge gaps where further research is needed to identify the potential for future applications of postbiotics.}, }
@article {pmid36358119, year = {2022}, author = {Calatayud, M and Duysburgh, C and Van den Abbeele, P and Franckenstein, D and Kuchina-Koch, A and Marzorati, M}, title = {Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGut[TM] SHIME Model.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36358119}, issn = {2079-6382}, abstract = {Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and an important nosocomial infection with different severity degrees. Disruption of the gut microbiota by broad-spectrum antibiotics creates a proper environment for C. difficile colonization, proliferation, and clinical disease onset. Restoration of the gut microbial ecosystem through prebiotic interventions can constitute an effective complementary treatment of CDI. Using an adapted simulator of the human gut microbial ecosystem, the PathoGut[TM] SHIME, the effect of different long-term and repeated dose lactulose treatments was tested on C. difficile germination and growth in antibiotic-induced dysbiotic gut microbiota environments. The results showed that lactulose reduced the growth of viable C. difficile cells following clindamycin treatment, shifted the antibiotic-induced dysbiotic microbial community, and stimulated the production of health-promoting metabolites (especially butyrate). Recovery of the gut microenvironment by long-term lactulose administration following CDI was also linked to lactate production, decrease in pH and modulation of bile salt metabolism. At a structural level, lactulose showed a significant bifidogenic potential and restored key commensal members of the gut ecosystem such as Lactobacillaceae, Veillonellaceae and Lachnospiraceae. These results support further human intervention studies aiming to validate the in vitro beneficial effects of lactulose on gut microbiome recovery during antibiotic exposure and CDI.}, }
@article {pmid36356812, year = {2022}, author = {Kim, M and Cui, F}, title = {Identification of bacterial communities in conventional wastewater treatment sludge to inform inoculation of the anammox process.}, journal = {Chemosphere}, volume = {311}, number = {Pt 2}, pages = {137167}, doi = {10.1016/j.chemosphere.2022.137167}, pmid = {36356812}, issn = {1879-1298}, abstract = {This study uses 16 S rRNA gene pyrosequencing for the identification of a vast number of wastewater bacterial communities to investigate the evolution of bacterial communities in the Anammox process. Four lab-scale Anammox reactors inoculated with different conventional wastewater treatment sludge (activated sludge, livestock wastewater treatment sludge, denitrification sludge, and anaerobic digestion sludge) were operated under identical operating conditions for more than 400 days. The phylum Planctomycetes was present in all seeds of conventional sludge with a relative abundance of 1-3%. In particular, the known Anammox bacteria Candidatus Brocadia was found in the seed of the denitrification sludge. The reactor inoculated with denitrification sludge demonstrated the most effective nitrogen removal of ∼80% with successful cultivation of Anammox bacteria. This study found that the performance of the Anammox process is related to the presence of Nitrospira genus (nitrite-oxidizing bacteria) and that symbiotic association with other functional groups can lead to nitrogen removal. The outcomes of this study can provide vital insight into the study of microbial ecology for the cultivation of Anammox bacteria.}, }
@article {pmid36355167, year = {2022}, author = {Yoon, KH and Indong, RA and Lee, JI}, title = {Making "Sense" of Ecology from a Genetic Perspective: Caenorhabditis elegans, Microbes and Behavior.}, journal = {Metabolites}, volume = {12}, number = {11}, pages = {}, pmid = {36355167}, issn = {2218-1989}, abstract = {Our knowledge of animal and behavior in the natural ecology is based on over a century's worth of valuable field studies. In this post-genome era, however, we recognize that genes are the underpinning of ecological interactions between two organisms. Understanding how genes contribute to animal ecology, which is essentially the intersection of two genomes, is a tremendous challenge. The bacterivorous nematode Caenorhabditis elegans, one of the most well-known genetic animal model experimental systems, experiences a complex microbial world in its natural habitat, providing us with a window into the interplay of genes and molecules that result in an animal-microbial ecology. In this review, we will discuss C. elegans natural ecology, how the worm uses its sensory system to detect the microbes and metabolites that it encounters, and then discuss some of the fascinating ecological dances, including behaviors, that have evolved between the nematode and the microbes in its environment.}, }
@article {pmid36354324, year = {2022}, author = {Saati-Santamaría, Z and Baroncelli, R and Rivas, R and García-Fraile, P}, title = {Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0237022}, doi = {10.1128/spectrum.02370-22}, pmid = {36354324}, issn = {2165-0497}, abstract = {Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.}, }
@article {pmid36352414, year = {2022}, author = {Pitiriga, V and Bakalis, J and Theodoridou, K and Kanellopoulos, P and Saroglou, G and Tsakris, A}, title = {Lower risk of bloodstream infections for peripherally inserted central catheters compared to central venous catheters in critically ill patients.}, journal = {Antimicrobial resistance and infection control}, volume = {11}, number = {1}, pages = {137}, pmid = {36352414}, issn = {2047-2994}, mesh = {Adult ; Humans ; *Central Venous Catheters/adverse effects ; *Catheter-Related Infections/epidemiology/etiology ; *Catheterization, Central Venous/adverse effects ; Retrospective Studies ; Critical Illness ; Risk Factors ; *Sepsis/epidemiology ; }, abstract = {BACKGROUND: Peripherally inserted central venous catheters (PICCs) serve as an alternative to short-term central venous catheters (CVCs) for providing intravenous access in hospitalized patients. Although a number of studies suggest that PICCs are associated with a lower risk of central line-associated bloodstream infections (CLABSIs) than CVCs, recent data concerning specific patient groups support the contrary. In this regard, we are comparing CVC- and PICC-related CLABSI rates developed in a selected group of critically ill inpatients and evaluating the CLABSI microbiological distribution.<br><br>METHODS: The study was conducted at a tertiary care hospital in Greece between May 2017 and May 2019. We performed a two-year retrospective analysis of the data collected from medical records of consecutive adult patients who underwent PICC or CVC placement.<br><br>RESULTS: A total of 1187 CVCs placed for 9774 catheter-days and 639 PICCs placed for 11,110 catheter-days, were reported and analyzed during the study period. Among CVCs, a total of 59 (4.9%) CLABSIs were identified, while among PICCs, 18 (2.8%) cases presented CLABSI (p&#x2009;=&#x2009;0.029). The CLABSI incidence rate per 1,000 catheter-days was 6.03 for CVC group and 1.62 for PICC group (p&#x2009;<&#x2009;0.001). The CLABSI rate due to multidrug-resistant organisms (MDROs) among the two groups was 3.17 in CVC group and 0.36 in PICC group (p&#x2009;<&#x2009;0.001). Within CLABSI-CVC group, the most common microorganism detected was MDR Acinetobacter baumannii (27.1%) followed by MDR Klebsiella pneumoniae (22%). In CLABSI-PICC group, the predominant microorganism was Candida spp. (33.3%) followed by non-MDR gram-negative pathogens (22.2%).<br><br>CONCLUSIONS: PICC lines were associated with significantly lower CLABSI rates comparing to CVC although they were in place longer than CVC lines. Given their longer time to the development of infection, PICCs may be a safer alternative for prolonged inpatient IV access. The high prevalence of CLABSI-MDROs depicts the local microbial ecology, emphasizing the need of&#xa0;public health awareness.}, }
@article {pmid36352137, year = {2022}, author = {Graber, LC and Ramalho, MO and Powell, S and Moreau, CS}, title = {Identifying the Role of Elevation, Geography, and Species Identity in Structuring Turtle Ant (Cephalotes Latreille, 1802) Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36352137}, issn = {1432-184X}, abstract = {Bacterial communities in animals are often necessary for hosts to survive, particularly for hosts with nutrient-limited diets. The composition, abundance, and richness of these bacterial communities may be shaped by host identity and external ecological factors. The turtle ants (genus Cephalotes) are predominantly herbivorous and known to rely on bacterial communities to enrich their diet. Cephalotes have a broad Neotropical distribution, with high diversity in the South American Cerrado, a geologically and biologically diverse savanna. Using 16S rRNA amplicon sequencing, we examined the bacterial communities of forty-one Cephalotes samples of sixteen different species collected from multiple locations across two sites in the Cerrado (MG, Brazil) and compared the bacterial communities according to elevation, locality, species, and species group, defined by host phylogeny. Beta diversity of bacterial communities differed with respect to all categories but particularly strongly when compared by geographic location, species, and species group. Differences seen in species and species groups can be partially explained by the high abundance of Mesorhizobium in Cephalotes pusillus and Cephalotes depressus species groups, when compared to other clades via the Analysis of Composition of Microbiome (ANCOM). Though the Cephalotes bacterial community is highly conserved, results from this study indicate that multiple external factors can affect and change bacterial community composition and abundance.}, }
@article {pmid36350347, year = {2022}, author = {Ayilara, MS and Adeleke, BS and Babalola, OO}, title = {Correction to: Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-022-02141-2}, pmid = {36350347}, issn = {1432-184X}, }
@article {pmid36350260, year = {2022}, author = {Collin, B and Auffan, M and Doelsch, E and Proux, O and Kieffer, I and Ortet, P and Santaella, C}, title = {Bacterial Metabolites and Particle Size Determine Cerium Oxide Nanomaterial Biotransformation.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {23}, pages = {16838-16847}, doi = {10.1021/acs.est.2c05280}, pmid = {36350260}, issn = {1520-5851}, mesh = {Particle Size ; *Cerium/chemistry ; Soil/chemistry ; *Metal Nanoparticles/chemistry ; Bacteria ; *Nanostructures ; }, abstract = {Soil is a major receptor of manufactured nanomaterials (NMs) following unintentional releases or intentional uses. Ceria NMs have been shown to undergo biotransformation in plant and soil organisms with a partial Ce(IV) reduction into Ce(III), but the influence of environmentally widespread soil bacteria is poorly understood. We used high-energy resolution fluorescence-detected X-ray absorption spectroscopy (HERFD-XAS) with an unprecedented detection limit to assess Ce speciation in a model soil bacterium (Pseudomonas brassicacearum) exposed to CeO2 NMs of different sizes and shapes. The findings revealed that the CeO2 NM's size drives the biotransformation process. No biotransformation was observed for the 31 nm CeO2 NMs, contrary to 7 and 4 nm CeO2 NMs, with a Ce reduction of 64 ± 14% and 70 ± 15%, respectively. This major reduction appeared quickly, from the early exponential bacterial growth phase. Environmentally relevant organic acid metabolites secreted by Pseudomonas, especially in the rhizosphere, were investigated. The 2-keto-gluconic and citric acid metabolites alone were able to induce a significant reduction in 4 nm CeO2 NMs. The high biotransformation measured for <7 nm NMs would affect the fate of Ce in the soil and biota.}, }
@article {pmid36349407, year = {2022}, author = {Hu, J and Vandenkoornhuyse, P and Khalfallah, F and Causse-Védrines, R and Mony, C}, title = {Ecological corridors homogenize plant root endospheric mycobiota.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18606}, pmid = {36349407}, issn = {1469-8137}, abstract = {Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind while microorganisms, the invisible majority of biodiversity, were disregarded. We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of one meter over two years (i.e. at five time points) by combining an experimental corridor-mesocosm with high-throughput amplicon sequencing. We show that the plant root endospheric mycobiota was sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta-diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants. Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions.}, }
@article {pmid36349406, year = {2022}, author = {Chen, H and Fang, Y and Zwaenepoel, A and Huang, S and Van de Peer, Y and Li, Z}, title = {Revisiting ancient polyploidy in leptosporangiate ferns.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18607}, pmid = {36349406}, issn = {1469-8137}, abstract = {Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building KS -age distributions and applying substitution rate corrections, and by conducting statistical gene tree - species tree reconciliation analyses. Our integrative analyses confidently identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree - species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.}, }
@article {pmid36346444, year = {2022}, author = {Palmer, B and Lawson, D and Lipson, DA}, title = {Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36346444}, issn = {1432-184X}, abstract = {Microbial communities are integral for ecosystem processes and their taxonomic composition and function may be altered by a disturbance such as fire. Biocrusts are composed of macroscopic and microscopic organisms and are important for a variety of ecosystem functions, such as nutrient cycling and erosion control. We sought to understand if biocrust community composition and function were altered 1 year after a prescribed fire and 6 years after a wildfire in a coastal California grassland on San Clemente Island. We used shotgun metagenomic sequencing and measurements of chlorophyll content, exopolysaccharide production related to soil stability, and nitrogen fixation. There were no differences in the community composition between unburned samples and the samples burned in the prescribed fire and wildfire. Chlorophyll content differed between the prescribed fire and the controls; however, there were no measured differences in exopolysaccharide production, and nitrogen fixation. However, the wildfire and their respective unburned samples had different functions based on the gene annotations. We compiled one Actinobacteria metagenome-assembled genome from the shotgun sequences which had genes for oxidative and heat stress tolerance. These results suggest that the biocrust community can reach a community composition and function similar to the unburned biocrusts within a year after a prescribed burn and 6 years after a wildfire. However, legacy effects of the wildfire may present themselves in the differences between functional gene sequences. Due to their ability to match the undisturbed community composition and function within years and without intervention, future restoration work should consider the biocrusts in their restoration plans as they may provide valuable ecosystem functions after a disturbance.}, }
@article {pmid36345526, year = {2022}, author = {DeWitt, ME and Polk, C and Williamson, J and Shetty, AK and Passaretti, CL and McNeil, CJ and Fairman, RT and Sampson, MM and Dalton, C and Sanders, JW}, title = {Global monkeypox case hospitalisation rates: A rapid systematic review and meta-analysis.}, journal = {EClinicalMedicine}, volume = {54}, number = {}, pages = {101710}, pmid = {36345526}, issn = {2589-5370}, abstract = {BACKGROUND: Estimates of the case hospitalization rate and case fatality rate when hospital care is available for monkeypox (MPX) infections have not been well defined. This rapid systematic review and meta-analysis aimed to estimate the case hospitalisation rate and case fatality rate where hospital care is available.<br><br>METHODS: We systematically searched PubMed, Embase, the Lancet Preprints, and MedRxiv for studies published between Jan 1, 1950 and Aug 2, 2022. We included documents which contained both the number of cases and associated hospitalisations of MPX infections. From eligible studies we extracted the country, the year of the study, the study design type, the clade of MPX, the participant characteristics, transmission type, any treatments used, number of cases (including suspected, probable, or laboratory confirmed diagnosis), number of hospitalizations, hospitalized patient outcomes, and case definition. Case hospitalization rate (CHR) was defined as the proportion of cases that were admitted to hospital care while case fatality rate (CFR) was defined as the proportion of cases that died. CHR and CFR were analysed in a fully Bayesian meta-analytic framework using random effects models, including sub-group analysis with heterogeneity assessed using I[2].<br><br>FINDINGS: Of the 259 unique documents identified, 19 studies were eligible for inclusion. Included studies represented 7553 reported cases among which there were 555 hospitalizations. Of the 7540 cases for which outcomes were available, there were 15 recorded deaths. The median age of cases was 35 years (interquartile range 28-38, n&#xa0;=&#xa0;2010) and primarily male (7339/7489, 98%) in studies where age or sex were available. Combined CHR was estimated to be 14.1% (95% credible interval, 7.5-25.0, I[2] 97.4%), with a high degree of heterogeneity. Further analysis by outbreak period indicates CHRs of 49.8% (28.2-74.0, I[2] 81.4%), 21.7% (7.2-52.1, I[2] 57.7%), and 5.8% (3.2-9.4, I[2] 92.4%) during the pre-2017, 2017-2021, and 2022 outbreaks, respectively, again with high levels of heterogeneity. CFR was estimated to be 0.03% (0.0-0.44, I[2] 99.9%), with evidence of large heterogeneity between the studies.<br><br>INTERPRETATION: There is limited data for MPX hospitalization rates in countries where MPX has been traditionally non-endemic until the current outbreak. Due to substantial heterogeneity, caution is needed when interpreting these findings. Health care organizations should be cognizant of the potential increase in healthcare utilization. Rapid identification of infection and use of appropriate therapies such as antivirals play a role reducing the CHR and associated CFR.<br><br>FUNDING: None.}, }
@article {pmid36345334, year = {2022}, author = {Verbeelen, T and Van Houdt, R and Leys, N and Ganigué, R and Mastroleo, F}, title = {Optimization of RNA extraction for bacterial whole transcriptome studies of low-biomass samples.}, journal = {iScience}, volume = {25}, number = {11}, pages = {105311}, pmid = {36345334}, issn = {2589-0042}, abstract = {We developed a procedure for extracting maximal amounts of high-quality RNA from low-biomass producing (autotrophic) bacteria for experiments where sample volume is limited. Large amounts of high-quality RNA for downstream analyses cannot be obtained using larger quantities of culture volume. The performance of standard commercial silica-column based kit protocols and these procedures amended by ultrasonication or enzymatic lysis were assessed. The ammonium-oxidizing Nitrosomonas europaea and nitrite-oxidizing Nitrobacter winogradskyi were used as model organisms for optimization of the RNA isolation protocol. Enzymatic lysis through lysozyme digestion generated high-quality, high-yield RNA samples. Subsequent RNA-seq analysis resulted in qualitative data for both strains. The RNA extraction procedure is suitable for experiments with volume and/or biomass limitations, e.g., as encountered during space flight experiments. Furthermore, it will also result in higher RNA yields for whole transcriptome experiments where sample volume and/or biomass was increased to compensate the low-biomass characteristic of autotrophs.}, }
@article {pmid36344828, year = {2022}, author = {Bringhurst, B and Allert, M and Greenwold, M and Kellner, K and Seal, JN}, title = {Environments and Hosts Structure the Bacterial Microbiomes of Fungus-Gardening Ants and their Symbiotic Fungus Gardens.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36344828}, issn = {1432-184X}, abstract = {The fungus gardening-ant system is considered a complex, multi-tiered symbiosis, as it is composed of ants, their fungus, and microorganisms associated with either ants or fungus. We examine the bacterial microbiome of Trachymyrmex septentrionalis and Mycetomoellerius turrifex ants and their symbiotic fungus gardens, using 16S rRNA Illumina sequencing, over a region spanning approximately 350 km (east and central Texas). Typically, microorganisms can be acquired from a parent colony (vertical transmission) or from the environment (horizontal transmission). Because the symbiosis is characterized by co-dispersal of the ants and fungus, elements of both ant and fungus garden microbiome could be characterized by vertical transmission. The goals of this study were to explore how both the ant and fungus garden bacterial microbiome are acquired. The main findings were that different mechanisms appear to explain the structure the microbiomes of ants and their symbiotic fungus gardens. Ant associated microbiomes had a strong host ant signature, which could be indicative of vertical inheritance of the ant associated bacterial microbiome or an unknown mechanism of active uptake or screening. On the other hand, the bacterial microbiome of the fungus garden was more complex in that some bacterial taxa appear to be structured by the ant host species, whereas others by fungal lineage or the environment (geographic region). Thus bacteria in fungus gardens appear to be acquired both horizontally and vertically.}, }
@article {pmid36342171, year = {2022}, author = {Jin, H and Li, X and Wang, H and Cápiro, NL and Li, X and Löffler, FE and Yan, J and Yang, Y}, title = {Anaerobic Biohydrogenation of Isoprene by Acetobacterium wieringae Strain Y.}, journal = {mBio}, volume = {}, number = {}, pages = {e0208622}, doi = {10.1128/mbio.02086-22}, pmid = {36342171}, issn = {2150-7511}, abstract = {Isoprene is a ubiquitously distributed, biogenic, and climate-active organic compound. Microbial isoprene degradation in oxic environments is fairly well understood; however, studies exploring anaerobic isoprene metabolism remain scarce, with no isolates for study available. Here, we obtained an acetogenic isolate, designated Acetobacterium wieringae strain Y, which hydrogenated isoprene to a mixture of methyl-1-butenes at an overall rate of 288.8 ± 20.9 μM day[-1] with concomitant acetate production at a rate of 478.4 ± 5.6 μM day[-1]. Physiological characterization demonstrated that isoprene was not utilized in a respiratory process; rather, isoprene promoted acetogenesis kinetically. Bioinformatic analysis and proteomics experiments revealed the expression of candidate ene-reductases responsible for isoprene biohydrogenation. Notably, the addition of isoprene to strain Y cultures stimulated the expression of proteins associated with the Wood-Ljungdahl pathway, indicating unresolved impacts of isoprene on carbon cycling and microbial ecology in anoxic environments (e.g., promoting CO2 plus H2 reductive acetogenesis while inhibiting methanogenesis). Our new findings advance understanding of microbial transformation of isoprene under anoxic conditions and suggest that anoxic environments are isoprene sinks. IMPORTANCE Isoprene is the most abundant, biologically generated, volatile organic compound on Earth, with estimated emissions in the same magnitude as methane. Nonetheless, a comprehensive knowledge of isoprene turnover in the environment is lacking, impacting global isoprene flux models and our understanding of the environmental fate and longevity of isoprene. A critical knowledge gap that has remained largely unexplored until recently is the microbiology and associated molecular mechanisms involved in the anaerobic biotransformation of isoprene. By integrating culture-dependent approaches with omics techniques, we isolated an acetogen, Acetobacterium wieringae strain Y, capable of anaerobic biohydrogenation of isoprene. We obtained the complete genome of strain Y, and proteomic experiments identified candidate ene-reductases for catalyzing the asymmetric reduction of the electronically activated carbon-carbon double bond of isoprene. We also demonstrated that isoprene biohydrogenation stimulates the expression of Wood-Ljungdahl pathway enzymes. This study emphasizes the ecological roles of specialized Acetobacterium on the natural cycling of isoprene in anoxic environments and the potential effects of isoprene biohydrogenation on acetogens and methanogens, which have implications for global climate change and bioenergy production.}, }
@article {pmid36338036, year = {2022}, author = {Kraemer, SA and Barbosa da Costa, N and Oliva, A and Huot, Y and Walsh, DA}, title = {A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {995418}, pmid = {36338036}, issn = {1664-302X}, abstract = {Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome - the diversity of ARGs - under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.}, }
@article {pmid36334202, year = {2022}, author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y}, title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36334202}, issn = {1614-7499}, abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.}, }
@article {pmid36334118, year = {2022}, author = {Stouvenakers, G and Massart, S and Jijakli, MH}, title = {First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36334118}, issn = {1432-184X}, abstract = {Aquaponics is defined as a sustainable and integrated system that combines fish aquaculture and hydroponic plant production in the same recirculated water loop. A recent study using high-throughput sequencing (HTS) technologies highlighted that microbial communities from an aquaponic system could control one of the most problematic pathogens in soilless lettuce culture, namely, Pythium aphanidermatum. Therefore, this study aims at isolating the microorganisms responsible for this biocontrol action. Based on the most promising genera identified by HTS, an innovative strategy for isolating and testing original biocontrol agents from aquaponic water was designed to control P. aphanidermatum. Eighty-two bacterial strains and 18 fungal strains were isolated, identified by Sanger sequencing, and screened in vivo to control damping-off of lettuce seeds caused by P. aphanidermatum. Out of these 100 isolates, the eight most efficacious ones were selected and further tested individually to control root rot disease caused by the same pathogen at a later stage of lettuce growth. Strains SHb30 (Sphingobium xenophagum), G2 (Aspergillus flavus), and Chito13 (Mycolicibacterium fortuitum) decreased seed damping-off at a better rate than a propamocarb fungicide and a Pseudomonas chlororaphis registered biocontrol agent did. In root rot bioassays, lettuce mortality was prevented by applying strains G2 and Chito13, which were at least as efficacious as the fungicide or biopesticide controls. Lettuce disease symptoms and mortality were eradicated by strain SHb30 in the first bioassay, but not in the second one. These results show that aquaponic systems are promising sources of original biocontrol agents, and that HTS-guided strategies could represent interesting approaches to identify new biocontrol agents.}, }
@article {pmid36333944, year = {2022}, author = {Zhang, S and Yang, Q and Defoirdt, T}, title = {Indole analogues decreasing the virulence of Vibrio campbellii towards brine shrimp larvae.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14160}, pmid = {36333944}, issn = {1751-7915}, abstract = {Indole signalling has been proposed as a potential target for the development of novel virulence inhibitors to control bacterial infections. However, the major structural features of indole analogues that govern antivirulence activity remain unexplored. Therefore, we investigated the impact of 26 indole analogues on indole-regulated virulence phenotypes in Vibrio campbellii and on the virulence of the bacterium in a gnotobiotic brine shrimp model. The results demonstrated that 10 indole analogues significantly increased the fluorescence of indole reporter strain Vibrio cholerae S9149, 21 of them decreased the swimming motility of V. campbellii, and 13 of them significantly decreased the biofilm formation of V. campbellii. Further, we found that 1-methylindole, indene, 2,3-benzofuran, thianaphthene, indole-3-acetonitrile, methyl indole-3-carboxylate, 3-methylindole, and indole-2-carboxaldehyde exhibited a significant protective effect on brine shrimp larvae against V. campbellii infection, resulting in survival rates of challenged brine shrimp above 80%. The highest survival of shrimp larvae (98%) was obtained with indole-3-acetonitrile, even at a relatively low concentration of 20 μM. Importantly, the indole analogues did not affect bacterial growth, both in vitro and in vivo. These results indicate the potential of indole analogues in applications aiming at the protection of shrimp from vibriosis.}, }
@article {pmid36333915, year = {2022}, author = {Berry, O and Briand, E and Bagot, A and Chaigné, M and Meslet-Cladière, L and Wang, J and Grovel, O and Jansen, JJ and Ruiz, N and du Pont, TR and Pouchus, YF and Hess, P and Bertrand, S}, title = {Deciphering interactions between the marine dinoflagellate Prorocentrum lima and the fungus Aspergillus pseudoglaucus.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16271}, pmid = {36333915}, issn = {1462-2920}, abstract = {The comprehension of microbial interactions is one of the key challenges in marine microbial ecology. This study focused on exploring chemical interactions between the toxic dinoflagellate Prorocentrum lima and a filamentous fungal species, Aspergillus pseudoglaucus, which has been isolated from the microalgal culture. Such interspecies interactions are expected to occur even though they were rarely studied. Here, a co-culture system was designed in a dedicated microscale marine-like condition. This system allowed to explore microalgal-fungal physical and metabolic interactions in presence and absence of the bacterial consortium. Microscopic observation showed an unusual physical contact between the fungal mycelium and dinoflagellate cells. To delineate specialized metabolome alterations during microalgal-fungal co-culture metabolomes were monitored by high-performance liquid chromatography coupled to high-resolution mass spectrometry. In-depth multivariate statistical analysis using dedicated approaches highlighted (1) the metabolic alterations associated with microalgal-fungal co-culture, and (2) the impact of associated bacteria in microalgal metabolome response to fungal interaction. Unfortunately, only a very low number of highlighted features were fully characterized. However, an up-regulation of the dinoflagellate toxins okadaic acid and dinophysistoxin 1 was observed during co-culture in supernatants. Such results highlight the importance to consider microalgal-fungal interactions in the study of parameters regulating toxin production.}, }
@article {pmid36333353, year = {2022}, author = {Barret, M and Gandois, L and Thalasso, F and Martinez Cruz, K and Sepulveda Jauregui, A and Lavergne, C and Teisserenc, R and Aguilar, P and Gerardo Nieto, O and Etchebehere, C and Martins Dellagnezze, B and Bovio Winkler, P and Fochesatto, GJ and Tananaev, N and Svenning, MM and Seppey, C and Tveit, A and Chamy, R and Astorga España, MS and Mansilla, A and Van de Putte, A and Sweetlove, M and Murray, AE and Cabrol, L}, title = {A combined microbial and biogeochemical dataset from high-latitude ecosystems with respect to methane cycle.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {674}, pmid = {36333353}, issn = {2052-4463}, mesh = {Carbon Dioxide/analysis ; *Greenhouse Gases ; Methane/analysis ; *Microbiota ; Soil ; Wetlands ; }, abstract = {High latitudes are experiencing intense ecosystem changes with climate warming. The underlying methane (CH4) cycling dynamics remain unresolved, despite its crucial climatic feedback. Atmospheric CH4 emissions are heterogeneous, resulting from local geochemical drivers, global climatic factors, and microbial production/consumption balance. Holistic studies are mandatory to capture CH4 cycling complexity. Here, we report a large set of integrated microbial and biogeochemical data from 387 samples, using a concerted sampling strategy and experimental protocols. The study followed international standards to ensure inter-comparisons of data amongst three high-latitude regions: Alaska, Siberia, and Patagonia. The dataset encompasses different representative environmental features (e.g. lake, wetland, tundra, forest soil) of these high-latitude sites and their respective heterogeneity (e.g. characteristic microtopographic patterns). The data included physicochemical parameters, greenhouse gas concentrations and emissions, organic matter characterization, trace elements and nutrients, isotopes, microbial quantification and composition. This dataset addresses the need for a robust physicochemical framework to conduct and contextualize future research on the interactions between climate change, biogeochemical cycles and microbial communities at high-latitudes.}, }
@article {pmid36332310, year = {2023}, author = {Daille, LK and Aguirre, J and Anguita, J and Galarce, C and Caro-Lara, L and Armijo, F and Vargas, IT and Pizarro, G and Walczak, M and De la Iglesia, R}, title = {When material science meets microbial ecology: Bacterial community selection on stainless steels in natural seawater.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {221}, number = {}, pages = {112955}, doi = {10.1016/j.colsurfb.2022.112955}, pmid = {36332310}, issn = {1873-4367}, mesh = {Humans ; *Steel ; *Stainless Steel ; Materials Science ; Corrosion ; Seawater/microbiology ; Biofilms ; Bacteria ; Oxides ; }, abstract = {The passive film depends on the alloy's composition and the exposure conditions. How the surface composition affects the selection of microbial biofilms though, has not been fully elucidated or incorporated into the analysis of corrosive biofilms. The degradation of stainless steel (SS) exposed to natural seawater was studied to understand how the oxide layer composition of SS could affect the selection and variability of the bacterial community. To accomplish this goal, austenitic and superferritic SS grades were exposed to natural seawater on the central coast of Chile. The deterioration of steel and qualitative description of biofilm formation was monitored at different exposure periods. Biofilms were evaluated based on massive sequencing analysis of the bacterial community and subsequent ecological studies. The results revealed that variability of the calculated corrosion rate correlated with the similarity of the bacterial community within samples from each SS and its corrosion inferred capacity. The associated bacterial families showed a higher representation in SSs with a more significant increase in the Fe/Cr ratio over the exposure time. These findings revealed that iron content in the oxide layer represents a key feature of the surface composition for selecting bacterial assemblages in marine environments.}, }
@article {pmid36332298, year = {2022}, author = {Lin, Q and De Vrieze, J and Fang, X and Li, L and Li, X}, title = {Microbial life strategy with high rRNA operon copy number facilitates the energy and nutrient flux in anaerobic digestion.}, journal = {Water research}, volume = {226}, number = {}, pages = {119307}, doi = {10.1016/j.watres.2022.119307}, pmid = {36332298}, issn = {1879-2448}, mesh = {Swine ; Animals ; *rRNA Operon ; RNA, Ribosomal, 16S/genetics ; *Manure ; Anaerobiosis ; DNA Copy Number Variations ; Nutrients ; Bioreactors ; Methane ; }, abstract = {Microbial life strategy, reflected by rRNA operon (rrn) copy number, determines microbial ecological roles. However, the relationship between microbial life strategy and the energy and nutrient flux in anaerobic digestion (AD) remains elusive. This study investigated microbial rrn copy number and expression ratio using amplicon sequencing of 16S rRNA gene and 16S rRNA, and monitored CH4 daily production to approximate the status of energy and nutrient flux in semi-continuous AD. A significantly positive correlation between the mean rrn copy number of microbial communities in digestate and CH4 daily production was detected in the control treatment fed swine manure. The reduced feedstock complexity, by replacing parts of swine manure with fructose or apple waste, weakened the correlation. When feedstock complexity was increased again, the correlation was strengthened again. Similar results were detected in mean rrn expression ratio of microbial communities. The responses of mean rrn copy number and expression ratio of communities to feedstock addition differed between the reduced feedstock complexity and the control treatment, as well as between in digestate and in straw. Our findings reveal a novel relationship between microbial community life strategy and the energy and nutrient flux, and the roles of feedstock characteristics therein in AD.}, }
@article {pmid36331579, year = {2022}, author = {Cortés-Pérez, S and Ferrera-Cerrato, R and Rodríguez-Zaragoza, S and Alarcón, A}, title = {Short-Term Evaluation of the Spatial Distribution of Trophic Groups of Amoebae in the Rhizosphere of Zea mays Inoculated with Rhizophagus intraradices.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36331579}, issn = {1432-184X}, abstract = {Primary production in terrestrial ecosystems is sustained by plants, microbiota, and fungi, which are the major organic matter providers in the root zone, setting in motion the soil food webs. Predators like soil amoebae voraciously feed on bacteria, fungi, and microbial eukaryotes releasing the nutrients sequestered in their biomass. Early food web setting up is crucial for seedling nutrition and its further development after establishment. Mycorrhizal fungi are more than phosphorus providers, and we wonder what their role is in structuring the predators' trophic groups in the root zone. We evaluated the effect of Rhizophagus intraradices inoculated in Zea mays (mycorrhizosphere), on the structuration of amoebae trophic groups along vertical and horizontal (3, 6, and 9 cm) soil distribution when compared to un-inoculated plants, after 20 days in microcosms. Amoebae species richness was highest in non-mycorrhizal seedlings in the root zone at 6- to 9-cm depth, and 3 cm away from plants. More bacterial species are needed when plants are devoid of mycorrhiza, and their influence is constrained 3 cm away from roots. Higher diversity of trophic groups was recorded at mycorrhizal seedlings and at the compartment influenced by the mycelium at 6- to 9-cm depth. The highest bacterivorous diversity, higher number of rare species and protozoa-eating amoebae, and the absence of fungivorous group recorded at the mycorrhizosphere of Z. mays, indicate that the community was very different from the non-mycorrhizal plants. We conclude that the arbuscular mycorrhizal fungus exerts significant changes on the community of trophic groups of amoebae.}, }
@article {pmid36331034, year = {2022}, author = {Schrad, N and Pensky, J and Gorski, G and Beganskas, S and Fisher, AT and Saltikov, C}, title = {Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, doi = {10.1093/femsec/fiac130}, pmid = {36331034}, issn = {1574-6941}, mesh = {Soil/chemistry ; *Groundwater/chemistry ; *Microbiota ; Carbon/analysis ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.}, }
@article {pmid36330300, year = {2022}, author = {Klein, M and Stewart, JD and Porter, SS and Weedon, JT and Kiers, ET}, title = {Evolution of manipulative microbial behaviors in the rhizosphere.}, journal = {Evolutionary applications}, volume = {15}, number = {10}, pages = {1521-1536}, pmid = {36330300}, issn = {1752-4571}, abstract = {The rhizosphere has been called "one of the most complex ecosystems on earth" because it is a hotspot for interactions among millions of microbial cells. Many of these are microbes are also participating in a dynamic interplay with host plant tissues, signaling pathways, and metabolites. Historically, breeders have employed a plant-centric perspective when trying to harness the potential of microbiome-derived benefits to improve productivity and resilience of economically important plants. This is potentially problematic because: (i) the evolution of the microbes themselves is often ignored, and (ii) it assumes that the fitness of interacting plants and microbes is strictly aligned. In contrast, a microbe-centric perspective recognizes that putatively beneficial microbes are still under selection to increase their own fitness, even if there are costs to the host. This can lead to the evolution of sophisticated, potentially subtle, ways for microbes to manipulate the phenotype of their hosts, as well as other microbes in the rhizosphere. We illustrate this idea with a review of cases where rhizosphere microbes have been demonstrated to directly manipulate host root growth, architecture and exudation, host nutrient uptake systems, and host immunity and defense. We also discuss indirect effects, whereby fitness outcomes for the plant are a consequence of ecological interactions between rhizosphere microbes. If these consequences are positive for the plant, they can potentially be misconstrued as traits that have evolved to promote host growth, even if they are a result of selection for unrelated functions. The ubiquity of both direct microbial manipulation of hosts and context-dependent, variable indirect effects leads us to argue that an evolutionary perspective on rhizosphere microbial ecology will become increasingly important as we continue to engineer microbial communities for crop production.}, }
@article {pmid36329848, year = {2022}, author = {Xu, H and Xue, Y and Na, N and Wu, N and Zhao, Y and Sun, L and Qili, M and Wang, T and Zhong, J}, title = {Fermentation quality, bacterial community, and aerobic stability of ensiling Leymus chinensis with lactic acid bacteria or/and water after long-term storage.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {959018}, pmid = {36329848}, issn = {1664-302X}, abstract = {Leymus chinensis is a major forage resource for herbivores on typical steppe and meadow steppes in Northern China. This study aimed to reveal the fermentation quality, bacterial community, and aerobic stability of L. chinensis silage treated with lactic acid bacteria or/and water after long-term storage. Leymus chinensis was harvested at the heading stage and ensiled with lactic acid bacteria [LAB, 2.00 ml/kg fresh weight (FW) of LAB, L], water (100 ml/kg FW of distilled water, W), or a combination of both [2.00 ml/kg fresh weight (FW) of LAB and 100 ml/kg FW of distilled water, LW] in polyethylene laboratory-scale silos (diameter, 20 cm; height, 30 cm) at a density of 650 kg/m[3]. As a control silage (CK), untreated L. chinensis silage was also assessed. The samples were taken at 0 day of opening after 300 days of ensiling (CK_0d, L_0d, W_0d, and LW_0d) and at 10 days of opening (CK_10d, L_10d, W_10d, and LW_10d). The fermentation quality, microbial counts, bacterial community, and aerobic stability of the silage were assessed. The CK_0d contained higher pH and aerobic bacteria count, and lower LA and BC concentrations than L_0d, W_0d, and LW_0d (p < 0.05), and the LAB and yeasts were only detected in CK at 0 day of opening. Lactobacillus had the most abundance among bacterial genera in all silages at 0 day of opening. Just CK had 2°C above the ambient temperature during aerobic exposure (at 224 h). During aerobic exposure, the pH and microbial counts in CK increased (p < 0.05), and Lactobacillus in L and LW had decreasing abundance (p < 0.05). The CK_10d had higher pH and microbial counts, and lower lactic acid and buffering capacity than L_10d, W_10d, and LW_10d (p < 0.05). At 10 days of opening, the coliforms and yeasts were just detected in CK, and Lactobacillus also had the most abundance among bacterial genera in all silages at 10 days of opening. Overall, inoculating LAB and adding water improved the fermentation quality and the aerobic exposure of L. chinensis silage after long-term storage. The activities of coliforms and yeasts during aerobic exposure contributed to the aerobic deterioration of L. chinensis silage without any treating. Lactobacillus dominated the bacterial communities of all silage at 0 and 10 days of opening. During aerobic exposure, the abundance of Lactobacillus reduced in L. chinensis silage treated with LAB or water.}, }
@article {pmid36329282, year = {2022}, author = {Fang, FZ and Chen, SL and Gui, HY and Li, ZJ and Zhang, XF}, title = {Long-Read Sequencing Analysis Revealed the Impact of Forest Conversion on Soil Fungal Diversity in Limu Mountain, Hainan.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36329282}, issn = {1432-184X}, abstract = {Soil fungi are essential to soil microorganisms that play an important role in the ecosystem's soil carbon cycle and mineral nutrient transformation. Understanding the structural characteristics and diversity of soil fungal communities helps understand the health of forest ecosystems. The transition from tropical rainforest to artificial forest greatly impacts the composition and diversity of fungal communities. Hainan Limushan tropical rainforest National Park has a large area of artificial forests. Ecologists have conducted in-depth studies on the succession of animals and plants to regenerate tropical rainforests. There are few reports on the diversity of soil fungi and its influencing factors in the succession of tropical rainforests in Limu Mountain. In this study, 44 soil samples from five different stands were collected in the tropical rainforest of Limushan, Hainan. High-throughput sequencing of rDNA in its region was used to analyze fungal communities and study their α and β diversity. Analysis of variance and multiple regression models was used to analyze soil variables and fungal functional groups to determine the effects of interaction between fungi and environmental factors. A total of 273,996 reads and 1290 operational taxonomic units (OTUs) were obtained, belonging to 418 species, 325 genera, 159 families, eight phyla, 30 classes, and 73 orders. The results showed that the composition of soil fungal communities in the five stands was similar, with ascomycetes accounting for 70.5% and basidiomycetes accounting for 14.7%. α and β diversity analysis showed that soil fungi in Limushan tropical rainforest had high abundance and diversity. Multiple regression analysis between soil variables and functional groups showed that organic matter, TN, TP, TK, and AK were excellent predictors for soil fungi. TP was the strongest predictor in all functional groups except soil saprotroph. Organic matter and total nitrogen were the strongest predictors of soil rot. The transformation from tropical rainforest to artificial forest in Limushan did not change the soil fungal community structure, but the richness and diversity of soil fungi changed. The forest transformation did not lead to decreased soil fungal abundance and diversity. Different vegetation types and soil properties affect the diversity of soil fungal communities. We found that Caribbean pine plantations can improve soil fungal diversity, while long-term Eucalyptus spp. plantations may reduce soil fungal diversity.}, }
@article {pmid36329197, year = {2022}, author = {van Spanning, RJM and Guan, Q and Melkonian, C and Gallant, J and Polerecky, L and Flot, JF and Brandt, BW and Braster, M and Iturbe Espinoza, P and Aerts, JW and Meima-Franke, MM and Piersma, SR and Bunduc, CM and Ummels, R and Pain, A and Fleming, EJ and van der Wel, NN and Gherman, VD and Sarbu, SM and Bodelier, PLE and Bitter, W}, title = {Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem.}, journal = {Nature microbiology}, volume = {7}, number = {12}, pages = {2089-2100}, pmid = {36329197}, issn = {2058-5276}, mesh = {*Ecosystem ; Proteomics ; Phylogeny ; Methane/metabolism ; *Mycobacterium/genetics ; }, abstract = {So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gaseous chemocline interface between volcanic gases and the Earth's atmosphere. This Mycobacterium, for which we propose the name Candidatus Mycobacterium methanotrophicum, is closely related to well-known obligate pathogens such as M. tuberculosis and M. leprae. Genomic and proteomic analyses revealed that Candidatus M. methanotrophicum expresses a full suite of enzymes required for aerobic growth on methane, including a soluble methane monooxygenase that catalyses the hydroxylation of methane to methanol and enzymes involved in formaldehyde fixation via the ribulose monophosphate pathway. Growth experiments combined with stable isotope probing using [13]C-labelled methane confirmed that Candidatus M. methanotrophicum can grow on methane as a sole carbon and energy source. A broader survey based on 16S metabarcoding suggests that species closely related to Candidatus M. methanotrophicum may be abundant in low-pH, high-methane environments.}, }
@article {pmid36329192, year = {2022}, author = {Slack, E and Diard, M}, title = {Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution.}, journal = {Mucosal immunology}, volume = {15}, number = {6}, pages = {1188-1198}, pmid = {36329192}, issn = {1935-3456}, mesh = {Animals ; Humans ; Immunoglobulin A, Secretory ; Mucous Membrane ; *Gastrointestinal Microbiome ; Bacteria ; *Vaccines ; Inflammation ; Intestinal Mucosa ; Mammals ; }, abstract = {In the beginning it was simple: we injected a protein antigen and studied the immune responses against the purified protein. This elegant toolbox uncovered thousands of mechanisms via which immune cells are activated. However, when we consider immune responses against real infectious threats, this elegant simplification misses half of the story: the infectious agents are typically evolving orders-of-magnitude faster than we are. Nowhere is this more pronounced than in the mammalian large intestine. A bacterium representing only 0.1% of the human gut microbiota will have a population size of 10[9] clones, each actively replicating. Moreover, the evolutionary pressure from other microbes is at least as profound as direct effects of the immune system. Therefore, to really understand intestinal immune mechanisms, we need to understand both the host response and how rapid microbial evolution alters the apparent outcome of the response. In this review we use the examples of intestinal inflammation and secretory immunoglobulin A (SIgA) to highlight what is already known (Fig. 1). Further, we will explore how these interactions can inform immunotherapy and prophylaxis. This has major implications for how we design effective mucosal vaccines against increasingly drug-resistant bacterial pathogens Fig. 1 THE IMMUNE RESPONSE SHAPES THE FITNESS LANDSCAPE IN THE GASTRO-INTESTINAL TRACT.: The red arrows depict possible evolutionary paths of a novel colonizer along adaptive peaks in the intestinal fitness landscapes that change with the status of the host immune system. The flat surfaces represent the non-null fitness baselines (values x or y) at which a bacterium can establish at minimum carrying capacity. a In the healthy gut, metabolic competence, resistance to aggressions by competitors and predators, swift adaptation to rapid fluctuations as well as surviving acidic pH and the flow of the intestinal content, represent potent selective pressures and as many opportunities for bacteria to increase fitness by phenotypic or genetic variations. b When pathogens trigger acute inflammation, bacteria must adapt to iron starvation, killing by immune cells and antimicrobial peptides, and oxidative stress, while new metabolic opportunities emerge. c When high-affinity SIgA are produced against a bacterium, e.g., after oral vaccination, escape of SIgA by altering or losing surface epitopes becomes crucial for maximum fitness. However, escaping polyvalent SIgA responses after vaccination with "evolutionary trap" vaccines leads to evolutionary trade-offs: A fitness maximum is reached in the vaccinated host gut that represents a major disadvantage for transmission into naïve hosts (fitness diminished below x) (d).}, }
@article {pmid36328255, year = {2023}, author = {Abdullah Al, M and Wang, W and Jin, L and Chen, H and Xue, Y and Jeppesen, E and Majaneva, M and Xu, H and Yang, J}, title = {Planktonic ciliate community driven by environmental variables and cyanobacterial blooms: A 9-year study in two subtropical reservoirs.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 2}, pages = {159866}, doi = {10.1016/j.scitotenv.2022.159866}, pmid = {36328255}, issn = {1879-1026}, mesh = {Plankton ; Ecosystem ; Phylogeny ; *Cyanobacteria ; Lakes ; *Ciliophora ; Eutrophication ; }, abstract = {It is well-established that environmental variability and cyanobacterial blooms have major effects on the assembly and functioning of bacterial communities in both marine and freshwater habitats. It remains unclear, however, how the ciliate community responds to such changes over the long-term, particularly in subtropical lake and reservoir ecosystems. We analysed 9-year planktonic ciliate data series from the surface water of two subtropical reservoirs to elucidate the role of cyanobacterial bloom and environmental variabilities on the ciliate temporal dynamics. We identified five distinct periods of cyanobacterial succession in both reservoirs. Using multiple time-scale analyses, we found that the interannual variability of ciliate communities was more strongly related to cyanobacterial blooms than to other environmental variables or to seasonality. Moreover, the percentage of species turnover across cyanobacterial bloom and non-bloom periods increased significantly with time over the 9-year period. Phylogenetic analyses further indicated that 84 %-86 % of ciliate community turnover was governed by stochastic dispersal limitation or undominated processes, suggesting that the ciliate communities in subtropical reservoirs were mainly controlled by neutral processes. However, short-term blooms increased the selection pressure and drove 30 %-53 % of the ciliate community turnover. We found that the ciliate community composition was influenced by environmental conditions with nutrients, cyanobacterial biomass and microzooplankton having direct and/or indirect significant effects on the ciliate taxonomic or functional community dynamics. Our results provide new insights into the long-term temporal dynamics of planktonic ciliate communities under cyanobacterial bloom disturbance.}, }
@article {pmid36327936, year = {2022}, author = {Wong, YY and Lee, CW and Chai, SCY and Lim, JH and Bong, CW and Sim, EUH and Narayanan, K and Hii, YS and Wang, AJ}, title = {Distribution of faecal indicator bacteria in tropical waters of Peninsular Malaysia and their decay rates in tropical seawater.}, journal = {Marine pollution bulletin}, volume = {185}, number = {Pt A}, pages = {114297}, doi = {10.1016/j.marpolbul.2022.114297}, pmid = {36327936}, issn = {1879-3363}, mesh = {*Escherichia coli/physiology ; Malaysia ; *Seawater/microbiology ; Feces/microbiology ; Bacteria ; Water Microbiology ; }, abstract = {We investigated the appropriateness of faecal indicator bacteria in tropical waters. We compared total coliform (undetectable to 7.2 × 10[5] cfu 100 mL[-1]), faecal coliform (undetectable to 6.1 × 10[5] cfu 100 mL[-1]) and enterococci (undetectable to 3.1 × 10[4] cfu 100 mL[-1]) distribution in Peninsular Malaysia. Faecal indicator bacteria was highest in freshwater, and lowest in seawater (q > 4.18, p < 0.01). We also measured the decay rates of Escherichia coli and Enterococcus faecium in microcosms. In seawater, average decay rate for E. coli was 0.084 ± 0.029 h[-1], and higher than E. faecium (0.048 ± 0.024 h[-1]) (t = 2.527, p < 0.05). Grazing accounted for 54 % of both E. coli and E. faecium decay. E. coli decayed in the <0.02 μm seawater fraction (0.023 ± 0.012 h[-1]) but E. faecium sometimes grew. Seawater warming further uncoupled the response from both E. coli and E. faecium as E. faecium grew and E. coli decayed with warming. Our results suggested that the prevalence of faecal indicator bacteria in tropical waters was not due to faecal pollution alone, and this will have serious implications towards the use of these faecal indicator bacteria.}, }
@article {pmid36327839, year = {2023}, author = {Moreira, VA and Cravo-Laureau, C and de Carvalho, ACB and Baldy, A and Bidone, ED and Sabadini-Santos, E and Duran, R}, title = {Microbial indicators along a metallic contamination gradient in tropical coastal sediments.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130244}, doi = {10.1016/j.jhazmat.2022.130244}, pmid = {36327839}, issn = {1873-3336}, mesh = {Geologic Sediments ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Brazil ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; *Metals, Heavy/analysis ; }, abstract = {The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.}, }
@article {pmid36326874, year = {2022}, author = {Chen, T and Zhao, M and Tang, X and Wang, W and Zhang, M and Tang, J and Wang, W and Wei, W and Ma, B and Zou, Y and Zhang, N and Mi, J and Wang, Y and Liao, X and Wu, Y}, title = {Serious Risk of Tigecycline Resistance in Escherichia coli Isolated from Swine Manure.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36326874}, issn = {1432-184X}, abstract = {The emergence of the plasmid-mediated tigecycline resistance gene tetX family in pig farms has attracted worldwide attention. The use of tetracycline antibiotics in pig farms has a facilitating effect on the prevalence of the tetX family, but the relationship among its presence, expression, and resistance phenotype in resistant bacteria is unknown. In this study, the presence and expression characteristics of tetracycline resistance genes (TRGs) in 89 strains of doxycycline-resistant E. coli (DRE) isolated from pig manure samples from 20 pig farms under low concentrations of doxycycline stress (2 μg/mL) were analyzed. The detection rate of tetO was 96.63%, which is higher than those of other TRGs, such as tetA (94.38%), tetX (76.40%), tetB (73.03%), and tet(X4) (69.66%). At least three TRG types were present in DRE strains, which thus showed extensive resistance to tetracycline antibiotics, and 37% of these strains were resistant to tigecycline. In the presence of a low concentration of doxycycline, tetA played an important role, and the expression and existence ratio of TRGs indicated low expression of TRGs. Furthermore, the doxycycline resistance of DRE was jointly determined by the total absolute abundance of TRGs, and the absolute abundance of tetX and tet(X4) was significantly positively associated with tigecycline resistance in DRE (P < 0.05). Overall, DRE isolated from swine manure is an important reservoir of the tetX family, which suggests that DRE in swine manure has a high risk of tigecycline resistance, poses a potential threat to human health, and should be of public concern.}, }
@article {pmid36326287, year = {2022}, author = {Bandekar, M and Abdolahpur Monikh, F and Kekäläinen, J and Tahvanainen, T and Kortet, R and Zhang, P and Guo, Z and Akkanen, J and Leskinen, JTT and Gomez-Gonzalez, MA and Krishna Darbha, G and Grossart, HP and Valsami-Jones, E and Kukkonen, JVK}, title = {Submicron Plastic Adsorption by Peat, Accumulation in Sphagnum Mosses and Influence on Bacterial Communities in Peatland Ecosystems.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {22}, pages = {15661-15671}, pmid = {36326287}, issn = {1520-5851}, mesh = {*Sphagnopsida/chemistry/microbiology ; Soil/chemistry ; Adsorption ; Plastics ; Bacteria ; *Microbiota ; }, abstract = {The smallest fraction of plastic pollution, submicron plastics (SMPs <1 μm) are expected to be ubiquitous in the environment. No information is available about SMPs in peatlands, which have a key role in sequestering carbon in terrestrial ecosystems. It is unknown how these plastic particles might behave and interact with (micro)organisms in these ecosystems. Here, we show that the chemical composition of polystyrene (PS) and poly(vinyl chloride) (PVC)-SMPs influenced their adsorption to peat. Consequently, this influenced the accumualtion of SMPs by Sphagnum moss and the composition and diversity of the microbial communities in peatland. Natural organic matter (NOM), which adsorbs from the surrounding water to the surface of SMPs, decreased the adsorption of the particles to peat and their accumulation by Sphagnum moss. However, the presence of NOM on SMPs significantly altered the bacterial community structure compared to SMPs without NOM. Our findings show that peatland ecosystems can potentially adsorb plastic particles. This can not only impact mosses themselves but also change the local microbial communities.}, }
@article {pmid36324386, year = {2022}, author = {Li, Y and Xin, X and Song, W and Zhang, X and Chen, S and Wang, Q and Li, A and Li, Y}, title = {VHL syndrome without clear family history: A rare case report and literature review of Chinese patients.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {951054}, pmid = {36324386}, issn = {1664-2295}, abstract = {OBJECTIVE: To analyze the clinical manifestations and imaging features of a hospitalized patient with intermittent headache who was finally diagnosed with von Hippel-Lindau (VHL) syndrome and to perform whole-exon gene detection to improve the understanding of the diagnosis and treatment strategies of the disease.<br><br>METHODS: A case of suspected VHL syndrome in Shanxi Provincial People's Hospital was analyzed. Proband DNA was also extracted for whole exome sequencing and screened for causative mutation sites, which were validated by Sanger sequencing. The literature about VHL gene mutations in Chinese patients in the past 10 years were also reviewed.<br><br>RESULTS: There is a heterozygous mutation site c.499C > G on the VHL gene on the short arm of chromosome 3 of the patient, which is a missense mutation. The mutation results in the substitution of arginine with glycine at amino acid 167 of the encoded protein, which may be primarily responsible for the disease in the patient with VHL syndrome. However, the mutation did not occur in other family members.<br><br>CONCLUSION: Early recognition and treatment of VHL syndrome can be available with genetic testing technology. Strengthening the understanding of this complex genetic disease and improving the diagnostic rate of VHL syndrome are helpful for the precise treatment of patients with this disease, which may help prolong the survival time of patients to a certain extent and improve their quality of life.}, }
@article {pmid36323973, year = {2022}, author = {Ma, Y and Li, P and Zhong, H and He, M and Wang, B and Mou, X and Wu, L}, title = {The Ecological Differentiation of Particle-Attached and Free-Living Bacterial Communities in a Seasonal Flooding Lake-the Poyang Lake.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36323973}, issn = {1432-184X}, abstract = {Particle-attached (PA) and free-living (FL) bacterial communities play essential roles in the biogeochemical cycling of essential nutrients in aquatic environments. However, little is known about the factors that drive the differentiation of bacterial lifestyles, especially in flooding lake systems. Here we assessed the compositional and functional similarities between the FL and PA bacterial fractions in a typical flooding lake-the Poyang Lake (PYL) of China. The results revealed that PA communities had significantly different compositions and functions from FL communities in every hydrological period, and the diversity of both PA and FL communities was affected mainly by the water regime rather than bacterial lifestyles. PA communities were more diverse and enriched with Proteobacteria and Bacteroidetes, while FL communities had more Actinobacteria. There was a higher abundance of photosynthetic and nitrogen-cycling bacterial groups in PA communities, but a higher abundance of members involved in hydrocarbon degradation, aromatic hydrocarbon degradation, and methylotrophy in FL communities. Water properties (e.g., temperature, pH, total phosphorus) significantly regulated the lifestyle variations of PA and FL bacteria in PYL. Collectively, our results have demonstrated a clear ecological differentiation of PA and FL bacterial communities in flooding lakes, suggesting that the connectivity between FL and PA bacterial fractions is water property-related rather than water regime-related.}, }
@article {pmid36322177, year = {2022}, author = {Stupar, M and Savković, &#x17d; and Breka, K and Stamenković, S and Krizmanić, I and Vukojević, J and Grbić, ML}, title = {A Variety of Fungal Species on the Green Frogs' Skin (Pelophylax esculentus complex) in South Banat.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36322177}, issn = {1432-184X}, abstract = {In the last several decades, amphibian populations have been declining worldwide. Many factors have been linked to global amphibian decline, including habitat destruction, pollution, introduced species, global environmental changes, and emerging infectious diseases. Recent studies of amphibian skin infections were mainly focused on the presence of chytridiomycosis, neglecting other members of the frogs' skin communities. The diversity pattern of fungal dwellers on the skin of green frogs (Pelophylax esculentus complex) was investigated. A total of 100 adults were sampled from three localities in South Banat (northern Serbia) over three consecutive years and detected fungal dwellers were identified using light microscopy and ITS and BenA gene sequencing. Structures belonging to fungi and fungus-like organisms including a variety of spores and different mycelia types were documented in the biofilm formed on amphibian skin, and are classified into 10 groups. In total, 42 fungal isolates were identified to species, section, or genus level. The difference in mycobiota composition between sampling points (localities and green frog taxa) was documented. The highest number of fungal structures and isolates was recorded on the hybrid taxon P. esculentus and locality Stevanove ravnice. Parental species showed a markedly lower diversity than the hybrid taxon and were more similar in diversity patterns and were placed in the same homogenous group. The locality Stevanove ravnice exhibited more pronounced differences in diversity pattern than the other two localities and was placed in a distinct and separate homogenous group. Among the fungal isolates, the highest isolation frequency was documented for Alternaria alternata, Aspergillus sp. sect. Nigri, Epicoccum nigrum, Fusarium proliferatum, and Trichoderma atroviride. Among the documented species, dematiaceous fungi, causative agents of chromomycosis in amphibians, were also recorded in this research with high isolation frequency. Also, some rare fungal species such as Quambalaria cyanescens and Pseudoteniolina globosa are documented for the first time in this research as microbial inhabitants of amphibian skin.}, }
@article {pmid36321898, year = {2022}, author = {Spencer-Williams, I and Balangoda, A and Dabundo, R and Elliott, E and Haig, SJ}, title = {Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0215822}, doi = {10.1128/spectrum.02158-22}, pmid = {36321898}, issn = {2165-0497}, abstract = {Many cities across the nation are plagued by lead contamination in drinking water. As such, many drinking water utilities have undertaken lead service line (LSL) replacement to prevent further lead contamination. However, given the urgency of lead mitigation, and the socioeconomic challenges associated with LSL replacement, cities have used phosphate-based corrosion inhibitors (i.e., orthophosphate) alongside LSL replacement. While necessary to ensure public health protection from lead contamination, the addition of orthophosphate into an aging and leaking drinking water system may increase the concentration of phosphate leaching into urban streams characterized by century-old failing water infrastructure. Such increases in phosphate availability may cascade into nutrient and microbial community composition shifts. The purpose of this study was to determine how this occurs and to understand whether full-scale distribution system orthophosphate addition impacts the microbial ecology of urban streams. Through monthly collection of water samples from five urban streams before and after orthophosphate addition, significant changes in microbial community composition (16S rRNA amplicon sequencing) and in the relative abundance of typical freshwater taxa were observed. In addition, key microbial phosphorus and nitrogen metabolism genes (e.g., two component regulatory systems) were predicted to change via BugBase. No significant differences in the absolute abundances of total bacteria, Cyanobacteria, and "Candidatus Accumulibacter" were observed. Overall, the findings from this study provide further evidence that urban streams are compromised by unintentional hydrologic connections with drinking water infrastructure. Moreover, our results suggest that infiltration of phosphate-based corrosion inhibitors can impact urban streams and have important, as-yet-overlooked impacts on urban stream microbial communities. IMPORTANCE Elevated lead levels in drinking water supplies are a public health risk. As such, it is imperative for cities to urgently address lead contamination from aging drinking water supplies by way of lead service line replacements and corrosion control methods. However, when applying corrosion control methods, it is also important to consider the chemical and microbiological effects that can occur in natural settings, given that our water infrastructure is aging and more prone to leaks and breaks. Here, we examine the impacts on the microbial ecology of five urban stream systems before and after full-scale distribution system orthophosphate addition. Overall, the results suggest that infiltration of corrosion inhibitors may impact microbial communities; however, future work should be done to ascertain the true impact to protect both public and environmental health.}, }
@article {pmid36320358, year = {2022}, author = {Simões, ACP and Fernandes, RP and Barreto, MS and Marques da Costa, GB and de Godoy, MG and Freire, DMG and Pereira, N}, title = {Growth of Methylobacterium organophilum in Methanol for the Simultaneous Production of Single-Cell Protein and Metabolites of Interest.}, journal = {Food technology and biotechnology}, volume = {60}, number = {3}, pages = {338-349}, pmid = {36320358}, issn = {1330-9862}, abstract = {RESEARCH BACKGROUND: This study aims to monitor the growth of the methylotrophic bacteria Methylobacterium organophilum in a culture medium with methanol as a carbon source and to verify the production of unicellular proteins and other biomolecules, such as carotenoids, exopolysaccharides and polyhydroxyalkanoates, making them more attractive as animal feed.<br><br>EXPERIMENTAL APPROACH: Bacterial growth was studied in shake flasks using different carbon/nitrogen (C:N) ratios to determine their best ratio for achieving the highest volumetric productivity of cells and substrate consumption rate. This optimal parameter was further used in a fed-batch operating bioreactor system to define the kinetic profile of cell growth. Methanol consumption was measured by HPLC analysis and the extracted pigments were analyzed by liquid chromatography/mass spectrometry. Chemical composition and rheological properties of the produced exopolysaccharides were also determined.<br><br>RESULTS AND CONCLUSIONS: The best experimental parameters were verified using an initial methanol concentration of 7 g/L in the culture medium. The same initial substrate concentration was used in the fed-batch operation and after 60 h of cultivation 5 g/L of biomass were obtained. The accumulation of carotenoids associated with cell growth was monitored, reaching a concentration of 1.6 mg/L at the end of the process. These pigments were then analyzed and characterized as a set of xanthophylls (oxidized carotenoids). In addition, two other product types were identified during the fed-batch operation: exopolysaccharides, which reached a concentration of 8.9 g/L at the end of the cultivation, and an intracellular granular structure that was detected by transmission electron microscopy (TEM), suggesting the accumulation of polyhydroxyalkanoate (PHA), most likely polyhydroxybutyrate.<br><br>Methylobacterium organophilum demonstrated a unique ability to produce compounds of commercial interest. The distinct metabolic diversity of this bacterium makes room for its use in biorefineries.}, }
@article {pmid36319743, year = {2022}, author = {Ayilara, MS and Adeleke, BS and Babalola, OO}, title = {Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36319743}, issn = {1432-184X}, abstract = {This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.}, }
@article {pmid36318280, year = {2022}, author = {Hill, AJ and Grisnik, M and Walker, DM}, title = {Bacterial Skin Assemblages of Sympatric Salamanders Are Primarily Shaped by Host Genus.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36318280}, issn = {1432-184X}, abstract = {Bacterial assemblages on the skins of amphibians are known to influence pathogen resistance and other important physiological functions in the host. Host-specific factors and the environment play significant roles in structuring skin assemblages. This study used high-throughput 16S rRNA sequencing and multivariate analyses to examine differences in skin-bacterial assemblages from 246 salamanders belonging to three genera in the lungless family Plethodontidae along multiple spatial gradients. Composition and α- and β-diversity of bacterial assemblages were defined, indicator species were identified for each host group, and the relative influences of host- versus environment-specific ecological factors were evaluated. At the broadest spatial scale, host genus, host species, and sampling site were predictive of skin assemblage structure, but host genus and species were more influential after controlling for the marginal effects of site, as well as nestedness of site. Furthermore, assemblage similarity within each host genus did not change with increasing geographic distance. At the smallest spatial scale, site-specific climate analyses revealed different relationships to climatic variables for each of the three genera, and these relationships were determined by host ecomode. Variation in bacterial assemblages of terrestrial hosts correlated with landscape-level climatic variability, and this pattern decayed with increasing water dependence of the host. Results from this study highlight host-specific considerations for researchers studying wildlife diseases in co-occurring, yet ecologically divergent, species.}, }
@article {pmid36317499, year = {2022}, author = {Bachimanchi, H and Midtvedt, B and Midtvedt, D and Selander, E and Volpe, G}, title = {Microplankton life histories revealed by holographic microscopy and deep learning.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36317499}, issn = {2050-084X}, mesh = {Animals ; *Phytoplankton ; *Deep Learning ; Microscopy ; Zooplankton ; Oceans and Seas ; Seawater ; }, abstract = {The marine microbial food web plays a central role in the global carbon cycle. However, our mechanistic understanding of the ocean is biased toward its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages. Yet, resolution at the level of the individual microplankton is required to advance our understanding of the microbial food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons throughout their lifespan, continuously measuring their three-dimensional position and dry mass. The deep-learning algorithms circumvent the computationally intensive processing of holographic data and allow rapid measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates, and handling times for individual microplanktons. The method is particularly useful to detail the rates and routes of organic matter transfer in micro-zooplankton, the most important and least known group of primary consumers in the oceans. Studying individual interactions in idealized small systems provides insights that help us understand microbial food webs and ultimately larger-scale processes. We exemplify this by detailed descriptions of micro-zooplankton feeding events, cell divisions, and long-term monitoring of single cells from division to division.}, }
@article {pmid36316374, year = {2022}, author = {Noiset, P and Cabirol, N and Rojas-Oropeza, M and Warrit, N and Nkoba, K and Vereecken, NJ}, title = {Honey compositional convergence and the parallel domestication of social bees.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18280}, pmid = {36316374}, issn = {2045-2322}, mesh = {Bees ; Animals ; *Honey/analysis ; Domestication ; Magnetic Resonance Spectroscopy ; Thailand ; Mexico ; }, abstract = {Honey collection evolved from simple honey hunting to the parallel and independent domestication of different species of bees in various parts of the world. In this study, we investigate the extent to which the composition of Apis and stingless bee honeys has been a driver in the selection of different bee species for domestication in Mesoamerica (Mexico) and Asia (Thailand) using a sampling design that combines peak honey profiling by H1 NMR spectroscopy with the collection of honeys from domesticated and undomesticated bee species. Our results show that, independently of the region of the world considered, domesticated stingless bees produce honey whose compositional profiles differ from those of the non-domesticated species and exhibit more similarities towards honeys produced by the domesticated Apis species. Our results provide evidence for the first time that the search for natural sweeteners in the environment by our ancestors led to the parallel and independent domestication of social bees producing honeys with similar compositional profiles.}, }
@article {pmid36314760, year = {2022}, author = {Florent, P and Cauchie, HM and Herold, M and Ogorzaly, L}, title = {Bacteriophages pass through candle-shaped porous ceramic filters: Application for the collection of viruses in soil water.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1314}, pmid = {36314760}, issn = {2045-8827}, mesh = {*Bacteriophages/genetics ; Soil ; Porosity ; Water ; *Viruses ; Ceramics ; }, abstract = {Despite the ubiquity of viruses in soils, their diversity in soil water has not been explored, mainly due to the difficulty of collecting them. In hydrology, soil water is usually collected using porous candles. This study proposes using these porous candles as a new tool for sampling viruses in soil water to analyze their passage through the ceramic part of the candles. The recovery of the viruses was determined after filtration under laboratory conditions using three model bacteriophages (MS2, ΦX174, and Φ6) and Escherichia coli, at neutral and acidic pH. Then, a field experiment was carried out where soil water filtration and viral identification by metagenomic shotgun were performed. At neutral pH, all bacteriophages tested successfully passed through the porous candles during the filtration process, with reductions of 0.02 log, 0.16 log, and 0.55 log for MS2 ΦX174 and Φ6, respectively. At pH 4.4, the passage of MS2 was not affected while ΦX174 underwent a slight reduction in recovery, probably caused by adsorption onto the filter material. Regarding the application of the porous candles in the field, the results obtained allowed the successful recovery of viruses, exposing porous candles as a new method suitable for the collection of viruses from soil water in the context of the study of viral communities.}, }
@article {pmid36314757, year = {2022}, author = {Brauer, A and Bengtsson, MM}, title = {DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1323}, pmid = {36314757}, issn = {2045-8827}, mesh = {*Eukaryota/genetics ; Archaea/genetics ; Bacteria/genetics ; *Microbiota/genetics ; DNA/genetics ; }, abstract = {DNA extraction and preservation bias is a recurring topic in DNA sequencing-based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft-bodied and hard-shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities.}, }
@article {pmid36314752, year = {2022}, author = {Orsini, M and Ianni, A and Zinzula, L}, title = {Brucella ceti and Brucella pinnipedialis genome characterization unveils genetic features that highlight their zoonotic potential.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1329}, pmid = {36314752}, issn = {2045-8827}, mesh = {Animals ; Humans ; *Brucella/genetics ; *Brucellosis/microbiology ; *Caniformia/microbiology ; Cetacea/microbiology ; }, abstract = {The Gram-negative bacteria Brucella ceti and Brucella pinnipedialis circulate in marine environments primarily infecting marine mammals, where they cause an often-fatal disease named brucellosis. The increase of brucellosis among several species of cetaceans and pinnipeds, together with the report of sporadic human infections, raises concerns about the zoonotic potential of these pathogens on a large scale and may pose a threat to coastal communities worldwide. Therefore, the characterization of the B. ceti and B. pinnipedialis genetic features is a priority to better understand the pathological factors that may impact global health. Moreover, an in-depth functional analysis of the B. ceti and B. pinnipedialis genome in the context of virulence and pathogenesis was not undertaken so far. Within this picture, here we present the comparative whole-genome characterization of all B. ceti and B. pinnipedialis genomes available in public resources, uncovering a collection of genetic tools possessed by these aquatic bacterial species compared to their zoonotic terrestrial relatives. We show that B. ceti and B. pinnipedialis genomes display a wide host-range infection capability and a polyphyletic phylogeny within the genus, showing a genomic structure that fits the canonical definition of closeness. Functional genome annotation led to identifying genes related to several pathways involved in mechanisms of infection, others conferring pan-susceptibility to antimicrobials and a set of virulence genes that highlight the similarity of B. ceti and B. pinnipedialis genotypes to those of Brucella spp. displaying human-infecting phenotypes.}, }
@article {pmid36312987, year = {2022}, author = {Ma, K and Tu, Q}, title = {Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1011269}, pmid = {36312987}, issn = {1664-302X}, abstract = {Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup-Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined.}, }
@article {pmid36312976, year = {2022}, author = {Quagliariello, A and Ramiro, RS and Couce, A and Martino, ME}, title = {Editorial: Integrating multi-scale approaches for predicting microbiome ecology and evolution.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1045045}, pmid = {36312976}, issn = {1664-302X}, }
@article {pmid36309426, year = {2023}, author = {Jääskeläinen, E and Säde, E and Rönkkö, T and Hultman, J and Johansson, P and Riekkola, ML and Björkroth, J}, title = {Marination increased tyramine levels in rainbow trout fillet strips packaged under modified atmosphere.}, journal = {Food microbiology}, volume = {109}, number = {}, pages = {104099}, doi = {10.1016/j.fm.2022.104099}, pmid = {36309426}, issn = {1095-9998}, mesh = {Animals ; *Oncorhynchus mykiss ; Tyramine ; Meat/microbiology ; Atmosphere ; }, abstract = {Marinades are increasingly used to manufacture raw fish products. In corresponding meats, marinating is known to have a major effect on the composition of the microbiome, but the effect of marinating on fish is not known as well. This knowledge gap prompted our study of the microbial ecology and amine formation in marinated and unmarinated modified atmosphere commercially packaged rainbow trout fillet strips. According to our findings, marination increased the maximum concentrations (7-8 log CFU/g) of psychrotrophic bacteria by one logarithmic unit and led to 5 times higher average tyramine concentrations than the corresponding unmarinated product. Instead, trimethylamine concentrations were 30 times higher in the unmarinated product than those in the marinated one. According to the 16 S rRNA sequence analyses, lactic acid bacteria (LAB) predominated in the marinated strips one day after the use-by date, whereas in the unmarinated strips Fusobacteriaceae and LAB were the dominating taxa. Based on the culture-dependent analysis, Latilactobacillus fuchuensis was the prevailing LAB in both products. Since the subset of L. fuchuensis strains tested was able to produce tyramine in vitro, we hypothesise that the use of the acidic marinade activated the production of tyrosine-decarboxylating enzymes in L. fuchuensis and led to the increased tyramine concentrations.}, }
@article {pmid36307735, year = {2022}, author = {Hladnik, M and Unković, N and Janakiev, T and Grbić, ML and Arbeiter, AB and Stanković, S and Janaćković, P and Gavrilović, M and Rančić, D and Bandelj, D and Dimkić, I}, title = {An Insight into an Olive Scab on the "Istrska Belica" Variety: Host-Pathogen Interactions and Phyllosphere Mycobiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36307735}, issn = {1432-184X}, abstract = {The olive tree is one of the most important agricultural plants, affected by several pests and diseases that cause a severe decline in health status leading to crop losses. Olive leaf spot disease caused by the fungus Venturia oleaginea can result in complete tree defoliation and consequently lower yield. The aim of the study was to obtain new knowledge related to plant-pathogen interaction, reveal mechanisms of plant defense against the pathogen, and characterize fungal phyllosphere communities on infected and symptomless leaves that could contribute to the development of new plant breeding strategies and identification of novel biocontrol agents. The highly susceptible olive variety "Istrska Belica"' was selected for a detailed evaluation. Microscopy analyses led to the observation of raphides in the mesophyll and parenchyma cells of infected leaves and gave new insight into the complex V. oleaginea pathogenesis. Culturable and total phyllosphere mycobiota, obtained via metabarcoding approach, highlighted Didymella, Aureobasidium, Cladosporium, and Alternaria species as overlapping between infected and symptomless leaves. Only Venturia and Erythrobasidium in infected and Cladosporium in symptomless samples with higher abundance showed statistically significant differences. Based on the ecological role of identified taxa, it can be suggested that Cladosporium species might have potential antagonistic effects on V. oleaginea.}, }
@article {pmid36306091, year = {2023}, author = {Jameson, E and Taubert, M and Angel, R and Coyotzi, S and Chen, Y and Eyice, &#xd6; and Schäfer, H and Murrell, JC and Neufeld, JD and Dumont, MG}, title = {DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {261-282}, pmid = {36306091}, issn = {1940-6029}, mesh = {RNA, Ribosomal, 16S/genetics/chemistry ; Carbon Isotopes/chemistry ; Isotope Labeling/methods ; *DNA/chemistry ; *Proteins/chemistry ; Biomarkers ; RNA, Messenger ; }, abstract = {Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of [13]C, [18]O, or [15]N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.}, }
@article {pmid36305941, year = {2022}, author = {Costas-Selas, C and Martínez-García, S and Logares, R and Hernández-Ruiz, M and Teira, E}, title = {Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36305941}, issn = {1432-184X}, abstract = {We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ría de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.}, }
@article {pmid36304282, year = {2022}, author = {Saenz, C and Nigro, E and Gunalan, V and Arumugam, M}, title = {MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {846922}, pmid = {36304282}, issn = {2673-7647}, abstract = {Omics technologies have revolutionized microbiome research allowing the characterization of complex microbial communities in different biomes without requiring their cultivation. As a consequence, there has been a great increase in the generation of omics data from metagenomes and metatranscriptomes. However, pre-processing and analysis of these data have been limited by the availability of computational resources, bioinformatics expertise and standardized computational workflows to obtain consistent results that are comparable across different studies. Here, we introduce MIntO (Microbiome Integrated meta-Omics), a highly versatile pipeline that integrates metagenomic and metatranscriptomic data in a scalable way. The distinctive feature of this pipeline is the computation of gene expression profile through integrating metagenomic and metatranscriptomic data taking into account the community turnover and gene expression variations to disentangle the mechanisms that shape the metatranscriptome across time and between conditions. The modular design of MIntO enables users to run the pipeline using three available modes based on the input data and the experimental design, including de novo assembly leading to metagenome-assembled genomes. The integrated pipeline will be relevant to provide unique biochemical insights into microbial ecology by linking functions to retrieved genomes and to examine gene expression variation. Functional characterization of community members will be crucial to increase our knowledge of the microbiome's contribution to human health and environment. MIntO v1.0.1 is available at https://github.com/arumugamlab/MIntO.}, }
@article {pmid36304272, year = {2022}, author = {Karaoz, U and Brodie, EL}, title = {microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {918853}, pmid = {36304272}, issn = {2673-7647}, abstract = {Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.}, }
@article {pmid36303775, year = {2021}, author = {Hu, B and Canon, S and Eloe-Fadrosh, EA and Anubhav,  and Babinski, M and Corilo, Y and Davenport, K and Duncan, WD and Fagnan, K and Flynn, M and Foster, B and Hays, D and Huntemann, M and Jackson, EKP and Kelliher, J and Li, PE and Lo, CC and Mans, D and McCue, LA and Mouncey, N and Mungall, CJ and Piehowski, PD and Purvine, SO and Smith, M and Varghese, NJ and Winston, D and Xu, Y and Chain, PSG}, title = {Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.}, journal = {Frontiers in bioinformatics}, volume = {1}, number = {}, pages = {826370}, pmid = {36303775}, issn = {2673-7647}, abstract = {The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.}, }
@article {pmid36303759, year = {2021}, author = {Giulia, A and Anna, S and Antonia, B and Dario, P and Maurizio, C}, title = {Extending Association Rule Mining to Microbiome Pattern Analysis: Tools and Guidelines to Support Real Applications.}, journal = {Frontiers in bioinformatics}, volume = {1}, number = {}, pages = {794547}, pmid = {36303759}, issn = {2673-7647}, abstract = {Boosted by the exponential growth of microbiome-based studies, analyzing microbiome patterns is now a hot-topic, finding different fields of application. In particular, the use of machine learning techniques is increasing in microbiome studies, providing deep insights into microbial community composition. In this context, in order to investigate microbial patterns from 16S rRNA metabarcoding data, we explored the effectiveness of Association Rule Mining (ARM) technique, a supervised-machine learning procedure, to extract patterns (in this work, intended as groups of species or taxa) from microbiome data. ARM can generate huge amounts of data, making spurious information removal and visualizing results challenging. Our work sheds light on the strengths and weaknesses of pattern mining strategy into the study of microbial patterns, in particular from 16S rRNA microbiome datasets, applying ARM on real case studies and providing guidelines for future usage. Our results highlighted issues related to the type of input and the use of metadata in microbial pattern extraction, identifying the key steps that must be considered to apply ARM consciously on 16S rRNA microbiome data. To promote the use of ARM and the visualization of microbiome patterns, specifically, we developed microFIM (microbial Frequent Itemset Mining), a versatile Python tool that facilitates the use of ARM integrating common microbiome outputs, such as taxa tables. microFIM implements interest measures to remove spurious information and merges the results of ARM analysis with the common microbiome outputs, providing similar microbiome strategies that help scientists to integrate ARM in microbiome applications. With this work, we aimed at creating a bridge between microbial ecology researchers and ARM technique, making researchers aware about the strength and weaknesses of association rule mining approach.}, }
@article {pmid36303234, year = {2022}, author = {Yin, G and Chen, F and Chen, G and Yang, X and Huang, Q and Chen, L and Chen, M and Zhang, W and Ou, M and Cao, M and Lin, H and Chen, M and Xu, H and Ren, J and Chen, Y and Chen, Z}, title = {Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals.}, journal = {Journal of ovarian research}, volume = {15}, number = {1}, pages = {117}, pmid = {36303234}, issn = {1757-2215}, mesh = {Humans ; Female ; *Polycystic Ovary Syndrome ; *Mycobiome ; Overweight/complications ; RNA, Ribosomal, 16S ; Metabolome ; Bacteria/genetics ; }, abstract = {To characterize the gut bacteriome, mycobiome and serum metabolome profiles in polycystic ovary syndrome (PCOS) patients with normal/overweight individuals and evaluate a potential microbiota-related diagnostic method development for PCOS, 16S rRNA and ITS2 gene sequencing using 88 fecal samples and 87 metabolome analysis from serum samples are conducted and PCOS classifiers based on multiomics markers are constructed. There are significant bacterial, fungal community and metabolite differences among PCOS patients and healthy volunteers with normal/overweight individuals. Healthy individuals with overweight/obesity display less abnormal metabolism than PCOS patients and uniquely higher abundance of the fungal genus Mortierella. Nine bacterial genera, 4 predicted pathways, 11 fungal genera and top 30 metabolites are screened out which distinguish PCOS from healthy controls, with AUCs of 0.84, 0.64, 0.85 and 1, respectively. The metabolite-derived model is more accurate than the microbe-based model in discriminating normal BMI PCOS (PCOS-LB) from normal BMI healthy (Healthy-LB), PCOS-HB from Healthy-HB. Featured bacteria, fungi, predicted pathways and serum metabolites display higher associations with free androgen index (FAI) in the cooccurrence network. In conclusion, our data reveal that hyperandrogenemia plays a central role in the dysbiosis of intestinal microecology and the change in metabolic status in patients with PCOS and that its effect exceeds the role of BMI. Healthy women with high BMI showed unique microbiota and metabolic features.The priority of predictive models in discriminating PCOS from healthy status in this study were serum metabolites, fungal taxa and bacterial taxa.}, }
@article {pmid36303146, year = {2022}, author = {Xu, X and Dodd, AN}, title = {Is there crosstalk between circadian clocks in plants and the rhizomicrobiome?.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {241}, pmid = {36303146}, issn = {1741-7007}, mesh = {Rhizosphere ; *Circadian Clocks ; Circadian Rhythm ; Soil Microbiology ; *Microbiota ; Plants/microbiology ; *Arabidopsis ; Soil ; }, abstract = {Circadian clocks occur across the kingdoms of life, including some fungi and bacteria present in the root-associated soil known as the rhizosphere. Recent work from Amy Newman and colleagues, published in BMC Biology, has discovered that the circadian clock in Arabidopsis plants affects the rhythmicity of rhizosphere microbial communities This brings into play the exciting question of whether there is a bidirectional rhythmic interaction between plants and their rhizomicrobiome. Here, we discuss how the findings of Newman et al. suggest that soil microbiomes can have both self-sustained and plant-imposed rhythmicity, and the challenges of plant-microbiome circadian clock research.}, }
@article {pmid36301703, year = {2022}, author = {Xiang, L and Harindintwali, JD and Wang, F and Redmile-Gordon, M and Chang, SX and Fu, Y and He, C and Muhoza, B and Brahushi, F and Bolan, N and Jiang, X and Ok, YS and Rinklebe, J and Schaeffer, A and Zhu, YG and Tiedje, JM and Xing, B}, title = {Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {23}, pages = {16546-16566}, doi = {10.1021/acs.est.2c02976}, pmid = {36301703}, issn = {1520-5851}, mesh = {Humans ; Soil/chemistry ; *Soil Pollutants/analysis ; *Environmental Pollutants ; Ecosystem ; Biodegradation, Environmental ; Plants ; Bacteria ; }, abstract = {The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.}, }
@article {pmid36301451, year = {2022}, author = {Woo, C and Bhuiyan, MIU and Kim, D and Kumari, P and Lee, SK and Park, JY and Dong, K and Lee, K and Yamamoto, N}, title = {DNA metabarcoding-based study on bacteria and fungi associated with house dust mites (Dermatophagoides spp.) in settled house dust.}, journal = {Experimental &amp; applied acarology}, volume = {}, number = {}, pages = {}, pmid = {36301451}, issn = {1572-9702}, abstract = {House dust mites (HDMs) including Dermatophagoides spp. are an important cause of respiratory allergies. However, their relationship with microorganisms in house dust has not been fully elucidated. Here, we characterized bacteria and fungi associated with HDMs in house dust samples collected in 107 homes in Korea by using DNA barcode sequencing of bacterial 16S rRNA gene, fungal internal transcribed spacer 2 (ITS2) region, and arthropod cytochrome c oxidase I (COI) gene. Our inter-kingdom co-occurrence network analysis and/or indicator species analysis identified that HDMs were positively related with a xerophilic fungus Wallemia, mycoparasitic fungi such as Cystobasidium, and some human skin-related bacterial and fungal genera, and they were negatively related with the hygrophilous fungus Cephalotrichum. Overall, our study has succeeded in adding novel insights into HDM-related bacteria and fungi in the house dust ecosystem, and in confirming the historically recognized fact that HDMs are associated with xerophilic fungi such as Wallemia. Understanding the microbial ecology in house dust is thought to be important for elucidating the etiology of human diseases including allergies, and our study revealed baseline information of house dust ecology in relation to HDMs. The findings could be useful from a perspective of human health.}, }
@article {pmid36300970, year = {2022}, author = {Deng, Y and Mauri, M and Vallet, M and Staudinger, M and Allen, RJ and Pohnert, G}, title = {Dynamic Diatom-Bacteria Consortia in Synthetic Plankton Communities.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0161922}, pmid = {36300970}, issn = {1098-5336}, mesh = {*Diatoms ; Plankton ; Phytoplankton ; *Flavobacteriaceae ; Ecosystem ; *Microalgae/microbiology ; }, abstract = {Microalgae that form phytoplankton live and die in a complex microbial consortium in which they co-exist with bacteria and other microorganisms. The dynamics of species succession in the plankton depends on the interplay of these partners. Bacteria utilize substrates produced by the phototrophic algae, while algal growth can be supported by bacterial exudates. Bacteria might also use chemical mediators with algicidal properties to attack algae. To elucidate whether specific bacteria play universal or context-specific roles in the interaction with phytoplankton, we investigated the effect of cocultured bacteria on the growth of 8 microalgae. An interaction matrix revealed that the function of a given bacterium is highly dependent on the cocultured partner. We observed no universally algicidal or universally growth-promoting bacteria. The activity of bacteria can even change during the aging of an algal culture from inhibitory to stimulatory or vice versa. We further established a synthetic phytoplankton/bacteria community with the centric diatom, Coscinodiscus radiatus, and 4 phylogenetically distinctive bacterial isolates, Mameliella sp., Roseovarius sp., Croceibacter sp., and Marinobacter sp. Supported by a Lotka-Volterra model, we show that interactions within the consortium are specific and that the sum of the pairwise interactions can explain algal and bacterial growth in the community. No synergistic effects between bacteria in the presence of the diatom was observed. Our survey documents highly species-specific interactions that are dependent on algal fitness, bacterial metabolism, and community composition. This species specificity may underly the high complexity of the multi-species plankton communities observed in nature. IMPORTANCE The marine food web is fueled by phototrophic phytoplankton. These algae are central primary producers responsible for the fixation of ca. 40% of the global CO2. Phytoplankton always co-occur with a diverse bacterial community in nature. This diversity suggests the existence of ecological niches for the associated bacteria. We show that the interaction between algae and bacteria is highly species-specific. Furthermore, both, the fitness stage of the algae and the community composition are relevant in determining the effect of bacteria on algal growth. We conclude that bacteria should not be sorted into algicidal or growth supporting categories; instead, a context-specific function of the bacteria in the plankton must be considered. This functional diversity of single players within a consortium may underly the observed diversity in the plankton.}, }
@article {pmid36296484, year = {2022}, author = {Gao, J and Wang, M and Huang, W and You, Y and Zhan, J}, title = {Indigenous Saccharomyces cerevisiae Could Better Adapt to the Physicochemical Conditions and Natural Microbial Ecology of Prince Grape Must Compared with Commercial Saccharomyces cerevisiae FX10.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {20}, pages = {}, pmid = {36296484}, issn = {1420-3049}, mesh = {Saccharomyces cerevisiae ; *Vitis/chemistry ; Glycerol ; *Wine/analysis ; Fermentation ; }, abstract = {Indigenous Saccharomyces cerevisiae, as a new and useful tool, can be used in fermentation to enhance the aroma characteristic qualities of the wine-production region. In this study, we used indigenous S. cerevisiae L59 and commercial S. cerevisiae FX10 to ferment Prince (a new hybrid variety from Lion Winery) wine, detected the basic physicochemical parameters and the dynamic changes of fungal communities during fermentation, and analyzed the correlations between fungal communities and volatile compounds. The results showed that the indigenous S. cerevisiae L59 could quickly adapt to the specific physicochemical conditions and microbial ecology of the grape must, showing a strong potential for winemaking. Compared with commercial S. cerevisiae FX10, the wine fermented by indigenous S. cerevisiae L59 contained more glycerol and less organic acids, contributing to a rounder taste. The results of volatile compounds indicated that the indigenous S. cerevisiae L59 had a positive effect on adding rosy, honey, pineapple and other sweet aroma characteristics to the wine. Overall, the study we performed showed that selection of indigenous S. cerevisiae from the wine-producing region as a starter for wine fermentation is conducive to improving the aroma profile of wine and preserving the aroma of the grape variety.}, }
@article {pmid36296348, year = {2022}, author = {Lorenzi, AS and Bonatelli, ML and Chia, MA and Peressim, L and Quecine, MC}, title = {Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296348}, issn = {2076-2607}, abstract = {Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view.}, }
@article {pmid36296237, year = {2022}, author = {Trego, A and Keating, C and Nzeteu, C and Graham, A and O'Flaherty, V and Ijaz, UZ}, title = {Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296237}, issn = {2076-2607}, support = {14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 16/RC/3889/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.}, }
@article {pmid36296177, year = {2022}, author = {Leite, MFA and van den Broek, SWEB and Kuramae, EE}, title = {Current Challenges and Pitfalls in Soil Metagenomics.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296177}, issn = {2076-2607}, abstract = {Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.}, }
@article {pmid36292810, year = {2022}, author = {Ghosh, S and Namin, SM and Jung, C}, title = {Differential Bacterial Community of Bee Bread and Bee Pollen Revealed by 16s rRNA High-Throughput Sequencing.}, journal = {Insects}, volume = {13}, number = {10}, pages = {}, pmid = {36292810}, issn = {2075-4450}, abstract = {We investigated the bacterial community of bee bread and bee pollen samples using an approach through 16 s rRNA high-throughput sequencing. The results revealed a higher bacterial diversity in bee bread than in bee pollen as depicted in taxonomic profiling, as well as diversity indices such as the Shannon diversity index (3.7 to 4.8 for bee bread and 1.1 to 1.7 for bee pollen samples) and Simpson's index (>0.9 for bee bread and 0.4-0.5 for bee pollen). Principal component analysis showed a distinct difference in bacterial communities. The higher bacterial diversity in the bee bread than bee pollen could presumably be due to factors such as storage period, processing of food, fermentation, and high sugar environment. However, no effect of the feed (rapeseed or oak pollen patties or even natural inflow) was indicated on the bacterial composition of bee bread, presumably because of the lack of restriction of foraged pollen inflow in the hive. The diverse bacterial profile of the bee bread could contribute to the nutritional provisioning as well as enhance the detoxification process; however, a thorough investigation of the functional role of individual bacteria genera remains a task for future studies.}, }
@article {pmid36286524, year = {2022}, author = {Akob, DM and Sutton, JM and Bushman, TJ and Baesman, SM and Klein, E and Shrestha, Y and Andrews, R and Fierst, JL and Kolton, M and Gushgari-Doyle, S and Oremland, RS and Freeman, JL}, title = {Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from TCE-Contaminated Soils.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0121922}, pmid = {36286524}, issn = {1098-5336}, mesh = {*Bradyrhizobium ; *Trichloroethylene/metabolism ; Nitrogen Fixation/genetics ; Soil/chemistry ; Acetylene/metabolism ; Phylogeny ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {Acetylene (C2H2) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus' economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. IMPORTANCE The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.}, }
@article {pmid36286523, year = {2022}, author = {Van Peteghem, L and Sakarika, M and Matassa, S and Rabaey, K}, title = {The Role of Microorganisms and Carbon-to-Nitrogen Ratios for Microbial Protein Production from Bioethanol.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0118822}, pmid = {36286523}, issn = {1098-5336}, mesh = {Humans ; *Nitrogen ; *Carbon ; Biomass ; Ethanol/metabolism ; Yeasts/metabolism ; Fermentation ; Biofuels ; }, abstract = {With industrial agriculture increasingly challenging our ecological limits, alternative food production routes such as microbial protein (MP) production are receiving renewed interest. Among the multiple substrates so far evaluated for MP production, renewable bioethanol (EtOH) is still underexplored. Therefore, the present study investigated the cultivation of five microorganisms (2 bacteria, 3 yeasts) under carbon (C), nitrogen (N), and dual C-N-limiting conditions (molar C/N ratios of 5, 60, and 20, respectively) to evaluate the production (specific growth rate, protein and biomass yield, production cost) as well as the nutritional characteristics (protein and carbohydrate content, amino acid [AA] profile) of MP production from bioethanol. Under C-limiting conditions, all the selected microorganisms showed a favorable AA profile for human nutrition (average AA score of 1.5 or higher), with a negative correlation between protein content and growth rate. Maximal biomass yields were achieved under conditions where no extracellular acetate was produced. Cyberlindnera saturnus and Wickerhamomyces anomalus displayed remarkably high biomass yields (0.40 to 0.82 g cell dry weight [CDW]/g EtOHconsumed), which was reflected in the lowest estimated biomass production costs when cultivated with a C/N ratio of 20. Finally, when the production cost was evaluated on a protein basis, Corynebacterium glutamicum grown under C-limiting conditions showed the most promising economic outlook. IMPORTANCE The global protein demand is rapidly increasing at rates that cannot be sustained, with projections showing 78% increased global protein needs by 2050 (361 compared to 202 million tonprotein/year in 2017). In the absence of dedicated mitigation strategies, the environmental effects of our current food production system (relying on agriculture) are expected to surpass the planetary boundaries-the safe operating space for humanity-by 2050. Here, we illustrate the potential of bioethanol-renewable ethanol produced from side streams-as a main resource for the production of microbial protein, a radically different food production strategy in comparison to traditional agriculture, with the potential to be more sustainable. This study unravels the kinetic, productive, and nutritional potential for microbial protein production from bioethanol using the bacteria Methylorubrum extorquens and Corynebacterium glutamicum and the yeasts Wickerhamomyces anomalus, Cyberlindnera saturnus, and Metschnikowia pulcherrima, setting the scene for microbial protein production from renewable ethanol.}, }
@article {pmid36282736, year = {2022}, author = {Sarkar, A and Prescott, SM and Dutra, S and Yoo, JY and Gordon, J and Shaffer, E and McSkimming, D and Groer, ME}, title = {Relationships of the very low birth weight infant microbiome with neurodevelopment at 2 and 4 years of age.}, journal = {Developmental psychobiology}, volume = {64}, number = {7}, pages = {e22317}, pmid = {36282736}, issn = {1098-2302}, support = {R01 NR015446/NR/NINR NIH HHS/United States ; R21 NR013094/NR/NINR NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Infant, Newborn ; Infant ; Adult ; Humans ; Child, Preschool ; *Infant, Very Low Birth Weight ; Intensive Care Units, Neonatal ; Gestational Age ; Birth Weight ; *Microbiota ; Anti-Bacterial Agents ; }, abstract = {Very low birth weight (VLBW) infants (<1500 g) are at risk for poor neurodevelopmental outcomes depending on gestational age (GA), birth weight (BW), and morbidity in early life. The contribution of the gut microbiome is not well understood. Stool samples were collected weekly in the neonatal intensive care unit (NICU) from 24 VLBW infants for 6 weeks after admission and then again at 2 and 4 years of age. The Battelle Development Inventory-2 Screening Test (BDI-2 ST) was administered at 2- and 4-year time points. VLBW infants had dysbiotic microbiota in the NICU that progressed for most to an adult-type microbiota by 4 years of age. The BDI-2 ST results at age of 2 years triggered referral for further testing in 14 toddlers (70%), and by 4 years of age only seven of these 14 continued to require referral. Both NICU infant stool diversity and particular microbial amplicon sequence variants were associated with BDI-2 ST subscales, particularly for cognition, adaptive, and communication subscales, when controlled for GA, BW, and antibiotic exposure. Network analysis of the NICU infant stool microbial ecology showed differences in children needing neurodevelopmental referral. The results of this preliminary study indicate that the neonatal gut microbiome plays a role in early cognitive and behavioral neurodevelopment.}, }
@article {pmid36282286, year = {2022}, author = {Ortiz, WE and Carlos-Shanley, C and Huertas, M}, title = {Impact of Sublethal Concentrations of Nitrite on Goldfish (Carassius auratus) Microbiomes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36282286}, issn = {1432-184X}, abstract = {Elevated concentrations of nitrite are toxic to fish and can cause a myriad of well documented issues. However, the effects of sublethal concentrations of nitrite on fish health, and specifically, fish tissue microbiomes have not been studied. To test the effects of nitrite exposure, goldfish were exposed to sublethal concentrations of nitrite, 0.0 mM, 0.1 mM, and 1.0 mM, for 2 months. The bacteria in the nose, skin, gills, and water were then extracted and sequenced to identify changes to the microbial composition. The water microbiome was not significantly changed by the added nitrite; however, each of the tissue microbiomes was changed by at least one of the treatments. The skin and gill microbiomes were significantly different between the control and 1.0 mM treatment and the nose microbiome showed significant changes between the control and both the 0.1 mM and 1.0 mM treatments. Thus, sublethal concentrations of nitrite in the environment caused a shift in the fish tissue microbiomes independently of the water microbiome. These changes could lead to an increased chance of infection, disrupt organ systems, and raise the mortality rate of fish. In systems with high nitrite concentrations, like intensive aquaculture setups or polluted areas, the effects of nitrite on the microbiomes could negatively affect fish populations.}, }
@article {pmid36280326, year = {2022}, author = {Narendrakumar, L and Ray, A}, title = {Respiratory tract microbiome and pneumonia.}, journal = {Progress in molecular biology and translational science}, volume = {192}, number = {1}, pages = {97-124}, doi = {10.1016/bs.pmbts.2022.07.002}, pmid = {36280326}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Dysbiosis ; *Pneumonia ; *Respiratory Tract Infections/microbiology ; Lung ; }, abstract = {The respiratory system, like the gut, harbors a vast variety of microorganisms which include bacteria, viruses and fungi. The advent of next generation sequencing and multi-omic approaches has revealed the diversity and functional significances of microorganisms in the respiratory health. It has been identified that there has been a co-evolution of indigenous respiratory microbiota and the human immune system. However, an immune response is usually generated when the homeostasis of the microbiota is disturbed. The respiratory microbiome has been identified to be important in shaping the respiratory immunity. Gut microbiota and oral microbiota are also known to be pivotal in shaping the immune system of the respiratory tract and influence its microbial dynamics. Proteobacteria, Firmicutes, and Bacteroidetes have been identified to be predominant in the respiratory system. While, Streptococcus, Prevotella, Fusobacteria, and Veillonella forms the major part, potential pathogens, such as Haemophilus and Neisseria, also form a small fraction of the healthy lung microbiome. Dysbiosis of respiratory microbiome can lead to increased colonization of opportunistic pathogens that can lead to respiratory infections such as pneumonia. This chapter describes the microbial diversity of respiratory system and the role of respiratory microbiome during respiratory infections like pneumonia. The chapter also discusses few strategies that have been proved effective in preventing pneumonia.}, }
@article {pmid36275752, year = {2022}, author = {Xin, X and Wang, Q and Qing, J and Song, W and Gui, Y and Li, X and Li, Y}, title = {Th17 cells in primary Sjögren's syndrome negatively correlate with increased Roseburia and Coprococcus.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {974648}, pmid = {36275752}, issn = {1664-3224}, mesh = {Humans ; *Th17 Cells ; RNA, Ribosomal, 16S/genetics ; *Sjogren's Syndrome ; Galactose ; Peptidoglycan ; Bacteria/genetics ; Inflammation/complications ; Pyrimidines ; Amino Acids ; Glyoxylates ; Glucuronates ; Pentoses ; Butyrates ; }, abstract = {BACKGROUND: Dysbiosis of the gut microbiota is closely related to chronic systemic inflammation and autoimmunity, playing an essential role in the pathogenesis of primary Sjögren's syndrome (pSS). Abnormalities in the proportions of blood T lymphocyte subtype, that is Th17/Treg, were detected in pSS patients. We aimed to determine the associations between gut microbiota and Th17/Treg in pSS.<br><br>METHOD: 98 pSS patients and 105 healthy controls (NC) were enrolled between Dec 1, 2018, and Aug 31, 2019. The baseline information and clinical parameters on pSS patients and healthy controls were collected. 16S rRNA sequencing was performed to characterize the gut microbiome and identify gut microbes that are differentially abundant between patients and healthy controls. Lastly, associations between relative abundances of specific bacterial taxa in the gut and clinical outcome parameters were evaluated.<br><br>RESULTS: Patients with pSS show decreased gut microbial diversity and richness, decreased abundance of butyrate producing bacteria, such as Roseburia and Coprococcus, and increased abundance of other taxa, such as Eubacterium rectale and Roseburia inulinivorans. These bacteria are enriched with functions related to glycolytic and lipogenic, energy, substance, galactose, pentose metabolism pathways and glucuronate interconversions, decreased with functions related to peptidoglycan biosynthesis, pyrimidine metabolism pathways. An integrative analysis identified pSS-related specific bacterial taxa in the gut, for which the abundance of Eubacterium rectale is negatively correlated with Th17/Treg. Furthermore, the pathways of biosynthesis of secondary metabolites, biosynthesis of amino acids, peptidoglycan biosynthesis and pyrimidine, galactose, pentose, microbial metabolism in diverse environments, glyoxylate and dicarboxylate metabolism are associated with Treg or Th17/Treg.<br><br>CONCLUSIONS: Primary Sj&#xf6;gren's syndrome could lead to decreased gut microbial diversity and richness of intestinal flora in patients. The proportions of Th17 and Treg cells induced by microbiota were predictive pSS manifestations and accounted for the pSS severity.}, }
@article {pmid36274442, year = {2022}, author = {Tims, S and Marsaux, C and Pinto, A and Daly, A and Karall, D and Kuhn, M and Santra, S and Roeselers, G and Knol, J and MacDonald, A and Scholl-Bürgi, S}, title = {Altered gut microbiome diversity and function in patients with propionic acidemia.}, journal = {Molecular genetics and metabolism}, volume = {137}, number = {3}, pages = {308-322}, doi = {10.1016/j.ymgme.2022.09.012}, pmid = {36274442}, issn = {1096-7206}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Propionic Acidemia ; Propionates ; Feces/microbiology ; Butyrates ; }, abstract = {Propionic acidemia (PA) is an inherited metabolic disorder of propionate metabolism, where the gut microbiota may play a role in pathophysiology and therefore, represent a relevant therapeutic target. Little is known about the gut microbiota composition and activity in patients with PA. Although clinical practice varies between metabolic treatment centers, management of PA requires combined dietary and pharmaceutical treatments, both known to affect the gut microbiota. This study aimed to characterize the gut microbiota and its metabolites in fecal samples of patients with PA compared with healthy controls from the same household. Eight patients (aged 3-14y) and 8 controls (4-31y) were recruited from Center 1 (UK) and 7 patients (11-33y) and 6 controls (15-54y) from Center 2 (Austria). Stool samples were collected 4 times over 3 months, alongside data on dietary intakes and medication usage. Several microbial taxa differed between patients with PA and controls, particularly for Center 1, e.g., Proteobacteria levels were increased, whereas butyrate-producing genera, such as Roseburia and Faecalibacterium, were decreased. Most measured microbial metabolites were lower in patients with PA, and butyrate was particularly depleted in patients from Center 1. Furthermore, microbiota profile of these patients showed the lowest compositional and functional diversity, and lowest stability over 3 months. As the first study to map the gut microbiota of patients with PA, this work represents an important step forward for developing new therapeutic strategies to further improve PA clinical status. New dietary strategies should consider microbial propionate production as well as butyrate production and microbiota stability.}, }
@article {pmid36270682, year = {2022}, author = {Ahrodia, T and Das, S and Bakshi, S and Das, B}, title = {Structure, functions, and diversity of the healthy human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {53-82}, doi = {10.1016/bs.pmbts.2022.07.003}, pmid = {36270682}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Bacteria/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Archaea ; }, abstract = {Taxonomic composition and functional potency of microbes associated with different parts of the human body have largely been explored by culture-independent metagenome sequencing. The diverse microbiota living throughout the human body is made up of thousands of microbial taxa from all three domains of life: Archaea, Bacteria, and Eukarya. Microbial load and functional potency in different body sites are well distinct and have minimal resemblance at higher taxonomic levels between the two habitats. The highest microbial load, diversity, and functional potency including biosynthesis of essential nutrients, chemical modifications of dietary components, and sources of immunomodulatory molecules, are found in the gut microbiome. However, the inter-individual diversity and dynamics of the human microbiome in a given body habitat vary greatly over time. Both environmental factors and host genetics contribute significantly to shaping microbial community structure and its stability. A basic understanding of native microbial compositions and their functional potency and stability in different parts of healthy humans living across geography will help us to identify disease-specific microbiota and develop potential microbiome-based therapeutics. Here, we updated our current understanding of the diversity, dynamics, and functional potency of microbiomes associated with different parts of the human body.}, }
@article {pmid36270678, year = {2022}, author = {Purohit, A and Alam, MJ and Kandiyal, B and Shalimar,  and Das, B and Banerjee, SK}, title = {Gut microbiome and non-alcoholic fatty liver disease.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {187-206}, doi = {10.1016/bs.pmbts.2022.07.004}, pmid = {36270678}, issn = {1878-0814}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Non-alcoholic Fatty Liver Disease/therapy/complications/microbiology ; Prebiotics ; Dysbiosis ; Fecal Microbiota Transplantation ; *Probiotics/therapeutic use ; }, abstract = {The human gastrointestinal tract (GIT) contains a dynamic and diverse collection of bacteria, archaea, and fungi termed the "gut microbiome." The gut microbiome has a major impact on the host during homeostasis and disease. The connection between both the host and the microbiome is complex, although its manipulation may assist prevent or treating a multitude of morbidities. These microorganisms play a critical role in the host's energy metabolism and homeostasis. According to new research, the microbes in the gastrointestinal tract play a substantial role in host health, and alterations in its composition and function might lead to the emergence of metabolic disorders like non-alcoholic fatty liver disease (NAFLD). The resilience of the GIT microbial ecology and its tolerance to perturbation are robust but not ideal. Several factors may disrupt the GIT microbiome's homeostasis leading to dysbiosis, characterized by an imbalanced equilibrium and perturbations in gut homeostasis. Irritable bowel disease (IBD), malnutrition, and metabolic disorders, such as NAFLD, have been associated with the dysbiotic gut microbiome. Recent evidence suggests that utilizing medications, prebiotics, probiotics, and fecal microbiota transplantation (FMT) to manipulate the microbiome could be a viable method for treating NAFLD.}, }
@article {pmid36270674, year = {2022}, author = {Das, B}, title = {An introduction to human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {1-28}, doi = {10.1016/bs.pmbts.2022.06.026}, pmid = {36270674}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Dysbiosis ; Bacteria ; Archaea ; Host Microbial Interactions ; }, abstract = {The microbiome is an assemblage of a complex community of microbes (bacteria, archaea, fungi, algae, protists, and viruses) and their biomolecules occupying a well-defined habitat in or on a living or non-living object. All the environmentally exposed surfaces of the human body are colonized with trillions of microbes from all three major domains of life, including bacteria, archea, and microscopic eukarya. However, the richness, abundance, and functional potency of microbial taxa living in different parts of the human body are distinct. The Presence of common microbial taxa in different body habitats is also very rare. With the recent development of next generation sequencing technologies, it has been established that the indigenous microbial community in the human body and their functional attributes within a given body habitat vary over time, between ethnic groups and health status of the host. Perturbation of homeostasis in community structures or functions due to any extrinsic factors can alter mutualistic host-microbe interactions and may lead to disease. In addition, the dysbiotic state of the microbiome can also affect the efficacy of therapeutics, prolong treatment duration and lead to undesired treatment outcomes. In this chapter, structure, functions, diversity and dynamics of human microbiome in health and diseases, factors that alter microbial composition, interactions between microbial taxa and xenobiotics, and therapeutic efficacy of drugs in dysbiotic conditions are highlighted.}, }
@article {pmid36270377, year = {2023}, author = {Evariste, L and Mouchet, F and Pinelli, E and Flahaut, E and Gauthier, L and Barret, M}, title = {Gut microbiota impairment following graphene oxide exposure is associated to physiological alterations in Xenopus laevis tadpoles.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159515}, doi = {10.1016/j.scitotenv.2022.159515}, pmid = {36270377}, issn = {1879-1026}, mesh = {Animals ; *Gastrointestinal Microbiome ; Larva ; *Graphite/toxicity ; Xenopus laevis ; *Microbiota ; Bacteria/genetics ; }, abstract = {Graphene-based nanomaterials such as graphene oxide (GO) possess unique properties triggering high expectations for the development of technological applications. Thus, GO is likely to be released in aquatic ecosystems. It is essential to evaluate its ecotoxicological potential to ensure a safe use of these nanomaterials. In amphibians, previous studies highlighted X. laevis tadpole growth inhibitions together with metabolic disturbances and genotoxic effects following GO exposure. As GO is known to exert bactericidal effects whereas the gut microbiota constitutes a compartment involved in host homeostasis regulation, it is important to determine if this microbial compartment constitutes a toxicological pathway involved in known GO-induced host physiological impairments. This study investigates the potential link between gut microbial communities and host physiological alterations. For this purpose, X. laevis tadpoles were exposed during 12 days to GO. Growth rate was monitored every 2 days and genotoxicity was assessed through enumeration of micronucleated erythrocytes. Genomic DNA was also extracted from the whole intestine to quantify gut bacteria and to analyze the community composition. GO exposure led to a dose dependent growth inhibition and genotoxic effects were detected following exposure to low doses. A transient decrease of the total bacteria was noticed with a persistent shift in the gut microbiota structure in exposed animals. Genotoxic effects were associated to gut microbiota remodeling characterized by an increase of the relative abundance of Bacteroides fragilis. The growth inhibitory effects would be associated to a shift in the Firmicutes/Bacteroidetes ratio while metagenome inference suggested changes in metabolic pathways and upregulation of detoxification processes. This work indicates that the gut microbiota compartment is a biological compartment of interest as it is integrative of host physiological alterations and should be considered for ecotoxicological studies as structural or functional impairments could lead to later life host fitness loss.}, }
@article {pmid36270363, year = {2023}, author = {Regueira, A and Turunen, R and Vuoristo, KS and Carballa, M and Lema, JM and Uusitalo, J and Mauricio-Iglesias, M}, title = {Model-aided targeted volatile fatty acid production from food waste using a defined co-culture microbial community.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159521}, doi = {10.1016/j.scitotenv.2022.159521}, pmid = {36270363}, issn = {1879-1026}, mesh = {Food ; Caproates ; Coculture Techniques ; *Refuse Disposal ; Fatty Acids, Volatile ; Butyrates ; *Microbiota ; Carbon ; Bioreactors ; Fermentation ; Hydrogen-Ion Concentration ; }, abstract = {The production of volatile fatty acids (VFA) is gaining momentum due to their central role in the emerging carboxylate platform. Particularly, the production of the longest VFA (from butyrate to caproate) is desired due to their increased economic value and easier downstream processing. While the use of undefined microbial cultures is usually preferred with organic waste streams, the use of defined microbial co-culture processes could tackle some of their drawbacks such as poor control over the process outcome, which often leads to low selectivity for the desired products. However, the extensive experimentation needed to design a co-culture system hinders the use of this technology. In this work, a workflow based on the combined use of mathematical models and wet experimentation is proposed to accelerate the design of novel bioprocesses. In particular, a co-culture consisting of Pediococcus pentosaceus and Megaphaera cerevisiae is used to target the production of high-value odd- and even‑carbon VFA. An unstructured kinetic model was developed, calibrated and used to design experiments with the goal of increasing the selectivity for the desired VFA, which were experimentally validated. In the case of even‑carbon VFA, the experimental validation showed an increase of 38 % in caproate yield and, in the case of enhanced odd‑carbon VFA experiments, the yield of butyrate and caproate diminished by 62 % and 94 %, respectively, while propionate became one of the main end products and valerate yield value increased from 0.007 to 0.085 gvalearte per gconsumed sugar. The workflow followed in this work proved to be a sound tool for bioprocess design due to its capacity to explore and design new experiments in silico in a fast way and ability to quickly adapt to new scenarios.}, }
@article {pmid36267243, year = {2022}, author = {Huang, W and Zhu, L and Song, W and Zhang, M and Teng, L and Wu, M}, title = {Crosstalk between the Gut and Brain in Ischemic Stroke: Mechanistic Insights and Therapeutic Options.}, journal = {Mediators of inflammation}, volume = {2022}, number = {}, pages = {6508046}, pmid = {36267243}, issn = {1466-1861}, mesh = {Humans ; Prebiotics ; *Ischemic Stroke ; Fecal Microbiota Transplantation ; *Probiotics/therapeutic use ; Brain/metabolism ; *Stroke/therapy/metabolism ; }, abstract = {There has been a significant amount of interest in the past two decades in the study of the evolution of the gut microbiota, its internal and external impacts on the gut, and risk factors for cerebrovascular disorders such as cerebral ischemic stroke. The network of bidirectional communication between gut microorganisms and their host is known as the microbiota-gut-brain axis (MGBA). There is mounting evidence that maintaining gut microbiota homeostasis can frequently enhance the effectiveness of ischemic stroke treatment by modulating immune, metabolic, and inflammatory responses through MGBA. To effectively monitor and cure ischemic stroke, restoring a healthy microbial ecology in the gut may be a critical therapeutic focus. This review highlights mechanistic insights on the MGBA in disease pathophysiology. This review summarizes the role of MGBA signaling in the development of stroke risk factors such as aging, hypertension, obesity, diabetes, and atherosclerosis, as well as changes in the microbiota in experimental or clinical populations. In addition, this review also examines dietary changes, the administration of probiotics and prebiotics, and fecal microbiota transplantation as treatment options for ischemic stroke as potential health benefits. It will become more apparent how the MGBA affects human health and disease with continuing advancements in this emerging field of biomedical sciences.}, }
@article {pmid36267180, year = {2022}, author = {Wang, M and Tu, Q}, title = {Effective data filtering is prerequisite for robust microbial association network construction.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1016947}, pmid = {36267180}, issn = {1664-302X}, abstract = {Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.}, }
@article {pmid36266277, year = {2022}, author = {Sauvaitre, T and Van Landuyt, J and Durif, C and Roussel, C and Sivignon, A and Chalancon, S and Uriot, O and Van Herreweghen, F and Van de Wiele, T and Etienne-Mesmin, L and Blanquet-Diot, S}, title = {Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {86}, pmid = {36266277}, issn = {2055-5008}, mesh = {Humans ; *Enterotoxigenic Escherichia coli/physiology ; Interleukin-8/genetics ; Virulence ; Diarrhea ; Caco-2 Cells ; *Escherichia coli Infections/microbiology ; Travel ; *Microbiota ; Bacteria ; Mucus ; Mucins ; }, abstract = {The intestinal mucus layer has a dual role in human health constituting a well-known microbial niche that supports gut microbiota maintenance but also acting as a physical barrier against enteric pathogens. Enterotoxigenic Escherichia coli (ETEC), the major agent responsible for traveler's diarrhea, is able to bind and degrade intestinal mucins, representing an important but understudied virulent trait of the pathogen. Using a set of complementary in vitro approaches simulating the human digestive environment, this study aimed to describe how the mucus microenvironment could shape different aspects of the human ETEC strain H10407 pathophysiology, namely its survival, adhesion, virulence gene expression, interleukin-8 induction and interactions with human fecal microbiota. Using the TNO gastrointestinal model (TIM-1) simulating the physicochemical conditions of the human upper gastrointestinal (GI) tract, we reported that mucus secretion and physical surface sustained ETEC survival, probably by helping it to face GI stresses. When integrating the host part in Caco2/HT29-MTX co-culture model, we demonstrated that mucus secreting-cells favored ETEC adhesion and virulence gene expression, but did not impede ETEC Interleukin-8 (IL-8) induction. Furthermore, we proved that mucosal surface did not favor ETEC colonization in a complex gut microbial background simulated in batch fecal experiments. However, the mucus-specific microbiota was widely modified upon the ETEC challenge suggesting its role in the pathogen infectious cycle. Using multi-targeted in vitro approaches, this study supports the major role played by mucus in ETEC pathophysiology, opening avenues in the design of new treatment strategies.}, }
@article {pmid36265143, year = {2022}, author = {Zhu, M and Duan, X and Cai, P and Qiu, Z and Li, Z}, title = {Genome Sequence Resource of Trichothecium roseum (ZM-Tr2021), the causal agent of postharvest pink rot.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-03-22-0655-A}, pmid = {36265143}, issn = {0191-2917}, abstract = {Trichothecium roseum is an economically and agriculturally important fungal pathogen that causes postharvest pink rot on a variety of fruits and vegetables. In addition, it is a biocontrol agent against insects and phytopathogens. However, few genome-sequence resources of T. roseum are publicly available, and this has likely limited progress in understanding genes involved in pathogenicity and other processes in the fungus. In the current study, we used Illumina and PacBio DNA sequencing technologies to generate a chromosome-scale genome sequence assembly of a T. roseum strain (ZM-Tr2021) isolated from colonies of the wheat powdery mildew, Blumeria graminis f. sp. tritici, in China. In total, 26.06 Gb polymerase reads for raw data and 25.86 Gb subreads were obtained. These reads were processed into a 33.80 Mb genome assembly containing 19 contigs, resulting in nine superscaffolds that likely correspond to nearly full-length chromosomes, with an N50 of 4.31 Mb and scaffold lengths ranging from 2.02 Mb to 6.06 Mb. Combining the data of transcriptome and genome, we predicted 8695 protein-coding genes, of which 8488 genes were annotated with known functions. To the best of our knowledge, this is the first chromosome-scale genome of a Trichothecium species. The assembled genome sequence will facilitate studies of comparative genomics, genome evolution, pathogenicity and parasitism of T. roseum and, thereby, provide insights into control of crop diseases caused by the fungus and its use as a biocontrol agent.}, }
@article {pmid36262799, year = {2022}, author = {Faust, V and van Alen, TA and Op den Camp, HJM and Vlaeminck, SE and Ganigué, R and Boon, N and Udert, KM}, title = {Ammonia oxidation by novel "Candidatus Nitrosacidococcus urinae" is sensitive to process disturbances at low pH and to iron limitation at neutral pH.}, journal = {Water research X}, volume = {17}, number = {}, pages = {100157}, pmid = {36262799}, issn = {2589-9147}, abstract = {Acid-tolerant ammonia-oxidizing bacteria (AOB) can open the door to new applications, such as partial nitritation at low pH. However, they can also be problematic because chemical nitrite oxidation occurs at low pH, leading to the release of harmful nitrogen oxide gases. In this publication, the role of acid-tolerant AOB in urine treatment was explored. On the one hand, the technical feasibility of ammonia oxidation under acidic conditions for source-separated urine with total nitrogen concentrations up to 3.5 g-N L[-1] was investigated. On the other hand, the abundance and growth of acid-tolerant AOB at more neutral pH was explored. Under acidic conditions (pH of 5), ammonia oxidation rates of 500 mg-N L[-1] d[-1] and 10 g-N g-VSS[-1] d[-1] were observed, despite high concentrations of 15 mg-N L[-1] of the AOB-inhibiting compound nitrous acid and low concentration of 0.04 mg-N L[-1] of the substrate ammonia. However, ammonia oxidation under acidic conditions was very sensitive to process disturbances. Even short periods of less than 12 h without oxygen or without influent resulted in a complete cessation of ammonia oxidation with a recovery time of up to two months, which is a problem for low maintenance applications such as decentralized treatment. Furthermore, undesirable nitrogen losses of about 10% were observed. Under acidic conditions, a novel AOB strain was enriched with a relative abundance of up to 80%, for which the name "Candidatus (Ca.) Nitrosacidococcus urinae" is proposed. While Nitrosacidococcus members were present only to a small extent (0.004%) in urine nitrification reactors operated at pH values between 5.8 and 7, acid-tolerant AOB were always enriched during long periods without influent, resulting in an uncontrolled drop in pH to as low as 2.5. Long-term experiments at different pH values showed that the activity of "Ca. Nitrosacidococcus urinae" decreased strongly at a pH of 7, where they were also outcompeted by the acid-sensitive AOB Nitrosomonas halophila. The experiment results showed that the decreased activity of "Ca. Nitrosacidococcus urinae" correlated with the limited availability of dissolved iron at neutral pH.}, }
@article {pmid36261994, year = {2022}, author = {De La Fuente, MJ and De la Iglesia, R and Farias, L and Glasner, B and Torres-Rojas, F and Muñoz, D and Daims, H and Lukumbuzya, M and Vargas, IT}, title = {Enhanced nitrogen and carbon removal in natural seawater by electrochemical enrichment in a bioelectrochemical reactor.}, journal = {Journal of environmental management}, volume = {323}, number = {}, pages = {116294}, doi = {10.1016/j.jenvman.2022.116294}, pmid = {36261994}, issn = {1095-8630}, mesh = {Nitrogen/chemistry ; Denitrification ; Nitrification ; Waste Water ; Carbon ; Nitrates ; Bioreactors ; RNA, Ribosomal, 16S ; Nitrites ; *Graphite ; In Situ Hybridization, Fluorescence ; *Ammonium Compounds ; Seawater ; }, abstract = {Municipal and industrial wastewater discharges in coastal and marine environments are of major concern due to their high carbon and nitrogen loads and the resulted phenomenon of eutrophication. Bioelectrochemical reactors (BERs) for simultaneous nitrogen and carbon removal have gained attention owing to their cost efficiency and versatility, as well as the possibility of electrochemical enrich specific groups. This study presented a scalable two-chamber BERs using graphite granules as electrode material. BERs were inoculated and operated for 37 days using natural seawater with high concentrations of ammonium and acetate. The BERs demonstrated a maximum current density of 0.9 A m[-3] and removal rates of 7.5 mg NH4[+]-N L[-1] d[-1] and 99.5 mg L[-1] d[-1] for total organic carbon (TOC). Removals observed for NH4[+]-N and TOC were 96.2% and 68.7%, respectively. The results of nutrient removal (i.e., ammonium, nitrate, nitrite and TOC) and microbial characterization (i.e., next-generation sequencing of the 16S rRNA gene and fluorescence in situ hybridization) showed that BERs operated with a poised cathode at -260 mV (vs. Ag/AgCl) significantly enriched nitrifying microorganisms in the anode and denitrifying microorganisms and planctomycetes in the cathode. Interestingly, the electrochemical enrichment did not increase the total number of microorganisms in the formed biofilms but controlled their composition. Thus, this work shows the first successful attempt to electrochemically enrich marine nitrifying and denitrifying microorganisms and presents a technique to accelerate the start-up process of BERs to remove dissolved inorganic nitrogen and total organic carbon from seawater.}, }
@article {pmid36259773, year = {2022}, author = {Eliades, SJ and Colston, TJ and Siler, CD}, title = {Gut microbial ecology of Philippine gekkonids: ecoevolutionary effects on microbiome compositions.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, pmid = {36259773}, issn = {1574-6941}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Philippines ; *Microbiota/genetics ; Symbiosis ; }, abstract = {Given the rapidly changing landscapes of habitats across the globe, a sound understanding of host-associated microbial communities and the ecoevolutionary forces that shape them is needed to assess general organismal adaptability. Knowledge of the symbiotic endogenous microbiomes of most reptilian species worldwide remains limited. We sampled gut microbiomes of geckos spanning nine species and four genera in the Philippines to (i) provide baseline data on gut microbiota in these host species, (ii) test for significant associations between host phylogenetic relationships and observed microbial assemblages, potentially indicative of phylosymbiosis, and (iii) identify correlations between multiple ecoevolutionary factors (e.g. species identity, habitat tendencies, range extents, and maximum body sizes) and gut microbiomes in Philippine gekkonids. We recovered no significant association between interspecific host genetic distances and observed gut microbiomes, providing limited evidence for phylosymbiosis in this group. Philippine gekkonid microbiomes were associated most heavily with host species identity, though marked variation among conspecifics at distinct sampling sites indicates that host locality influences gut microbiomes as well. Interestingly, individuals grouped as widespread and microendemic regardless of host species identity displayed significant differences in alpha and beta diversity metrics examined, likely driven by differences in rare OTU presence between groups. These results provide much needed insight in host-associated microbiomes in wild reptiles and the ecoevolutionary forces that structure such communities.}, }
@article {pmid36259715, year = {2022}, author = {Conacher, CG and Naidoo-Blassoples, RK and Rossouw, D and Bauer, FF}, title = {A Transcriptomic Analysis of Higher-Order Ecological Interactions in a Eukaryotic Model Microbial Ecosystem.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0043622}, doi = {10.1128/msphere.00436-22}, pmid = {36259715}, issn = {2379-5042}, abstract = {Nonlinear ecological interactions within microbial ecosystems and their contribution to ecosystem functioning remain largely unexplored. Higher-order interactions, or interactions in systems comprised of more than two members that cannot be explained by cumulative pairwise interactions, are particularly understudied, especially in eukaryotic microorganisms. The wine fermentation ecosystem presents an ideal model to study yeast ecosystem establishment and functioning. Some pairwise ecological interactions between wine yeast species have been characterized, but very little is known about how more complex, multispecies systems function. Here, we evaluated nonlinear ecosystem properties by determining the transcriptomic response of Saccharomyces cerevisiae to pairwise versus tri-species culture. The transcriptome revealed that genes expressed during pairwise coculture were enriched in the tri-species data set but also that just under half of the data set comprised unique genes attributed to a higher-order response. Through interactive protein-association network visualizations, a holistic cell-wide view of the gene expression data was generated, which highlighted known stress response and metabolic adaptation mechanisms which were specifically activated during tri-species growth. Further, extracellular metabolite data corroborated that the observed differences were a result of a biotic stress response. This provides exciting new evidence showing the presence of higher-order interactions within a model microbial ecosystem. IMPORTANCE Higher-order interactions are one of the major blind spots in our understanding of microbial ecosystems. These systems remain largely unpredictable and are characterized by nonlinear dynamics, in particular when the system is comprised of more than two entities. By evaluating the transcriptomic response of S. cerevisiae to an increase in culture complexity from a single species to two- and three-species systems, we were able to confirm the presence of a unique response in the more complex setting that could not be explained by the responses observed at the pairwise level. This is the first data set that provides molecular targets for further analysis to explain unpredictable ecosystem dynamics in yeast.}, }
@article {pmid36258041, year = {2022}, author = {Wang, J and Shi, X and Tan, Y and Wang, L and Zhang, G}, title = {Elevated O3 Exerts Stronger Effects than Elevated CO2 on the Functional Guilds of Fungi, but Collectively Increase the Structural Complexity of Fungi in a Paddy Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36258041}, issn = {1432-184X}, abstract = {Global climate change is characterized by altered global atmospheric composition, including elevated CO2 and O3, with important consequences on soil fungal communities. However, the function and community composition of soil fungi in response to elevated CO2 together with elevated O3 in paddy soils remain largely unknown. Here we used twelve open-top chamber facilities (OTCs) to evaluate the interactive effect of CO2 (+ 200 ppm) and O3 (+ 40 ppb) on the diversity, gene abundance, community structure, and functional composition of soil fungi during the growing seasons of two rice cultivars (Japonica, Wuyujing 3 vs. Nangeng 5055) in a Chinese paddy soil. Elevated CO2 and O3 showed no individual or combined effect on the gene abundance or relative abundance of soil fungi, but increased structural complexity of soil fungal communities, indicating that elevated CO2 and/or O3 promoted the competition of species-species interactions. When averaged both cultivars, elevated CO2 showed no individual effect on the diversity or abundance of functional guilds of soil fungi. By contrast, elevated O3 significantly reduced the relative abundance and diversity of symbiotrophic fungi by an average of 47.2% and 39.1%, respectively. Notably, elevated O3 exerts stronger effects on the functional processes of fungal communities than elevated CO2. The structural equation model revealed that elevated CO2 and/or O3 indirectly affected the functional composition of soil fungi through community structure and diversity of soil fungi. Root C/N and soil environmental parameters were identified as the top direct predictors for the community structure of soil fungi. Furthermore, significant correlations were identified between saprotrophic fungi and root biomass, symbiotrophic fungi and root carbon, the pathotroph-symbiotroph and soil pH, as well as pathotroph-saprotroph-symbiotroph and soil microbial biomass carbon. These results suggest that climatic factors substantially affected the functional processes of soil fungal, and threatened soil function and food production, highlighting the detrimental impacts of high O3 on the function composition of soil biota.}, }
@article {pmid36257429, year = {2023}, author = {Chen, H and Liu, K and Yang, E and Chen, J and Gu, Y and Wu, S and Yang, M and Wang, H and Wang, D and Li, H}, title = {A critical review on microbial ecology in the novel biological nitrogen removal process: Dynamic balance of complex functional microbes for nitrogen removal.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159462}, doi = {10.1016/j.scitotenv.2022.159462}, pmid = {36257429}, issn = {1879-1026}, mesh = {*Nitrogen ; *Denitrification ; Acyl-Butyrolactones ; Quorum Sensing ; Bacteria ; }, abstract = {The novel biological nitrogen removal process has been extensively studied for its high nitrogen removal efficiency, energy efficiency, and greenness. A successful novel biological nitrogen removal process has a stable microecological equilibrium and benign interactions between the various functional bacteria. However, changes in the external environment can easily disrupt the dynamic balance of the microecology and affect the activity of functional bacteria in the novel biological nitrogen removal process. Therefore, this review focuses on the microecology in existing the novel biological nitrogen removal process, including the growth characteristics of functional microorganisms and their interactions, together with the effects of different influencing factors on the evolution of microbial communities. This provides ideas for achieving a stable dynamic balance of the microecology in a novel biological nitrogen removal process. Furthermore, to investigate deeply the mechanisms of microbial interactions in novel biological nitrogen removal process, this review also focuses on the influence of quorum sensing (QS) systems on nitrogen removal microbes, regulated by which bacteria secrete acyl homoserine lactones (AHLs) as signaling molecules to regulate microbial ecology in the novel biological nitrogen removal process. However, the mechanisms of action of AHLs on the regulation of functional bacteria have not been fully determined and the composition of QS system circuits requires further investigation. Meanwhile, it is necessary to further apply molecular analysis techniques and the theory of systems ecology in the future to enhance the exploration of microbial species and ecological niches, providing a deeper scientific basis for the development of a novel biological nitrogen removal process.}, }
@article {pmid36257158, year = {2022}, author = {Yang, Y and Lu, Z and Azari, M and Kartal, B and Du, H and Cai, M and Herbold, CW and Ding, X and Denecke, M and Li, X and Li, M and Gu, JD}, title = {Discovery of a new genus of anaerobic ammonium oxidizing bacteria with a mechanism for oxygen tolerance.}, journal = {Water research}, volume = {226}, number = {}, pages = {119165}, doi = {10.1016/j.watres.2022.119165}, pmid = {36257158}, issn = {1879-2448}, mesh = {*Ammonium Compounds/metabolism ; Anaerobiosis ; Catalase ; Nitrates/metabolism ; Oxygen/metabolism ; Bacteria, Anaerobic/genetics/metabolism ; Oxidation-Reduction ; Bacteria/metabolism ; }, abstract = {In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems.}, }
@article {pmid36255374, year = {2022}, author = {Castillo, DJ and Dithugoe, CD and Bezuidt, OK and Makhalanyane, TP}, title = {Microbial ecology of the Southern Ocean.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {11}, pages = {}, doi = {10.1093/femsec/fiac123}, pmid = {36255374}, issn = {1574-6941}, mesh = {*Ecosystem ; Seawater/microbiology ; Phytoplankton ; Carbon Cycle ; *Microbiota ; Oceans and Seas ; }, abstract = {The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.}, }
@article {pmid36252671, year = {2023}, author = {Wang, Z and Li, K and Shen, X and Yan, F and Zhao, X and Xin, Y and Ji, L and Xiang, Q and Xu, X and Li, D and Ran, J and Xu, X and Chen, Q}, title = {Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159439}, doi = {10.1016/j.scitotenv.2022.159439}, pmid = {36252671}, issn = {1879-1026}, mesh = {*Methane ; *Wetlands ; Nitrogen ; Anaerobiosis ; Soil ; Rivers ; Oxidation-Reduction ; }, abstract = {Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH4). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO3[-]), sulfate (SO4[2-]), and nitrous oxide (N2O) flux, among them, soil N substances (TN, NO3[-], N2O) have essential regulatory roles in the AOM process, while NO3[-] and N2O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH4 sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH4 biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.}, }
@article {pmid36252516, year = {2022}, author = {Calatayud, M and Xiong, C and Selma-Royo, M and van de Wiele, T}, title = {Arsenolipids reduce butyrate levels and influence human gut microbiota in a donor-dependent way.}, journal = {Ecotoxicology and environmental safety}, volume = {246}, number = {}, pages = {114175}, doi = {10.1016/j.ecoenv.2022.114175}, pmid = {36252516}, issn = {1090-2414}, mesh = {Humans ; *Gastrointestinal Microbiome ; Butyrates/pharmacology ; *Arsenic/toxicity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; }, abstract = {Arsenolipids are organic arsenic species with variable toxicity. Accurate assessment of the risks derived from arsenic-contaminated seafood intake requires studying the interplay between arsenolipids and the human gut microbiota. This research used the in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) to assess the effect of defined chemical standards of arsenolipids (AsFA 362 and AsHC 332) on a simulated healthy human gut microbiota (n = 4). Microbial-derived metabolites were quantified by gas chromatography and microbiota structure was characterized by 16S rRNA gene sequencing. A specific reduction in butyrate production (control=5.28 ± 0.3 mM; AsFAs=4.56 ± 0.4 mM; AsHC 332=4.4 ± 0.6 mM, n = 4 donors), concomitant with a reduction in the abundance of Lachnospiraceae UCG-004 group and the Faecalibacterium genus was observed, albeit in a donor-dependent manner. Furthermore, an increase in Escherichia/Shigella, Proteobacteria and Fusobacterium abundance was observed after arsenolipid treatments, depending on individual microbiota background. These alterations in microbial functionality and microbial community structure suggest a detrimental effect of arsenolipids intake towards the commensal gut microbiome, and consequently, on human health.}, }
@article {pmid36251278, year = {2022}, author = {Ross, DE and Lipus, D and Gulliver, D}, title = {Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16251}, pmid = {36251278}, issn = {1462-2920}, abstract = {Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes (MAGs) to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin (AppB). Our analyses resulted in the recovery of over 40 MAGs from 8 coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. The data presented herein provides novel insights into AppB coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.}, }
@article {pmid36246995, year = {2022}, author = {Mörkl, S and Oberascher, A and Tatschl, JM and Lackner, S and Bastiaanssen, TFS and Butler, MI and Moser, M and Frühwirth, M and Mangge, H and Cryan, JF and Dinan, TG and Holasek, SJ}, title = {Cardiac vagal activity is associated with gut-microbiome patterns in women-An exploratory pilot study.}, journal = {Dialogues in clinical neuroscience}, volume = {24}, number = {1}, pages = {1-9}, pmid = {36246995}, issn = {1958-5969}, mesh = {Female ; *Gastrointestinal Microbiome/physiology ; Humans ; Interleukin-6 ; *Microbiota ; Pilot Projects ; }, abstract = {INTRODUCTION: A functional reciprocity between the gut microbiome and vagal nerve activity has been suggested, however, human studies addressing this phenomenon are limited.<br><br>METHODS: Twenty-four-hour cardiac vagal activity (CVA) was assessed from 73 female participants (aged 24.5&#x2009;&#xb1;&#x2009;4.3&#x2009;years). Additionally, stool samples were subjected to 16SrRNA gene analysis (V1-V2). Quantitative Insights Into Microbial Ecology (QIIME) was used to analyse microbiome data. Additionally, inflammatory parameters (such as CRP and IL-6) were derived from serum samples.<br><br>RESULTS: Daytime CVA correlated significantly with gut microbiota diversity (r sp&#x2009;=&#x2009;0.254, p&#x2009;=&#x2009;0.030), CRP (r sp&#x2009;=&#x2009;-0.348, p&#x2009;=&#x2009;0.003), and IL-6 (r sp&#x2009;=&#x2009;-0.320, p&#x2009;=&#x2009;0.006). When the group was divided at the median of 24&#x2009;h CVA (Mdn = 1.322), the following features were more abundant in the high CVA group: Clostridia (Linear discriminant analysis effect size (LDA)&#x2009;=&#x2009;4.195, p&#x2009;=&#x2009;0.029), Clostridiales (LDA = 4.195, p&#x2009;=&#x2009;0.029), Lachnospira (LDA = 3.489, p&#x2009;=&#x2009;0.004), Ruminococcaceae (LDA = 4.073, p&#x2009;=&#x2009;0.010), Faecalibacterium (LDA = 3.982, p&#x2009;=&#x2009;0.042), Lactobacillales (LDA = 3.317, p&#x2009;=&#x2009;0.029), Bacilli (LDA = 3.294, p&#x2009;=&#x2009;0.0350), Streptococcaceae (LDA = 3.353, p&#x2009;=&#x2009;0.006), Streptococcus (LDA = 3.332, p&#x2009;=&#x2009;0.011). Based on Dirichlet multinomial mixtures two enterotypes could be detected, which differed significantly in CVA, age, BMI, CRP, IL-6, and diversity.<br><br>CONCLUSIONS: As an indicator of gut-brain communication, gut microbiome analysis could be extended by measurements of CVA to enhance our understanding of signalling via microbiota-gut-brain-axis and its alterations through psychobiotics.}, }
@article {pmid36243459, year = {2022}, author = {Pinnell, LJ and Morley, PS}, title = {The Microbial Ecology of Liver Abscesses in Cattle.}, journal = {The Veterinary clinics of North America. Food animal practice}, volume = {38}, number = {3}, pages = {367-381}, doi = {10.1016/j.cvfa.2022.08.004}, pmid = {36243459}, issn = {1558-4240}, mesh = {Animals ; Bacteroidetes/genetics ; Cattle ; *Cattle Diseases ; Humans ; *Liver Abscess/veterinary ; *Microbiota/genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Emerging evidence regarding the microbiome of liver abscesses (LAs) and the gastrointestinal tract of cattle suggests that a reexamination of the etiopathogenesis of LAs is warranted. Microbiome studies using 16S rRNA gene sequencing have demonstrated that LAs are highly polymicrobial, and hundreds of bacterial taxa are typically found in these lesions at slaughter. Fusobacteria and Bacteroidetes are equally dominant phyla within LAs, followed by Proteobacteria. The gut-liver axis (ie, bidirectional crosstalk between the gut and liver) is linked with a variety of liver diseases in humans, and investigation of host-microbiome interactions in cattle may lead to improved methods of prevention.}, }
@article {pmid36242623, year = {2022}, author = {Li, W and Li, X and Wang, W and Zhang, S and Cui, J and Peng, Y and Zhao, Y}, title = {Impact of Sulfoxaflor Exposure on Bacterial Community and Developmental Performance of the Predatory Ladybeetle Propylea japonica.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36242623}, issn = {1432-184X}, abstract = {Insects maintain a vast number of symbiotic bacteria, and these symbionts play key roles in the hosts' life processes. Propylea japonica (Coleoptera: Coccinellidae) is an abundant and widespread ladybeetle in agricultural fields in Asia. Both larvae and adults of P. japonica are likely to be exposed to insecticide residue in the field during their predatory activity. Sulfoxaflor is a highly powerful insecticide that has strong efficacy in controlling sap-sucking pests. To date, there have been several studies on the acute and long-term toxicity of sulfoxaflor to insects, but few studies have reported the impact of sulfoxaflor on the predators' micro-ecosystems. This study was to determine the impact of sulfoxaflor on the symbiotic bacteria and developmental performance of P. japonica. In the present study, two concentrations (1 mg/L and 5 mg/L) and two exposure periods (1 day and 5 days) were set for P. japonica under sulfoxaflor exposure. The survival rate, developmental duration, pupation rate, emergence rate, and body weight of P. japonica were examined. Moreover, the bacterial community of P. japonica was investigated by high-throughput 16S ribosomal RNA gene sequencing. Our results indicated that bacterial community of P. japonica was mainly composed of Staphylococcus, Pantoea, Acinetobacter, Rhodococcus, and Ralstonia at the genus level. The bacterial community of P. japonica in 1 mg/L and 5 mg/L sulfoxaflor groups was significantly altered on day 1, compared with that in control group. The results also showed that the larval duration was significantly prolonged but the pupal duration was significantly shortened in both sulfoxaflor groups. Meanwhile, the pupation and emergence rate was not significantly changed, but the body weights of adults were significantly decreased in both sulfoxaflor groups. Our study will provide a new perspective for evaluating the safety of pesticides to beneficial arthropods.}, }
@article {pmid36239777, year = {2022}, author = {Tian, C and Lv, Y and Yang, Z and Zhang, R and Zhu, Z and Ma, H and Li, J and Zhang, Y}, title = {Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36239777}, issn = {1432-184X}, abstract = {Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.}, }
@article {pmid36239764, year = {2022}, author = {Nissen, L and Aniballi, C and Casciano, F and Elmi, A and Ventrella, D and Zannoni, A and Gianotti, A and Bacci, ML}, title = {Maternal amoxicillin affects piglets colon microbiota: microbial ecology and metabolomics in a gut model.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {22}, pages = {7595-7614}, pmid = {36239764}, issn = {1432-0614}, mesh = {Animals ; Swine ; Female ; *Gastrointestinal Microbiome ; Amoxicillin/pharmacology ; Colon ; *Microbiota ; Metabolomics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The first weeks of life represent a crucial stage for microbial colonization of the piglets' gastrointestinal tract. Newborns' microbiota is unstable and easily subject to changes under stimuli or insults. Nonetheless, the administration of antibiotics to the sow is still considered as common practice in intensive farming for pathological conditions in the postpartum. Therefore, transfer of antibiotic residues through milk may occurs, affecting the piglets' colon microbiota. In this study, we aimed to extend the knowledge on antibiotic transfer through milk, employing an in vitro dedicated piglet colon model (MICODE-Multi Unit In vitro Colon Model). The authors' focus was set on the shifts of the piglets' microbiota composition microbiomics (16S r-DNA MiSeq and qPCR-quantitative polymerase chain reaction) and on the production of microbial metabolites (SPME GC/MS-solid phase micro-extraction gas chromatography/mass spectrometry) in response to milk with different concentrations of amoxicillin. The results showed an effective influence of amoxicillin in piglets' microbiota and metabolites production; however, without altering the overall biodiversity. The scenario is that of a limitation of pathogens and opportunistic taxa, e.g., Staphylococcaceae and Enterobacteriaceae, but also a limitation of commensal dominant Lactobacillaceae, a reduction in commensal Ruminococcaceae and a depletion in beneficial Bifidobactericeae. Lastly, an incremental growth of resistant species, such as Enterococcaceae or Clostridiaceae, was observed. To the authors' knowledge, this study is the first evaluating the impact of antibiotic residues towards the piglets' colon microbiota in an in vitro model, opening the way to include such approach in a pipeline of experiments where a reduced number of animals for testing is employed. KEY POINTS: • Piglet colon model to study antibiotic transfer through milk. • MICODE resulted a robust and versatile in vitro gut model. • Towards the "3Rs" Principles to replace, reduce and refine the use of animals used for scientific purposes (Directive 2010/63/UE).}, }
@article {pmid36238597, year = {2022}, author = {Sinclair, P and Longyear, J and Reynolds, K and Finnie, AA and Brackley, CA and Carballo-Pacheco, M and Allen, RJ}, title = {A computational model for microbial colonization of an antifouling surface.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {920014}, pmid = {36238597}, issn = {1664-302X}, abstract = {Biofouling of marine surfaces such as ship hulls is a major industrial problem. Antifouling (AF) paints delay the onset of biofouling by releasing biocidal chemicals. We present a computational model for microbial colonization of a biocide-releasing AF surface. Our model accounts for random arrival from the ocean of microorganisms with different biocide resistance levels, biocide-dependent proliferation or killing, and a transition to a biofilm state. Our computer simulations support a picture in which biocide-resistant microorganisms initially form a loosely attached layer that eventually transitions to a growing biofilm. Once the growing biofilm is established, immigrating microorganisms are shielded from the biocide, allowing more biocide-susceptible strains to proliferate. In our model, colonization of the AF surface is highly stochastic. The waiting time before the biofilm establishes is exponentially distributed, suggesting a Poisson process. The waiting time depends exponentially on both the concentration of biocide at the surface and the rate of arrival of resistant microorganisms from the ocean. Taken together our results suggest that biofouling of AF surfaces may be intrinsically stochastic and hence unpredictable, but immigration of more biocide-resistant species, as well as the biological transition to biofilm physiology, may be important factors controlling the time to biofilm establishment.}, }
@article {pmid36229976, year = {2022}, author = {De Spiegeleer, A and Wynendaele, E and Descamps, A and Debunne, N and Braeckman, BP and De Mey, M and Coudenys, J and Crombez, L and Verbeke, F and Janssens, Y and Janky, R and Goossens, E and Vlaeminck, C and Duchi, D and Andries, V and Dumas, E and Petrovic, M and Van de Wiele, T and Knappe, D and Hoffmann, R and Mouly, V and Bigot, A and Vereecke, L and Van Immerseel, F and Van Den Noortgate, N and De Spiegeleer, B and Elewaut, D}, title = {The bacterial quorum sensing peptide iAM373 is a novel inducer of sarcopenia.}, journal = {Clinical and translational medicine}, volume = {12}, number = {10}, pages = {e1053}, pmid = {36229976}, issn = {2001-1326}, mesh = {Bacteria ; Humans ; Oligopeptides ; Peptides ; *Quorum Sensing ; *Sarcopenia ; }, }
@article {pmid36224329, year = {2022}, author = {Bayer, N and Hausman, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G}, title = {Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.}, journal = {Leukemia}, volume = {36}, number = {11}, pages = {2705-2714}, pmid = {36224329}, issn = {1476-5551}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology ; *Gastrointestinal Microbiome ; Immunity ; }, abstract = {The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45[+] leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.}, }
@article {pmid36224114, year = {2022}, author = {Rohrbach, S and Gkoutselis, G and Hink, L and Weig, AR and Obst, M and Diekmann, A and Ho, A and Rambold, G and Horn, MA}, title = {Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16234}, pmid = {36224114}, issn = {1462-2920}, abstract = {Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments.}, }
@article {pmid36216061, year = {2023}, author = {Sabba, F and Farmer, M and Jia, Z and Di Capua, F and Dunlap, P and Barnard, J and Qin, CD and Kozak, JA and Wells, G and Downing, L}, title = {Impact of operational strategies on a sidestream enhanced biological phosphorus removal (S2EBPR) reactor in a carbon limited wastewater plant.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159280}, doi = {10.1016/j.scitotenv.2022.159280}, pmid = {36216061}, issn = {1879-1026}, mesh = {*Waste Water ; *Phosphorus ; Carbon ; Bioreactors ; Sewage ; }, abstract = {Water resource recovery facilities are faced with stringent effluent phosphorus limits to reduce nutrient pollution. Enhanced biological phosphorus removal (EBPR) is the most common biological route to remove phosphorus; however, many facilities struggle to achieve consistent performance due to limited carbon availability in the influent wastewater. A promising process to improve carbon availability is through return activated sludge (RAS) fermentation via sidestream EBPR (S2EBPR). In this study, a full-scale S2EBPR pilot was operated with a sidestream plus carbon configuration (SSRC) at a carbon-limited facility. A model based on the pilot test was developed and calibrated in the SUMO platform and used to explore routes for improving orthophosphate (OP) effluent compliance. Modeling results showed that RAS diversion by itself was not sufficient to drive OP removal to permit limits of 1 mg L[-1], therefore, other strategies were evaluated. Supplemental carbon addition of MicroC® at 1.90 L min[-1] and controlling the phosphorus concentration below 3.5 mgP L[-1] in the primary effluent (PE) proved to be valid supplemental strategies to achieve OP removal below 1 mg L[-1] most of the time. In particular, the proposed supplemental carbon flow rate would result in an improvement of the rbCOD:P ratio from 17:1 to 26:1. The synergistic approach of RAS diversion and supplemental carbon addition increased the polyphosphate accumulating organisms (PAO) population while minimizing the supplemental carbon needed to achieve consistent phosphorus removal. Overall, this pilot and modeling study shows that joint strategies, including RAS diversion, carbon addition and PE control, can be effective to achieve optimal control of OP effluent.}, }
@article {pmid36215761, year = {2022}, author = {Uroosa,  and Kazmi, SSUH and Warren, A and Zhong, X and Xu, H}, title = {Effects of nitrofurazone on ecosystem function in marine environments: A case study on microbial fauna.}, journal = {Marine pollution bulletin}, volume = {184}, number = {}, pages = {114216}, doi = {10.1016/j.marpolbul.2022.114216}, pmid = {36215761}, issn = {1879-3363}, mesh = {*Ecosystem ; Nitrofurazone/toxicity ; Environmental Monitoring ; *Ciliophora ; Anti-Bacterial Agents ; }, abstract = {To evaluate the effects of nitrofurazone on functional processes in marine ecosystems, periphytic protozoan communities were exposed to different concentrations of the antibiotic for a 10-day duration. Species trait distributions in the tested communities were observed during exposure to five concentrations of nitrofurazone. A fuzzy coding system with seven traits and seventeen categories was used to summarize the changes in functional patterns of the test organisms. Nitrofurazone had a significant influence on the function process of the periphytic ciliate communities. Bacterivores with flattened bodies were sensitive to the toxicant whereas sessile and cylindrical raptors showed a high tolerance to nitrofurazone, invariably dominating communities exposed to high concentrations. Bootstrapped-average analysis demonstrated a significant change in functional patterns at highest nitrofurazone concentrations (8 mg l[-1]). Based on these findings, it is suggested that nitrofurazone may negatively influence ecosystem function in marine environments.}, }
@article {pmid36215464, year = {2022}, author = {Chevrette, MG and Thomas, CS and Hurley, A and Rosario-Meléndez, N and Sankaran, K and Tu, Y and Hall, A and Magesh, S and Handelsman, J}, title = {Microbiome composition modulates secondary metabolism in a multispecies bacterial community.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {42}, pages = {e2212930119}, pmid = {36215464}, issn = {1091-6490}, support = {T32 GM135066/GM/NIGMS NIH HHS/United States ; S10 RR029531/RR/NCRR NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; Benzamides ; Humans ; *Microbiota ; Secondary Metabolism ; *Siderophores/genetics/metabolism ; }, abstract = {Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions and responses to environmental change. Despite the importance of secondary metabolites in human health and microbial ecology, little is known about their roles and regulation in the context of multispecies communities. In a simplified model of the rhizosphere composed of Bacillus cereus, Flavobacterium johnsoniae, and Pseudomonas koreensis, we show that the dynamics of secondary metabolism depend on community species composition and interspecies interactions. Comparative metatranscriptomics and metametabolomics reveal that the abundance of transcripts of biosynthetic gene clusters (BGCs) and metabolomic molecular features differ between monocultures or dual cultures and a tripartite community. In both two- and three-member cocultures, P. koreensis modified expression of BGCs for zwittermicin, petrobactin, and other secondary metabolites in B. cereus and F. johnsoniae, whereas the BGC transcriptional response to the community in P. koreensis itself was minimal. Pairwise and tripartite cocultures with P. koreensis displayed unique molecular features that appear to be derivatives of lokisin, suggesting metabolic handoffs between species. Deleting the BGC for koreenceine, another P. koreensis metabolite, altered transcript and metabolite profiles across the community, including substantial up-regulation of the petrobactin and bacillibactin BGCs in B. cereus, suggesting that koreenceine represses siderophore production. Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.}, }
@article {pmid36214570, year = {2022}, author = {Utter, DR and Cavanaugh, CM and Borisy, GG}, title = {Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations.}, journal = {mBio}, volume = {}, number = {}, pages = {e0241422}, doi = {10.1128/mbio.02414-22}, pmid = {36214570}, issn = {2150-7511}, abstract = {Two major viewpoints have been put forward for how microbial populations change, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to study bacterial intrapopulation genome dynamics. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven time points obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera. The vast majority of genes in each MAG were tightly linked over the 2-week sampling window, indicating that the majority of the population's genomes were temporally stable at the MAG level. MAG-defined populations were composed of up to 5 strains, as determined by single-nucleotide-variant frequencies. Although most were stable over time, individual strains carrying over 100 distinct genes that rose from low abundance to dominance in a population over a period of days were detected. These results indicate a genome-wide as opposed to a gene-level process of population change. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations over short timescales. IMPORTANCE The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dynamics. However, bacterial populations and their genomes are neither monolithic nor static; their genomes are constantly evolving to lose, gain, or alter their functional potential. To better understand how microbial genomes change in complex communities, we used culture-independent approaches to reconstruct the genomes (MAGs) for bacterial populations that approximated different species, in 17 healthy donors' mouths over a 2-week window. Our results underscored the importance of strain-level dynamics, which agrees with and expands on the conclusions of previous research. Altogether, these observations reveal patterns of genomic dynamics among strains of oral bacteria occurring over a matter of days.}, }
@article {pmid36213689, year = {2022}, author = {He, KJ and Zhang, YF and Liang, LY and Cheng, XS and Gong, G and Ouyang, XM and Lin, Y and Guleng, B}, title = {ncRNAs-mediated high expression of TICRR promotes tumor cell proliferation and migration and is correlated with poor prognosis and tumor immune infiltration of hepatocellular carcinoma.}, journal = {Molecular therapy. Nucleic acids}, volume = {30}, number = {}, pages = {80-94}, pmid = {36213689}, issn = {2162-2531}, abstract = {TICRR is a regulatory factor of DNA replication with ToPBP1 interaction. At present, the underlying function and mechanisms of TICRR remain unclear in LIHC. Our objective was to assess the function and prognosis of TICRR in LIHC. We conducted a differential expression analysis, GO/KEGG, and GSEA enrichment analysis of TICRR in LIHC. We also carried out the gene frequency and SCNA of TICRR. We found that TICRR could serve as an independent prognostic marker in LIHC by univariate and multivariate analysis. In addition, we observed that TICRR was related to immune infiltration, and TICRR had positive correlation with PD1/PD-L1 and CTLA-4 in LIHC. The hsa-miR-126-3p/IPO9-AS1 may be the candidate ncRNAs to regulate the expression of TICRR. The high rate of SCNV of TICRR might have critical effect on the function of CTL cells in LIHC. We further demonstrate through a series of experiments that TICRR facilitated the proliferation and metastasis of liver cancer cells in vitro. Altogether, TICRR might be a potential biomarker and therapeutic target in LIHC.}, }
@article {pmid36213308, year = {2022}, author = {Vinyard, JR and Faciola, AP}, title = {Unraveling the pros and cons of various in vitro methodologies for ruminant nutrition: a review.}, journal = {Translational animal science}, volume = {6}, number = {4}, pages = {txac130}, pmid = {36213308}, issn = {2573-2102}, abstract = {To decrease the time and cost of experiments as well as the use of animals in nutrition research, in vitro methodologies have become more commonplace in the field of ruminant nutrition. Therefore, the objectives of this review are 1) to describe the development of different in vitro methodologies, 2) to discuss the application, utilization, and advantages of in vitro methodologies, 3) to discuss shortcomings of in vitro methodologies, and 4) to describe the potential developments that may be able to improve in vitro methods. Having been used for decades, some in vitro methodologies such as pure, batch, and continuous cultures have been very well documented and utilized to investigate a wide array of different aspects of nutrition, including the effects of different dietary compositions, individual fermentation end products, and impacts on the microbiome of the rumen. However, both batch and pure cultures can result in a build-up of end products that may inhibit fermentation, as they culture ruminal contents or defined strains of bacteria, respectfully. Continuous culture; however, allows for the removal of end products but, similar to pure and batch cultures, is applicable only to ruminal fermentation and cannot provide information regarding intestinal digestion and bioavailability. This information for in vitro can only be provided using an assay designed for total tract digestibility, which is the three-step procedure (TSP). The TSP may be improved by coupling it with cell culture to investigate the absorption of nutrients in both the ruminal and intestinal phases of the methodology; however, the TSP needs further development to investigate all nutrients and the methodologies available for cell culture are still relatively new to ruminant nutrition. Therefore, while in vitro methodologies provide useful data in the field of ruminant nutrition without the continuous use of animals, there is still much work to be done to improve the methodologies to further apply them.}, }
@article {pmid36208750, year = {2023}, author = {Gros, M and Mas-Pla, J and Sànchez-Melsió, A and Čelić, M and Castaño, M and Rodríguez-Mozaz, S and Borrego, CM and Balcázar, JL and Petrović, M}, title = {Antibiotics, antibiotic resistance and associated risk in natural springs from an agroecosystem environment.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159202}, doi = {10.1016/j.scitotenv.2022.159202}, pmid = {36208750}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/analysis ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Tetracyclines/analysis ; *Natural Springs ; Sulfonamides ; Water ; China ; }, abstract = {This study investigates the occurrence, transport, and risks associated to antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic resistant Escherichia coli (AR-E. coli) in eleven natural springs in an agroecosystem environment with intense livestock production, where groundwater nitrate concentration usually sets above 50 mg L[-1]. Out of 23 multiple-class antibiotics monitored, tetracycline and sulfonamide residues were the most ubiquitous, and they were detected at concentrations ranging from ng L[-1] to μg L[-1]. Five ARGs were monitored, conferring resistance to the antibiotic classes of major use in livestock production. Thus, genes conferring resistance to sulfonamides (sul1 and sul2) and tetracyclines (tetW) as well as a gene proxy for anthropogenic pollution (intI1) were present in most springs. sul1 was the most abundant, with absolute concentrations ranging from 4 × 10[2] to 5.6 × 10[6] gene copies L[-1] water. AR-E. coli showing resistance to sulfonamides and tetracyclines was also detected, with a prevalence up to approximately 40 % in some sites but with poor correlations with the concentration of antibiotic residues and ARGs. The occurrence of antibiotics, ARGs and AR-E. coli was characterized by large seasonal variations which were mostly associated to both hydrological factors and reactive transport processes. Finally, a risk assessment approach pointed out towards low risk for both the groundwater environment and human health, when spring water is used for direct human consumption, associated with the occurrence of antibiotics, ARGs and AR-E. coli. However, long-term effects cannot be neglected, and proper actions must be taken to preserve groundwater quality.}, }
@article {pmid36207335, year = {2022}, author = {Tao, J and Wang, W and Weissman, JL and Zhang, Y and Chen, S and Zhu, Y and Zhang, C and Hou, S}, title = {Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {605}, pmid = {36207335}, issn = {2052-4463}, mesh = {*Bays/microbiology ; China ; Genome, Microbial ; Metagenome ; *Microbiota ; Oceans and Seas ; }, abstract = {Jiaozhou Bay is a typical semi-enclosed bay with a temperate climate imposed by strong anthropogenic influence. To investigate microbial biodiversity and ecosystem services in this highly dynamic coastal environment, we conducted a monthly microbial survey spanning eight months at two stations in the bay and the open Yellow Sea starting in April 2015. This report provides a comprehensive inventory of amplicon sequences and environmental microbial genomes from this survey. In total, 2,543 amplicon sequence variants were obtained with monthly relative abundance profiles in three size fractions (>2.7 μm, 2.7-0.7 μm, and 0.7-0.22 μm). Shotgun metagenomes yielded 915 high-quality metagenome-assembled genomes with ≥50% completeness and ≤5% contamination. These environmental genomes comprise 27 bacterial and 5 archaeal phyla. We expect this comprehensive dataset will facilitate a better understanding of coastal microbial ecology.}, }
@article {pmid36206900, year = {2023}, author = {Sauter, D and Steuer, A and Wasmund, K and Hausmann, B and Szewzyk, U and Sperlich, A and Gnirss, R and Cooper, M and Wintgens, T}, title = {Microbial communities and processes in biofilters for post-treatment of ozonated wastewater treatment plant effluent.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159265}, doi = {10.1016/j.scitotenv.2022.159265}, pmid = {36206900}, issn = {1879-1026}, mesh = {Filtration/methods ; RNA, Ribosomal, 16S ; *Water Purification/methods ; Charcoal ; *Microbiota ; Coal ; *Water Pollutants, Chemical ; }, abstract = {Ozonation is an established solution for organic micropollutant (OMP) abatement in tertiary wastewater treatment. Biofiltration is the most common process for the biological post-treatment step, which is generally required to remove undesired oxidation products from the reaction of ozone with water matrix compounds. This study comparatively investigates the effect of filter media on the removal of organic contaminants and on biofilm properties for biologically activated carbon (BAC) and anthracite biofilters. Biofilms were analysed in two pilot-scale filters that have been operated for >50,000 bed volumes as post-treatment for ozonated wastewater treatment plant effluent. In parallel, the removal performance of bulk organics and OMP, including differentiation of adsorption and biotransformation through sodium azide inhibition, were carried out in bench-scale filter columns filled with material from the pilot filters. The use of BAC instead of anthracite resulted in an improved removal of organic bulk parameters, dissolved oxygen, and OMP. The OMP removal observed in the BAC filter but not in the anthracite filter was based on adsorption for most of the investigated compounds. For valsartan, however, biotransformation was found to be the dominant pathway, indicating that conditions for biotransformation of certain OMP are better on BAC than on anthracite. Adenosine triphosphate analyses in the media-attached biofilms of the pilot filters showed that biomass concentrations in the BAC filter were significantly higher than in the anthracite filter. The microbial communities (16S rRNA gene sequencing) appeared to be similar with respect to the types of organisms occurring on both filter materials. Alpha diversity also exhibited little variation between filter media. Beta diversity analysis, however, revealed that filter media and bed depth substantially influenced the biofilm composition. In practice, the impact of filter media on biofilm properties and biotransformation processes should be considered for the design of biofilters.}, }
@article {pmid36205738, year = {2022}, author = {Quero, GM and Piredda, R and Basili, M and Maricchiolo, G and Mirto, S and Manini, E and Seyfarth, AM and Candela, M and Luna, GM}, title = {Host-associated and Environmental Microbiomes in an Open-Sea Mediterranean Gilthead Sea Bream Fish Farm.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36205738}, issn = {1432-184X}, abstract = {Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host's tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.}, }
@article {pmid36205737, year = {2022}, author = {Feng, SW and Lu, JL and Liang, JL and Wu, ZH and Yi, X and Wen, P and Li, FL and Liao, B and Jia, P and Shu, WS and Li, JT}, title = {Functional Guilds, Community Assembly, and Co-occurrence Patterns of Fungi in Metalliferous Mine Tailings Ponds in Mainland China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36205737}, issn = {1432-184X}, abstract = {Metalliferous mine tailings ponds are generally characterized by low levels of nutrient elements, sustained acidic conditions, and high contents of toxic metals. They represent one kind of extreme environments that are believed to resemble the Earth's early environmental conditions. There is increasing evidence that the diversity of fungi inhabiting mine tailings ponds is much higher than previously thought. However, little is known about functional guilds, community assembly, and co-occurrence patterns of fungi in such habitats. As a first attempt to address this critical knowledge gap, we employed high-throughput sequencing to characterize fungal communities in 33 mine tailings ponds distributed across 18 provinces of mainland China. A total of 5842 fungal phylotypes were identified, with saprotrophic fungi being the major functional guild. The predictors of fungal diversity in whole community and sub-communities differed considerably. Community assembly of the whole fungal community and individual functional guilds were primarily governed by stochastic processes. Total soil nitrogen and total phosphorus mediated the balance between stochastic and deterministic processes of the fungal community assembly. Co-occurrence network analysis uncovered a high modularity of the whole fungal community. The observed main modules largely consisted of saprotrophic fungi as well as various phylotypes that could not be assigned to known functional guilds. The richness of core fungal phylotypes, occupying vital positions in co-occurrence network, was positively correlated with edaphic properties such as soil enzyme activity. This indicates the important roles of core fungal phylotypes in soil organic matter decomposition and nutrient cycling. These findings improve our understanding of fungal ecology of extreme environments.}, }
@article {pmid36204622, year = {2022}, author = {Banerjee, S and Bedics, A and Tóth, E and Kriszt, B and Soares, AR and Bóka, K and Táncsics, A}, title = {Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m- and p-xylene under microaerobic conditions.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {929128}, pmid = {36204622}, issn = {1664-302X}, abstract = {Members of the genus Pseudomonas are known to be widespread in hydrocarbon contaminated environments because of their remarkable ability to degrade a variety of petroleum hydrocarbons, including BTEX (benzene, toluene, ethylbenzene and xylene) compounds. During an enrichment investigation which aimed to study microaerobic xylene degradation in a legacy petroleum hydrocarbon-contaminated groundwater, a novel Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated as MAP12[T] was isolated. It was capable of degrading benzene, toluene, meta- and para- xylene effectively under both aerobic and microaerobic conditions. The 16S rRNA gene sequence analysis revealed that strain MAP12[T] belongs to the genus Pseudomonas, with the highest 16S rRNA gene similarity to Pseudomonas linyingensis LYBRD3-7 [T] (98.42%), followed by Pseudomonas sagittaria JCM 18195 [T] (98.29%) and Pseudomonas alcaliphila JCM 10630 [T] (98.08%). Phylogenomic tree constructed using a concatenated alignment of 92 core genes indicated that strain MAP12[T] is distinct from any known Pseudomonas species. The draft genome sequence of strain MAP12[T] is 4.36 Mb long, and the G+C content of MAP12[T] genome is 65.8%. Orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) analyses confirmed that strain MAP12[T] is distinctly separated from its closest neighbors (OrthoANI < 89 %; dDDH < 36%). Though several members of the genus Pseudomonas are well known for their aerobic BTEX degradation capability, this is the first report of a novel Pseudomonas species capable of degrading xylene under microaerobic conditions. By applying genome-resolved metagenomics, we were able to partially reconstruct the genome of strain MAP12 [T] from metagenomics sequence data and showed that strain MAP12 [T] was an abundant member of the xylene-degrading bacterial community under microaerobic conditions. Strain MAP12[T] contains ubiquinone 9 (Q9) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine as major polar lipids. The major cellular fatty acids of strain MAP12[T] are summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The results of this polyphasic study support that strain MAP12[T] represents a novel species of the genus Pseudomonas, hence the name of Pseudomonas aromaticivorans sp. nov. is proposed for this strain considering its aromatic hydrocarbon degradation capability. The type strain is MAP12[T] (=LMG 32466, =NCAIM B.02668).}, }
@article {pmid36204070, year = {2022}, author = {Zhang, H and Ma, Y and Shao, J and Di, R and Zhu, F and Yang, Z and Sun, J and Zhang, X and Zheng, C}, title = {Changes in soil bacterial community and functions by substituting chemical fertilizer with biogas slurry in an apple orchard.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1013184}, pmid = {36204070}, issn = {1664-462X}, abstract = {Growing concerns about the negative environmental effects of excessive chemical fertilizer input in fruit production have resulted in many attempts looking for adequate substitution. Biogas slurry as a representative organic fertilizer has the potential to replace chemical fertilizer for improvement of sustainability. However, it is still poorly known how biogas slurry applications may affect the composition of soil microbiome. Here, we investigated different substitution rates of chemical fertilizer with biogas slurry treatment (the control with no fertilizer and biogas slurry, CK; 100% chemical fertilizer, CF; biogas slurry replacing 50% of chemical fertilizer, CBS; and biogas slurry replacing 100% of chemical fertilizer, BS) in an apple orchard. Soil bacterial community and functional structure among treatments were determined using Illumina sequencing technology coupled with Functional Annotation of Prokaryotic Taxonomy (FAPROTAX) analysis. Leaf nutrient contents, apple fruit and soil parameters were used to assess plant and soil quality. Results showed that most of fruit parameters and soil properties were significantly varied in the four treatments. CBS treatment increased the contents of soil organic matter, alkali nitrogen and available potassium average by 49.8%, 40.7% and 27.9%, respectively. Treatments with biogas slurry application increased the single fruit weight, fresh weight, and dry weight of apple fruit average by 15.6%, 18.8% and 17.8, respectively. Soil bacterial community dominance and composition were significantly influenced by substituting of chemical fertilizer with biogas slurry. Biogas slurry application enhanced the relative abundance of some beneficial taxa (e.g. Acidobacteria Gp5 and Gp7, Parasegetibacter) and functional groups related to carbon and nitrogen cycling such as chemoheterotrophy, cellulolysis, and nitrogen fixation. Soil available phosphorus and potassium, pH and electrical conductivity were identified having a high potential for regulating soil bacterial specific taxa and functional groups. This study showed that the proper ratio application (50%: 50%) of biogas slurry with chemical fertilizer could regulate soil bacterial composition and functional structure via changes in soil nutrients. The variations of bacterial community could potentially take significant ecological roles in maintaining apple plant growth, soil fertility and functionality.}, }
@article {pmid36202959, year = {2022}, author = {Guerrero-Latorre, L and Collado, N and Abasolo, N and Anzaldi, G and Bofill-Mas, S and Bosch, A and Bosch, L and Busquets, S and Caimari, A and Canela, N and Carcereny, A and Chacón, C and Ciruela, P and Corbella, I and Domingo, X and Escoté, X and Espiñeira, Y and Forés, E and Gandullo-Sarró, I and Garcia-Pedemonte, D and Girones, R and Guix, S and Hundesa, A and Itarte, M and Mariné-Casadó, R and Martínez, A and Martínez-Puchol, S and Mas-Capdevila, A and Mejías-Molina, C and Rafa, MMI and Munné, A and Pintó, RM and Pueyo-Ros, J and Robusté-Cartró, J and Rusiñol, M and Sanfeliu, R and Teichenné, J and Torrell, H and Corominas, L and Borrego, CM}, title = {The Catalan Surveillance Network of SARS-CoV-2 in Sewage: design, implementation, and performance.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16704}, pmid = {36202959}, issn = {2045-2322}, mesh = {*COVID-19/epidemiology ; Humans ; Pandemics ; RNA, Viral ; *SARS-CoV-2 ; Sewage ; Waste Water ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {Wastewater-based epidemiology has shown to be an efficient tool to track the circulation of SARS-CoV-2 in communities assisted by wastewater treatment plants (WWTPs). The challenge comes when this approach is employed to help Health authorities in their decision-making. Here, we describe the roadmap for the design and deployment of SARSAIGUA, the Catalan Surveillance Network of SARS-CoV-2 in Sewage. The network monitors, weekly or biweekly, 56 WWTPs evenly distributed across the territory and serving 6 M inhabitants (80% of the Catalan population). Each week, samples from 45 WWTPs are collected, analyzed, results reported to Health authorities, and finally published within less than 72 h in an online dashboard (https://sarsaigua.icra.cat). After 20 months of monitoring (July 20-March 22), the standardized viral load (gene copies/day) in all the WWTPs monitored fairly matched the cumulative number of COVID-19 cases along the successive pandemic waves, showing a good fit with the diagnosed cases in the served municipalities (Spearman Rho = 0.69). Here we describe the roadmap of the design and deployment of SARSAIGUA while providing several open-access tools for the management and visualization of the surveillance data.}, }
@article {pmid36202936, year = {2022}, author = {Fournier, E and Denis, S and Dominicis, A and Van de Wiele, T and Alric, M and Mercier-Bonin, M and Etienne-Mesmin, L and Blanquet-Diot, S}, title = {A child is not an adult: development of a new in vitro model of the toddler colon.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {21}, pages = {7315-7336}, pmid = {36202936}, issn = {1432-0614}, mesh = {Adult ; Infant ; Humans ; Child, Preschool ; Child ; *Propionates ; Colon ; Fatty Acids, Volatile ; Feces ; *Microbiota ; Butyrates ; Methane ; }, abstract = {Early life is a critical period where gut ecosystem and functions are being established with significant impact on health. For regulatory, technical, and cost reasons, in vitro gut models can be used as a relevant alternative to in vivo assays. An exhaustive literature review was conducted to adapt the Mucosal Artificial Colon (M-ARCOL) to specific physicochemical (pH, transit time, and nutritional composition of ileal effluents) and microbial parameters from toddlers in the age range of 6 months-3 years, resulting in the Tm-ARCOL. In vitro fermentations were performed to validate this newly developed colonic model compared to in vivo toddler data. Results were also compared to those obtained with the classical adult configuration. Fecal samples from 5 toddlers and 4 adults were used to inoculate bioreactors, and continuous fermentations were performed for 8 days. Gut microbiota structure (lumen and mucus-associated microbiota) and functions (gas and short-chain fatty acids) were monitored. Clearly distinct microbial signatures were obtained between the two in vitro conditions, with lower α-diversity indices and higher abundances of infant-related microbial populations (e.g., Bifidobacteriaceae, Enterobacteriaceae) in toddler versus adult conditions. In accordance with in vivo data, methane was found only in adult bioreactors, while higher percentage of acetate but lower proportions of propionate and butyrate was measured in toddlers compared to adults. This new in vitro model will provide a powerful platform for gut microbiome mechanistic studies in a pediatric context, both in nutritional- (e.g., nutrients, probiotics, prebiotics) and health-related (e.g., drugs, enteric pathogens) studies. KEY POINTS: • Development of a novel in vitro colonic model recapitulating the toddler environment. • Specific toddler versus adult digestive conditions are preserved in vitro. • The new model provides a powerful platform for microbiome mechanistic studies.}, }
@article {pmid36198042, year = {2022}, author = {Yan, C and Kwek, E and Ding, HF and He, Z and Ma, KY and Zhu, H and Chen, ZY}, title = {Dietary Oxidized Cholesterol Aggravates Chemically Induced Murine Colon Inflammation and Alters Gut Microbial Ecology.}, journal = {Journal of agricultural and food chemistry}, volume = {70}, number = {41}, pages = {13289-13301}, doi = {10.1021/acs.jafc.2c05001}, pmid = {36198042}, issn = {1520-5118}, mesh = {Mice ; Humans ; Animals ; *Gastrointestinal Microbiome ; Dextran Sulfate/adverse effects ; Cholesterol, Dietary ; Mice, Inbred C57BL ; *Colitis/chemically induced/microbiology ; Colon/microbiology ; Fatty Acids, Volatile/pharmacology ; Inflammation ; Disease Models, Animal ; }, abstract = {Western diet with a higher intake of fat and cholesterol has been claimed as an intestinal inflammation trigger. Human diet contains both cholesterol and oxidized cholesterol. Oxidized cholesterol has been claimed to be associated with various inflammation diseases, but its effects on colitis and gut microbiome remain largely unknown. The present study was the first time to investigate the effect of the oxidized cholesterol on gut microbiota and dextran sodium sulfate-induced colitis using mice as a model. The results showed that oxidized cholesterol promoted colitis by exacerbating bleeding, body weight decrease, colon shortening, gut barrier damage, oxidative stress, and gut inflammation, whereas non-oxidized cholesterol had no effect. Meanwhile, oxidized cholesterol could adversely modulate the gut microbiota by increasing the relative abundance of pro-inflammatory bacteria (including Escherichia-Shigella and Bacteroides) and decreasing that of beneficial bacteria (Lachnospiraceae_NK4A136_group and Odoribacter). In addition, oxidized cholesterol significantly reduced the production of fecal short-chain fatty acids in colitis mice. It was concluded that oxidized cholesterol was a potential dietary factor of gut dysbiosis.}, }
@article {pmid36197502, year = {2022}, author = {Pin Viso, ND and Rizzo, PF and Young, BJ and Gabioud, E and Bres, P and Riera, NI and Merino, L and Farber, MD and Crespo, DC}, title = {The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36197502}, issn = {1432-184X}, abstract = {Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.}, }
@article {pmid36196151, year = {2022}, author = {Zhang, YW and Cao, MM and Li, YJ and Lu, PP and Dai, GC and Zhang, M and Wang, H and Rui, YF}, title = {Fecal microbiota transplantation ameliorates bone loss in mice with ovariectomy-induced osteoporosis via modulating gut microbiota and metabolic function.}, journal = {Journal of orthopaedic translation}, volume = {37}, number = {}, pages = {46-60}, pmid = {36196151}, issn = {2214-031X}, abstract = {BACKGROUND: Osteoporosis (OP) is a systemic metabolic bone disease characterized by decreased bone mass and destruction of bone microstructure, which tends to result in enhanced bone fragility and related fractures. The postmenopausal osteoporosis (PMOP) has a relatively high proportion, and numerous studies reveal that estrogen-deficiency is related to the imbalance of gut microbiota (GM), impaired intestinal mucosal barrier function and enhanced inflammatory reactivity. However, the underlying mechanisms remain unclear and the existing interventions are also scarce.<br><br>METHODS: In this study, we established a mouse model induced by ovariectomy (OVX) and conducted fecal microbiota transplantation (FMT) by gavage every day for 8 weeks. Subsequently, the bone mass and microarchitecture of mice were evaluated by the micro computed tomography (Micro-CT). The intestinal permeability, pro-osteoclastogenic cytokines expression, osteogenic and osteoclastic activities were detected by the immunohistological analysis, histological examination, enzyme-linked immunosorbent assay (ELISA) and western blot analysis accordingly. Additionally, the composition and abundance of GM were assessed by 16S rRNA sequencing and the fecal short chain fatty acids (SCFAs) level was measured by metabolomics.<br><br>RESULTS: Our results demonstrated that FMT inhibited the excessive osteoclastogenesis and prevented the OVX-induced bone loss. Specifically, compared with the OVX group, FMT enhanced the expressions of tight junction proteins (zonula occludens protein 1 (ZO-1) and Occludin) and suppressed the release of pro-osteoclastogenic cytokines (tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and interleukin-1&#x3b2; (IL-1&#x3b2;)). Furthermore, FMT also optimized the composition and abundance of GM, and increased the fecal SCFAs level (mainly acetic acid and propionic acid).<br><br>CONCLUSIONS: Collectively, based on GM-bone axis, FMT prevented the OVX-induced bone loss by correcting the imbalance of GM, improving the SCFAs level, optimizing the intestinal permeability and suppressing the release of pro-osteoclastogenic cytokines, which may be an alternative option to serve as a promising candidate for the prevention and treatment of PMOP in the future.<br><br>This study indicates the ingenious involvement of GM-bone axis in PMOP and the role of FMT in reshaping the status of GM and ameliorating the bone loss in OVX-induced mice. FMT might serve as a promising candidate for the prevention and treatment of PMOP in the future.}, }
@article {pmid36196117, year = {2022}, author = {Dong, H and Huang, L and Zhao, L and Zeng, Q and Liu, X and Sheng, Y and Shi, L and Wu, G and Jiang, H and Li, F and Zhang, L and Guo, D and Li, G and Hou, W and Chen, H}, title = {A critical review of mineral-microbe interaction and co-evolution: mechanisms and applications.}, journal = {National science review}, volume = {9}, number = {10}, pages = {nwac128}, pmid = {36196117}, issn = {2053-714X}, abstract = {Mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation and precipitation of minerals through their activity, resulting in either genetically controlled or metabolism-induced biomineralization. Through these interactions, minerals and microbes co-evolve through Earth history. Mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.}, }
@article {pmid36194291, year = {2022}, author = {Lomelí-Ortega, CO and Barajas-Sandoval, DR and Martínez-Villalobos, JM and Jaramillo, CR and Chávez, EM and Gómez-Gil, B and Balcázar, JL and Quiroz-Guzmán, E}, title = {A Broad-Host-Range Phage Cocktail Selectively and Effectively Eliminates Vibrio Species from Shrimp Aquaculture Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36194291}, issn = {1432-184X}, abstract = {The protective effects of a phage cocktail composed of vB_Vc_SrVc2 and vB_Vc_SrVc9 were tested in Pacific white shrimp (Litopenaeus vannamei) postlarvae, which were originally isolated from diseased shrimps and selected due to their broad-host-range properties against several pathogenic Vibsrio species. We used culture-dependent and culture-independent approaches to explore its effect on bacterial communities associated with shrimp postlarvae. Both methods revealed that the levels of Vibrio species were significantly reduced after phage cocktail administration. Phage-treated shrimp also exhibisuppted lesser damage and higher lipid accumulation in B cells of the hepatopancreas, as revealed by histopathological examination. Taken together, this study provides clear evidence that phage therapy can selectively and effectively reduce Vibrio species, thereby providing an environmentally safe alternative to the prophylactic use of antibiotics in shrimp aquaculture.}, }
@article {pmid36194136, year = {2022}, author = {Fang, Y and Stanford, K and Yang, X}, title = {Lactic Acid Resistance and Population Structure of Escherichia coli from Meat Processing Environment.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0135222}, pmid = {36194136}, issn = {2165-0497}, mesh = {Cattle ; Animals ; Escherichia coli ; Lactic Acid ; Phylogeny ; Meat ; Anti-Bacterial Agents/pharmacology ; Food Handling ; *Anti-Infective Agents/pharmacology ; *Disinfectants/pharmacology ; Sugar Acids/analysis/pharmacology ; Colony Count, Microbial ; Food Microbiology ; Food Contamination/analysis ; }, abstract = {To explore the effect of beef processing on Escherichia coli populations in relation to lactic acid resistance, this study investigated the links among acid response, phylogenetic structure, genome diversity, and genotypes associated with acid resistance of meat plant E. coli. Generic E. coli isolates (n = 700) were from carcasses, fabrication equipment, and beef products. Acid treatment was carried out in Luria-Bertani broth containing 5.5% lactic acid (pH 2.9). Log reductions of E. coli ranged from <0.5 to >5 log CFU/mL (median: 1.37 log). No difference in lactic acid resistance was observed between E. coli populations recovered before and after a processing step or antimicrobial interventions. E. coli from the preintervention carcasses were slightly more resistant than E. coli isolated from equipment, differing by <0.5 log unit. Acid-resistant E. coli (log reduction <1, n = 45) had a higher prevalence of genes related to energy metabolism (ydj, xap, ato) and oxidative stress (fec, ymjC) than the less resistant E. coli (log reduction >1, n = 133). The ydj and ato operons were abundant in E. coli from preintervention carcasses. In contrast, fec genes were abundant in E. coli from equipment surfaces. The preintervention E. coli contained phylogroups A and B1 in relatively equal proportions. Phylogroup B1 predominated (95%) in the population from equipment. Of note, E. coli collected after sanitation shared either the antigens of O8 or H21. Additionally, genome diversity decreased after chilling and equipment sanitation. Overall, beef processing did not select for E. coli resistant to lactic acid but shaped the population structure. IMPORTANCE Antimicrobial interventions have significantly reduced the microbial loads on carcasses/meat products; however, the wide use of chemical and physical biocides has raised concerns over their potential for selecting resistant populations in the beef processing environment. Phenotyping of acid resistance and whole-genome analysis described in this study demonstrated beef processing practices led to differences in acid resistance, genotype, and population structure between carcass- and equipment-associated E. coli but did not select for the acid-resistant population. Results indicate that genes coding for the metabolism of long-chain sugar acids (ydj) and short-chain fatty acids (ato) were more prevalent in carcass-associated than equipment-associated E. coli. These results suggest E. coli from carcasses and equipment surfaces have been exposed to different selective pressures. The findings improve our understanding of the microbial ecology of E. coli in food processing environments and in general.}, }
@article {pmid36192537, year = {2022}, author = {Zaremba, M and Dakineviciene, D and Golovinas, E and Zagorskaitė, E and Stankunas, E and Lopatina, A and Sorek, R and Manakova, E and Ruksenaite, A and Silanskas, A and Asmontas, S and Grybauskas, A and Tylenyte, U and Jurgelaitis, E and Grigaitis, R and Timinskas, K and Venclovas, &#x10c; and Siksnys, V}, title = {Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD[+] depletion.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1857-1869}, pmid = {36192537}, issn = {2058-5276}, mesh = {*NAD/genetics/metabolism ; Prokaryotic Cells/metabolism ; Argonaute Proteins/genetics ; DNA/metabolism ; *Bacteriophages/genetics/metabolism ; Interspersed Repetitive Sequences ; }, abstract = {Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). The majority (~60%) of pAgos identified bioinformatically are shorter (comprising only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here we show that Geobacter sulfurreducens short pAgo and the NAD[+]-bound Sir2 protein form a stable heterodimeric complex. The GsSir2/Ago complex presumably recognizes invading plasmid or phage DNA and activates the Sir2 subunit, which triggers endogenous NAD[+] depletion and cell death, and prevents the propagation of invading DNA. We reconstituted NAD[+] depletion activity in vitro and showed that activated GsSir2/Ago complex functions as a NADase that hydrolyses NAD[+] to ADPR. Thus, short Sir2-associated pAgos provide defence against phages and plasmids, underscoring the diversity of mechanisms of prokaryotic Agos.}, }
@article {pmid36192536, year = {2022}, author = {Garb, J and Lopatina, A and Bernheim, A and Zaremba, M and Siksnys, V and Melamed, S and Leavitt, A and Millman, A and Amitai, G and Sorek, R}, title = {Multiple phage resistance systems inhibit infection via SIR2-dependent NAD[+] depletion.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1849-1856}, pmid = {36192536}, issn = {2058-5276}, mesh = {*NAD/metabolism ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/genetics/metabolism ; Sirtuin 2/genetics ; *Bacteriophages/genetics/metabolism ; NAD+ Nucleosidase ; }, abstract = {Defence-associated sirtuins (DSRs) comprise a family of proteins that defend bacteria from phage infection via an unknown mechanism. These proteins are common in bacteria and harbour an N-terminal sirtuin (SIR2) domain. In this study we report that DSR proteins degrade nicotinamide adenine dinucleotide (NAD[+]) during infection, depleting the cell of this essential molecule and aborting phage propagation. Our data show that one of these proteins, DSR2, directly identifies phage tail tube proteins and then becomes an active NADase in Bacillus subtilis. Using a phage mating methodology that promotes genetic exchange between pairs of DSR2-sensitive and DSR2-resistant phages, we further show that some phages express anti-DSR2 proteins that bind and repress DSR2. Finally, we demonstrate that the SIR2 domain serves as an effector NADase in a diverse set of phage defence systems outside the DSR family. Our results establish the general role of SIR2 domains in bacterial immunity against phages.}, }
@article {pmid36190138, year = {2022}, author = {Weissman, JL and Peras, M and Barnum, TP and Fuhrman, JA}, title = {Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0074522}, pmid = {36190138}, issn = {2379-5077}, abstract = {Trait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metagenome to (meta)phenotype are needed. Recently, we developed a tool, gRodon, that enables the prediction of the maximum growth rate of an organism from genomic data on the basis of codon usage patterns. Our work and that of other groups suggest that such predictors can be applied to mixed-species communities in order to derive estimates of the average community-wide maximum growth rate. Here, we present an improved maximum growth rate predictor designed for metagenomes that corrects a persistent GC bias in the original gRodon model for metagenomic prediction. We benchmark this predictor with simulated metagenomic data sets to show that it has superior performance on mixed-species communities relative to earlier models. We go on to provide guidance on data preprocessing and show that calling genes from assembled contigs rather than directly from reads dramatically improves performance. Finally, we apply our predictor to large-scale metagenomic data sets from marine and human microbiomes to illustrate how community-wide growth prediction can be a powerful approach for hypothesis generation. Altogether, we provide an updated tool with clear guidelines for users about the uses and pitfalls of metagenomic prediction of the average community-wide maximal growth rate. IMPORTANCE Microbes dominate nearly every known habitat, and therefore tools to survey the structure and function of natural microbial communities are much needed. Metagenomics, in which the DNA content of an entire community of organisms is sequenced all at once, allows us to probe the genetic diversity contained in a habitat. Yet, mapping metagenomic information to the actual traits of community members is a difficult and largely unsolved problem. Here, we present and validate a tool that allows users to predict the average maximum growth rate of a microbial community directly from metagenomic data. Maximum growth rate is a fundamental characteristic of microbial species that can give us a great deal of insight into their ecological role, and by applying our community-level predictor to large-scale metagenomic data sets from marine and human-associated microbiomes, we show how community-wide growth prediction can be a powerful approach for hypothesis generation.}, }
@article {pmid36189957, year = {2022}, author = {Hunter, BT and Flury, JD and Cocioba, SS and Cope-Arguello, ML and Helms, JM and García, KH and Dominguez, G and Taniguchi, DA and Becket, E}, title = {Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies.}, journal = {BioTechniques}, volume = {73}, number = {4}, pages = {183-191}, pmid = {36189957}, issn = {1940-9818}, support = {R25 GM066341/GM/NIGMS NIH HHS/United States ; R15 ES033027/ES/NIEHS NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Temperature ; }, abstract = {Coastal environments are dynamic and can vary widely on short- or long-term scales depending on location and weather. Incubation equipment that reflects these changes through programmable gradient light and temperature cycles would permit more precise in vitro coastal microbiome studies. Here we present an open-source incubation environment that mimics in situ conditions for in vitro coastal microbiome studies using a modified shaking water bath that has fully customizable temperature and light gradients that can also mimic real-time field conditions. We compared coastal microbial community profiles incubated in situ and in our build mimicking field conditions over 48 h. Analyses of congruence indicated significant overlap (p > 0.2) between microbial communities incubated in situ and in vitro at each time point.}, }
@article {pmid36189437, year = {2022}, author = {Moussa, DG and Sharma, AK and Mansour, TA and Witthuhn, B and Perdigão, J and Rudney, JD and Aparicio, C and Gomez, A}, title = {Functional signatures of ex-vivo dental caries onset.}, journal = {Journal of oral microbiology}, volume = {14}, number = {1}, pages = {2123624}, pmid = {36189437}, issn = {2000-2297}, abstract = {BACKGROUND: The etiology of dental caries remains poorly understood. With the advent of next-generation sequencing, a number of studies have focused on the microbial ecology of the disease. However, taxonomic associations with caries have not been consistent. Researchers have also pursued function-centric studies of the caries microbial communities aiming to identify consistently conserved functional pathways. A major question is whether changes in microbiome are a cause or a consequence of the disease. Thus, there is a critical need to define conserved functional signatures at the onset of dental caries.<br><br>METHODS: Since it is unethical to induce carious lesions clinically, we developed an innovative longitudinal ex-vivo model integrated with the advanced non-invasive multiphoton second harmonic generation bioimaging to spot the very early signs of dental caries, combined with 16S rRNA short amplicon sequencing and liquid chromatography-mass spectrometry-based targeted metabolomics.<br><br>FINDINGS: For the first time, we induced longitudinally monitored caries lesions validated with the scanning electron microscope. Consequently, we spotted the caries onset and, associated with it, distinguished five differentiating metabolites - Lactate, Pyruvate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate (upregulated) and Fumarate (downregulated). Those metabolites co-occurred with certain bacterial taxa; Streptococcus, Veillonella, Actinomyces, Porphyromonas, Fusobacterium, and Granulicatella, regardless of the abundance of other taxa.<br><br>INTERPRETATION: These findings are crucial for understanding the etiology and dynamics of dental caries, and devising targeted interventions to prevent disease progression.}, }
@article {pmid36188424, year = {2022}, author = {Geldenhuys, J and Redelinghuys, MJ and Lombaard, HA and Ehlers, MM and Cowan, D and Kock, MM}, title = {Diversity of the gut, vaginal and oral microbiome among pregnant women in South Africa with and without pre-eclampsia.}, journal = {Frontiers in global women's health}, volume = {3}, number = {}, pages = {810673}, pmid = {36188424}, issn = {2673-5059}, abstract = {BACKGROUND: Changes in microbial communities are a known characteristic of various inflammatory diseases and have been linked to adverse pregnancy outcomes, such as preterm birth. However, there is a paucity of information regarding the taxonomic composition and/or diversity of microbial communities in pre-eclampsia. The aim of this study was to determine the diversity of the gut, vaginal and oral microbiome in a cohort of South African pregnant women with and without pre-eclampsia. The diversity of the gut, vaginal and oral microbiome was determined by targeted next generation sequencing (NGS) of the V3 and V4 region of the 16S rRNA gene on the Illumina MiSeq platform.<br><br>RESULTS: In this study population, pre-eclampsia was associated with a significantly higher alpha diversity (P = 0.0472; indicated by the Shannon index) in the vaginal microbiome accompanied with a significant reduction in Lactobacillus spp. (P = 0.0275), compared to normotensive pregnant women. Lactobacillus iners was identified as the predominant species of the vaginal microbiome in both cohorts. High inter-individual variation in alpha diversity was observed in the gut and oral microbiome in both cohorts. Although differences in the relative abundance of bacteria at all phylogenetic levels were observed, overall microbial composition of the gut, oral and vaginal microbiome was not significantly different in the pre-eclampsia cohort compared to the normotensive cohort.<br><br>CONCLUSION: Collectively, a reduction of Lactobacillus spp., and predominance of L. iners in pregnant women with pre-eclampsia could suggest an unstable vaginal microbiome that might predispose pregnant women to develop pre-eclampsia. The lack of significant structural changes in the gut, oral and vaginal microbiome does not suggest that the characterized communities play a role in pre-eclampsia, but could indicate a characteristic unique to the study population. The current study provided novel information on the diversity of the gut, oral and vaginal microbiome among pregnant women in South Africa with and without pre-eclampsia. The current study provides a baseline for further investigations on the potential role of microbial communities in pre-eclampsia.}, }
@article {pmid36187988, year = {2022}, author = {Zufiaurre, A and Felip, M and Camarero, L and Sala-Faig, M and Juhanson, J and Bonilla-Rosso, G and Hallin, S and Catalan, J}, title = {Bacterioplankton seasonality in deep high-mountain lakes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {935378}, pmid = {36187988}, issn = {1664-302X}, abstract = {Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.}, }
@article {pmid36187961, year = {2022}, author = {Yang, X and Yu, X and He, Q and Deng, T and Guan, X and Lian, Y and Xu, K and Shu, L and Wang, C and Yan, Q and Yang, Y and Wu, B and He, Z}, title = {Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {956860}, pmid = {36187961}, issn = {1664-302X}, abstract = {Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.}, }
@article {pmid36187958, year = {2022}, author = {Li, Y and Zhang, Y and Xue, S}, title = {pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {952285}, pmid = {36187958}, issn = {1664-302X}, abstract = {Microorganisms are the core drivers of biogeochemistry processes in petroleum reservoirs and have been widely used to enhance petroleum recovery. However, systematic information about the microbial communities related to the C-N-S cycle in petroleum reservoirs under different pH conditions remains poorly understood. In this study, 16S rRNA gene data from 133 petroleum samples were collected, and 756 C-N-S related genera were detected. The Chao1 richness and Shannon diversity indices for the C-N-S-related microbial communities showed significant differences among different pH conditions and at the lowest levels in acidic conditions with pH values of 4.5-6.5. In addition, pH was the most important factor influencing the C-N-S related microbial communities and contributed to 17.95% of the variation in the methanogenesis community. A total of 55 functional genera were influenced by pH, which accounted for 42.08% of the C-N-S related genera. Among them, the genera Pseudomonas and Arcobacter were the highest and were concentrated in acidic conditions with pH values of 4.5-6.5. In parallel, 56 predicted C-N-S related genes were examined, and pH affected 16 of these genes, including putative chitinase, mcrA, mtrB, cysH, narGHIVYZ, nirK, nirB, nifA, sat, aprAB, and dsrAB. Furthermore, the co-occurrence networks of the C-N-S related microbial communities distinctly varied among the different pH conditions. The acidic environment exhibited the lowest complex network with the lowest keystone taxa number, and Escherichia-Shigella was the only keystone group that existed in all three networks. In summary, this study strengthened our knowledge regarding the C-N-S related microbial communities in petroleum reservoirs under different pH conditions, which is of great significance for understanding the microbial ecology and geochemical cycle of petroleum reservoirs.}, }
@article {pmid36185017, year = {2022}, author = {Zhang, Y and Xue, S and Chang, X and Li, Y and Yue, X}, title = {Nutrients Changed the Assembly Processes of Profuse and Rare Microbial Communities in Coals.}, journal = {Polish journal of microbiology}, volume = {71}, number = {3}, pages = {359-370}, pmid = {36185017}, issn = {2544-4646}, mesh = {*Coal ; Firmicutes/genetics ; Methane ; *Microbiota ; Nutrients ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nutrient stimulation is considered effective for improving biogenic coalbed methane production potential. However, our knowledge of the microbial assembly process for profuse and rare microbial communities in coals under nutrient stimulation is still limited. This study collected 16S rRNA gene data from 59 microbial communities in coals for a meta-analysis. Among these communities, 116 genera were identified as profuse taxa, and the remaining 1,637 genera were identified as rare taxa. Nutrient stimulation increased the Chao1 richness of profuse and rare genera and changed the compositions of profuse and rare genera based on nonmetric multidimensional scaling with Bray-Curtis dissimilarities. In addition, many profuse and rare genera belonging to Proteobacteria and Acidobacteria were reduced, whereas those belonging to Euryarchaeota and Firmicutes were increased under nutrient stimulation. Concomitantly, the microbial co-occurrence relationship network was also altered by nutrient addition, and many rare genera mainly belonging to Firmicutes, Bacteroides, and Euryarchaeota also comprised the key microorganisms. In addition, the compositions of most of the profuse and rare genera in communities were driven by stochastic processes, and nutrient stimulation increased the relative contribution of dispersal limitation for both profuse and rare microbial community assemblages and that of variable selection for rare microbial community assemblages. In summary, this study strengthened our knowledge regarding the mechanistic responses of coal microbial diversity and community composition to nutrient stimulation, which are of great importance for understanding the microbial ecology of coals and the sustainability of methane production stimulated by nutrients.}, }
@article {pmid36182151, year = {2023}, author = {Wang, C and Yao, Z and Zhan, P and Yi, X and Chen, J and Xiong, J}, title = {Significant tipping points of sediment microeukaryotes forewarn increasing antibiotic pollution.}, journal = {Journal of environmental sciences (China)}, volume = {124}, number = {}, pages = {429-439}, doi = {10.1016/j.jes.2021.10.031}, pmid = {36182151}, issn = {1001-0742}, mesh = {*Ammonium Compounds ; *Anti-Bacterial Agents ; Environmental Biomarkers ; Phosphates ; Tetracyclines ; Waste Water ; }, abstract = {Antibiotic pollution imposes urgent threats to public health and microbial-mediated ecological processes. Existing studies have primarily focused on bacterial responses to antibiotic pollution, but they ignored the microeukaryotic counterpart, though microeukaryotes are functionally important (e.g., predators and saprophytes) in microbial ecology. Herein, we explored how the assembly of sediment microeukaryotes was affected by increasing antibiotic pollution at the inlet (control) and across the outlet sites along a shrimp wastewater discharge channel. The structures of sediment microeukaryotic community were substantially altered by the increasing nutrient and antibiotic pollutions, which were primarily controlled by the direct effects of phosphate and ammonium (-0.645 and 0.507, respectively). In addition, tetracyclines exerted a large effect (0.209), including direct effect (0.326) and indirect effect (-0.117), on the microeukaryotic assembly. On the contrary, the fungal subcommunity was relatively resistant to antibiotic pollution. Segmented analysis depicted nonlinear responses of microeukaryotic genera to the antibiotic pollution gradient, as supported by the significant tipping points. We screened 30 antibiotic concentration-discriminatory taxa of microeukaryotes, which can quantitatively and accurately predict (98.7% accuracy) the in-situ antibiotic concentration. Sediment microeukaryotic (except fungal) community is sensitive to antibiotic pollution, and the identified bioindicators could be used for antibiotic pollution diagnosis.}, }
@article {pmid36181942, year = {2022}, author = {Shen, Z and Xie, G and Zhang, Y and Yu, B and Shao, K and Gao, G and Tang, X}, title = {Similar assembly mechanisms but distinct co-occurrence patterns of free-living vs. particle-attached bacterial communities across different habitats and seasons in shallow, eutrophic Lake Taihu.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120305}, doi = {10.1016/j.envpol.2022.120305}, pmid = {36181942}, issn = {1873-6424}, mesh = {*Lakes/microbiology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; Seasons ; Bacteria/genetics ; Phosphorus ; Nitrogen ; Methane ; Carbon ; }, abstract = {Eutrophication due to nitrogen and phosphorus input is an increasing problem in lake ecosystems. Free-living (FL) and particle-attached (PA) bacterial communities play a primary role in mediating biogeochemical processes in these lakes and in responding to eutrophication. However, knowledge of factors governing function, assembly mechanisms, and co-occurrence patterns of these communities remain poorly understood and are key challenges in microbial ecology. To address this knowledge gap, we collected 96 samples from Lake Taihu across four seasons and investigated the bacterial community using 16S rRNA gene sequencing. Our results demonstrate that the α-diversity, β-diversity, community composition, and functional composition of FL and PA bacterial communities exhibited differing spatiotemporal dynamics. FL and PA bacterial communities displayed similar distance-decay relationships across seasons. Deterministic processes (i.e., environmental filtering and species interaction) were the primary factors shaping community assembly in both FL and PA bacteria. Similar environmental factors shaped bacterial community structure while different environmental factors drove bacterial functional composition. Habitat filtering influenced enrichment of bacteria within specific functional groups. Among them, the FL bacterial community appeared to play a critical role in methane-utilization, whereas the PA bacteria contributed more to biogeochemical cycling of carbon. FL and PA bacterial communities exhibited distinct co-occurrence pattern across different seasons. In the FL network, Methylotenera and Methylophilaceae were identified as keystone taxa, while Burkholderiaceae and the hgcI clade were keystone taxa in the PA network. The PA bacterial community appeared to possess greater stability in the face of environmental change than did FL counterparts. These results broaden our knowledge of the driving factors, co-occurrence patterns, and assembly processes in FL and PA bacterial communities in eutrophic ecosystems and provide improved insight into the underlying mechanisms responsible for these results.}, }
@article {pmid36180800, year = {2022}, author = {Uroosa,  and Kazmi, SSUH and Rahman, MS and Xu, H}, title = {Can functional units of periphytic protozoan communities be used to evaluate the effects of harmful algal blooms on ecological quality in marine ecosystems?.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36180800}, issn = {1614-7499}, abstract = {Based on biological traits, the ecological quality status under the pressure of two harmful algal bloom (HAB) species was evaluated using functional units (FUs) of periphytic protozoan communities. Five treatments with different concentrations of Alexandrium tamarense and Gymnodinium catenatum, i.e., 10[0], 10[2], 10[3], 10[4], and 10[5] cells ml[-1], were used. A total of 20 FUs were identified from 25 test protozoan species. Among these FUs, vagile algivores with large sizes showed a decreasing trend (i.e., in diversity and abundance) with increasing concentrations of algae, while vagile bacterivores and non-selectives with small sizes dominated at concentrations of 10[4] cells ml[-1] of both algal species. Ellipse tests on pair-wise functional distinctness indices revealed a significant departure of test protozoan communities from an expected functional distinctness breadth when algal concentrations exceeded 10[4] cells ml[-1]. Based on these findings, it was concluded that FUs of periphytic protozoa may be a useful tool for evaluating the effects of HABs on ecological quality status in marine ecosystems.}, }
@article {pmid36180621, year = {2022}, author = {Signorini, M and Midolo, G and Cesco, S and Mimmo, T and Borruso, L}, title = {A Matter of Metals: Copper but Not Cadmium Affects the Microbial Alpha-Diversity of Soils and Sediments - a Meta-analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36180621}, issn = {1432-184X}, abstract = {Heavy metal (HM) accumulation in soil affects plants and soil fauna, yet the effect on microbial alpha-diversity remains unclear, mainly due to the absence of dedicated research synthesis (e.g. meta-analysis). Here, we report the first meta-analysis of the response of soil microbial alpha-diversity to the experimental addition of cadmium (Cd) and copper (Cu). We considered studies conducted between 2013 and 2022 using DNA metabarcoding of bacterial and fungal communities to overcome limitations of other cultivation- and electrophoresis-based techniques. Fungi were discarded due to the limited study number (i.e. 6 studies). Bacterial studies resulted in 66 independent experiments reported in 32 primary papers from four continents. We found a negative dose-dependent response for Cu but not for Cd for bacterial alpha-diversity in the environments, only for Cu additions exceeding 29.6 mg kg[-1] (first loss of - 0.06% at 30 mg kg[-1]). The maximal loss of bacterial alpha-diversity registered was 13.89% at 3837 mg kg[-1]. Our results first highlight that bacterial communities behave differently to soil pollution depending on the metal. Secondly, our study suggests that even extreme doses of Cu do not cause a dramatic loss in alpha-diversity, highlighting how the behaviour of bacterial communities diverges from soil macro-organisms.}, }
@article {pmid36179845, year = {2023}, author = {Dziurzynski, M and Gorecki, A and Pawlowska, J and Istel, L and Decewicz, P and Golec, P and Styczynski, M and Poszytek, K and Rokowska, A and Gorniak, D and Dziewit, L}, title = {Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) - Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159072}, doi = {10.1016/j.scitotenv.2022.159072}, pmid = {36179845}, issn = {1879-1026}, mesh = {*Bioprospecting ; Soil Microbiology ; *Permafrost ; Ecosystem ; Biodiversity ; Svalbard ; Bacteria/genetics ; Soil ; Fungi/genetics ; Arctic Regions ; }, abstract = {Arctic soils are constantly subjected to extreme environmental conditions such as low humidity, strong winds, high salinity, freeze-thaw cycles, UV exposition, and low nutrient availability, therefore, they have developed unique microbial ecosystems. These environments provide excellent opportunities to study microbial ecology and evolution within pristine (i.e. with limited anthropogenic influence) regions since the High Arctic is still considered one of the wildest and least explored environments on the planet. This environment is also of interest for the screening and recovery of unique microbial strains suitable for various biotechnological applications. In this study, a combination of culture-depended and culture-independent approaches was used to determine the cultivation bias in studies of the diversity of cold-active microorganisms. Cultivation bias is a reduction in recovered diversity, introduced when applying a classical culturing technique. Six different soil types, collected in the vicinity of the Polish Polar Station Hornsund (Spitsbergen, Norway), were tested. It was revealed that the used media allowed recovery of only 6.37 % of bacterial and 20 % of fungal genera when compared with a culture-independent approach. Moreover, it was shown that a combination of R2A and Marine Broth media recovered as much as 93.6 % of all cultivable bacterial genera detected in this study. Based on these results, a novel protocol for genome-guided bioprospecting, combining a culture-dependent approach, metabarcoding, next-generation sequencing, and genomic data reuse was developed. With this methodology, 14 psychrotolerant, multi-metal-resistant strains, including the highly promising Rhodococcus spp., were obtained. These strains, besides increased metal tolerance, have a petroleum hydrocarbon utilization capacity, and thus may be good candidates for future bioremediation technologies, also suited to permanently cold regions.}, }
@article {pmid36179842, year = {2023}, author = {Romans-Casas, M and Perona-Vico, E and Dessì, P and Bañeras, L and Balaguer, MD and Puig, S}, title = {Boosting ethanol production rates from carbon dioxide in MES cells under optimal solventogenic conditions.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159124}, doi = {10.1016/j.scitotenv.2022.159124}, pmid = {36179842}, issn = {1879-1026}, mesh = {*Carbon Dioxide ; *Ethanol ; Biofuels ; Electricity ; Acetic Acid ; Electrodes ; }, abstract = {Microbial Electrosynthesis (MES) has been widely applied for acetic acid (HA) production from CO2 and electricity. Ethanol (EtOH) has a higher market value than HA, and wide application in industry and as a biofuel. However, it has only been obtained sporadically and at low concentrations, probably due to sub-optimal operating conditions. This study aimed at enhancing EtOH productivity in MES cells by jointly optimising key operation parameters, including pH, H2 and CO2 partial pressure (pH2 and pCO2), and HA concentration, to promote solventogenesis. Two H-type cells were operated in fed-batch mode at -0.8 V vs. SHE with CO2 as the sole carbon source. A mixed culture, enriched with Clostridium ljungdahlii was used as the biocatalyst. The combination of low pH (<4.5) and pCO2 (<0.3 atm), along with high HA concentration (about 6 g L[-1]) and pH2 (>3 atm), were mandatory conditions for maintaining an efficient solventogenic culture, dominated by Clostridium sp., capable of high-rate EtOH production. The maximum EtOH production rate was 10.95 g m[-2] d[-1], and a concentration of 5.28 g L[-1] was achieved. Up to 30 % of the electrons and 15.2 % of the carbon provided were directed towards EtOH production, and 28.1 kWh were required for the synthesis of 1 kg of EtOH from CO2. These results highlight that strict conditions are required for a continuous, reliable, EtOH production in MES cells. Future investigation should focus on improving cell configuration to achieve EtOH production at higher current densities while minimizing the electric energy input.}, }
@article {pmid36178538, year = {2022}, author = {Ishigami, K and Jang, S and Itoh, H and Kikuchi, Y}, title = {Obligate Gut Symbiotic Association with Caballeronia in the Mulberry Seed Bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36178538}, issn = {1432-184X}, abstract = {Many insects possess symbiotic bacteria in their bodies, and microbial symbionts play pivotal metabolic roles for their hosts. Members of the heteropteran superfamilies Coreoidea and Lygaeoidea stinkbugs harbor symbionts of the genus Caballeronia in their intestinal tracts. Compared with symbiotic associations in Coreoidea, those in Lygaeoidea insects are still less understood. Here, we investigated a symbiotic relationship involving the mulberry seed bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae) using histological observations, cultivation of the symbiont, 16S rRNA gene amplicon sequencing, and infection testing of cultured symbionts. Histological observations and cultivation revealed that P. dissimilis harbors Caballeronia symbionts in the crypts of its posterior midgut. 16S rRNA gene amplicon sequencing of field-collected P. dissimilis confirmed that the genus Caballeronia is dominant in the midgut of natural populations of P. dissimilis. In addition, PCR diagnostics showed that the eggs were free of symbiotic bacteria, and hatchlings horizontally acquired the symbionts from ambient soil. Infection and rearing experiments revealed that symbiont-free aposymbiotic individuals had abnormal body color, small body size, and, strikingly, a low survival rate, wherein no individuals reached adulthood, indicating an obligate cooperative mutualism between the mulberry seed bug and Caballeronia symbionts.}, }
@article {pmid36175476, year = {2022}, author = {Gan, L and Zheng, J and Xu, WH and Lin, J and Liu, J and Zhang, Y and Wu, Z and Lv, Z and Jia, Y and Guo, Q and Chen, S and Liu, C and Defoirdt, T and Qin, Q and Liu, Y}, title = {Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16296}, pmid = {36175476}, issn = {2045-2322}, mesh = {Animals ; Humans ; Lithium ; Muscle Fibers, Skeletal ; *Penaeidae ; Seafood ; *Vibrio ; *Vibrio cholerae ; }, abstract = {The muscle of aquatic crustaceans is perishable and susceptible to environmental contamination. Vibrio harveyi is a widely occurring pathogen in aquatic animals. Here, bath treatment with a virulent V. harveyi strain (which was added directly in the rearing water to imitate environmental contamination) isolated from the muscle of the whiteleg shrimp, Litopenaeus vannamei, caused the muscle of Li. vannamei to display a whitish-opaque appearance due to microscopic changes including muscle lysis, muscle fiber damage and microbial colonization. When administered orally by incorporating this isolate in feed (which is an imitation of infection via natural route), rather than direct invasion followed by colonization in the muscle, this isolate indirectly stimulated severe muscle necrosis in Li. vannamei via steering the enrichment of two important (human) pathogens, V. cholerae and V. vulnificus, and one environmental bacterium Pseudomonas oleovorans, based on the meta-taxonomic analyses. In addition to the scientifically proven viral diseases, our research proved that bacterial agents are also capable of causing muscle spoilage in crustaceans via changing the microbial composition, and that the crustaceans might be exploited as the wide-spectrum sensitive bio-detector to indicate the extent of microbial contamination.}, }
@article {pmid36173731, year = {2022}, 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 = {Legionella bononiensis sp. nov., isolated from a hotel water distribution system in northern Italy.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.005512}, pmid = {36173731}, issn = {1466-5034}, mesh = {Agar ; Bacterial Typing Techniques ; Base Composition ; Catalase/genetics ; Charcoal ; Ciprofloxacin ; Cycloheximide ; Cysteine/genetics ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Gelatinases/genetics ; Glycine/genetics ; Hippurates ; *Legionella ; Nucleotides ; Phylogeny ; Polymyxin B/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Vancomycin ; Water ; }, abstract = {Legionella-like isolates, strains 27fs60, 30fs61 and 30cs62[T], were isolated from a hotel water distribution system in the Emilia-Romagna region, Italy. Isolates were Gram- and Ziehl Neelsen-stain-negative, rod-shaped, with transitory flagella presence and able to grow at 32-37 °C (with an optimum at 32 °C) on buffered charcoal-yeast extract agar with l-cysteine, glycine-vancomycin-polymyxin B-cycloheximide agar and Wadowsky-Yee medium agar. The strains showed positive reactions for oxidase, hippurate and gelatinase and a weakly positive reaction for catalase. Based on the EUCAST cut-off, strain 30cs62[T] was resistant to ciprofloxacin (5 mg l[-1]). The mip and rpoB gene sequences of the three strains showed close matches to those of Legionella quateirensis ATCC 49507[T] with similarity values of 98.2 and 94.5 %, respectively. Whole genome sequencing of the three strains was performed, resulting in G+C contents of 39.0, 39.1 and 39.0 mol%, respectively. The identity percentage measured by average nucleotide identity between the three strains and their respective closest strains were: 91.32 % L. quateirensis NCTC 12376[T], 91.45 % L. quateirensis ATCC 49507[T] and 91.45 % L. quateirensis ATCC 49507[T], respectively. The digital DNA-DNA hybridization analysis demonstrated how the isolates were separated from the most related phylogenetic Legionella species (L. quateirensis ATCC 49507[T], ≤40.10 % DNA-DNA relatedness). The concatenated phylogenetic tree based on 16S rRNA, mip, rpoB and rnpB genes, shows a close relationship with L. quateirensis ATCC 49507[T]. The results obtained confirm the status of an independent species. The name proposed for this species is Legionella bononiensis sp. nov. with 30cs62[T] (=ATCC TSD-262[T]=DSM 112526[T]) as the type strain.}, }
@article {pmid36173132, year = {2022}, author = {Izcue, J and Palacios-García, I and Rojas Traverso, F and Koller, M and Parada, FJ}, title = {Perspectives on Inequity and Health Disparities in Chile and Their Relationship to Microbial Ecology.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0149621}, pmid = {36173132}, issn = {2379-5077}, abstract = {Among countries in the Organisation for Economic Cooperation and Development (OECD), Chile stands out as having important inequalities in income distribution, dietary quality, access to urban green spaces, and health outcomes. People in lower socioeconomic groups consistently show higher rates of noncommunicable chronic diseases and are being hit the hardest by the COVID-19 pandemic. These chronic conditions are increasingly considered to be shaped, or affected by, the human gut microbiome. Moreover, inequity as an overarching concept might also be associated with microbial patterns and if so, this may represent a novel pathway through which to address health and other disparities. Focusing on the case of Chile, our goal is to contribute to a critical discussion and motivate researchers and policymakers to consider the role of the microbiome in social equity in future endeavors.}, }
@article {pmid36172557, year = {2022}, author = {Li, J and Yu, X and Shan, Q and Shi, Z and Li, J and Zhao, X and Chang, C and Yu, J}, title = {Integrated volatile metabolomic and transcriptomic analysis provides insights into the regulation of floral scents between two contrasting varieties of Lonicera japonica.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {989036}, pmid = {36172557}, issn = {1664-462X}, abstract = {Lonicera japonica Thunb., belonging to the Caprifoliaceae family, is an important traditional Chinese medicinal plant. The L. japonica flower (LJF) is widely used in medicine, cosmetics, drinks, and food due to its medicinal and sweet-smelling properties. Considerable efforts have been devoted to investigating the pharmacological activities of LJF; however, the regulatory mechanism of the floral scents remains unknown. We previously selected and bred an elite variety of L. japonica var. chinensis Thunb. called 'Yujin2', which has a strong aroma and is used in functional drinks and cosmetics. In order to reveal the regulatory mechanism of the floral scents of LJF, volatile metabolomic and transcriptomic analyses of the LJF at the silver flowering stage of 'Yujin2' (strong aroma) and 'Fengjin1' (bland odor) were performed. Our results revealed that a total of 153 metabolites and 9,523 genes were differentially regulated in LJF between 'Yujin2' and 'Fengjin1'. The integrated analysis of omics data indicated that the biosynthetic pathways of terpenoids (i.e., monoterpenoids, including geraniol and alpha-terpineol; sesquiterpenoids, including farnesol, farnesal, and alpha-farnesene; triterpenoid squalene), tryptophan and its derivatives (methyl anthranilate), and fatty acid derivatives, were major contributors to the stronger aroma of 'Yujin2' compared to 'Fengjin1'. Moreover, several genes involved in the terpenoid biosynthetic pathway were characterized using quantitative real-time PCR. These results provide insights into the metabolic mechanisms and molecular basis of floral scents in LJF, enabling future screening of genes related to the floral scent regulation, such as alpha-terpineol synthase, geranylgeranyl diphosphate synthase, farnesyl pyrophosphate synthase, anthranilate synthase, as well as transcription factors such as MYB, WRKY, and LFY. The knowledge from this study will facilitate the breeding of quality-improved and more fragrant variety of L. japonica for ornamental purpose and functional beverages and cosmetics.}, }
@article {pmid36171563, year = {2022}, author = {Junghare, M and Frey, J and Naji, KM and Spiteller, D and Vaaje-Kolstad, G and Schink, B}, title = {Isophthalate:coenzyme A ligase initiates anaerobic degradation of xenobiotic isophthalate.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {227}, pmid = {36171563}, issn = {1471-2180}, mesh = {Acetyl Coenzyme A/metabolism ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Anaerobiosis ; Base Composition ; Benzoates/metabolism ; Carbon ; Carcinogens ; Coenzyme A/metabolism ; Coenzyme A Ligases ; *Diphosphates ; *Environmental Pollutants ; Escherichia coli/metabolism ; Glutarates ; Hydroxybenzoates ; Mutagens ; Oxygen ; Phenylacetates/metabolism ; Phthalic Acids ; Phylogeny ; Plastics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Sulfur ; Xenobiotics ; }, abstract = {BACKGROUND: Environmental contamination from synthetic plastics and their additives is a widespread problem. Phthalate esters are a class of refractory synthetic organic compounds which are widely used in plastics, coatings, and for several industrial applications such as packaging, pharmaceuticals, and/or paints. They are released into the environment during production, use and disposal, and some of them are potential mutagens and carcinogens. Isophthalate (1,3-benzenedicarboxylic acid) is a synthetic chemical that is globally produced at a million-ton scale for industrial applications and is considered a priority pollutant. Here we describe the biochemical characterization of an enzyme involved in anaerobic degradation of isophthalate by the syntrophically fermenting bacterium Syntrophorhabdus aromaticivorans strain UI that activate isophthalate to isophthalyl-CoA followed by its decarboxylation to benzoyl-CoA.<br><br>RESULTS: Isophthalate:Coenzyme A ligase (IPCL, AMP-forming) that activates isophthalate to isophthalyl-CoA was heterologously expressed in E. coli (49.6&#x2009;kDa) for biochemical characterization. IPCL is homologous to phenylacetate-CoA ligase that belongs to the family of ligases that form carbon-sulfur bonds. In the presence of coenzyme A, Mg[2+] and ATP, IPCL converts isophthalate to isophthalyl-CoA, AMP and pyrophosphate (PPi). The enzyme was specifically induced after anaerobic growth of S. aromaticivorans in a medium containing isophthalate as the sole carbon source. Therefore, IPCL exhibited high substrate specificity and affinity towards isophthalate. Only substrates that are structurally related to isophthalate, such as glutarate and 3-hydroxybenzoate, could be partially converted to the respective coenzyme A esters. Notably, no activity could be measured with substrates such as phthalate, terephthalate&#xa0;and benzoate. Acetyl-CoA or succinyl-CoA did not serve as CoA donors. The enzyme has a theoretical pI of 6.8 and exhibited optimal activity between&#xa0;pH 7.0 to 7.5. The optimal temperature was between 25&#x2009;&#xb0;C and 37&#x2009;&#xb0;C. Denaturation temperature (Tm) of IPCL was found to be at about&#xa0;63&#x2009;&#xb0;C. The apparent KM values for isophthalate, CoA, and ATP were 409&#x2009;&#x3bc;M, 642&#x2009;&#x3bc;M, and 3580&#x2009;&#x3bc;M, respectively. Although S. aromaticivorans is a strictly anaerobic bacterium, the enzyme was found to be&#xa0;oxygen-insensitive and catalysed isophthalyl-CoA formation under both anoxic and oxic conditions.<br><br>CONCLUSION: We have successfully cloned&#xa0;the ipcl gene, expressed and characterized the corresponding IPCL&#xa0;enzyme, which plays a key role in isophthalate activation that initiates its activation and&#xa0;further degradation by S. aromaticivorans. Its biochemical characterization represents an important step in the elucidation of the complete degradation pathway of isophthalate.}, }
@article {pmid36170274, year = {2022}, author = {Mohammed, A and Hu, J and Murugesan, R and Cheng, HW}, title = {Effects of a synbiotic as an antibiotic alternative on behavior, production performance, cecal microbial ecology, and jejunal histomorphology of broiler chickens under heat stress.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0274179}, pmid = {36170274}, issn = {1932-6203}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Diet/veterinary ; Dietary Supplements ; Escherichia coli ; *Escherichia coli Infections ; *Heat Stress Disorders ; Heat-Shock Response ; Male ; *Synbiotics ; }, abstract = {The aim of this study was to examine if synbiotics present similar efficiency to a common antibiotic used in poultry production under heat stress (HS) conditions. Two hundred and forty-one-day-old male Ross 708 broiler chicks were distributed among 3 treatments with 8 pens per treatment of 80 birds each for a 42-day trial. From day 15, birds were heat stressed (32°C for 9 h daily, HS) and fed the basal diet (CONT), the basal diet mixed with an antibiotic (Bactiracin Methylene Disalicylate) (0.05 g/kg of feed, BMD) or a synbiotic (0.5 g/kg of feed, SYN). The treatment effects on bird behavior, production performance, jejunal histomorphology, and cecal microbial ecology were examined. Behavioral observation was recorded by using instantaneous scan sampling technique. Production parameters were measured on day 14, 28, and 42. Cecal microbial populations of Escherichia coli and Lactobacilli and jejunal histomorphological parameters were measured at day 42. The results showed that, SYN birds exhibited more feeding and preening but less drinking and panting behaviors compared with both BMD and CONT birds (P < 0.05). The SYN birds also had higher body weight (BW) at both day 28 and 42 compared to CONT birds (P < 0.05). At the end of the experiment, the counts of Escherichia coli of SYN birds were at the similar levels of BMD but were lower than that of CONT birds (P < 0.05); while there were no treatment effects on the populations of Lactobacilli (P > 0.05). In addition, SYN birds had greater villus height compared with both CONT and BMD birds (P < 0.05). These findings suggest that the dietary synbiotic supplement has significant performance and welfare benefits, with the potential to be used as an alternative to antibiotics for poultry meat production, especially during hot seasons.}, }
@article {pmid36167684, year = {2022}, author = {Seong, HJ and Roux, S and Hwang, CY and Sul, WJ}, title = {Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {157}, pmid = {36167684}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics ; DNA ; DNA Methylation/genetics ; Metagenome/genetics ; Metagenomics ; Methyltransferases/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.<br><br>RESULTS: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.<br><br>CONCLUSIONS: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.}, }
@article {pmid36166154, year = {2022}, author = {Duarte, IO and Hissa, DC and Quintela, BCSF and Rabelo, MC and Oliveira, FADS and Lima, NCB and Melo, VMM}, title = {Genomic Analysis of Surfactant-Producing Bacillus vallismortis TIM68: First Glimpse at Species Pangenome and Prediction of New Plipastatin-Like Lipopeptide.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {36166154}, issn = {1559-0291}, abstract = {Surfactants are applied in several industrial processes when the modification of interface activity and the stability of colloidal systems are required. Lipopeptides are a class of microbial biosurfactants produced by species of the Bacillus genus. The present study aimed at assembling and analyzing the genome of a new Bacillus vallismortis strain, TIM68, that was shown to produce surfactant lipopeptides. The draft genome was also screened for common virulence factors and antibiotics resistance genes to investigate the strain biosafety. Comparative genomics analyses, i.e., synteny, average nucleotide identity (ANI), and pangenome, were also carried out using strain TIM68 and publicly available B. vallismortis complete and partial genomes. Three peptide synthetase operons were found in TIM68 genome, and they were surfactin A, mojavensin, and a novel plipastatin-like lipopeptide named vallisin. No virulence factors that render pathogenicity to the strain have been identified, but a region of prophage, that may contain unknown pathogenic factors, has been predicted. The pangenome of the species was characterized as closed, with 57% of genes integrating the core genome. The results obtained here on the genetic potential of TIM68 strain should contribute to its exploration in biotechnological applications.}, }
@article {pmid36166070, year = {2022}, author = {Alcantara, DMC and Ikeda, P and Souza, CS and de Mello, VVC and Torres, JM and Lourenço, EC and Bassini-Silva, R and Herrera, HM and Machado, RZ and Barros-Battesti, DM and Graciolli, G and André, MR}, title = {Multilayer Networks Assisting to Untangle Direct and Indirect Pathogen Transmission in Bats.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36166070}, issn = {1432-184X}, abstract = {The importance of species that connect the different types of interactions is becoming increasingly recognized, and this role may be related to specific attributes of these species. Multilayer networks have two or more layers, which represent different types of interactions, for example, between different parasites and hosts that are nonetheless connected. The understanding of the ecological relationship between bats, ectoparasites, and vector-borne bacteria could shed some light on the complex transmission cycles of these pathogens. In this study, we investigated a multilayer network in Brazil formed by interactions between bat-bacteria, bat-ectoparasite, and ectoparasite-bacteria, and asked how these interactions overlap considering different groups and transmission modes. The multilayer network was composed of 31 nodes (12 bat species, 14 ectoparasite species, and five bacteria genera) and 334 links, distributed over three layers. The multilayer network has low modularity and shows a core-periphery organization, that is, composed of a few generalist species with many interactions and many specialist species participating in few interactions in the multilayer network. The three layers were needed to accurately describe the multilayer structure, while aggregation leads to loss of information. Our findings also demonstrated that the multilayer network is influenced by a specific set of species that can easily be connected to the behavior, life cycle, and type of existing interactions of these species. Four bat species (Artibeus lituratus, A. planirostris, Phyllostomus discolor, and Platyrrhinus lineatus), one ectoparasite species (Steatonyssus) and three bacteria genera (Ehrlichia, hemotropic Mycoplasma and Neorickettsia) are the most important species for the multilayer network structure. Finally, our study brings an ecological perspective under a multilayer network approach on the interactions between bats, ectoparasites, and pathogens. By using a multilayer approach (different types of interactions), it was possible to better understand these different ecological interactions and how they affect each other, advancing our knowledge on the role of bats and ectoparasites as potential pathogen vectors and reservoirs, as well as the modes of transmission of these pathogens.}, }
@article {pmid36164984, year = {2022}, author = {Li, HB and Xu, ML and Xu, XD and Tang, YY and Jiang, HL and Li, L and Xia, WJ and Cui, N and Bai, J and Dai, ZM and Han, B and Li, Y and Peng, B and Dong, YY and Aryal, S and Manandhar, I and Eladawi, MA and Shukla, R and Kang, YM and Joe, B and Yang, T}, title = {Faecalibacterium prausnitzii Attenuates CKD via Butyrate-Renal GPR43 Axis.}, journal = {Circulation research}, volume = {131}, number = {9}, pages = {e120-e134}, pmid = {36164984}, issn = {1524-4571}, support = {R21 AG079357/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Butyrates/pharmacology/therapeutic use ; Disease Models, Animal ; *Faecalibacterium prausnitzii ; Inflammation ; Kidney/physiology ; Receptors, G-Protein-Coupled/genetics ; *Renal Insufficiency, Chronic ; }, abstract = {BACKGROUND: Despite available clinical management strategies, chronic kidney disease (CKD) is associated with severe morbidity and mortality worldwide, which beckons new solutions. Host-microbial interactions with a depletion of Faecalibacterium prausnitzii in CKD are reported. However, the mechanisms about if and how F prausnitzii can be used as a probiotic to treat CKD remains unknown.<br><br>METHODS: We evaluated the microbial compositions in 2 independent CKD populations for any potential probiotic. Next, we investigated if supplementation of such probiotic in a mouse CKD model can restore gut-renal homeostasis as monitored by its effects on suppression on renal inflammation, improvement in gut permeability and renal function. Last, we investigated the molecular mechanisms underlying the probiotic-induced beneficial outcomes.<br><br>RESULTS: We observed significant depletion of Faecalibacterium in the patients with CKD in both Western (n=283) and Eastern populations (n=75). Supplementation of F prausnitzii to CKD mice reduced renal dysfunction, renal inflammation, and lowered the serum levels of various uremic toxins. These are coupled with improved gut microbial ecology and intestinal integrity. Moreover, we demonstrated that the beneficial effects in kidney induced by F prausnitzii-derived butyrate were through the GPR (G protein-coupled receptor)-43.<br><br>CONCLUSIONS: Using a mouse CKD model, we uncovered a novel beneficial role of F prausnitzii in the restoration of renal function in CKD, which is, at least in part, attributed to the butyrate-mediated GPR-43 signaling in the kidney. Our study provides the necessary foundation to harness the therapeutic potential of F prausnitzii for ameliorating CKD.}, }
@article {pmid36163700, year = {2022}, author = {Orsi, WD}, title = {Quantitative microbial ecology: Future challenges and opportunities.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16204}, pmid = {36163700}, issn = {1462-2920}, }
@article {pmid36161873, year = {2022}, author = {Orner, KD and Deleu, E and Rabaey, K and Nelson, KL}, title = {Accelerating urea hydrolysis in fresh urine by modifying operating conditions of a sequencing batch reactor.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/09593330.2022.2129456}, pmid = {36161873}, issn = {1479-487X}, abstract = {A number of existing and emerging technologies can recover nitrogen from urine. A preliminary step in many nitrogen recovery processes is hydrolyzing urea to ammonium, a biologically-mediated process that can take days to weeks without intervention. The ability to achieve urea hydrolysis quickly and reliably would increase the feasibility of decentralized nitrogen recovery, especially where space and treatment time are constrained. The goal of this research was to determine whether urea hydrolysis could be accelerated by providing an inoculum containing microorganisms likely to have urease activity (feces or soil), providing a carrier to support attached growth (plastic carriers, granular activated carbon, or no carrier), and modifying the hydraulic retention time (HRT; 1.3, 2, and 4 days) and feeding frequency (Δt = 4, 24 h). Inoculated reactors achieved significantly more urea hydrolysis, and reactors inoculated with soil were able to sustain higher urea hydrolysis rates over time than those inoculated with feces. The mean zero-order rate constants (mM/hr) for reactors with a soil inoculum (15.1) were about three times higher than that of reactors with an inoculum of feces (4.9). A reactor with GAC and an inoculum of soil fed daily with fresh urine achieved greater than 90% hydrolysis with an HRT of 2 days; results suggest the HRT could be reduced to 16 h without reducing performance. No significant benefit was provided by increasing the frequency of feedings for the same HRT, likely because urease enzymes were saturated and operating at maximum hydrolysis rates during most of the reaction period.}, }
@article {pmid36161499, year = {2022}, author = {Alonso-Reyes, DG and Galván, FS and Irazoqui, JM and Amadio, A and Tschoeke, D and Thompson, F and Albarracín, VH and Farias, ME}, title = {Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36161499}, issn = {1432-184X}, abstract = {Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.}, }
@article {pmid36160194, year = {2022}, author = {Guajardo-Leiva, S and Alarcón, J and Gutzwiller, F and Gallardo-Cerda, J and Acuña-Rodríguez, IS and Molina-Montenegro, M and Crandall, KA and Pérez-Losada, M and Castro-Nallar, E}, title = {Source and acquisition of rhizosphere microbes in Antarctic vascular plants.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {916210}, pmid = {36160194}, issn = {1664-302X}, abstract = {Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.}, }
@article {pmid36159733, year = {2022}, author = {Van de Walle, A and Torfs, E and Gaublomme, D and Rabaey, K}, title = {In silico assessment of household level closed water cycles: Towards extreme decentralization.}, journal = {Environmental science and ecotechnology}, volume = {10}, number = {}, pages = {100148}, pmid = {36159733}, issn = {2666-4984}, abstract = {Water management in most of the developed world is currently practiced in a highly centralized manner, leading to major infrastructure and energy costs to transport water. To decrease the impacts of water scarcity and climate change, the decentralization of water can increase local robustness. In extremis, decentralization can involve building or house level water supply and treatment. Here, we constructed a MATLAB/Simulink model for two decentralized water management configurations at the household level, assuming the socio-environmental setting of Flanders, Belgium. Independence from the potable water grid and sewer system was pursued through rainwater harvesting, reuse of wastewater streams fit-for-purpose, and discharge via infiltration. The mass balance for water was calculated over the system boundaries showing high potential for independence from the grid with a reasonable treatment train and storage options. Next, the risk of contaminant accumulation within the circular system was assessed, showing a key limitation on decentralized system performance necessitating a system purge. Up to 59% of system rainwater usage was due to the replacement of this purge. Employing treatment units with high (95%) contaminant rejection efficiencies eliminated contaminant accumulation issues. The raw model output was quantitatively assessed by constructing four newly proposed key performance indicators (KPIs), quantifying system independence, circularity, drought tolerance and local water body recharge, which allowed for facilitated system comparison and communication to stakeholders. A sensitivity analysis was performed in which the effect of input parameter variability and uncertainty on system performance was quantified. The sensitivity analysis showed the importance of water recovery and contaminant removal efficiencies of the applied treatment technologies on system performance when contaminant accumulation in the system forms an issue. In systems not severely affected by pollutant accumulation, parameters such as inhabitant number and roof surface had the largest effect. As a whole, this work shows the potential of extreme decentralization of water systems and addresses the obstacle towards implementation formed by the accumulation of contaminants due to system circularity. Additionally, this study provides a framework for operational and technological decision support of decentralized household-scale water systems and, by extension, for future water policy-making.}, }
@article {pmid36158753, year = {2022}, author = {Ostermeyer, P and Van Landuyt, J and Bonin, L and Folens, K and Williamson, A and Hennebel, T and Rabaey, K}, title = {High rate production of concentrated sulfides from metal bearing wastewater in an expanded bed hydrogenotrophic sulfate reducing bioreactor.}, journal = {Environmental science and ecotechnology}, volume = {11}, number = {}, pages = {100173}, pmid = {36158753}, issn = {2666-4984}, abstract = {Metallurgical wastewaters contain high concentrations of sulfate, up to 15 g L[-1]. Sulfate-reducing bioreactors are employed to treat these wastewaters, reducing sulfates to sulfides which subsequently co-precipitate metals. Sulfate loading and reduction rates are typically restricted by the total H2S concentration. Sulfide stripping, sulfide precipitation and dilution are the main strategies employed to minimize inhibition by H2S, but can be adversely compromised by suboptimal sulfate reduction, clogging and additional energy costs. Here, metallurgical wastewater was treated for over 250 days using two hydrogenotrophic granular activated carbon expanded bed bioreactors without additional removal of sulfides. H2S toxicity was minimized by operating at pH 8 ± 0.15, resulting in an average sulfate removal of 7.08 ± 0.08 g L[-1], sulfide concentrations of 2.1 ± 0.2 g L[-1] and peaks up to 2.3 ± 0.2 g L[-1]. A sulfate reduction rate of 20.6 ± 0.9 g L[-1] d[-1] was achieved, with maxima up to 27.2 g L[-1] d[-1], which is among the highest reported considering a literature review of 39 studies. The rates reported here are 6-8 times higher than those reported for other reactors without active sulfide removal and the only reported for expanded bed sulfate-reducing bioreactors using H2. By increasing the influent sulfate concentration and maintaining high sulfide concentrations, sulfate reducers were promoted while fermenters and methanogens were suppressed. Industrial wastewater containing 4.4 g L[-1] sulfate, 0.036 g L[-1] nitrate and various metals (As, Fe, Tl, Zn, Ni, Sb, Co and Cd) was successfully treated with all metal(loid)s, nitrates and sulfates removed below discharge limits.}, }
@article {pmid36154441, year = {2022}, author = {Zhang, S and Yang, Q and Defoirdt, T}, title = {Halogenated Indoles Decrease the Virulence of Vibrio campbellii in a Gnotobiotic Brine Shrimp Model.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0268922}, pmid = {36154441}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Artemia/microbiology ; Germ-Free Life ; Indoles/pharmacology ; Peptide Hydrolases/pharmacology ; *Vibrio ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Indole signaling is viewed as a potential target for antivirulence therapy against antibiotic-resistant pathogens because of its link with the production of virulence factors. This study examined the antimicrobial and antivirulence properties of 44 indoles toward Vibrio campbellii. Based on the results, 17 halogenated indole analogues were selected, as they significantly improved the survival of brine shrimp larvae challenged with V. campbellii. Specifically, 6-bromoindole, 7-bromoindole, 4-fluoroindole, 5-iodoindole, and 7-iodoindole showed a high protective effect, improving the survival of brine shrimp to over 80% even at a low concentration of 10 μM. To explore the impact of selected indole analogues on bacterial virulence phenotypes, swimming motility, biofilm formation, protease activity, and hemolytic activity of V. campbellii were determined. The results showed that all of the 17 selected indole analogues decreased swimming motility at both 10 μM and 100 μM. Most of the indole analogues decreased biofilm formation at a concentration of 100 μM. In contrast, only a slightly decreased protease activity and no effect on hemolytic activity were observed at both concentrations. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system, and the results demonstrate the potential of these compounds in applications aiming at the protection of shrimp from vibriosis, a major disease in aquaculture. IMPORTANCE Bacterial diseases are a major problem in the aquaculture industry. In order to counter this problem, farmers have been using antibiotics, and this has led to the evolution and spread of antibiotic resistance. In order for the aquaculture industry to further grow in a sustainable way, novel and sustainable methods to control diseases are needed. We previously reported that indole signaling is a valid target for the development of novel therapies to control disease caused by Vibrio campbellii and related bacteria, which are among the major bacterial pathogens in aquaculture. In the present study, we identified indole analogues that are more potent in protecting brine shrimp (a model organism for shrimp) from V. campbellii. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system.}, }
@article {pmid36153325, year = {2022}, author = {Zhu, H and Xu, L and Luan, G and Zhan, T and Kang, Z and Li, C and Lu, X and Zhang, X and Zhu, Z and Zhang, Y and Li, Y}, title = {A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5608}, pmid = {36153325}, issn = {2041-1723}, mesh = {*Bioelectric Energy Sources ; Bionics ; Hydrogels ; *Microbiota ; Oceans and Seas ; }, abstract = {Marine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.}, }
@article {pmid36152855, year = {2023}, author = {Zhang, X and Shen, M and Wang, C and Gao, M and Wang, L and Jin, Z and Xia, X}, title = {Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii).}, journal = {The Science of the total environment}, volume = {855}, number = {}, pages = {158902}, doi = {10.1016/j.scitotenv.2022.158902}, pmid = {36152855}, issn = {1879-1026}, mesh = {Animals ; *Astacoidea ; *Aluminum/toxicity ; Hemocytes ; Oxidative Stress ; Immunity ; }, abstract = {Aluminum (Al) is an abundant metal that has been classified as a threatening pollutant due to indiscriminate use and anthropogenic activities. This study aimed to evaluate the impacts of Al on crayfish (Procambarus clarkii), including biochemical change, histological alteration, gut microbial community diversification, and immune changes. The bioaccumulation of Al was detected in the hemolymph and intestine of crayfish after Al exposure at different time points. Results showed that Al exposure significantly induced oxidative stress and caused pathohistological changes on intestinal barrier structures in crayfish. It was found that the intestinal microbiota was affected by retained Al and the intestinal community diversity was changed after Al treated in the crayfish. Furthermore, Al exposure affected the immunity in crayfish, by altering the expression of a set of immune-related genes, as well as reducing the phenoloxidase and lysozyme activities. Moreover, Al exposure promoted hemocytes apoptosis and impaired hemophagocytic capacity against Vibro parahamolyticus, resulting in higher mortality of crayfish upon bacterial infection. Taken these results together, we conclude that excessive Al exposure caused adverse effects on multiple biological processes of crayfish and Al pollution is a potential threat to crayfish culture.}, }
@article {pmid36152034, year = {2022}, author = {Weingarten, EA and Jackson, CR}, title = {Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36152034}, issn = {1432-184X}, abstract = {As sea level rise impacts coastal wetlands, saltmarsh will overtake coastal freshwater marsh in many areas, but changes in the sediment microbiome in response to saltwater intrusion are difficult to predict. Coastal freshwater marsh sediment was exposed to ambient, brackish, and saline conditions as well as to elevated nitrate and phosphate to model the combined stresses of saltwater intrusion and coastal eutrophication. Initially, sediment prokaryotic composition was similar to prior studies of freshwater marsh but diverged over time, reflecting the magnitude of increase in saltwater. There was no observed effect of nutrient amendment, potentially ranking seawater intrusion as a higher-importance compositional driver. Although the previously described loss of methanogenic populations and promotion of sulfate reducers in response to saltwater exposure was observed, taxonomic distribution was not similar to typical meso-polyhaline wetlands. Without colonization by marine taxa, such a community may be short-lived naturally, ultimately equilibrating with more common saltmarsh species. However, the recapitulation of salinity concentration by freshwater sediment microbial composition demonstrates the overwhelming nature of saltwater intrusion relative to other drivers like eutrophication.}, }
@article {pmid36151709, year = {2022}, author = {Prosser, JI}, title = {How and why in microbial ecology: An appeal for scientific aims, questions, hypotheses and theories.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {4973-4980}, doi = {10.1111/1462-2920.16221}, pmid = {36151709}, issn = {1462-2920}, mesh = {*Ecology ; *Environmental Microbiology ; }, abstract = {This article precedes a series of articles on the important questions, hypotheses and theories in microbial ecology. It considers why, as scientists, we ask questions and propose hypotheses and what makes them important, good or significant. Emphasis is placed on 'scientific' questions, the need for scientific aims and on possible reasons for, and inadequacy of aim-less studies and question free studies. Current global issues surrounding the climate crisis, pandemics and antibiotic resistance focus attention on science and scientists. They exemplify the urgent need for greater understanding of the interactions between microbes and their biological and physicochemical environments, that is, of microbial ecology. They also provide examples of reaction against science and scientists and highlight why we must be clear regarding what defines (good) science, its power and limitations, and ensure that this is communicated to stakeholders and the general public.}, }
@article {pmid36151339, year = {2022}, author = {Zhou, X and Lee, J and Yun, J and Kim, J and Yang, Y and Kang, H}, title = {Distinct Nitrification Rates and Nitrifiers in Needleleaf and Evergreen Broadleaf Forest Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36151339}, issn = {1432-184X}, abstract = {Research on niche specialization in the microbial communities of ammonia oxidizers is important for assessing the consequences of vegetation shift on nitrogen (N) cycling. In this study, soils were sampled from three tree stands (needleleaf, mixed, and evergreen broadleaf) from the Hannam experimental forest in South Korea in spring (May 2019), summer (August 2019), autumn (November 2019), and winter (January 2020). Quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to measure the abundance and community structure of various nitrifiers: ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) as well as complete ammonia oxidizers (comammox). Nitrification rates and total ammonia oxidizer abundance were significantly higher in needleleaf forest soil than those in other forest stands, and they were lowest in evergreen broadleaf forest soil. Comammox clade B was most abundant in needleleaf and evergreen broadleaf forest soils, while AOA were significantly more abundant in mixed forest soil. The abundances of comammox clade B and AOA were negatively correlated with dissolved organic carbon. Phylogenetic analysis showed that NT-alpha and NS-gamma-2.3.2 were the most abundant AOA lineages in all the samples. The seasonal of AOA, AOB, and comammox varied with the sites, suggesting the need to examine the combinations of environmental factors when considering the effects of seasonal changes in the environment. Overall, the results suggest that potential vegetation shifts in forest ecosystems might affect nitrification activities by regulating the abundance and community structure of ammonia oxidizers.}, }
@article {pmid36150718, year = {2022}, author = {Kritzberg, E and Bååth, E}, title = {Seasonal variation in temperature sensitivity of bacterial growth in a temperate soil and lake.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {10}, pages = {}, pmid = {36150718}, issn = {1574-6941}, mesh = {Bacteria/metabolism ; *Lakes ; Seasons ; *Soil ; Temperature ; Tin/metabolism ; Water/metabolism ; }, abstract = {Faster bacterial biomass turnover is expected in water compared to soil, which would result in more rapid community adaption to changing environmental conditions, including temperature. Bacterial community adaptation for growth is therefore predicted to have larger seasonal amplitudes in lakes than in soil. To test this prediction, we compared the seasonal variation in temperature adaptation of bacterial community growth in a soil and lake in Southern Sweden (Tin situ 0-20°C, mean 10°C) during 1.5 years, based on monthly samplings including two winters and summers. An indicator of community adaptation, minimum temperature for growth (Tmin), was calculated from bacterial growth measurements (Leu incorporation) using the Ratkowsky model. The seasonal variation in Tmin (sinusoidal function, R2 = 0.71) was most pronounced for the lake bacterial community, with an amplitude for Tmin of 3.0°C (-4.5 to -10.5°C) compared to 0.6°C (-7 to -8°C) for the soil. Thus, Tmin in water increased by 0.32°C/degree change of Tin situ. Similar differences were also found when comparing four lakes and soils in the winter and summer (amplitudes 2.9°C and 0.9°C for lakes and soils, respectively). Thus, seasonal variation in temperature adaptation has to be taken into account in lakes, while for soils a constant Tmin can be used.}, }
@article {pmid36150364, year = {2022}, author = {Mitrović, M and Kostešić, E and Marković, T and Selak, L and Hausmann, B and Pjevac, P and Orlić, S}, title = {Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {6}, pages = {126359}, doi = {10.1016/j.syapm.2022.126359}, pmid = {36150364}, issn = {1618-0984}, mesh = {RNA, Ribosomal, 16S/genetics ; Ammonia/metabolism ; Croatia ; Phylogeny ; *Hot Springs/microbiology ; Archaea ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by Hydrogenophilus, Sulfuricurvum, Sulfurovum, Thiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.}, }
@article {pmid36145836, year = {2022}, author = {Vidal, C and González, F and Santander, C and Pérez, R and Gallardo, V and Santos, C and Aponte, H and Ruiz, A and Cornejo, P}, title = {Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {18}, pages = {}, pmid = {36145836}, issn = {2223-7747}, abstract = {Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil-plant-microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.}, }
@article {pmid36145178, year = {2022}, author = {Overbeeke, A and Lang, M and Hausmann, B and Watzka, M and Nikolov, G and Schwarz, J and Kohl, G and De Paepe, K and Eislmayr, K and Decker, T and Richter, A and Berry, D}, title = {Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria.}, journal = {Nutrients}, volume = {14}, number = {18}, pages = {}, pmid = {36145178}, issn = {2072-6643}, support = {741623/ERC_/European Research Council/International ; }, mesh = {Bacteria ; Butyrates/metabolism ; *Dietary Fiber/metabolism ; Homeostasis ; Intestinal Mucosa/metabolism ; *Mucus/metabolism ; }, abstract = {The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders.}, }
@article {pmid36144291, year = {2022}, author = {Kuzyk, SB and Ma, X and Yurkov, V}, title = {Seasonal Dynamics of Lake Winnipeg's Microbial Communities Reveal Aerobic Anoxygenic Phototrophic Populations Coincide with Sunlight Availability.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144291}, issn = {2076-2607}, abstract = {In this first comprehensive study of Lake Winnipeg's microbial communities, limnetic and littoral euphotic zones were examined during each season from 2016 through 2020. Classical cultivation and modern high-throughput sequencing techniques provided quantification and identification of key phototrophic populations, including aerobic anoxygenic phototrophs (AAP). Annual dynamics found total heterotrophs reached 4.23 × 10[6] CFU/g in littoral sands, and 7.69 × 10[4] CFU/mL in summer littoral waters on oligotrophic media, higher counts than for copiotrophic compositions. Limnetic numbers inversely dipped to 4.34 × 10[3] CFU/mL midsummer. Cultured AAP did not follow heterotrophic trends, instead peaking during the spring in both littoral and limnetic waters as 19.1 and 4.7% of total copiotrophs, or 3.9 and 4.9% of oligotrophs, decreasing till autumn each year. Complementary observations came from environmental 16S V4 rRNA gene analysis, as AAP made up 1.49 and 1.02% of the littoral and limnetic sequenced communities in the spring, declining with seasonal progression. Spatial and temporal fluctuations of microbes compared to environmental factors exposed photosynthetic populations to independently and regularly fluctuate in the ecosystem. Oxygenic phototrophic numbers expectantly matched the midsummer peak of Chl a and b, oxygenic photosynthesis related carbon fixation, and water temperature. Independently, AAP particularly colonized spring littoral areas more than limnetic, and directly corresponded to habitat conditions that specifically promoted growth: the requirement of light and organic material.}, }
@article {pmid36143410, year = {2022}, author = {Johnston-Monje, D and Gutiérrez, JP and Becerra Lopez-Lavalle, LA}, title = {Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {36143410}, issn = {2075-1729}, abstract = {A plant's health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant-microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.}, }
@article {pmid36139115, year = {2022}, author = {Qing, J and Zheng, F and Zhi, H and Yaigoub, H and Tirichen, H and Li, Y and Zhao, J and Qiang, Y and Li, Y}, title = {Identification of Unique Genetic Biomarkers of Various Subtypes of Glomerulonephritis Using Machine Learning and Deep Learning.}, journal = {Biomolecules}, volume = {12}, number = {9}, pages = {}, pmid = {36139115}, issn = {2218-273X}, mesh = {Biomarkers/analysis ; *Deep Learning ; *Glomerulonephritis/genetics/metabolism ; Humans ; Kidney Glomerulus/chemistry/metabolism/pathology ; Macrophages/metabolism ; }, abstract = {(1) Objective: Identification of potential genetic biomarkers for various glomerulonephritis (GN) subtypes and discovering the molecular mechanisms of GN. (2) Methods: four microarray datasets of GN were downloaded from Gene Expression Omnibus (GEO) database and merged to obtain the gene expression profiles of eight GN subtypes. Then, differentially expressed immune-related genes (DIRGs) were identified to explore the molecular mechanisms of GN, and single-sample gene set enrichment analysis (ssGSEA) was performed to discover the abnormal inflammation in GN. In addition, a nomogram model was generated using the R package "glmnet", and the calibration curve was plotted to evaluate the predictive power of the nomogram model. Finally, deep learning (DL) based on a multilayer perceptron (MLP) network was performed to explore the characteristic genes for GN. (3) Results: we screened out 274 common up-regulated or down-regulated DIRGs in the glomeruli and tubulointerstitium. These DIRGs are mainly involved in T-cell differentiation, the RAS signaling pathway, and the MAPK signaling pathway. ssGSEA indicates that there is a significant increase in DC (dendritic cells) and macrophages, and a significant decrease in neutrophils and NKT cells in glomeruli, while monocytes and NK cells are increased in tubulointerstitium. A nomogram model was constructed to predict GN based on 7 DIRGs, and 20 DIRGs of each subtype of GN in glomeruli and tubulointerstitium were selected as characteristic genes. (4) Conclusions: this study reveals that the DIRGs are closely related to the pathogenesis of GN and could serve as genetic biomarkers in GN. DL further identified the characteristic genes that are essential to define the pathogenesis of GN and develop targeted therapies for eight GN subtypes.}, }
@article {pmid36138209, year = {2022}, author = {Liu, Q and Zhang, H and Huang, X}, title = {Strong Linkage Between Symbiotic Bacterial Community and Host Age and Morph in a Hemipteran Social Insect.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36138209}, issn = {1432-184X}, abstract = {The relationships between symbionts and insects are complex, and symbionts usually have diverse ecological and evolutionary effects on their hosts. The phloem sap-sucking aphids are good models to study the interactions between insects and symbiotic microorganisms. Although aphids usually exhibit remarkable life cycle complexity, most previous studies on symbiotic diversity sampled only apterous viviparous adult females or very few morphs. In this study, high-throughput 16S rDNA amplicon sequencing was used to assess the symbiotic bacterial communities of eleven morphs or developmental stages of the social aphid Pseudoregma bambucicola. We found there were significant differences in bacterial composition in response to different morphs and developmental stages, and for the first time, we revealed male aphids hosted very different symbiotic composition featured with low abundance of dominant symbionts but high diversity of total symbionts. The relative abundance of Pectobacterium showed relatively stable across different types of samples, while that of Wolbachia fluctuated greatly, indicating the former may have a consistent function in this species and the latter may provide specific function for certain morphs or developmental stages. Our study presents new evidence of complexity of symbiotic associations and indicates strong linkage between symbiotic bacterial community and host age and morph.}, }
@article {pmid36138151, year = {2022}, author = {Simpson, RC and Shanahan, ER and Batten, M and Reijers, ILM and Read, M and Silva, IP and Versluis, JM and Ribeiro, R and Angelatos, AS and Tan, J and Adhikari, C and Menzies, AM and Saw, RPM and Gonzalez, M and Shannon, KF and Spillane, AJ and Velickovic, R and Lazar, AJ and Damania, AV and Mishra, AK and Chelvanambi, M and Banerjee, A and Ajami, NJ and Wargo, JA and Macia, L and Holmes, AJ and Wilmott, JS and Blank, CU and Scolyer, RA and Long, GV}, title = {Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome.}, journal = {Nature medicine}, volume = {28}, number = {11}, pages = {2344-2352}, pmid = {36138151}, issn = {1546-170X}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Prospective Studies ; Immunotherapy/adverse effects ; *Melanoma/therapy ; Diet ; }, abstract = {The gut microbiota shapes the response to immune checkpoint inhibitors (ICIs) in cancer, however dietary and geographic influences have not been well-studied in prospective trials. To address this, we prospectively profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events (irAEs). Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline. Together, these data provide insight into the relevance of native gut microbiota signatures, dietary intake and systemic inflammation in shaping the response to and toxicity from ICIs, prompting the need for further studies in this area.}, }
@article {pmid36135386, year = {2022}, author = {Mason, AR and McKee-Zech, HS and Hoeland, KM and Davis, MC and Campagna, SR and Steadman, DW and DeBruyn, JM}, title = {Body Mass Index (BMI) Impacts Soil Chemical and Microbial Response to Human Decomposition.}, journal = {mSphere}, volume = {7}, number = {5}, pages = {e0032522}, pmid = {36135386}, issn = {2379-5042}, mesh = {Humans ; *Soil/chemistry ; *Soil Microbiology ; Body Mass Index ; Bacteria ; Cadaver ; }, abstract = {Microorganisms are key decomposers of vertebrate mortalities, breaking down body tissues and impacting decomposition progress. During human decomposition, both extrinsic environmental factors and intrinsic cadaver-related factors have the potential to impact microbial decomposers either directly or indirectly via altered physical or chemical conditions. While extrinsic factors (e.g., temperature, humidity) explain some variation in microbial response during human decomposition in terrestrial settings, recent work has noted that even under the same environmental conditions, individuals can have different decomposition patterns, highlighting the potential for intrinsic factors to impact microbial decomposers. The goal of this study was to investigate the effects of several intrinsic factors (age, sex, diseases at time of death, and body mass index [BMI]) on chemical and microbial changes in decomposition-impacted soils. In a field study conducted at the University of Tennessee Anthropology Research Facility, soils were collected from the decomposition-impacted area surrounding 19 deceased human individuals through the end of active decomposition. Soil physicochemical parameters were measured, and microbial (bacterial and fungal) communities were assessed via amplicon sequencing. BMI was shown to explain some variation in soil pH and microbial response to human decomposition. Hierarchical linear mixed (HLM) effects models revealed that BMI category significantly explained variation in pH response within decomposition-impacted soils over time (HLM F = 9.647; P < 0.001). Additionally, the relative abundance of soil Saccharomycetes in decomposition soils under underweight donors displayed little to no changes (mean maximum change in relative abundance, +6.6%), while all other BMI categories displayed an increased relative abundance of these organisms over time (normal, +50.6%; overweight, +64.4%; and obese, +64.6%) (HLM F = 3.441; P = 0.11). Together, these results reveal intrinsic factors influencing decomposition patterns, especially within the soil environment, and suggest BMI is an important factor for controlling decomposition processes. IMPORTANCE This work begins to address questions about interindividual variation in vertebrate decomposition attributed to intrinsic factors, that is, properties of the carcass or cadaver itself. Most research on factors affecting decomposition has focused on the extrinsic environment, such as temperature or humidity. While these extrinsic factors do explain some variation in decomposition patterns, interindividual variability is still observed. Understanding how intrinsic factors influence microbial decomposers will help reveal the ecological impacts of decomposition. This work also has forensic applications, as soil chemical and biological changes have been suggested as indicators of postmortem interval. We reveal factors that explain variation in the decomposition environment that should be considered in these estimates. This is particularly important as we consider the implications of variations in human populations due to diet, age, BMI, disease, toxicological loading, etc. on forensic investigations dealing with decomposing remains.}, }
@article {pmid36133177, year = {2022}, author = {Villegas-Plazas, M and Villamil, L and Martínez-Silva, MA and González-Jiménez, T and Salazar, M and Güiza, L and Mendoza, M and Junca, H}, title = {Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis.}, journal = {Access microbiology}, volume = {4}, number = {8}, pages = {acmi000405}, pmid = {36133177}, issn = {2516-8290}, abstract = {Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.}, }
@article {pmid36133174, year = {2022}, author = {Beirne, C and McCann, E and McDowell, A and Miliotis, G}, title = {Genetic determinants of antimicrobial resistance in three multi-drug resistant strains of Cutibacterium acnes isolated from patients with acne: a predictive in silico study.}, journal = {Access microbiology}, volume = {4}, number = {8}, pages = {acmi000404}, pmid = {36133174}, issn = {2516-8290}, abstract = {OBJECTIVES: Using available whole genome data, the objective of this in silico study was to identify genetic mechanisms that could explain the antimicrobial resistance profile of three multi-drug resistant (MDR) strains (CA17, CA51, CA39) of the skin bacterium Cutibacterium acnes previously recovered from patients with acne. In particular, we were interested in detecting novel genetic determinants associated with resistance to fluoroquinolone and macrolide antibiotics that could then be confirmed experimentally.<br><br>METHODS: A range of open source bioinformatics tools were used to 'mine' genetic determinants of antimicrobial resistance and plasmid borne contigs, and to characterise the phylogenetic diversity of the MDR strains.<br><br>RESULTS: As probable mechanisms of resistance to fluoroquinolones, we identified a previously described resistance associated allelic variant of the gyrA gene with a 'deleterious' S101L mutation in type IA1 strains CA51 (ST1) and CA39 (ST1), as well as a novel E761R 'deleterious' mutation in the type II strain CA17 (ST153). A distinct genomic sequence of the efflux protein YfmO which is potentially associated with resistance to MLSB antibiotics was also present in CA17; homologues in CA51, CA39, and other strains of Cutibacterium acnes , were also found but differed in amino acid content. Strikingly, in CA17 we also identified a circular 2.7&#x2009;kb non-conjugative plasmid (designated pCA17) that closely resembled a 4.8&#x2009;kb plasmid (pYU39) from the MDR Salmonella enterica strain YU39.<br><br>CONCLUSIONS: This study has provided a detailed explanation of potential genetic determinants for MDR in the Cutibacterium acnes strains CA17, CA39 and CA51. Further laboratory investigations will be required to validate these in silico results, especially in relation to pCA17.}, }
@article {pmid36132223, year = {2022}, author = {Yanez-Montalvo, A and Aguila, B and Gómez-Acata, ES and Guerrero-Jacinto, M and Oseguera, LA and Falcón, LI and Alcocer, J}, title = {Shifts in water column microbial composition associated to lakes with different trophic conditions: "Lagunas de Montebello" National Park, Chiapas, México.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13999}, pmid = {36132223}, issn = {2167-8359}, abstract = {Eutrophication is a global problem causing the reduction of water quality and the loss of ecosystem goods and services. The lakes of the "Lagunas de Montebello" National Park (LMNP), Chiapas, Mexico, not only represent unique and beautiful natural scenic sites in southern Mexico but are also a national protected area and RAMSAR site. Unfortunately, some of these lakes started showing eutrophication signs since 2003. Anthropogenic activities (e.g., land-use change from forested to agricultural and urban development) are leading to water quality and trophic state alterations of the lakes of the LMNP. This study shows the results of a coupled limnological characterization and high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene to analyze the microbial composition of the water column in a set of oligotrophic and eutrophic lakes. Chlorophyll a (Chl-a) was the main environmental parameter correlated with the trophic conditions of the lakes. Although the microbial diversity was similar, the microbial composition changed significantly from oligo to eutrophic lakes. Proteobacteria, Firmicutes, and Cyanobacteria were the main components of oligotrophic lakes, and Cyanobacteria, Proteobacteria, and Bacteroidetes of eutrophic lakes. While Acinetobacter (Proteobacteria) and Cyanobium (a unicellular cyanobacterium) dominated in oligotrophic lakes, the filamentous, bloom-forming, and toxin-producing cyanobacteria Planktothrix was the dominant genus in eutrophic lakes. High-throughput sequencing allowed the detection of changes in the composition of the microbial component in oligotrophic lakes, suggesting a shift towards eutrophication, highlighting the relevance of sensitive monitoring protocols of these ecosystems to implement remediation programs for eutrophicated lakes and conservation strategies for those yet pristine.}, }
@article {pmid36130296, year = {2022}, author = {Kerr, BJ and Trachsel, JM and Bearson, BL and Loving, CL and Bearson, SMD and Byrne, KA and Pearce, SC and Ramirez, SM and Gabler, NK and Schweer, WP and Helm, ET and De Mille, CM}, title = {Evaluation of digestively resistant or soluble fibers, short- and medium-chain fatty acids, trace minerals, and antibiotics in nonchallenged nursery pigs on performance, digestibility, and intestinal integrity.}, journal = {Journal of animal science}, volume = {100}, number = {11}, pages = {}, pmid = {36130296}, issn = {1525-3163}, mesh = {Swine ; Animals ; *Animal Nutritional Physiological Phenomena ; Animal Feed/analysis ; Digestion ; *Trace Elements/pharmacology ; Anti-Bacterial Agents/pharmacology ; Diet/veterinary ; Zea mays ; Fatty Acids, Volatile/pharmacology ; Starch/pharmacology ; Butyrates/pharmacology ; }, abstract = {Three experiments (EXP) were conducted to determine the effect of feed additives on performance, intestinal integrity, gastrointestinal volatile fatty acids (VFA), and energy and nutrient digestion in nonchallenged nursery pigs. In EXP 1, 480 pigs (6.36-kg body weight, BW) were placed into 96 pens with 5 pigs/pen, and allotted to 1 of 10 dietary treatments: 1) negative control containing no feed additive (NC), 2) NC + 44 mg chlortetracycline and 38.5 mg tiamulin/kg diet (CTsb), 3) NC + 5% resistant potato starch (RSpo), 4) NC + 5% soluble corn fiber (SCF), 5) NC + 5% sugar beet pulp (SBP), 6) NC + 0.30% fatty acid mix (FAM), 7) NC + 0.10% phytogenic blend of essential oils and flavoring compounds (PHY), 8) NC + 50 mg Cu and 1,600 mg zinc oxide/kg diet (CuZn), 9) NC + 5% resistant corn starch (RScn), and 10) NC + 0.05% β-glucan (BG) for 28 d. There was no impact of dietary treatment on BW gain or feed intake (P ≥ 0.22). Pigs fed diets containing SCF, CTsb, and RSpo resulted in microbial community differences compared to pigs fed the NC (P < 0.05). In EXP 2, 48 barrows (12.8 kg BW) were selected at the end of EXP 1 and fed the same dietary treatments they had previously received: 1) NC, 2) NC + 5% RScn, 3) NC + 5% SCF, and 4) NC + FAM for 8 d. There was no effect of feeding diets containing RScn, SCF, or FAM on in vivo intestinal permeability (P ≤ 0.21). Ileal or colon pH, concentrations of VFA did not differ due to dietary treatment (P ≥ 0.36), but pigs fed diets containing FAM resulted in a greater butyric acid concentration in the cecum compared to pigs fed the NC (P ≤ 0.05). In EXP 3, 156 pigs (6.11 kg BW) were placed into 52 pens with 3 pigs/pen and allotted to 1 of 4 dietary treatments arranged in a factorial manner: 1) NC, 2) NC + 5% RSpo, 3) NC + 0.30% FAM, and 4) NC + 5% RSpo + 0.30% FAM for 24 d. Feeding pigs diets containing RSpo did not affect BW gain (P = 0.91) while pigs fed diets containing FAM grew improved BW gain (P = 0.09). Colonic butyric acid concentrations were greater in pigs fed diets containing RSpo (P = 0.03), while pigs fed diets containing FAM exhibited reduced total VFA concentrations (P = 0.11). The results indicate that supplementing diets with digestively resistant but fermentable fibers, short- and medium-chain fatty acids, or antibiotics do not have a consistent effect, positive or negative, on markers of intestinal integrity or barrier function, intestinal VFA patterns, ATTD of energy and nutrients, or on pig performance.}, }
@article {pmid36128567, year = {2022}, author = {El Amrani, B}, title = {Aspects of the rhizospheric microbiota and their interactions with the soil ecosystem.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {26}, number = {5}, pages = {442-448}, doi = {10.18699/VJGB-22-54}, pmid = {36128567}, issn = {2500-0462}, abstract = {Soil microbial communities play a key role in the evolution of the rhizosphere. In addition, proper exploration of these microbial resources represents a promising strategy that guarantees the health and sustainability of all ecosystems connected to the ground. Under the inf luence of environmental conditions, microbial communities can change compositions in terms of abundance and diversity. Beyond the descriptive level, the current orientation of microbial ecology is to link these structures to the functioning of ecosystems; specif ically, to understand the effect of environmental factors on the functional structure of microbial communities in ecosystems. This review focuses on the main interactions between the indigenous soil microf lora and the major constituents of the rhizosphere to understand, on the one hand, how microbial biodiversity can improve plant growth and maintain homeostasis of the rhizospheric ecosystem, on the other hand, how the maintenance and enrichment of plant biodiversity can contribute to the conservation of soil microbial diversity; knowing that these microorganisms are also controlled by the abiotic properties of the soil. Overall, understanding the dynamics of the rhizosphere microbiome is essential for developing innovative strategies in the f ield of protecting and maintaining the proper functioning of the soil ecosystem.}, }
@article {pmid36128049, year = {2022}, author = {Külekci, B and Schwarz, S and Brait, N and Perkmann-Nagele, N and Jaksch, P and Hoetzenecker, K and Puchhammer-Stöckl, E and Goerzer, I}, title = {Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac076}, pmid = {36128049}, issn = {2057-1577}, abstract = {Mixed human cytomegalovirus (HCMV) strain infections are frequent in lung transplant recipients (LTRs). To date, the influence of the donor (D) and recipient (R) HCMV serostatus on intra-host HCMV strain composition and viral population dynamics after transplantation is only poorly understood. Here, we investigated ten pre-transplant lungs from HCMV-seropositive donors and 163 sequential HCMV-DNA-positive plasma and bronchoalveolar lavage samples from fifty LTRs with multiviremic episodes post-transplantation. The study cohort included D+R+ (38 per cent), D+R- (36 per cent), and D-R+ (26 per cent) patients. All samples were subjected to quantitative genotyping by short amplicon deep sequencing, and twenty-four of them were additionally PacBio long-read sequenced for genotype linkages. We find that D+R+ patients show a significantly elevated intra-host strain diversity compared to D+R- and D-R+ patients (P = 0.0089). Both D+ patient groups display significantly higher viral population dynamics than D- patients (P = 0.0061). Five out of ten pre-transplant donor lungs were HCMV DNA positive, whereof three multiple HCMV strains were detected, indicating that multi-strain transmission via lung transplantation is likely. Using long reads, we show that intra-host haplotypes can share distinctly linked genotypes, which limits overall intra-host diversity in mixed infections. Together, our findings demonstrate donor-derived strains as the main source of increased HCMV strain diversity and dynamics post-transplantation. These results foster strategies to mitigate the potential transmission of the donor strain reservoir to the allograft, such as ex vivo delivery of HCMV-selective immunotoxins prior to transplantation to reduce latent HCMV.}, }
@article {pmid36126627, year = {2022}, author = {Xu, G and He, J}, title = {Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge.}, journal = {Water research}, volume = {224}, number = {}, pages = {119055}, doi = {10.1016/j.watres.2022.119055}, pmid = {36126627}, issn = {1879-2448}, mesh = {Bacteria/chemistry ; Biodegradation, Environmental ; *Chloroflexi/genetics ; *Environmental Pollutants ; Halogenated Diphenyl Ethers ; Humans ; *Microbiota ; Oxygen ; Sewage ; *Tetrachloroethylene ; }, abstract = {Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.}, }
@article {pmid36123806, year = {2022}, author = {Zhang, Y and Yang, X and Van de Peer, Y and Chen, J and Marchal, K and Shi, T}, title = {Evolution of isoform-level gene expression patterns across tissues during lotus species divergence.}, journal = {The Plant journal : for cell and molecular biology}, volume = {112}, number = {3}, pages = {830-846}, pmid = {36123806}, issn = {1365-313X}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Lotus/genetics ; Gene Duplication ; Genes, Duplicate ; Protein Isoforms/genetics ; *Arabidopsis/genetics ; *Nelumbo/genetics ; Gene Expression ; Evolution, Molecular ; }, abstract = {Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small-scale duplicates, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus.}, }
@article {pmid36123554, year = {2022}, author = {Xu, MP and Zhi, RC and Jian, JN and Feng, YZ and Han, XH and Zhang, W}, title = {Changes in Soil Organic C Fractions and C Pool Stability Are Mediated by C-Degrading Enzymes in Litter Decomposition of Robinia pseudoacacia Plantations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36123554}, issn = {1432-184X}, abstract = {Litter decomposition is the main source of soil organic carbon (SOC) pool, regarding as an important part of terrestrial ecosystem C dynamics. The turnover of SOC is mainly regulated by extracellular enzymes secreted by microorganisms. However, the response mechanism of soil C-degrading enzymes and SOC in litter decomposition remains unclear. To clarify how SOC fraction dynamics respond to C-degrading enzymes in litter decomposition, we used field experiments to collect leaf litter and SOC fractions from the underlying layer in Robinia pseudoacacia plantations on the Loess Plateau. Our results showed that SOC, easily oxidizable organic C, dissolved organic C, and microbial biomass C increased significantly during the decomposition process. Litter decomposition significantly decreased soil hydrolase activity, but slightly increased oxidase activity. Correlation analysis results showed that SOC fractions were significantly positively correlated with the litter mass, lignin, soil moisture, and oxidase activity, but significantly negatively correlated with cellulose content and soil pH. Partial least squares path models revealed that soil C-degrading enzymes can directly or indirectly affect the changes of soil C fractions. The most direct factors affecting the SOC fractions of topsoil during litter decomposition were litter lignin and cellulose degradation, soil pH, and C-degrading enzymes. Furthermore, regression analysis showed that the decrease of SOC stability in litter decomposition was closely related to the decrease of soil hydrolase to oxidase ratio. These results highlighted that litter degradation-induced changes in C-degrading enzyme activity significantly affected SOC fractions. Furthermore, the distribution of soil hydrolases and oxidases affected the stability of SOC during litter decomposition. These findings provided a theoretical framework for a more comprehensive understanding of C turnover and stabilization mechanisms between plant and soil.}, }
@article {pmid36123442, year = {2022}, author = {Hedlund, BP and Chuvochina, M and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, IC and Venter, SN and Whitman, WB}, title = {SeqCode: a nomenclatural code for prokaryotes described from sequence data.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1702-1708}, pmid = {36123442}, issn = {2058-5276}, mesh = {*Metagenome ; *Prokaryotic Cells ; }, abstract = {Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.}, }
@article {pmid36122204, year = {2022}, author = {Peng, R and Xu, Y and Tian, S and Unver, T and Liu, Z and Zhou, Z and Cai, X and Wang, K and Wei, Y and Liu, Y and Wang, H and Hu, G and Zhang, Z and Grover, CE and Hou, Y and Wang, Y and Li, P and Wang, T and Lu, Q and Wang, Y and Conover, JL and Ghazal, H and Wang, Q and Zhang, B and Van Montagu, M and Van de Peer, Y and Wendel, JF and Liu, F}, title = {Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {39}, pages = {e2208496119}, pmid = {36122204}, issn = {1091-6490}, mesh = {Cotton Fiber ; *Evolution, Molecular ; Genetic Variation/genetics ; *Genome, Plant/genetics ; *Gossypium/classification/genetics ; Isomerases/genetics/metabolism ; Tetraploidy ; }, abstract = {Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)6, Ge] and Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates-including phenotypic differentiation, genetic isolation, and genetic convergence-that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.}, }
@article {pmid36118848, year = {2022}, author = {Rabapane, KJ and Ijoma, GN and Matambo, TS}, title = {Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {946449}, pmid = {36118848}, issn = {1664-8021}, abstract = {Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.}, }
@article {pmid36113308, year = {2022}, author = {Alves, KJ and Pylro, VS and Nakayama, CR and Vital, VG and Taketani, RG and Santos, DG and Rodrigues, JLM and Tsai, SM and Andreote, FD}, title = {Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127178}, doi = {10.1016/j.micres.2022.127178}, pmid = {36113308}, issn = {1618-0623}, mesh = {Archaea ; Bacteria ; Brazil ; *Euryarchaeota/genetics ; *Greenhouse Gases/analysis/metabolism ; Methane ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Amazonian forest conversion into agricultural and livestock areas is considered one of the activities that contribute most to the emission of greenhouse gases, including methane. Biogenic methane production is mainly performed by methanogenic Archaea, which underscores the importance of understanding the drivers shaping microbial communities involved in the methane cycling and changes in methane metabolism. Here, we aimed to investigate the composition and structure of bacterial and archaeal communities in tropical soils in response to land-use changes, emphasizing the methanogenic communities. We collected soil samples from primary forest, pasture, and secondary forest of the Amazonian region and used a strategy based on the enrichment of the methanogenic community with three different methanogenic substrates followed by measurements of methane emission, quantification of mcrA gene copies by qPCR, and total 16 S rRNA gene sequencing (metataxonomics). We observed variations in the structure of bacterial and archaeal communities of soils under different uses. The richness of methanogenic communities was higher in pasture than forest soils and this richness remained during the incubation period, and as a consequence, the enrichment induced earlier methane emission in pastures-derived samples. Furthermore, pastures enrichments exhibited methanogenic archaea networks more complex than primary and secondary forests. In conclusion, pastures harbor a richer and more responsive methanogenic community than forest samples, suggesting that conversion of forest areas to pasture may boost methane emission.}, }
@article {pmid36112603, year = {2022}, author = {Miller, JC and Satheesh Babu, AK and Petersen, C and Wankhade, UD and Robeson, MS and Putich, MN and Mueller, JE and O'Farrell, AS and Cho, JM and Chintapalli, SV and Jalili, T and Symons, JD and Anandh Babu, PV}, title = {Gut Microbes Are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome-Induced Vascular Inflammation.}, journal = {Molecular nutrition &amp; food research}, volume = {66}, number = {22}, pages = {e2200112}, pmid = {36112603}, issn = {1613-4133}, support = {R01 HL141540/HL/NHLBI NIH HHS/United States ; R03AGO52848/HL/NHLBI NIH HHS/United States ; R01 AT010247/AT/NCCIH NIH HHS/United States ; R01HL141540/HL/NHLBI NIH HHS/United States ; R01AT010247/AT/NCCIH NIH HHS/United States ; }, mesh = {Male ; Mice ; Animals ; *Fragaria/chemistry ; *Metabolic Syndrome/etiology/drug therapy ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Inflammation ; }, abstract = {SCOPE: Metabolic syndrome (MetS) alters the gut microbial ecology and increases the risk of cardiovascular disease. This study investigates whether strawberry consumption reduces vascular complications in an animal model of MetS and identifies whether this effect is associated with changes in the composition of gut microbes.<br><br>METHODS AND RESULTS: Seven-week-old male mice consume diets with 10% (C) or 60% kcal from fat (high-fat diet fed mice; HF) for 12 weeks and subgroups are fed a 2.35% freeze-dried strawberry supplemented diet (C+SB or HF+SB). This nutritional dose is equivalent to &#x2248;160 g of strawberry. After 12 weeks treatment, vascular inflammation is enhanced in HF versus C mice as shown by an increased monocyte binding to vasculature, elevated serum chemokines, and increased mRNA expression of inflammatory molecules. However, strawberry supplementation suppresses vascular inflammation in HF+SB versus HF mice. Metabolic variables, blood pressure, and indices of vascular function were similar among the groups. Further, the abundance of opportunistic microbe is decreased in HF+SB. Importantly, circulating chemokines are positively associated with opportunistic microbes and negatively associated with the commensal microbes (Bifidobacterium and Facalibaculum).<br><br>CONCLUSION: Dietary strawberry decreases the abundance of opportunistic microbe and this is associated with a decrease in vascular inflammation resulting from MetS.}, }
@article {pmid36112501, year = {2022}, author = {Abdel-Rahman, LIH and Morgan, XC}, title = {Searching for a Consensus Among Inflammatory Bowel Disease Studies: A Systematic Meta-Analysis.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izac194}, pmid = {36112501}, issn = {1536-4844}, abstract = {BACKGROUND: Numerous studies have examined the gut microbial ecology of patients with Crohn's disease (CD) and ulcerative colitis, but inflammatory bowel disease-associated taxa and ecological effect sizes are not consistent between studies.<br><br>METHODS: We systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyze how variables such as sample type (stool, biopsy, and lavage) affect results in inflammatory bowel disease gut microbiome studies, using uniform bioinformatic methods for all primary data.<br><br>RESULTS: Reduced alpha diversity was a consistent feature of both CD and ulcerative colitis but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD.<br><br>CONCLUSIONS: Our results indicate that sample type variation is an important contributor to study variability that should be carefully considered during study design, and stool is likely superior to biopsy for CD studies due to its lower heterogeneity.}, }
@article {pmid36112189, year = {2022}, author = {Peralta-Maraver, I and Rutere, C and Horn, MA and Reche, I and Behrends, V and Reiss, J and Robertson, AL}, title = {Intermediate Levels of Predation and Nutrient Enrichment Enhance the Activity of Ibuprofen-Degrading Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36112189}, issn = {1432-184X}, abstract = {Water is the most indispensable natural resource; yet, organic pollution of freshwater sources is widespread. In recent years, there has been increasing concern over the vast array of emerging organic contaminants (EOCs) in the effluent of wastewater treatment plants (WWTPs). Several of these EOCs are degraded within the pore space of riverbeds by active microbial consortia. However, the mechanisms behind this ecosystem service are largely unknown. Here, we report how phosphate concentration and predator-prey interactions drive the capacity of bacteria to process a model EOC (ibuprofen). The presence of phosphate had a significant positive effect on the population growth rate of an ibuprofen-degrading strain. Thus, when phosphate was present, ibuprofen removal efficiency increased. Moreover, low and medium levels of predation, by a ciliated protozoan, stimulated bacterial population growth. This unimodal effect of predation was lost under high phosphate concentration, resulting in the flattening of the relationships between predator density and population growth of ibuprofen degraders. Our results suggest that moderate nutrient and predation levels promote the growth rate of bacterial degraders and, consequently, the self-purifying capability of the system. These findings enhance our understanding of the mechanisms by which riverbed communities drive the processing of EOCs.}, }
@article {pmid36111808, year = {2022}, author = {Marzorati, M and Bubeck, S and Bayne, T and Krishnan, K and Giusto, M}, title = {Effects of combined prebiotic, probiotic, IgG and amino acid supplementation on the gut microbiome of patients with inflammatory bowel disease.}, journal = {Future microbiology}, volume = {17}, number = {}, pages = {1307-1324}, doi = {10.2217/fmb-2022-0066}, pmid = {36111808}, issn = {1746-0921}, mesh = {Amino Acids ; Caco-2 Cells ; Dietary Supplements ; Fatty Acids, Volatile/pharmacology ; Flavonoids ; *Gastrointestinal Microbiome ; Humans ; Immunoglobulin G ; *Inflammatory Bowel Diseases/drug therapy ; Interleukin-10 ; Interleukin-6 ; Prebiotics ; *Probiotics/pharmacology ; }, abstract = {Background: The effects of the Total Gut Restoration (TGR) system supplementation on the gut microbiome were evaluated. Materials &amp; methods: A mucosal in vitro simulation of the human gastrointestinal tract (M-SHIME[®]) system was inoculated with fecal samples from patients with inflammatory bowel disease. Chambers were supplemented for 5 days with the TGR system (five probiotic Bacillus strains, prebiotic mixture, immunoglobulin concentrate, amino acids and prebiotic flavonoids). Results: Compared with unsupplemented controls, supplementation was associated with a significant increase in short-chain fatty acid production, and changes to the microbiome were observed. Supernatants from supplemented chambers improved intestinal barrier function, increased IL-6 and IL-10 production and decreased MCP1 production versus control in Caco-2/THP1 coculture. Conclusion: Daily TGR supplementation facilitated changes to the gut microbiome of patients with inflammatory bowel disease.}, }
@article {pmid36110415, year = {2022}, author = {Song, W and Gong, H and Wang, Q and Zhang, L and Qiu, L and Hu, X and Han, H and Li, Y and Li, R and Li, Y}, title = {Using Bayesian networks with Max-Min Hill-Climbing algorithm to detect factors related to multimorbidity.}, journal = {Frontiers in cardiovascular medicine}, volume = {9}, number = {}, pages = {984883}, pmid = {36110415}, issn = {2297-055X}, abstract = {OBJECTIVES: Multimorbidity (MMD) is a medical condition that is linked with high prevalence and closely related to many adverse health outcomes and expensive medical costs. The present study aimed to construct Bayesian networks (BNs) with Max-Min Hill-Climbing algorithm (MMHC) algorithm to explore the network relationship between MMD and its related factors. We also aimed to compare the performance of BNs with traditional multivariate logistic regression model.<br><br>METHODS: The data was downloaded from the Online Open Database of CHARLS 2018, a population-based longitudinal survey. In this study, we included 10 variables from data on demographic background, health status and functioning, and lifestyle. Missing value imputation was first performed using Random Forest. Afterward, the variables were included into logistic regression model construction and BNs model construction. The structural learning of BNs was achieved using MMHC algorithm and the parameter learning was conducted using maximum likelihood estimation.<br><br>RESULTS: Among 19,752 individuals (9,313 men and 10,439 women) aged 64.73 &#xb1; 10.32 years, there are 9,129 ones without MMD (46.2%) and 10,623 ones with MMD (53.8%). Logistic regression model suggests that physical activity, sex, age, sleep duration, nap, smoking, and alcohol consumption are associated with MMD (P < 0.05). BNs, by establishing a complicated network relationship, reveals that age, sleep duration, and physical activity have a direct connection with MMD. It also shows that education levels are indirectly connected to MMD through sleep duration and residence is indirectly linked to MMD through sleep duration.<br><br>CONCLUSION: BNs could graphically reveal the complex network relationship between MMD and its related factors, outperforming traditional logistic regression model. Besides, BNs allows for risk reasoning for MMD through Bayesian reasoning, which is more consistent with clinical practice and thus holds some application prospects.}, }
@article {pmid36108399, year = {2022}, author = {Sun, H and Xia, J and Wu, B and Ren, H and Zhang, X and Ye, L}, title = {Aerobic starvation treatment of activated sludge enhances the degradation efficiency of refractory organic compounds.}, journal = {Water research}, volume = {224}, number = {}, pages = {119069}, doi = {10.1016/j.watres.2022.119069}, pmid = {36108399}, issn = {1879-2448}, mesh = {Benzhydryl Compounds ; Bioreactors/microbiology ; Fluorocarbons ; Gabapentin ; Humans ; Phenols ; RNA, Ribosomal, 16S/genetics ; *Sewage/chemistry ; *Waste Water ; }, abstract = {Many refractory organic compounds (ROCs) in wastewater are toxic to human and aquatic organisms. Here, we reported an aerobic starvation approach to improve the degradation efficiencies of ROCs in activated sludge systems. The highest degradation rates of bisphenol AF (BPAF) (11.4 mg/g VSS · h) and gabapentin (GBP) (8.9 mg/g VSS · h) were achieved on the second day of the starvation process. While, the degradation rate of bisphenol A (BPA) on the 43rd day reached the maximum value of 0.8 mg/g VSS ·h, which was significantly higher than that of the seeding sludge (0.01 mg/g VSS · h). To investigate the mechanisms of this finding, we applied magnetic-nanoparticle mediated isolation, 16S rRNA gene sequencing, metagenomic sequencing and metatranscriptomic sequencing to analyze the microbial community structures and functions during the starvation process. The results showed that the increase of the BPA degradation ability was caused by the increase of the relative abundance of BPA degrading bacteria (Sphingomonas, Achromobacter, etc.), while, the enhancement of BPAF and GBP degradation was attributed to the increase of the expression of ROC degrading genes. Overall, these results improve our understanding of the microbial ecology of starved activated sludge and provide useful information for the future development of ROC removal technologies.}, }
@article {pmid36106503, year = {2022}, author = {Law, CKY and Bolea-Fernandez, E and Liu, T and Bonin, L and Wallaert, E and Verbeken, K and De Gusseme, B and Vanhaecke, F and Boon, N}, title = {The influence of H2 partial pressure on biogenic palladium nanoparticle production assessed by single-cell ICP-mass spectrometry.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14140}, pmid = {36106503}, issn = {1751-7915}, abstract = {The production of biogenic palladium nanoparticles (bio-Pd NPs) is widely studied due to their high catalytic activity, which depends on the size of nanoparticles (NPs). Smaller NPs (here defined as <100 nm) are more efficient due to their higher surface/volume ratio. In this work, inductively coupled plasma-mass spectrometry (ICP-MS), flow cytometry (FCM) and transmission electron microscopy (TEM) were combined to obtain insight into the formation of these bio-Pd NPs. The precipitation of bio-Pd NPs was evaluated on a cell-per-cell basis using single-cell ICP-MS (SC-ICP-MS) combined with TEM images to assess how homogenously the particles were distributed over the cells. The results provided by SC-ICP-MS were consistent with those provided by "bulk" ICP-MS analysis and FCM. It was observed that heterogeneity in the distribution of palladium over an entire cell population is strongly dependent on the Pd[2+] concentration, biomass and partial H2 pressure. The latter three parameters affected the particle size, ranging from 15.6 to 560 nm, and exerted a significant impact on the production of the bio-Pd NPs. The TEM combined with SC-ICP-MS revealed that the mass distribution for bacteria with high Pd content (144 fg Pd cell[-1]) indicated the presence of a large number of very small NPs (D50 = 15.6 nm). These results were obtained at high cell density (1 × 10[5] ± 3 × 10[4] cells μl[-1]) and H2 partial pressure (180 ml H2). In contrast, very large particles (D50 = 560 nm) were observed at low cell density (3 × 10[4] ± 10 × 10[2] cells μl[-1]) and H2 partial pressure (10-100 ml H2). The influence of the H2 partial pressure on the nanoparticle size and the possibility of size-tuned nanoparticles are presented.}, }
@article {pmid36106339, year = {2022}, author = {Van Wyk, JC and Sewell, BT and Danson, MJ and Tsekoa, TL and Sayed, MF and Cowan, DA}, title = {Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase.}, journal = {Current research in structural biology}, volume = {4}, number = {}, pages = {256-270}, pmid = {36106339}, issn = {2665-928X}, abstract = {Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4-7.6 kJ/mol increase in the activation energy of thermal inactivation at 63 °C. High resolution X-ray crystal structures (1.15-1.80 Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising.}, }
@article {pmid36102128, year = {2022}, author = {Sampson, MM and Polk, CM and Fairman, RT and DeWitt, ME and Leonard, MK and Davidson, L and McCurdy, L and Passaretti, CL}, title = {Monkeypox testing delays: The need for drastic expansion of education and testing for monkeypox virus.}, journal = {Infection control and hospital epidemiology}, volume = {}, number = {}, pages = {1-2}, doi = {10.1017/ice.2022.237}, pmid = {36102128}, issn = {1559-6834}, }
@article {pmid36100598, year = {2022}, author = {Metz, S and Huber, P and Mateus-Barros, E and Junger, PC and de Melo, M and Bagatini, IL and Izaguirre, I and Câmara Dos Reis, M and Llames, ME and Accattatis, V and Quiroga, MV and Devercelli, M and Schiaffino, MR and Niño-García, JP and Bastidas Navarro, M and Modenutti, B and Vieira, H and Saraceno, M and Sabio Y García, CA and Pereira, E and González-Revello, A and Piccini, C and Unrein, F and Alonso, C and Sarmento, H}, title = {A georeferenced rRNA amplicon database of aquatic microbiomes from South America.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {565}, pmid = {36100598}, issn = {2052-4463}, mesh = {Bacteria/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; Water Microbiology ; }, abstract = {The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.}, }
@article {pmid36100325, year = {2022}, author = {Xu, Q and Vandenkoornhuyse, P and Li, L and Guo, J and Zhu, C and Guo, S and Ling, N and Shen, Q}, title = {Microbial generalists and specialists differently contribute to the community diversity in farmland soils.}, journal = {Journal of advanced research}, volume = {40}, number = {}, pages = {17-27}, pmid = {36100325}, issn = {2090-1224}, mesh = {Bacteria ; *Ecosystem ; Farms ; *Soil ; Soil Microbiology ; }, abstract = {INTRODUCTION: Microbial generalists and specialists are thought to have distinct impacts on community dynamics, while there have been limited efforts to estimate their contribution to microbial diversity.<br><br>OBJECTIVES: We aimed to resolve this research gap in microbial ecology to strengthen our understanding of the biogeography of microbial diversity, with implications for global-scale biodiversity mapping.<br><br>METHODS: Herein, we identified the ecological characteristics of microbial generalists and specialists across over 3,000 farmland soil samples from eleven countries that encompassed seven climate types.<br><br>RESULTS: Considering the distinct distributions of generalists and specialists in degree of connexions, betweenness and as key species in network topology, both generalists and specialists contributed to species interactions, though through different modalities. A stronger signature of deterministic processes in specialists indicated their lower tolerance to environment fluctuations. Generalists, in contrast, were more characterized by stochastic processes with higher diversification and transition rates that suggested more important roles in maintaining community stability when exposed to environmental disturbances. The relationship between latitude and diversity combining with distance-decay effects showed that generalists dampened microbial biogeographical patterns, with contrasting impacts by specialists.<br><br>CONCLUSION: By demonstrating the ecological characteristics of microbial generalists and specialists, this study deepens our understanding of microbial diversity and highlights the need to impart systematic distinctions among different categories of species when modelling and predicting the fate of ecosystems in the face of global climate change, rather than assuming that species are functionally equivalent.}, }
@article {pmid36098749, year = {2022}, author = {Angelella, G and Nalam, V and Nachappa, P and White, J and Kaplan, I}, title = {Correction to: Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-022-02107-4}, pmid = {36098749}, issn = {1432-184X}, }
@article {pmid36094300, year = {2022}, author = {Brugiroux, S and Berry, D and Ring, D and Barnich, N and Daims, H and Stecher, B}, title = {Specific Localization and Quantification of the Oligo-Mouse-Microbiota (OMM[12]) by Fluorescence In Situ Hybridization (FISH).}, journal = {Current protocols}, volume = {2}, number = {9}, pages = {e548}, doi = {10.1002/cpz1.548}, pmid = {36094300}, issn = {2691-1299}, mesh = {Animals ; In Situ Hybridization, Fluorescence/methods ; Mice ; *Microbiota ; Oligonucleotide Probes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The oligo-mouse-microbiota (OMM[12]) is a widely used syncom that colonizes gnotobiotic mice in a stable manner. It provides several fundamental functions to its murine host, including colonization resistance against enteric pathogens. Here, we designed and validated specific fluorescence in situ hybridization (FISH) probes to detect and quantify OMM[12] strains on intestinal tissue cross sections. 16S rRNA-specific probes were designed, and specificity was validated on fixed pure cultures. A hybridization protocol was optimized for sensitive detection of the individual bacterial cells in cryosections. Using this method, we showed that the intestinal mucosal niche of Akkermansia muciniphila can be influenced by global gut microbial community context. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Localization and quantification of OMM[12] single strains in mouse cecum cross section Support Protocol: Establishment of specific FISH probe set for OMM[12] syncom.}, }
@article {pmid36087683, year = {2022}, author = {Yaigoub, H and Fath, N and Tirichen, H and Wu, C and Li, R and Li, Y}, title = {Bidirectional crosstalk between dysbiotic gut microbiota and systemic lupus erythematosus: What is new in therapeutic approaches?.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {244}, number = {}, pages = {109109}, doi = {10.1016/j.clim.2022.109109}, pmid = {36087683}, issn = {1521-7035}, mesh = {*Autoimmune Diseases ; Autoimmunity ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Lupus Erythematosus, Systemic ; *Microbiota ; }, abstract = {Systemic lupus erythematosus is an autoimmune disease characterized by chronic inflammation and multiple organs damage. Its pathogenesis is complex and involves multiple factors including gut microbiota. Accumulating evidence indicates the interaction of microbial communities with the host immune system to maintain a state of homeostasis. Imbalances within the gut microbial composition and function may contribute to the development of many autoimmune diseases including SLE. In this review, we aim to highlight the dysregulation of commensal bacteria and their metabolites in the gastrointestinal tract and the resulting autoimmune responses in lupus and to decrypt the cross-link between the altered gut microbiota and the immune system in the SLE condition. We also provide new insights into targeting gut microbiota as a promising therapeutic approach to treat and manage SLE.}, }
@article {pmid36084824, year = {2022}, author = {Van Winckel, T and Ngo, N and Sturm, B and Al-Omari, A and Wett, B and Bott, C and Vlaeminck, SE and De Clippeleir, H}, title = {Enhancing bioflocculation in high-rate activated sludge improves effluent quality yet increases sensitivity to surface overflow rate.}, journal = {Chemosphere}, volume = {308}, number = {Pt 2}, pages = {136294}, doi = {10.1016/j.chemosphere.2022.136294}, pmid = {36084824}, issn = {1879-1298}, mesh = {Flocculation ; *Sewage ; *Waste Disposal, Fluid/methods ; }, abstract = {High-rate activated sludge (HRAS) relies on good bioflocculation and subsequent solid-liquid separation to maximize the capture of organics. However, full-scale applications often suffer from poor and unpredictable effluent suspended solids (ESS). While the biological aspects of bioflocculation are thoroughly investigated, the effects of fines (settling velocity < 0.6 m[3]/m[2]/h), shear and surface overflow rate (SOR) are unclear. This work tackled the impact of fines, shear, and SOR on the ESS in absence of settleable influent solids. This was assessed on a full-scale HRAS step-feed (SF) and pilot-scale HRAS contact-stabilization (CS) configuration using batch settling tests, controlled clarifier experiments, and continuous operation of reactors. Fines contributed up to 25% of the ESS in the full-scale SF configuration. ESS decreased up to 30 mg TSS/L when bioflocculation was enhanced with the CS configuration. The feast-famine regime applied in CS promoted the production of high-quality extracellular polymeric substances (EPS). However, this resulted in a narrow and unfavorable settling velocity distribution, with 50% ± 5% of the sludge mass settling between 0.6 and 1.5 m[3]/m[2]/h, thus increasing sensitivity towards SOR changes. A low shear environment (20 s[-1]) before the clarifier for at least one min was enough to ensure the best possible settling velocity distribution, regardless of prior shear conditions. Overall, this paper provides a more complete view on the drivers of ESS in HRAS systems, creating the foundation for the design of effective HRAS clarifiers. Tangible recommendations are given on how to manage fines and establish the optimal settling velocity of the sludge.}, }
@article {pmid36083443, year = {2022}, author = {Fournier, GP and Parsons, CW and Cutts, EM and Tamre, E}, title = {Standard Candles for Dating Microbial Lineages.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {41-74}, pmid = {36083443}, issn = {1940-6029}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Eukaryotic Cells ; Evolution, Molecular ; *Fossils ; Phylogeny ; Plants/genetics ; }, abstract = {Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.}, }
@article {pmid36081452, year = {2022}, author = {Duan, Q and Tian, L and Feng, J and Ping, X and Li, L and Yaigoub, H and Li, R and Li, Y}, title = {Trametenolic Acid Ameliorates the Progression of Diabetic Nephropathy in db/db Mice via Nrf2/HO-1 and NF-κB-Mediated Pathways.}, journal = {Journal of immunology research}, volume = {2022}, number = {}, pages = {6151847}, pmid = {36081452}, issn = {2314-7156}, mesh = {Albumins/metabolism ; Animals ; Antioxidants/metabolism ; Body Weight ; *Diabetes Mellitus ; *Diabetic Nephropathies/drug therapy ; Glutathione/metabolism ; Heme Oxygenase-1/metabolism ; Interleukin-6/metabolism ; Mice ; NF-E2-Related Factor 2/metabolism ; NF-kappa B/metabolism ; Oxidative Stress ; Superoxide Dismutase/metabolism ; *Triterpenes/therapeutic use ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Diabetic nephropathy (DN) is a fatal complication of diabetes and the main cause of end-stage renal disease. Due to the suboptimal effects of current treatments, there is an urgent need to develop new therapeutic strategies for DN. Trametenolic acid (TA), a lanostane-type tetracyclic triterpenoid, is one of the main active ingredients extracted from the natural product Inonotus obliquus. Our study was aimed at clarifying the potential protective effects of TA on DN and its underlying mechanism. In this research, C57BLKS/db (db/db) mice were used as the spontaneous DN model, and TA (10 mg/kg/d) was intraperitoneally injected for 4 consecutive weeks. Ratio of right kidney weight/body weight was calculated, and the contents of serum creatinine (Scr), blood urea nitrogen (BUN), and urine albumin were detected. The activities of superoxide dismutase (SOD) and catalase (CAT) and the contents of reductive glutathione (GSH) and malondialdehyde (MDA) were measured. The histopathological changes of renal tissues were observed by hematoxylin and eosin (HE), periodic acid-Schiff (PAS), and Masson staining. The protein expressions of nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), NAD(P)H:quinone oxidoreductase-1 (NQO-1), nuclear factor kappa B (NF-κB), proinflammation cytokine tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), Nephrin, and Podocin were detected by western blot assay. Immunohistochemistry was utilized to detect expressions of collagen III (COL-III) and fibronectin (FN). Our results showed that TA administration significantly reduced the ratio of right kidney weight/body weight, BUN, Scr, and urine albumin levels and alleviated the histopathological changes of DN mice. Moreover, TA administration remarkably increased GSH content and SOD and CAT activities and decreased MDA content. Western blot assay demonstrated that TA activated Nrf2 signaling and increased the expression of downstream antioxidant enzymes HO-1 and NQO-1. Further studies illustrated that NF-κB signaling was inhibited, and downstream proinflammation cytokine expressions of TNF-α, IL-6, and IL-1β were also downregulated. In addition, we also found that TA administration significantly increased the expression of nephrin and podocin proteins and reduced the protein expression of COL-III and FN. These findings suggested that TA exhibited a renoprotective effect by ameliorating oxidative stress and inflammation via Nrf2/HO-1 and NF-κB signaling pathways.}, }
@article {pmid36078654, year = {2022}, author = {Zou, J and Yang, J and He, H and Wang, X and Mei, R and Cai, L and Li, J}, title = {Effect of Seed Sludge Type on Aerobic Granulation, Pollutant Removal and Microbial Community in a Sequencing Batch Reactor Treating Real Textile Wastewater.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {17}, pages = {}, pmid = {36078654}, issn = {1660-4601}, mesh = {Aerobiosis ; Bioreactors/microbiology ; *Environmental Pollutants ; *Microbiota ; Nitrogen ; Sewage/microbiology ; Textiles ; Waste Disposal, Fluid/methods ; Waste Water ; }, abstract = {The aerobic granulation, pollutant removal, and microbial community in real textile wastewater (TWW) treatment were compared using conventional activated sludge (CAS) and preformed aerobic granular sludge (AGS) in synthetic wastewater as seed in two reactors, reactor-1 (R1) and reactor-2 (R2), respectively. The results showed that complete granulation was achieved in R1 (sludge volume index at 5 min (SVI5) and 30 min (SVI30): 19.4 mL/g; granule size: 210 μm) within 65 days, while it only required 28 days in R2 (SVI5 and SVI30: 27.3 mL/g; granule size: 496 μm). The removal of COD, NH4[+]-N and TN in R1 (49.8%, 98.8%, and 41.6%) and R2 (53.6%, 96.9%, and 40.8%) were comparable in 100% real TWW treatment, but stable performance was achieved much faster in R2. The real TWW had an inhibitory effect on heterotrophic bacteria activity, but it had no inhibition on ammonia-oxidizing bacteria activity. AGS with a larger particle size had a higher microbial tolerance to real TWW. Furthermore, filamentous Thiothrix in the AGS in R2 disappeared when treating real TWW, leading to the improvement of sludge settleability. Thus, seeding preformed AGS is suggested as a rapid start-up method for a robust AGS system in treating real TWW.}, }
@article {pmid36077481, year = {2022}, author = {Villalba, LA and Kasada, M and Zoccarato, L and Wollrab, S and Grossart, HP}, title = {Differing Escape Responses of the Marine Bacterium Marinobacter adhaerens in the Presence of Planktonic vs. Surface-Associated Protist Grazers.}, journal = {International journal of molecular sciences}, volume = {23}, number = {17}, pages = {}, pmid = {36077481}, issn = {1422-0067}, mesh = {Bacteria ; Ecosystem ; Humans ; Marinobacter ; *Plankton ; *Stramenopiles ; Water ; }, abstract = {Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.}, }
@article {pmid36076760, year = {2022}, author = {Mutalub, YB and Abdulwahab, M and Mohammed, A and Yahkub, AM and Al-Mhanna, SB and Yusof, W and Tang, SP and Rasool, AHG and Mokhtar, SS}, title = {Gut Microbiota Modulation as a Novel Therapeutic Strategy in Cardiometabolic Diseases.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {17}, pages = {}, pmid = {36076760}, issn = {2304-8158}, abstract = {The human gut harbors microbial ecology that is in a symbiotic relationship with its host and has a vital function in keeping host homeostasis. Inimical alterations in the composition of gut microbiota, known as gut dysbiosis, have been associated with cardiometabolic diseases. Studies have revealed the variation in gut microbiota composition in healthy individuals as compared to the composition of those with cardiometabolic diseases. Perturbation of host-microbial interaction attenuates physiological processes and may incite several cardiometabolic disease pathways. This imbalance contributes to cardiometabolic diseases via metabolism-independent and metabolite-dependent pathways. The aim of this review was to elucidate studies that have demonstrated the complex relationship between the intestinal microbiota as well as their metabolites and the development/progression of cardiometabolic diseases. Furthermore, we systematically itemized the potential therapeutic approaches for cardiometabolic diseases that target gut microbiota and/or their metabolites by following the pathophysiological pathways of disease development. These approaches include the use of diet, prebiotics, and probiotics. With the exposition of the link between gut microbiota and cardiometabolic diseases, the human gut microbiota therefore becomes a potential therapeutic target in the development of novel cardiometabolic agents.}, }
@article {pmid36076344, year = {2022}, author = {Xu, H and Qian, Y and Jia, S and Shi, Z and Zhong, Q}, title = {Comparative analysis of subgingival microbiota in patients with mild, moderate, and severe chronic periodontitis.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.14373}, pmid = {36076344}, issn = {1601-0825}, abstract = {In this study, we explored the suspected pathogens of chronic periodontitis at different stages of occurrence and development. We collected 100 gingival crevicular fluid samples, 27, 27, and 26 from patients with mild, moderate, and severe chronic periodontitis, respectively, and 20 from healthy individuals. Pathogens were detected using a 16S rRNA metagenomic approach. Quantitative Insights in Microbial Ecology, Mothur, and other software were used to analyze the original data, draw relative abundance histograms and heat maps, and calculate flora abundance and diversity indexes. We identified 429 operational taxonomic units, covering 13 phyla, 20 classes, 32 orders, 66 families, and 123 genera from the four groups of samples. Each group showed microbial diversity, and the number of new species of bacterial flora in the gingival crevicular fluid samples gradually increased from the healthy to the severe chronic periodontitis group. There was a significant difference in the relative abundance of the core flora at the phylum, class, order, family, and genus classification levels. Our data indicated a certain correlation between the changes in the subgingival microbial structure and the occurrence and development of chronic periodontitis, which might be able to provide a reference for the diagnosis, treatment and prevention of chronic periodontitis.}, }
@article {pmid36075785, year = {2022}, author = {Martín-Rodríguez, AJ}, title = {Respiration-induced biofilm formation as a driver for bacterial niche colonization.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2022.08.007}, pmid = {36075785}, issn = {1878-4380}, abstract = {Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.}, }
@article {pmid36075698, year = {2022}, author = {Van Holm, W and Verspecht, T and Carvalho, R and Bernaerts, K and Boon, N and Zayed, N and Teughels, W}, title = {Glycerol strengthens probiotic effect of Limosilactobacillus reuteri in oral biofilms: A synergistic synbiotic approach.}, journal = {Molecular oral microbiology}, volume = {37}, number = {6}, pages = {266-275}, doi = {10.1111/omi.12386}, pmid = {36075698}, issn = {2041-1014}, mesh = {Humans ; *Lactobacillus reuteri/metabolism ; Glycerol/pharmacology/metabolism ; *Synbiotics ; *Probiotics/pharmacology ; Biofilms ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; }, abstract = {Both in vitro and in vivo studies have shown that the probiotic Limosilactobacillus reuteri can improve oral health. Limosilactobacillus reuteri species are known to produce the antimicrobial "reuterin" from glycerol. In order to further increase its antimicrobial activity, this study evaluated the effect of the combined use of glycerol and Limosilactobacillus reuteri (ATCC PTA 5289) in view of using a synergistic synbiotic over a probiotic. An antagonistic agar growth and a multispecies biofilm model showed that the antimicrobial potential of the probiotic was significantly enhanced against periodontal pathobionts and anaerobic commensals when supplemented with glycerol. Synbiotic biofilms also showed a significant reduction in inflammatory expression of human oral keratinocytes (HOK-18A), but only when the keratinocytes were preincubated with the probiotic. Probiotic preincubation of keratinocytes or probiotic and synbiotic treatment of biofilms alone was insufficient to significantly reduce inflammatory expression. Overall, this study shows that combining glycerol with the probiotic L. reuteri into a synergistic synbiotic can greatly improve the effectiveness of the latter.}, }
@article {pmid36073497, year = {2022}, author = {Lammers, A and Nazipi, S and Zweers, H and Bilde, T and Schramm, A and Garbeva, P and Lalk, M}, title = {Antimicrobial volatiles emitted by members of the nest microbiome of social spiders.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, doi = {10.1093/femsle/fnac088}, pmid = {36073497}, issn = {1574-6968}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Antifungal Agents/pharmacology ; *Microbiota ; *Spiders ; *Streptomyces ; }, abstract = {Microbes produce and respond to a range of structurally and functionally diverse volatiles. Many microbial volatiles have antimicrobial properties. Since volatiles can diffuse through complex 3D systems like spider nests, they are promising pathogen protection for social arthropods. Here, we analyzed the volatilomes of five nest microbiome members of the Namibian, social spider Stegodyphus dumicola, namely the bacteria Massilia sp. IC2-278, Massilia sp. IC2-477, Sphingomonas sp. IC-11, Streptomyces sp. IC-207, and the fungus Aureobasidium sp. CE_32, and tested their antimicrobial activity against two putative spider pathogens, namely Bacillus thuringiensis and Purpureocillium lilacinum. Most nest microbiome members released volatilomes with antibacterial and/or antifungal activities under in vitro conditions. The analysis of their volatilomes using GC/Q-TOF revealed that they include numerous antimicrobial volatiles. We tested the antimicrobial activity of five pure volatile compounds found in the volatilomes and revealed that all of them were antibacterial and/or antifungal. We could not identify the same antimicrobial volatiles as in a previous in situ study, but our results indicate that social spider-associated microorganisms as a source of antimicrobial volatiles are important for pathogen inhibition. Additionally, we showed the influence of the volatilomes on the antibiotic sensitivity of B. thuringiensis offering novel approaches to counter antibiotic resistance.}, }
@article {pmid36073311, year = {2022}, author = {McLean, AR and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Site-tropism of streptococci in the oral microbiome.}, journal = {Molecular oral microbiology}, volume = {37}, number = {6}, pages = {229-243}, pmid = {36073311}, issn = {2041-1014}, support = {R01 DE030136/DE/NIDCR NIH HHS/United States ; R01 DE027958/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Streptococcus/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Mouth/microbiology ; Tropism ; Phylogeny ; }, abstract = {A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.}, }
@article {pmid36069784, year = {2022}, author = {Hahn, MW and Pitt, A and Schmidt, J and Koll, U and Wolf, J and Whitman, WB and Bodelier, PLE and Neumann-Schaal, M}, title = {Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.005513}, pmid = {36069784}, issn = {1466-5034}, mesh = {*Alcaligenaceae/genetics ; Animals ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Gastropoda ; Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by cultivation-independent methods in freshwater systems located in Europe, Asia, Africa and the Americas. The two strains, LF4-65[T] (=CCUG 56422[T]=DSM 107630[T]) and MWH-P2sevCIIIb[T] (=CCUG 56420[T]=DSM 107629[T]), are aerobic chemoorganotrophs, both with genome sizes of 3.2 Mbp and G+C values of 52.4 and 51.0 mol%, respectively. Phylogenomic analyses based on concatenated amino acid sequences of 120 proteins suggest an affiliation of the two strains with the family Alcaligenaceae and revealed Orrella amnicola and Orrella marina (= Algicoccus marinus) as being the closest related, previously described species. However, the calculated phylogenomic trees clearly suggest that the current genus Orrella represents a polyphyletic taxon. Based on the branching order in the phylogenomic trees, as well as the revealed phylogenetic distances and chemotaxonomic traits, we propose to establish the new genus Zwartia gen. nov. and the new species Z. hollandica sp. nov. to harbour strain LF4-65[T] and the new genus Jezberella gen. nov. and the new species J. montanilacus sp. nov. to harbour strain MWH-P2sevCIIIb[T]. Furthermore, we propose the reclassification of the species Orrella amnicola in the new genus Sheuella gen. nov. The new genera Zwartia, Jezberella and Sheuella together represent taxonomically the GKS98 cluster.}, }
@article {pmid36069437, year = {2022}, author = {Eddie, BJ and Bird, LJ and Pelikan, C and Mussmann, M and Martínez-Pérez, C and Pinamang, P and Malanoski, AP and Glaven, SM}, title = {Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales.}, journal = {mSphere}, volume = {7}, number = {5}, pages = {e0022322}, pmid = {36069437}, issn = {2379-5042}, mesh = {*Carbon Dioxide/metabolism ; *Chromatiaceae ; Sulfur ; Iron/metabolism ; Cytochromes ; Oxidoreductases ; Heme ; }, abstract = {Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.}, }
@article {pmid36068360, year = {2022}, author = {Xie, Z and Xu, G and Miao, F and Kong, H and Hu, M and Wang, Y}, title = {Predator Presence Alters Intestinal Microbiota in Mussel.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36068360}, issn = {1432-184X}, abstract = {Intestinal microbes are essential participants in host vital activities. The composition of the microbiota is closely related to the environmental factors. Predator presence may impact on intestinal microbiota of prey. In the present study, stone crab Charybdis japonica was used as potential predator, an external stress on mussel Mytilus coruscus, to investigate the intestinal microbiota alteration in M. coruscus. We set up two forms of predator presence including free crab and trapped crab, with a blank treatment without crab. The composition of intestinal microbiota in mussels among different treatments showed significant differences by 16S rRNA techniques. The biodiversity increased with trapped crab presence, but decreased with free crab presence. Neisseria, the most abundant genus, fell with the presence of crabs. Besides, the Arcobacter, a kind of pathogenic bacteria, increased with free crab presence. Regarding PICRUTs analysis, Environmental Information Processing, Genetic Information Processing and Metabolism showed differences in crab presence treatments compared with the blank, with a bit higher in the presence of free crab than trapped crab. In conclusion, trapped crab effects activated the metabolism and immunity of the intestinal flora, but free crabs made mussels more susceptible to disease and mortality, corresponding to the decreased biodiversity and the increased Arcobacter in their intestine.}, }
@article {pmid36067300, year = {2022}, author = {Saunders, JK and McIlvin, MR and Dupont, CL and Kaul, D and Moran, DM and Horner, T and Laperriere, SM and Webb, EA and Bosak, T and Santoro, AE and Saito, MA}, title = {Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {37}, pages = {e2200014119}, pmid = {36067300}, issn = {1091-6490}, support = {R01 GM135709/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/classification/enzymology ; *Archaeal Proteins/analysis ; Bacteria/classification/enzymology ; *Bacterial Proteins/analysis ; Biodiversity ; *Microbiota ; *Nitrification ; Nitrite Reductases/metabolism ; Pacific Ocean ; Proteomics/methods ; *Seawater/microbiology ; }, abstract = {Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.}, }
@article {pmid36067150, year = {2022}, author = {Wilberts, L and Vuts, J and Caulfield, JC and Thomas, G and Birkett, MA and Herrera-Malaver, B and Verstrepen, KJ and Sobhy, IS and Jacquemyn, H and Lievens, B}, title = {Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0273791}, pmid = {36067150}, issn = {1932-6203}, mesh = {Animals ; *Aphids/physiology ; *Beauveria/physiology ; *Capsicum ; Insecta ; Tobacco ; }, abstract = {Entomopathogenic fungi can adopt an endophytic lifestyle and provide protection against insect herbivores and plant pathogens. So far, most studies have focused on Beauveria bassiana to increase plant resistance against abiotic and biotic stresses, while only little is known for other entomopathogenic fungi. In this study, we investigated whether root inoculation of sweet pepper (Capsicum annuum L.) by the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128 and B. bassiana ARSEF 3097 can improve resistance against the tobacco peach aphid Myzus persicae var. nicotianae. First, dual-choice experiments were performed to test the hypothesis that the fungi deter aphids via modifying plant volatile profiles. Next, we tested the hypothesis that endophytic colonization negatively affects aphid life history traits, such as fecundity, development and mortality rate. Aphids were significantly attracted to the odor of plants inoculated with A. muscarius over non-inoculated plants. Plants inoculated with A. muscarius emitted significantly higher amounts of β-pinene than non-inoculated plants, and significantly higher amounts of indole than B. bassiana-inoculated and non-inoculated plants. Inoculation with the fungal strains also caused significantly higher emission of terpinolene. Further, both aphid longevity and fecundity were significantly reduced by 18% and 10%, respectively, when feeding on plants inoculated with A. muscarius, although intrinsic rate of population increase did not differ between inoculated and non-inoculated plants. Sweet pepper plants inoculated with B. bassiana ARSEF 3097 did not elicit a significant behavioral response nor affected the investigated life history traits. We conclude that endophytic colonization by entomopathogenic fungi has the potential to alter olfactory behavior and performance of M. persicae var. nicotianae, but effects are small and depend on the fungal strain used.}, }
@article {pmid36065063, year = {2022}, author = {Nottingham, AT and Scott, JJ and Saltonstall, K and Broders, K and Montero-Sanchez, M and Püspök, J and Bååth, E and Meir, P}, title = {Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1650-1660}, pmid = {36065063}, issn = {2058-5276}, mesh = {Carbon ; Carbon Dioxide/metabolism ; Respiration ; *Soil ; *Soil Microbiology ; }, abstract = {Perturbation of soil microbial communities by rising temperatures could have important consequences for biodiversity and future climate, particularly in tropical forests where high biological diversity coincides with a vast store of soil carbon. We carried out a 2-year in situ soil warming experiment in a tropical forest in Panama and found large changes in the soil microbial community and its growth sensitivity, which did not fully explain observed large increases in CO2 emission. Microbial diversity, especially of bacteria, declined markedly with 3 to 8 °C warming, demonstrating a breakdown in the positive temperature-diversity relationship observed elsewhere. The microbial community composition shifted with warming, with many taxa no longer detected and others enriched, including thermophilic taxa. This community shift resulted in community adaptation of growth to warmer temperatures, which we used to predict changes in soil CO2 emissions. However, the in situ CO2 emissions exceeded our model predictions threefold, potentially driven by abiotic acceleration of enzymatic activity. Our results suggest that warming of tropical forests will have rapid, detrimental consequences both for soil microbial biodiversity and future climate.}, }
@article {pmid36064650, year = {2022}, author = {Morillo-Lopez, V and Sjaarda, A and Islam, I and Borisy, GG and Mark Welch, JL}, title = {Corncob structures in dental plaque reveal microhabitat taxon specificity.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {145}, pmid = {36064650}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Biofilms ; *Dental Plaque ; Humans ; In Situ Hybridization, Fluorescence/methods ; Mouth/microbiology ; Streptococcus ; *Zea mays ; }, abstract = {BACKGROUND: The human mouth is a natural laboratory for studying how bacterial communities differ across habitats. Different bacteria colonize different surfaces in the mouth-teeth, tongue dorsum, and keratinized and non-keratinized epithelia-despite the short physical distance between these habitats and their connection through saliva. We sought to determine whether more tightly defined microhabitats might have more tightly defined sets of resident bacteria. A microhabitat may be characterized, for example, as the space adjacent to a particular species of bacterium. Corncob structures of dental plaque, consisting of coccoid bacteria bound to filaments of Corynebacterium cells, present an opportunity to analyze the community structure of one such well-defined microhabitat within a complex natural biofilm. Here, we investigate by fluorescence in situ hybridization and spectral imaging the composition of the cocci decorating the filaments.<br><br>RESULTS: The range of taxa observed in corncobs was limited to a small subset of the taxa present in dental plaque. Among four major groups of dental plaque streptococci, two were the major constituents of corncobs, including one that was the most abundant Streptococcus species in corncobs despite being relatively rare in dental plaque overall. Images showed both Streptococcus types in corncobs in all individual donors, suggesting that the taxa have different ecological roles or that mechanisms exist for stabilizing the persistence of functionally redundant taxa in the population. Direct taxon-taxon interactions were observed not only between the Streptococcus cells and the central corncob filament but also between Streptococcus cells and the limited subset of other plaque bacteria detected in the corncobs, indicating species ensembles involving these taxa as well.<br><br>CONCLUSIONS: The spatial organization we observed in corncobs suggests that each of the microbial participants can interact with multiple, albeit limited, potential partners, a feature that may encourage the long-term stability of the community. Additionally, our results suggest the general principle that a precisely defined microhabitat will be inhabited by a small and well-defined set of microbial taxa. Thus, our results are important for understanding the structure and organizing principles of natural biofilms and lay the groundwork for future work to modulate and control biofilms for human health. Video Abstract.}, }
@article {pmid36063938, year = {2022}, author = {Navarrete, AA and Aburto, F and González-Rocha, G and Guzmán, CM and Schmidt, R and Scow, K}, title = {Anthropogenic degradation alter surface soil biogeochemical pools and microbial communities in an Andean temperate forest.}, journal = {The Science of the total environment}, volume = {854}, number = {}, pages = {158508}, doi = {10.1016/j.scitotenv.2022.158508}, pmid = {36063938}, issn = {1879-1026}, abstract = {Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.}, }
@article {pmid36063436, year = {2022}, author = {Li, Y and Bletsa, M and Zisi, Z and Boonen, I and Gryseels, S and Kafetzopoulou, L and Webster, JP and Catalano, S and Pybus, OG and Van de Perre, F and Li, H and Li, Y and Li, Y and Abramov, A and Lymberakis, P and Lemey, P and Lequime, S}, title = {Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History.}, journal = {Molecular biology and evolution}, volume = {39}, number = {10}, pages = {}, pmid = {36063436}, issn = {1537-1719}, mesh = {Animals ; Evolution, Molecular ; Genome, Viral ; Humans ; *Pestivirus/genetics ; Phylogeny ; Shrews/genetics ; *Viruses/genetics ; *Zika Virus/genetics ; *Zika Virus Infection ; }, abstract = {As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.}, }
@article {pmid36061686, year = {2022}, author = {Liu, B and Chen, J and Li, Y}, title = {Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks.}, journal = {ACS omega}, volume = {7}, number = {34}, pages = {29901-29908}, pmid = {36061686}, issn = {2470-1343}, abstract = {Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.}, }
@article {pmid36061525, year = {2022}, author = {von Hoermann, C and Weithmann, S and Sikorski, J and Nevo, O and Szpila, K and Grzywacz, A and Grunwald, JE and Reckel, F and Overmann, J and Steiger, S and Ayasse, M}, title = {Linking bacteria, volatiles and insects on carrion: the role of temporal and spatial factors regulating inter-kingdom communication via volatiles.}, journal = {Royal Society open science}, volume = {9}, number = {8}, pages = {220555}, pmid = {36061525}, issn = {2054-5703}, abstract = {Multi-kingdom community complexity and the chemically mediated dynamics between bacteria and insects have recently received increased attention in carrion research. However, the strength of these inter-kingdom interactions and the factors that regulate them are poorly studied. We used 75 piglet cadavers across three forest regions to survey the relationship between three actors (epinecrotic bacteria, volatile organic compounds (VOCs) and flies) during the first 4 days of decomposition and the factors that regulate this interdependence. The results showed a dynamic bacterial change during decomposition (temperature-time index) and across the forest management gradient, but not between regions. Similarly, VOC emission was dynamic across a temperature-time index and the forest management gradient but did not differ between regions. However, fly occurrence was dynamic across both space and time. The strong interdependence between the three actors was mainly regulated by the temperature-time index and the study regions, thereby revealing regulation at temporal and spatial scales. Additionally, the actor interdependence was stable across a gradient of forest management intensity. By combining different actors of decomposition, we have expanded our knowledge of the holistic mechanisms regulating carrion community dynamics and inter-kingdom interactions, an important precondition for better describing food web dynamics and entire ecosystem functions.}, }
@article {pmid36061322, year = {2022}, author = {Jones, PA and Frischer, D and Mueller, S and Le, T and Schwanes, A and Govindaraju, A and Shalvarjian, K and Leducq, JB and Marx, CJ and Martinez-Gomez, NC and Lee, JA}, title = {Methylothon: a Versatile Course-Based High School Research Experience in Microbiology and Bioinformatics with Pink Bacteria.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {2}, pages = {}, pmid = {36061322}, issn = {1935-7877}, abstract = {Methylothon is an inquiry-based high school learning module in microbial ecology, molecular biology, and bioinformatics that centers around pink-pigmented plant-associated methylotrophic bacteria. Here, we present an overview of the module's learning goals, describe course resources (available for public use at http://methylothon.com), and relate lessons learned from adapting Methylothon for remote learning during the pandemic in spring of 2021. This curriculum description is intended not only for instructors but also for microbial ecology researchers with an interest in conducting K-12 outreach. The original in-person version of the module allows students to isolate their own strains of methylotrophic bacteria from plants they sample from the environment, to identify these using PCR, sequencing, and phylogenetic analysis, and to contribute their strains to original research in a university lab. The adapted version strengthens the focus on bioinformatics and increases its flexibility and accessibility by making the lab portion optional and adopting free web-based tools. Student feedback and graded assignments from spring 2021 revealed that the lesson was especially effective at introducing the concepts of BLAST and phylogenetic trees and that students valued and felt inspired by the opportunity to conduct hands-on work and to participate in community science.}, }
@article {pmid36059518, year = {2022}, author = {Qing, J and Hu, X and Li, C and Song, W and Tirichen, H and Yaigoub, H and Li, Y}, title = {Fucose as a potential therapeutic molecule against the immune-mediated inflammation in IgA nepharopathy: An unrevealed link.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {929138}, pmid = {36059518}, issn = {1664-3224}, mesh = {Fucose ; *Gene Expression Profiling ; *Glomerulonephritis, IGA/drug therapy/genetics/metabolism ; Humans ; Immunoglobulin A/genetics ; Inflammation/genetics ; }, abstract = {BACKGROUND: IgA nephropathy (IgAN) is an autoimmune disease that affects people of any age and is an important cause of end-stage renal disease. However, the pathogenesis and pathophysiology of IgAN is not clear. This article aimed to explore the immune-mediated inflammation and genetic mechanisms in IgAN.<br><br>METHODS: The transcriptome sequencing data of IgAN glomeruli in the Gene Expression Omnibus database were downloaded.&#xa0;Single-sample gene set enrichment analysis was used to estimate the immune microenvironment of the merged microarray data and GSE141295. IgAN samples were divided into two clusters by cluster analysis. "limma" and "DEseq2" package in R were used to identify differentially expressed genes (DEGs). The weighted gene co-expression network analysis (WGCNA) was used to identify the co-expression modules related to inflammation in IgAN. R software package "clusterProfiler" was used for enrichment analysis, whereas Short Time-Series Expression Miner (STEM) analysis was used to identify the trend of gene expression. Machine-learn (ML) was performed using the shiny app. Finally, Drug Signatures Database (DSigDB) was used to identify potential molecules for treating IgAN.<br><br>RESULTS: The infiltration of macrophages in IgAN glomeruli was increased, whereas CD4+ T cells, especially inducedregulatory T cells (iTregs) were decreased. A total of 1,104 common DEGs were identified from the merged data and GSE141295. Brown module was identified to have the highest inflammatory correlation with IgAN using WGCNA, and 15 hub genes were screened from this module. Among these 15 hub genes, 14 increased with the severity of IgAN inflammation based on STEM analysis. Neural network (nnet) is considered as the best model to predict the severity of IgAN. Fucose identified from DSigDB has a potential biological activity to treat IgAN.<br><br>CONCLUSION: The increase of macrophages and the decrease of iTregs in glomeruli represent the immune-mediated inflammation of IgAN, and fucose may be a potential therapeutic molecule against IgAN because it affects genes involved in the severe inflammation of IgAN.}, }
@article {pmid36056428, year = {2022}, author = {Ma, X and Wang, T and Shi, Z and Chiariello, NR and Docherty, K and Field, CB and Gutknecht, J and Gao, Q and Gu, Y and Guo, X and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Yuan, M and Yuan, T and Zhou, J and Yang, Y}, title = {Correction: Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {144}, pmid = {36056428}, issn = {2049-2618}, }
@article {pmid36056039, year = {2022}, author = {Arandia-Gorostidi, N and Berthelot, H and Calabrese, F and Stryhanyuk, H and Klawonn, I and Iversen, M and Nahar, N and Grossart, HP and Ploug, H and Musat, N}, title = {Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {14949}, pmid = {36056039}, issn = {2045-2322}, mesh = {Bacteria/metabolism ; Biomass ; Carbon/metabolism ; *Diatoms/metabolism ; Nitrogen/metabolism ; }, abstract = {Bacterial degradation of sinking diatom aggregates is key for the availability of organic matter in the deep-ocean. Yet, little is known about the impact of aggregate colonization by different bacterial taxa on organic carbon and nutrient cycling within aggregates. Here, we tracked the carbon (C) and nitrogen (N) transfer from the diatom Leptocylindrus danicus to different environmental bacterial groups using a combination of [13]C and [15]N isotope incubation (incubated for 72 h), CARD-FISH and nanoSIMS single-cell analysis. Pseudoalteromonas bacterial group was the first colonizing diatom-aggregates, succeeded by the Alteromonas group. Within aggregates, diatom-attached bacteria were considerably more enriched in [13]C and [15]N than non-attached bacteria. Isotopic mass balance budget indicates that both groups showed comparable levels of diatom C in their biomass, accounting for 19 ± 7% and 15 ± 11%, respectively. In contrast to C, bacteria of the Alteromonas groups showed significantly higher levels of N derived from diatoms (77 ± 28%) than Pseudoalteromonas (47 ± 17%), suggesting a competitive advantage for Alteromonas in the N-limiting environments of the deep-sea. Our results imply that bacterial succession within diatom aggregates may largely impact taxa-specific C and N uptake, which may have important consequences for the quantity and quality of organic matter exported to the deep ocean.}, }
@article {pmid36054689, year = {2022}, author = {Calvo-Martin, E and Teira, E and Álvarez-Salgado, XA and Rocha, C and Jiang, S and Justel-Díez, M and Ibánhez, JSP}, title = {On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16160}, pmid = {36054689}, issn = {1462-2920}, abstract = {Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.}, }
@article {pmid36054683, year = {2022}, author = {Fan, L and Chen, J and Pan, L and Xin, X and Geng, B and Yang, L and Wang, Q and Ma, W and Lou, Y and Bian, J and Cui, X and Li, J and Wang, L and Chen, Z and Wang, W and Cui, C and Li, S and Gao, Q and Song, Q and Deng, Y and Fan, J and Yu, J and Zhang, H and Li, Y and Cai, J}, title = {Alterations of gut microbiome, metabolome and lipidome in Takayasu arteritis.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/art.42331}, pmid = {36054683}, issn = {2326-5205}, abstract = {OBJECTIVE: Mounting evidences have linked microbiome and metabolome to systemic autoimmunity and cardiovascular diseases (CVDs). A rare disease sharing features of immune-related inflammatory diseases and CVDs, Takayasu arteritis (TA), has limited relative information. This study aimed to characterize gut microbial dysbiosis, and its crosstalk with phenotypes in TA.<br><br>METHODS: To address the discriminatory signatures, we performed shotgun sequencing of fecal metagenome across discovery cohort (n=97) and independent validation cohort (n=75) encompassing TA patients, healthy and Bechet's disease (BD) controls. Interrogation of untargeted metabolomics and lipidomics profiling of plasma and fecal samples was also employed to refine features mediating associations between microorganisms and TA phenotypes.<br><br>RESULTS: A combined model of bacterial species encompassing unclassified Escherichia, Veillonella parvula, Streptococcus parasanguinis, Dorea formicigenerans, Bifidobacterium adolescentis, Lachnospiraceae bacterium 7 1 58FAA, Escherichia coli, Streptococcus salivarius, Klebsiella pneumoniae, Bifidobacterium longum and Lachnospiraceae Bacterium 5 1 63FAA, discriminated TA from controls with area under curves (AUCs) of 87.8%, 85.9%, 81.1%, and 71.1% in training, test, validation sets including healthy or BD controls, respectively. Diagnostic species were directly or indirectly via metabolites or lipids correlated with TA phenotypes of vascular involvement, inflammation, discharge medication, and prognosis. External validation against publicly metagenomic studies (n=184) on hypertension, atrial fibrillation and healthy controls, confirmed the TA-diagnostic accuracy of the model.<br><br>CONCLUSION: This study firstly identifies the discriminatory gut microbes in TA. Dysbiotic microbes also link to TA phenotypes directly or indirectly via metabolic and lipid modules. Further explorations on microbiome-metagenome interface in TA subtype prediction and pathogenesis are indicated.}, }
@article {pmid36053304, year = {2022}, author = {Trumhová, K and Klimešová, V and Pichrtová, M}, title = {Seasonal Dynamics of Zygnema (Zygnematophyceae) Mats from the Austrian Alps.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36053304}, issn = {1432-184X}, abstract = {Filamentous green algae of the genus Zygnema are an essential part of hydro-terrestrial ecosystems. Despite several studies on their resistance to natural stresses, little is known about the composition of their assemblages and the changes they undergo over time. Two sites at altitudes above 2200 m a.s.l. in the Austrian Alps were selected for a 2-year observation period and sampled five times. Molecular phylogenetic analysis of the 152 isolated strains of Zygnema sp. was performed based on the rbcL and trnG sequences. Seven genotypes were found at these sites during the samplings, but their proportion varied throughout the seasons. The site with a more stable water regime also had a more stable representation of genotypes, in contrast to the site with fluctuating water availability. The mats formed resistant pre-akinetes at the end of the season with reduced photosynthetic activity. Contrary to expectations, the mats were not exposed to extremely cold temperatures in winter due to snow cover. Some genotypes have been previously observed at this site, indicating that the population composition is stable. This work highlights the importance of resistant pre-akinetes in surviving winter conditions, the ability of algae to re-establish mats, and the need to address the hidden diversity of the genus Zygnema.}, }
@article {pmid36050462, year = {2022}, author = {Fang, Y and Qin, X and Liao, Q and Du, R and Luo, X and Zhou, Q and Li, Z and Chen, H and Jin, W and Yuan, Y and Sun, P and Zhang, R and Zhang, J and Wang, L and Cheng, S and Yang, X and Yan, Y and Zhang, X and Zhang, Z and Bai, S and Van de Peer, Y and Lucas, WJ and Huang, S and Yan, J}, title = {The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences.}, journal = {Nature plants}, volume = {8}, number = {9}, pages = {1024-1037}, pmid = {36050462}, issn = {2055-0278}, support = {833522//European Research Council/International ; }, mesh = {*Adiantum/genetics ; *Ferns/genetics ; Genome, Plant ; Phylogeny ; }, abstract = {Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.}, }
@article {pmid36049255, year = {2022}, author = {Whitman, WB and Chuvochina, M and Hedlund, BP and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, I and Venter, SN}, title = {Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {5}, pages = {126305}, pmid = {36049255}, issn = {1618-0984}, support = {P20 GM103440/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Base Sequence ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming