@article {pmid32105920, year = {2020}, author = {Riaz, L and Wang, Q and Yang, Q and Li, X and Yuan, W}, title = {Potential of industrial composting and anaerobic digestion for the removal of antibiotics, antibiotic resistance genes and heavy metals from chicken manure.}, journal = {The Science of the total environment}, volume = {718}, number = {}, pages = {137414}, doi = {10.1016/j.scitotenv.2020.137414}, pmid = {32105920}, issn = {1879-1026}, abstract = {Composting and anaerobic digestion techniques are widely used for manure recycling, but these methods have shown conflicting results in the removal of antibiotics, antibiotic resistance genes (ARGs), and heavy metals. In the present study, anaerobically digested chicken manure and various types of composted chicken manure were investigated on an industrial scale. Antibiotics, ARGs, and heavy metals had shown inconsistent results for anaerobic digestion and composting. The different composting processes either declined or completely removed the blaCTX-M, intl1 and oqxB genes. In addition, composting processes decreased the absolute abundance of aac6'-Ib and aadA genes, while increased the absolute abundance of qnrD, sul1, and tet(A) genes. On the other hand, anaerobic digestion of chicken manure increased the absolute abundance of ere(A) and tet(A). High throughput sequencing showed that Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria dominated the total bacterial composition of composted and anaerobically digested samples. Network analysis revealed the co-occurrence of ARGs and intl1. The redundancy analysis showed a significant correlation between some heavy metals and ARGs. Similarly, the bacterial composition showed a positive correlation with the prevalence of ARGs in treated manure. These findings suggest that bacterial community, heavy metals, and mobile genetic elements can play a significant role in the abundance and variation of ARGs during composting and anaerobic digestion. In conclusion, anaerobic digestion and composting methods at industrial scale need to be improved for the effective removal of antibiotics, ARGs and heavy metals from chicken manure.}, }
@article {pmid32105814, year = {2020}, author = {Rizowy, GM and Poloni, S and Colonetti, K and Donis, KC and Dobbler, PT and Leistner-Segal, S and Roesch, LFW and Schwartz, IVD}, title = {Is the gut microbiota dysbiotic in patients with classical homocystinuria?.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2020.02.013}, pmid = {32105814}, issn = {1638-6183}, abstract = {Classical homocystinuria (HCU) is characterized by increased plasma levels of total homocysteine (tHcy) and methionine (Met). Treatment may involve supplementation of B vitamins and essential amino acids, as well as restricted Met intake. Dysbiosis has been described in some inborn errors of metabolism, but has not been investigated in HCU. The aim of this study was to investigate the gut microbiota of HCU patients on treatment. Six unrelated HCU patients (males= 5, median age= 25.5 years) and six age-and-sex-matched healthy controls (males= 5, median age= 24.5 years) had their fecal microbiota characterized through partial 16S rRNA gene sequencing. Fecal pH, a 3-day dietary record, medical history, and current medications were recorded for both groups. All patients were on a Met-restricted diet and presented with high tHcy. Oral supplementation of folate (n=6) and pyridoxine (n=5), oral intake of betaine (n=4), and IM vitamin B12 supplementation (n=4), were reported only in the HCU group. Patients had decreased daily intake of fat, cholesterol, vitamin D, and selenium compared to controls (p<0.05). There was no difference in alpha and beta diversity between the groups. HCU patients had overrepresentation of the Eubacterium coprostanoligenes group and underrepresentation of the Alistipes, Family XIII UCG-001, and Parabacteroidetes genera. HCU patients and controls had similar gut microbiota diversity, despite differential abundance of some bacterial genera. Diet, betaine, vitamin B supplementation, and host genetics may contribute to these differences in microbial ecology.}, }
@article {pmid32105635, year = {2020}, author = {Pushalkar, S and Paul, B and Li, Q and Yang, J and Vasconcelos, R and Makwana, S and González, JM and Shah, S and Xie, C and Janal, MN and Queiroz, E and Bederoff, M and Leinwand, J and Solarewicz, J and Xu, F and Aboseria, E and Guo, Y and Aguallo, D and Gomez, C and Kamer, A and Shelley, D and Aphinyanaphongs, Y and Barber, C and Gordon, T and Corby, P and Li, X and Saxena, D}, title = {Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection.}, journal = {iScience}, volume = {}, number = {}, pages = {100884}, doi = {10.1016/j.isci.2020.100884}, pmid = {32105635}, issn = {2589-0042}, abstract = {The trend of e-cigarette use among teens is ever increasing. Here we show the dysbiotic oral microbial ecology in e-cigarette users influencing the local host immune environment compared with non-smoker controls and cigarette smokers. Using 16S rRNA high-throughput sequencing, we evaluated 119 human participants, 40 in each of the three cohorts, and found significantly altered beta-diversity in e-cigarette users (p = 0.006) when compared with never smokers or tobacco cigarette smokers. The abundance of Porphyromonas and Veillonella (p = 0.008) was higher among vapers. Interleukin (IL)-6 and IL-1β were highly elevated in e-cigarette users when compared with non-users. Epithelial cell-exposed e-cigarette aerosols were more susceptible for infection. In vitro infection model of premalignant Leuk-1 and malignant cell lines exposed to e-cigarette aerosol and challenged by Porphyromonas gingivalis and Fusobacterium nucleatum resulted in elevated inflammatory response. Our findings for the first time demonstrate that e-cigarette users are more prone to infection.}, }
@article {pmid32105331, year = {2020}, author = {Schmidt, ML and Biddanda, BA and Weinke, AD and Chiang, E and Januska, F and Props, R and Denef, VJ}, title = {Microhabitats are associated with diversity-productivity relationships in freshwater bacterial communities.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa029}, pmid = {32105331}, issn = {1574-6941}, abstract = {Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer, and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production. pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. Our work adds to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.}, }
@article {pmid32050392, year = {2020}, author = {Chai, B and Tsoi, T and Sallach, JB and Liu, C and Landgraf, J and Bezdek, M and Zylstra, G and Li, H and Johnston, CT and Teppen, BJ and Cole, JR and Boyd, SA and Tiedje, JM}, title = {Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression.}, journal = {The Science of the total environment}, volume = {712}, number = {}, pages = {135525}, doi = {10.1016/j.scitotenv.2019.135525}, pmid = {32050392}, issn = {1879-1026}, abstract = {Polychlorinated dibenzo-p-dioxins and dibenzofurans are a group of chemically-related pollutants categorically known as dioxins. Some of their chlorinated congeners are among the most hazardous pollutants that persist in the environment. This persistence is due in part to the limited number of bacteria capable of metabolizing these compounds, but also to their limited bioavailability in soil. We used Sphingomonas wittichii strain RW1 (RW1), one of the few strains able to grow on dioxin, to characterize its ability to respond to and degrade clay-bound dioxin. We found that RW1 grew on and completely degraded dibenzo-p-dioxin (DD) intercalated into the smectite clay saponite (SAP). To characterize the effects of DD sorption on RW1 gene expression, we compared transcriptomes of RW1 grown with either free crystalline DD or DD intercalated clay, i.e. sandwiched between the clay interlayers (DDSAP). Free crystalline DD appeared to cause greater expression of toxicity and stress related functions. Genes coding for heat shock proteins, chaperones, as well as genes involved in DNA repair, and efflux were up-regulated during growth on crystalline dioxin compared to growth on intercalated dioxin. In contrast, growth on intercalated dioxin up-regulated genes that might be important in recognition and uptake mechanisms, as well as surface interaction/attachment/biofilm formation such as extracellular solute-binding protein and LuxR. These differences in gene expression may reflect the underlying adaptive mechanisms by which RW1 cells sense and deploy pathways to access dioxin intercalated into clay. These data show that intercalated DD remains bioavailable to the degrading bacterium with implications for bioremediation alternatives.}, }
@article {pmid32101723, year = {2020}, author = {Xavier, JB and Young, VB and Skufca, J and Ginty, F and Testerman, T and Pearson, AT and Macklin, P and Mitchell, A and Shmulevich, I and Xie, L and Caporaso, JG and Crandall, KA and Simone, NL and Godoy-Vitorino, F and Griffin, TJ and Whiteson, KL and Gustafson, HH and Slade, DJ and Schmidt, TM and Walther-Antonio, MRS and Korem, T and Webb-Robertson, BM and Styczynski, MP and Johnson, WE and Jobin, C and Ridlon, JM and Koh, AY and Yu, M and Kelly, L and Wargo, JA}, title = {The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.}, journal = {Trends in cancer}, volume = {6}, number = {3}, pages = {192-204}, doi = {10.1016/j.trecan.2020.01.004}, pmid = {32101723}, issn = {2405-8025}, abstract = {The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell-cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology - a systems biology approach.}, }
@article {pmid32100456, year = {2020}, author = {Wang, B and He, Y and Tang, J and Ou, Q and Lin, J}, title = {Alteration of the gut microbiota in tumor necrosis factor-α antagonist-treated collagen-induced arthritis mice.}, journal = {International journal of rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/1756-185X.13802}, pmid = {32100456}, issn = {1756-185X}, support = {81871710//National Natural Science Foundation of China/ ; 2017J01190//Fujian Provincial Department of Science and Technology/ ; 2018QH1056//Fujian Medical University Startup Fund for scientific research/ ; C18117//Fujian Medical University Innovation Training Program/ ; 2018J06022//Fujian Science Fund for Distinguished Young Scholars/ ; }, abstract = {AIM: Gut microbiota play an important role in rheumatoid arthritis (RA). Biological therapies targeting tumor necrosis factor-α (TNF-α) have been used for treatment in RA patients. However, whether TNF-α antagonist has some influence on gut microbiota is still unknown. This study aims to investigate the distribution of gut microbiota in collagen-induced arthritis (CIA) mice treated with the TNF-α antagonist etanercept.<br><br>METHODS: Collagen-induced arthritis mice were induced by type II collagen. Cytokine expression was detected by real-time polymerase chain reaction. 16S ribosomal RNA sequencing was performed to characterize the gut microbiota in CIA mice treated with vehicle or etanercept. Sequencing reads were processed by Microbial Ecology software program.<br><br>RESULTS: Compared with vehicle-treated mice, we showed that CIA mice treated with etanercept led to attenuation of inflammation and reduced expression of TNF-α, interferon (IFN)-γ, interleukin (IL)-6 and IL-21. Meanwhile, results showed operational taxonomic units, richness estimators and the diversity indices of gut microbiota in etanercept-treated mice were lower than that in vehicle-treated mice. Moreover, bacterial abundance analyses showed that genus Escherichia/Shigella was more abundant in etanercept-treated mice, and Lactobacillus, Clostridium XlVa, Tannerella were less abundant. The altered bacterial genus was correlated with TNF-α, IFN-γ, IL-6, IL-21 and IL-10.<br><br>CONCLUSION: Our results revealed that TNF-α antagonist treatment can reduce the abundance and diversity of gut microbiota in CIA mice. Targeted gut microbiota may be a new therapeutic strategy for the treatment of RA.}, }
@article {pmid32100127, year = {2020}, author = {Chen, K and Fu, Y and Wang, Y and Liao, L and Xu, H and Zhang, A and Zhang, J and Fan, L and Ren, J and Fang, B}, title = {Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01494-w}, pmid = {32100127}, issn = {1432-184X}, support = {81770558//National Natural Science Foundation of China/ ; 3502Z20149031//Xiamen Joint Projects for Major Diseases/ ; }, abstract = {Autism spectrum disorder (ASD) is a brain-based neurodevelopmental disorder characterized by behavioral abnormalities. Accumulating studies show that the gut microbiota plays a vital role in the pathogenesis of ASD, and gut microbiota transplantation (GMT) is a promising technique for the treatment of ASD. In clinical applications of GMT, it is challenging to obtain effective transplants because of the high costs of donor selection and heterogeneity of donors' gut microbiota, which can cause different clinical responses. In vitro batch culture is a fast, easy-to-operate, and repeatable method to culture gut microbiota. Thus, the present study investigates the feasibility of treating ASD with in vitro cultured gut microbiota as transplants. We cultured gut microbiota via the in vitro batch culture method and performed GMT in the maternal immune activation (MIA)-induced ASD mouse model with original donor microbiota and in vitro cultured microbiota. Open field, three-chamber social, marble burying, and self-grooming tests were used for behavioral improvement assessment. Serum levels of chemokines were detected. Microbial total DNA was extracted from mouse fecal samples, and 16S rDNA was sequenced using Illumina. Our results showed that GMT treatment with original and cultured donor gut microbiota significantly ameliorated anxiety-like and repetitive behaviors and improved serum levels of chemokines including GRO-α (CXCL1), MIP-1α (CCL3), MCP-3 (CCL7), RANTES (CCL5), and Eotaxin (CCL11) in ASD mice. Meanwhile, the gut microbial communities of the two groups that received GMT treatment were changed compared with the ASD mice groups. In the group treated with in vitro cultured donor gut microbiota, there was a significant decrease in the relative abundance of key differential taxa, including S24-7, Clostridiaceae, Prevotella_other, and Candidatus Arthromitus. The relative abundance of these taxa reached close to the level of healthy mice. Prevotella_other also decreased in the group treated with original donor gut microbiota, with a significant increase in Ruminococcaceae and Oscillospira. The present study demonstrated that GMT with in vitro cultured microbiota also improved behavioral abnormalities and chemokine disorders in an ASD mouse model compared with GMT with original donor gut microbiota. In addition, it significantly modified several key differential taxa in gut microbial composition.}, }
@article {pmid32097837, year = {2020}, author = {Abramov, SM and Tejada, J and Grimm, L and Schädler, F and Bulaev, A and Tomaszewski, EJ and Byrne, JM and Straub, D and Thorwarth, H and Amils, R and Kleindienst, S and Kappler, A}, title = {Role of biogenic Fe(III) minerals as a sink and carrier of heavy metals in the Rio Tinto, Spain.}, journal = {The Science of the total environment}, volume = {718}, number = {}, pages = {137294}, doi = {10.1016/j.scitotenv.2020.137294}, pmid = {32097837}, issn = {1879-1026}, abstract = {Oxidation of sulfide ores in the Iberian Pyrite Belt region leads to the presence of extremely high concentration of dissolved heavy metals (HMs) in the acidic water of the Rio Tinto. Fe(II) is microbially oxidized resulting in the formation of suspended particulate matter (SPM) consisting of microbial cells and Fe(III) minerals with co-precipitated HMs. Although substantial amount of HM-bearing SPM is likely deposited to river sediment, a portion can still be transported through estuary to the coastal ocean. Therefore, the mechanisms of SPM formation and transport along the Rio Tinto are important for coastal-estuarine zone. In order to reveal these mechanisms, we performed diurnal sampling of Rio Tinto water, mineralogical and elemental analysis of sediment from the middle course and the estuary of the river. We identified two divergent but interrelated pathways of HM transfer. The first longitudinal pathway is the transport of SPM-associated metals such as As (6.58 μg/L), Pb (3.51 μg/L) and Cr (1.30 μg/L) to the coastal ocean. The second sedimentation pathway contributes to the continuous burial of HMs in the sediment throughout the river. In the middle course, sediment undergoes mineralogical transformations during early diagenesis and traps HMs (e.g. 1.6 mg/g of As, 1.23 mg/g of Pb and 0.1 mg/g of Cr). In the estuary, HMs are accumulated in a distinct anoxic layer of sediment (e.g. 1.5 mg/g of As, 2.09 mg/g of Pb and 0.04 mg/g of Cr). Our results indicate that microbially precipitated Fe(III) minerals (identified as ferrihydrite and schwertmannite) play a key role in maintaining these divergent HM pathways and as a consequence are crucial for HM mobility in the Rio Tinto.}, }
@article {pmid32094388, year = {2020}, author = {Marsland, R and Cui, W and Mehta, P}, title = {A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3308}, doi = {10.1038/s41598-020-60130-2}, pmid = {32094388}, issn = {2045-2322}, support = {1R35GM119461//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Mathematical Modeling of Living Systems//Simons Foundation/ ; }, abstract = {Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) - a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization - can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.}, }
@article {pmid32094260, year = {2020}, author = {Samanta, P and Mandal, RS and Saha, RN and Shaw, S and Ghosh, P and Dutta, S and Ghosh, A and Imamura, D and Morita, M and Ohnishi, M and Ramamurthy, T and Mukhopadhyay, AK}, title = {A point mutation in carR involved in the emergence of polymyxin B-sensitive Vibrio cholerae O1 El Tor biotype by influencing gene transcription.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1128/IAI.00080-20}, pmid = {32094260}, issn = {1098-5522}, abstract = {Antimicrobial peptides play an important role in host-defence against Vibrio cholerae Generally, V. cholerae O1 classical biotype is polymyxin B (PB) sensitive and El Tor is relatively resistant. Detection of classical biotype traits like cholera toxin B-subunit gene ctxB1 and PB sensitivity in El Tor strains have been reported in recent years, including in the devastating Yemen cholera outbreak during 2016-18. To investigate the factor(s) responsible for the shift in the trend of sensitivity towards PB, we studied the two-component system carRS regulating the lipid A modification of El Tor vibrios and found that only carR contains a SNP in recently emerged PB-sensitive strains. We designated these two alleles present in PB-resistant and sensitive strains as carRR and carRS , respectively and replaced the carRS allele of a sensitive strain with carRR using allelic exchange approach. The sensitive strain then became resistant. PB-resistant N16961 was made susceptible to PB in a similar fashion. Our in-silico CarR models suggested that D89N substitution in more stable CarRS brings the two structural domains of CarR closer constricting the DNA binding cleft. This probably reduces the expression of carR-regulated almEFG operon inducing the PB-susceptibility. Expressions of almEFG in PB-sensitive strains were found to be down-regulated at natural culturing condition. In addition, the expression of carR and almEG decreased in all strains with increased concentration of extracellular Ca2+ but increased with the rise in pH. The down-regulation of almEFG in CarRS strains confirmed that G265A mutation is responsible for the emergence of PB-sensitive El Tor strains.}, }
@article {pmid32093252, year = {2020}, author = {Gómez Del Pulgar, EM and Benítez-Páez, A and Sanz, Y}, title = {Safety Assessment of Bacteroides Uniformis CECT 7771, a Symbiont of the Gut Microbiota in Infants.}, journal = {Nutrients}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/nu12020551}, pmid = {32093252}, issn = {2072-6643}, support = {613979//Seventh Framework Programme/ ; }, abstract = {The formulation of next-generation probiotics requires competent preclinical studies to show their efficacy and safety status. This study aims to confirm the safety of the prolonged oral use of Bacteroides uniformis CECT 7771, a strain that protected against metabolic disorders and obesity in preclinical trials, in a sub-chronic 90 day trial in animals. The safety assessment was conducted in male and female Wistar rats (n = 50) administered increasing doses (108 CFU/day, 109 CFU/day, or 1010 CFU/day) of B. uniformis CECT 7771, 1010 CFU/day of B. longum ATCC 15707T, which complies with the qualifying presumption of safety (QPS) status of the EU, or vehicle (placebo), as the control. Pancreatic, liver, and kidney functions and cytokine concentrations were analyzed. Bacterial translocation to peripheral tissues was evaluated, and colon integrity was investigated histologically. No adverse metabolic or tissue integrity alterations were associated with treatments; however, alanine aminotransferase levels and the ratio of anti-inflammatory to pro-inflammatory cytokines in serum indicated a potentially beneficial role of B. uniformis CECT 7771 at specific doses. Additionally, the microbial community structure was modified by the interventions, and potentially beneficial gut bacteria were increased. The results indicated that the oral consumption of B. uniformis CECT 7771 during a sub-chronic 90 day study in rats did not raise safety concerns.}, }
@article {pmid32092511, year = {2020}, author = {Wei, H and Gao, D and Liu, Y and Lin, X}, title = {Sediment nitrate reduction processes in response to environmental gradients along an urban river-estuary-sea continuum.}, journal = {The Science of the total environment}, volume = {718}, number = {}, pages = {137185}, doi = {10.1016/j.scitotenv.2020.137185}, pmid = {32092511}, issn = {1879-1026}, abstract = {Sediment denitrification (DEN), anaerobic ammonium oxidation (Anammox), and dissimilatory nitrate reduction to ammonium (DNRA) are three important nitrate (NO3-) reduction pathways in aquatic ecosystems. These processes modify nitrogen (N) loadings from land to the ocean, with important implications on the management of coastal eutrophication. While NO3- reduction has been studied intensively for various types of habitats, studies on its distributions along river-estuary-sea continua remain scarce. In this study, we examined these three pathways along a N-laden urban river-estuary-sea continuum comprised of three types of habitats (urban river, estuary, and adjacent sea) in the densely populated Shanghai-East China Sea area. The potential DEN, Anammox, and DNRA rates decreased seaward both in summer and winter in response to decreasing sediment organic matter (OM, 20 to 7 to 7 mg C g-1), ferrous oxide (9 to 2.7 to 2.8 mg Fe g-1), and bottom water dissolved inorganic nitrogen (543 to 112 to 21 μM). Among these pathways, DEN remained a major component (~69.6%) across habitats, while Anammox (47.9%) rivaled DEN (48.3%) in the urban river in winter. N retention index (NIRI), the ratio between retained and removed NO3-, ranged from 0 to 0.5 and increased downstream. Together, these results suggest that the decreasing gradients of OM and inorganic matter shape the distribution of NO3- reduction along the continuum, reflecting the diminishing impact of the river and human inputs from the urban river to the ocean. Our results highlight the importance of taking a continuum perspective in N cycling studies and emphasize the role of urban rivers as N removal hotspots, which should be a focus of research and management.}, }
@article {pmid32091935, year = {2020}, author = {Balachandran, M and Cross, KL and Podar, M}, title = {Single-Cell Genomics and the Oral Microbiome.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {22034520907380}, doi = {10.1177/0022034520907380}, pmid = {32091935}, issn = {1544-0591}, abstract = {The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. Studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.}, }
@article {pmid32090516, year = {2020}, author = {Hess, AL and Larsen, LH and Udesen, PB and Sanz, Y and Larsen, TM and Dalgaard, LT}, title = {Levels of Circulating miR-122 are Associated with Weight Loss and Metabolic Syndrome.}, journal = {Obesity (Silver Spring, Md.)}, volume = {28}, number = {3}, pages = {493-501}, doi = {10.1002/oby.22704}, pmid = {32090516}, issn = {1930-739X}, support = {115372//EU/EFPIA Innovative Medicines Initiative Joint Undertaking EMIF/ ; 613979//Seventh Framework Programme/ ; }, abstract = {OBJECTIVE: This study investigated whether the levels of specific serum microRNAs (miRNAs) were altered following diet-induced weight loss and whether the serum miRNAs differed in the presence of the metabolic syndrome.<br><br>METHODS: The study was a weight loss intervention trial with a prescribed energy deficit of approximately 500 kcal/d. Levels of 22 miRNAs were determined in serum samples from 85 participants with overweight or obesity. miRNAs were analyzed using TaqMan Array miRNA Cards and normalized to the geometric mean of spiked-in ath-miR-159a and U6 small nuclear RNA using the ΔCT method.<br><br>RESULTS: The average weight loss was 5.7 kg (P < 0.001). miR-122-5p (-0.18 ± 0.06 log fold relative to initial, P < 0.01) and miR-193a-5p (-0.12 ± 0.04, P < 0.01) levels decreased in response to weight loss. miR-126a-3p (0.11 ± 0.04, P = 0.01) and miR-222-3p (1.51 ± 0.12, P < 0.001) levels increased. Furthermore, a higher level of miR-122-5p was observed at baseline in participants with the metabolic syndrome compared with participants without (0.28 ± 0.08, P < 0.01).<br><br>CONCLUSIONS: Changes in circulating miR-122-5p, miR-126a-3p, miR-193a-5p, and miR-222-3p in response to diet-induced weight loss are demonstrated. Furthermore, assessment of miR-122-5p could be an indicator of an adverse metabolic health status independent of obesity.}, }
@article {pmid32088790, year = {2020}, author = {Zhang, S and Shao, Y and Zhao, X and Li, C and Guo, M and Lv, Z and Zhang, W}, title = {Indole contributes to tetracycline resistance via the outer membrane protein OmpN in Vibrio splendidus.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {36}, number = {3}, pages = {36}, doi = {10.1007/s11274-020-02813-6}, pmid = {32088790}, issn = {1573-0972}, support = {2018YFD0900603//the National Key R&amp;D Program of China/ ; 41676141//the National Natural Science Foundation of China/ ; }, abstract = {As an interspecies and interkingdom signaling molecule, indole has recently received attention for its diverse effects on the physiology of both bacteria and hosts. In this study, indole increased the tetracycline resistance of Vibrio splendidus. The minimal inhibitory concentration of tetracycline was 10 μg/mL, and the OD600 of V. splendidus decreased by 94.5% in the presence of 20 μg/mL tetracycline; however, the OD600 of V. splendidus with a mixture of 20 μg/mL tetracycline and 125 μM indole was 10- or 4.5-fold higher than that with only 20 μg/mL tetracycline at different time points. The percentage of cells resistant to 10 μg/mL tetracycline was 600-fold higher in the culture with an OD600 of approximately 2.0 (higher level of indole) than that in the culture with an OD600 of 0.5, which also meant that the level of indole was correlated to the tetracycline resistance of V. splendidus. Furthermore, one differentially expressed protein, which was identified as the outer membrane porin OmpN using SDS-PAGE combined with MALDI-TOF/TOF MS, was upregulated. Consequently, the expression of the ompN gene in the presence of either tetracycline or indole and simultaneously in the presence of indole and tetracycline was upregulated by 1.8-, 2.54-, and 6.01-fold, respectively, compared to the control samples. The combined results demonstrated that indole enhanced the tetracycline resistance of V. splendidus, and this resistance was probably due to upregulation of the outer membrane porin OmpN.}, }
@article {pmid32088758, year = {2020}, author = {Law, CKY and De Henau, R and De Vrieze, J}, title = {Feedstock thermal pretreatment selectively steers process stability during the anaerobic digestion of waste activated sludge.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-020-10472-8}, pmid = {32088758}, issn = {1432-0614}, support = {GA 826244//Horizon 2020/ ; }, abstract = {Strategies to enhance process performance of anaerobic digestion remain of key importance to promote wider usage of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e. organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process stability of the digesters fed sterile WAS, with a 92 ± 45% decrease in methane production, compared to a 42 ± 31% increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process stability between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na+ L-1. Feedstock sterilization through thermal pretreatment strongly impacted the microbial community in the digesters. In conclusion, feedstock thermal pretreatment strongly impacted anaerobic digestion process stability, due to feedstock inoculation and compositional modification.}, }
@article {pmid32086543, year = {2020}, author = {Bao, G and Song, M and Wang, Y and Saikkonen, K and Li, C}, title = {Does Epichloë Endophyte Enhance Host Tolerance to Root Hemiparasite?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01496-8}, pmid = {32086543}, issn = {1432-184X}, support = {31660690//National Natural Science Foundation of China/ ; 31700098//National Natural Science Foundation of China/ ; 1111126//Cooperation Program of Qinghai Province/ ; 295976//Academy of Finland/ ; 326226//Academy of Finland/ ; 2017-ZJ-Y12//QingHai Department of Science and Technology/ ; }, abstract = {Epichloë endophytes have been shown to be mutualistic symbionts of cool-season grasses under most environmental conditions. Although pairwise interactions between hemiparasites and their hosts are heavily affected by host-associated symbiotic microorganisms, little attention has been paid to the effects of microbe-plant interactions, particularly endophytic symbiosis, in studies examining the effects of parasitic plants on host performance. In this study, we performed a greenhouse experiment to examine the effects of hereditary Epichloë endophyte symbiosis on the growth of two host grasses (Stipa purpurea and Elymus tangutorum) in the presence or absence of a facultative root hemiparasite (Pedicularis kansuensis Maxim). We observed parasitism of both hosts by P. kansuensis: when grown with a host plant, the hemiparasite decreased the performance of the host while improving its own biomass and survival rate of the hemiparasite. Parasitized endophyte-infected S. purpurea plants had higher biomass, tillers, root:shoot ratio, and photosynthetic parameters and a lower number of functional haustoria than the endophyte-free S. purpurea conspecifics. By contrast, parasitized endophyte-infected E. tangutorum had a lower biomass, root:shoot ratio, and photosynthetic parameters and a higher number of haustoria and functional haustoria than their endophyte-free counterparts. Our results reveal that the interactions between the endophytes and the host grasses are context dependent and that plant-plant interactions can strongly affect their mutualistic interactions. Endophytes originating from S. purpurea alleviate the host biomass reduction by P. kansuensis and growth depression in the hemiparasite. These findings shed new light on using grass-endophyte symbionts as biocontrol methods for the effective and sustainable management of this weedy hemiparasite.}, }
@article {pmid32086129, year = {2020}, author = {Elhalis, H and Cox, J and Zhao, J}, title = {Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans.}, journal = {International journal of food microbiology}, volume = {321}, number = {}, pages = {108544}, doi = {10.1016/j.ijfoodmicro.2020.108544}, pmid = {32086129}, issn = {1879-3460}, abstract = {The microbial ecology in the fermentation of Australian coffee beans was investigated in this study. Pulped coffee beans were kept underwater for 36 h before air dried. Samples were collected periodically, and the microbial communities were analyzed by culture-dependent and independent methods. Changes in sugars, organic acids and microbial metabolites in the mucilage and endosperm of the coffee beans during fermentation were monitored by HPLC. Culture-dependent methods identified 6 yeast and 17 bacterial species, while the culture-independent methods, multiple-step total direct DNA extraction and high throughput sequencing, identified 212 fungal and 40 bacterial species. Most of the microbial species in the community have been reported for wet fermentation of coffee beans in other parts of the world, but the yeast Pichia kudriavzevii was isolated for the first time in wet coffee bean fermentation. The bacterial community was dominated by aerobic mesophilic bacteria (AMB) with Citrobacter being the predominant genus. Hanseniaspora uvarum and Pichia kudriavzevii were the predominant yeasts while Leuconostoc mesenteroides and Lactococcus lactis were the predominant LAB. The yeasts and bacteria grew significantly during fermentation, utilizing sugars in the mucilage and produced mannitol, glycerol, and lactic acid, leading to a significant decrease in pH. The results of this study provided a preliminary understanding of the microbial ecology of wet coffee fermentation under Australian conditions. Further studies are needed to explore the impact of microbial growth and metabolism on coffee quality, especially flavour.}, }
@article {pmid32084407, year = {2020}, author = {Lories, B and Roberfroid, S and Dieltjens, L and De Coster, D and Foster, KR and Steenackers, HP}, title = {Biofilm Bacteria Use Stress Responses to Detect and Respond to Competitors.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2020.01.065}, pmid = {32084407}, issn = {1879-0445}, abstract = {Bacteria use complex regulatory networks to cope with stress, but the function of these networks in natural habitats is poorly understood. The competition sensing hypothesis states that bacterial stress response systems can serve to detect ecological competition, but studying regulatory responses in diverse communities is challenging. Here, we solve this problem by using differential fluorescence induction to screen the Salmonella Typhimurium genome for loci that respond, at the single-cell level, to life in biofilms with competing strains of S. Typhimurium and Escherichia coli. This screening reveals the presence of competing strains drives up the expression of genes associated with biofilm matrix production (CsgD pathway), epithelial invasion (SPI1 invasion system), and, finally, chemical efflux and antibiotic tolerance (TolC efflux pump and AadA aminoglycoside 3-adenyltransferase). We validate that these regulatory changes result in the predicted phenotypic changes in biofilm, mammalian cell invasion, and antibiotic tolerance. We further show that these responses arise via activation of major stress responses, providing direct support for the competition sensing hypothesis. Moreover, inactivation of the type VI secretion system (T6SS) of a competitor annuls the responses to competition, indicating that T6SS-derived cell damage activates these stress response systems. Our work shows that bacteria use stress responses to detect and respond to competition in a manner important for major phenotypes, including biofilm formation, virulence, and antibiotic tolerance.}, }
@article {pmid32080691, year = {2020}, author = {Xu, J and Ma, Z and Li, X and Liu, L and Hu, X}, title = {A more pronounced effect of type III resistant starch vs. type II resistant starch on ameliorating hyperlipidemia in high fat diet-fed mice is associated with its supramolecular structural characteristics.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/c9fo02025j}, pmid = {32080691}, issn = {2042-650X}, abstract = {The anti-obesity effects of two categories of resistant starch (RS) including RS2 (isolated from untreated lentil starch, URS) and RS3 (isolated from autoclaved and retrograded lentil starch, ARS) on mice with high-fat (HF) diet-induced obesity and the supramolecular structure-in vivo physiological functionality relationship of RS were investigated. Following 6 consecutive weeks, the obese mice in the two RS administered groups displayed suppression of body/liver weight gain and an improvement in serum glucose/lipid profile, antioxidant status, and gut microbiota structure. Compared with the URS intervention group, the ARS administration resulted in a more pronounced effect in controlling body weight, together with a more prominent reduction in blood glucose and triglyceride concentration, as well as a significant increase in the HDL-c level in obese mice. The ARS group also showed an absolute advantage over URS in suppressing the oxidative stress and regulating the liver function induced by the HF diet. Simultaneously, the administration of URS and ARS efficiently suppressed the HF-diet induced alterations in gut microbial ecology, with an obviously decreased ratio of Firmicutes to Bacteroidetes, especially for the ARS group, suggesting its beneficial role in gastrointestinal tract health. The structural characterization results revealed that ARS and URS differed significantly in their supramolecular structural characteristics, where ARS exhibited a higher proportion of crystallinity and double helix content with an X-ray diffraction pattern of a CB type crystal polymorph and a low proportion of molecular inhomogeneity. This study suggested that the difference in the anti-obesity effect of resistant starches was a consequence of the diversity in their structural features.}, }
@article {pmid32076744, year = {2020}, author = {Chen, H and Wang, M and Chang, S}, title = {Disentangling Community Structure of Ecological System in Activated Sludge: Core Communities, Functionality, and Functional Redundancy.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01492-y}, pmid = {32076744}, issn = {1432-184X}, abstract = {The microbial ecosystems of the sludge were characterized in terms of the core community structure, functional pathways, and functional redundancy through Illumina MiSeq sequencing and PICRUSt analysis on the activated sludge (AS) samples from an extended activated aeration process. Based on the identified OTU distribution, we identified 125 core community genera, including 3 abundant core genera and 21 intermittent abundant core genera. Putative genera Nitrosomonas, Nitrotoga, Zoogloea, Novosphingobium, Thermomonas, Amaricoccus, Tetrasphaera, Candidatus Microthrix, and Haliscomenobacter, which are associated with functions of nitrifying, denitrifying, phosphorus accumulating, and bulking and foaming, were found to present as the core community organisms in the AS sampled from the conventional extended aeration AS processes. The high-abundant nitrogen metabolic pathways were associated with nitrate reduction to ammonium (DNRA and ANRA), denitrification, and nitrogen fixation, while the ammonia oxidation-related genes (amo) were rarely annotated in the AS samples. Strict functional redundancy was not found with the AS ecosystem as it showed a high correlation between the community composition similarity and function similarity. In addition, the classified dominant core genera community was found to be sufficient to characterize the functionality of AS, which could invigorate applications of 16S rDNA MiSeq sequencing and PICRUSt for the prediction of functions of AS ecosystems.}, }
@article {pmid32076743, year = {2020}, author = {Aubé, J and Senin, P and Bonin, P and Pringault, O and Jeziorski, C and Bouchez, O and Klopp, C and Guyoneaud, R and Goñi-Urriza, M}, title = {Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01493-x}, pmid = {32076743}, issn = {1432-184X}, support = {ANR11 BSV7 014 01//Agence Nationale de la Recherche/ ; }, abstract = {Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.}, }
@article {pmid32075981, year = {2020}, author = {Hernandez-Sanabria, E and Heiremans, E and Calatayud Arroyo, M and Props, R and Leclercq, L and Snoeys, J and Van de Wiele, T}, title = {Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {9}, doi = {10.1038/s41522-020-0119-0}, pmid = {32075981}, issn = {2055-5008}, support = {179PO8916W//Agentschap Innoveren en Ondernemen (Flanders Innovation &amp; Entrepreneurship)/ ; 12R2717N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {Celecoxib has been effective in the prevention and treatment of chronic inflammatory disorders through inhibition of altered cyclooxygenase-2 (COX-2) pathways. Despite the benefits, continuous administration may increase risk of cardiovascular events. Understanding microbiome-drug-host interactions is fundamental for improving drug disposition and safety responses of colon-targeted formulations, but little information is available on the bidirectional interaction between individual microbiomes and celecoxib. Here, we conducted in vitro batch incubations of human faecal microbiota to obtain a mechanistic proof-of-concept of the short-term impact of celecoxib on activity and composition of colon bacterial communities. Celecoxib-exposed microbiota shifted metabolic activity and community composition, whereas total transcriptionally active bacterial population was not significantly changed. Butyrate production decreased by 50% in a donor-dependent manner, suggesting that celecoxib impacts in vitro fermentation. Microbiota-derived acetate has been associated with inhibition of cancer markers and our results suggest uptake of acetate for bacterial functions when celecoxib was supplied, which potentially favoured bacterial competition for acetyl-CoA. We further assessed whether colon microbiota modulates anti-inflammatory efficacy of celecoxib using a simplified inflammation model, and a novel in vitro simulation of the enterohepatic metabolism. Celecoxib was responsible for only 5% of the variance in bacterial community composition but celecoxib-exposed microbiota preserved barrier function and decreased concentrations of IL-8 and CXCL16 in a donor-dependent manner in our two models simulating gut inflammatory milieu. Our results suggest that celecoxib-microbiome-host interactions may not only elicit adaptations in community composition but also in microbiota functionality, and these may need to be considered for guaranteeing efficient COX-2 inhibition.}, }
@article {pmid32075196, year = {2020}, author = {Dhakar, K and Pandey, A}, title = {Microbial Ecology from the Himalayan Cryosphere Perspective.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, doi = {10.3390/microorganisms8020257}, pmid = {32075196}, issn = {2076-2607}, abstract = {Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.}, }
@article {pmid32072187, year = {2020}, author = {Junges, DSB and Delabeneta, MF and Rosseto, LRB and Nascimento, BL and Paris, AP and Persel, C and Loth, EA and Simão, RCG and Menolli, RA and Paula, CR and Gandra, RF}, title = {Antibiotic Activity of Wickerhamomyces anomalus Mycocins on Multidrug-Resistant Acinetobacter baumannii.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01495-9}, pmid = {32072187}, issn = {1432-184X}, abstract = {To evaluate the susceptibility of multidrug-resistant Acinetobacter baumannii to mycocins produced by Wickerhamomyces anomalus and to verify the cytotoxicity of these compounds. Three culture supernatants of W. anomalus (WA40, WA45, and WA92), containing mycocins (WA40M1, WA45M2, and WA92M3), were tested on A. baumannii using broth microdilution methods, solid medium tests, and cytotoxicity tests in human erythrocytes and in Artemia saline Leach. W. anomalus was able to produce high antimicrobial mycocins, as even at high dilutions, they inhibited A. baumannii. In a solid medium, it was possible to observe the inhibition of A. baumannii, caused by the diffusion of mycocins between agar. Finally, the three supernatants were not cytotoxic when tested on human erythrocytes and Artemia salina. According to the evidence in this study, the mycocins of W. anomalus have been effective and could be used in the development of new antimicrobial substances.}, }
@article {pmid32071708, year = {2020}, author = {Klimenko, NS and Tyakht, AV and Toshchakov, SV and Shevchenko, MA and Korzhenkov, AA and Afshinnekoo, E and Mason, CE and Alexeev, DG}, title = {Co-occurrence patterns of bacteria within microbiome of Moscow subway.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {314-322}, doi = {10.1016/j.csbj.2020.01.007}, pmid = {32071708}, issn = {2001-0370}, abstract = {Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers. Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New-York City subway microbiome. Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, &quot;shotgun&quot; metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology and urban design.}, }
@article {pmid32071705, year = {2020}, author = {Chen, X and Krug, L and Yang, H and Li, H and Yang, M and Berg, G and Cernava, T}, title = {Nicotiana tabacum seed endophytic communities share a common core structure and genotype-specific signatures in diverging cultivars.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {287-295}, doi = {10.1016/j.csbj.2020.01.004}, pmid = {32071705}, issn = {2001-0370}, abstract = {Seed endophytes of crop plants have recently received increased attention due to their implications in plant health and the potential to be included in agro-biotechnological applications. While previous studies indicated that plants from the Solanaceae family harbor a highly diverse seed microbiome, genotype-specific effects on the community composition and structure remained largely unexplored. The present study revealed Enterobacteriaceae-dominated seed-endophytic communities in four Nicotiana tabacum L. cultivars originating from Brazil, China, and the USA. When the dissimilarity of bacterial communities was assessed, none of the cultivars showed significant differences in microbial community composition. Various unusual endophyte signatures were represented by Spirochaetaceae family members and the genera Mycobacterium, Clostridium, and Staphylococcus. The bacterial fraction shared by all cultivars was dominated by members of the phyla Proteobacteria and Firmicutes. In total, 29 OTUs were present in all investigated cultivars and accounted for 65.5% of the combined core microbiome reads. Cultivars from the same breeding line were shown to share a higher number of common OTUs than more distant lines. Moreover, the Chinese cultivar Yunyan 87 contained the highest number (33 taxa) of unique signatures. Our results indicate that a distinct proportion of the seed microbiome of N. tabacum remained unaffected by breeding approaches of the last century, while a substantial proportion co-diverged with the plant genotype. Moreover, they provide the basis to identify plant-specific endophytes that could be addressed for upcoming biotechnological approaches in agriculture.}, }
@article {pmid32071163, year = {2020}, author = {Röttjers, L and Faust, K}, title = {manta: a Clustering Algorithm for Weighted Ecological Networks.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSystems.00903-19}, pmid = {32071163}, issn = {2379-5077}, abstract = {Microbial network inference and analysis have become successful approaches to extract biological hypotheses from microbial sequencing data. Network clustering is a crucial step in this analysis. Here, we present a novel heuristic network clustering algorithm, manta, which clusters nodes in weighted networks. In contrast to existing algorithms, manta exploits negative edges while differentiating between weak and strong cluster assignments. For this reason, manta can tackle gradients and is able to avoid clustering problematic nodes. In addition, manta assesses the robustness of cluster assignment, which makes it more robust to noisy data than most existing tools. On noise-free synthetic data, manta equals or outperforms existing algorithms, while it identifies biologically relevant subcompositions in real-world data sets. On a cheese rind data set, manta identifies groups of taxa that correspond to intermediate moisture content in the rinds, while on an ocean data set, the algorithm identifies a cluster of organisms that were reduced in abundance during a transition period but did not correlate strongly to biochemical parameters that changed during the transition period. These case studies demonstrate the power of manta as a tool that identifies biologically informative groups within microbial networks.IMPORTANCE manta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.}, }
@article {pmid32071161, year = {2020}, author = {Clark, CM and Murphy, BT and Sanchez, LM}, title = {A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSystems.00813-19}, pmid = {32071161}, issn = {2379-5077}, }
@article {pmid32071158, year = {2020}, author = {McAllister, SM and Polson, SW and Butterfield, DA and Glazer, BT and Sylvan, JB and Chan, CS}, title = {Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSystems.00553-19}, pmid = {32071158}, issn = {2379-5077}, abstract = {Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.}, }
@article {pmid32070256, year = {2020}, author = {Ossowicki, A and Tracanna, V and Petrus, MLC and van Wezel, G and Raaijmakers, JM and Medema, MH and Garbeva, P}, title = {Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1921}, pages = {20192527}, doi = {10.1098/rspb.2019.2527}, pmid = {32070256}, issn = {1471-2954}, abstract = {In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.}, }
@article {pmid32068849, year = {2020}, author = {Pratama, AA and Jiménez, DJ and Chen, Q and Bunk, B and Spröer, C and Overmann, J and van Elsas, JD}, title = {Delineation of a subgroup of the genus Paraburkholderia, including P. terrae DSM 17804T, P. hospita DSM 17164T and four soil-isolated fungiphiles, reveals remarkable genomic and ecological features - Proposal for the definition of a P. hospita species cluster.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evaa031}, pmid = {32068849}, issn = {1759-6653}, abstract = {The fungal-interactive (fungiphilic) strains BS001, BS007, BS110 and BS437 have previously been preliminarily assigned to the species Paraburkholderia terrae. However, in the (novel) genus Paraburkholderia, an as-yet unresolved subgroup exists, that clusters around P. hospita (containing the species P. terrae, P. hospita and P. caribensis). To shed light on the precise relationships across the respective type strains and the novel fungiphiles, we here compare their genomic and ecophysiological features. To reach this goal, the genomes of the three type strains, with sizes ranging from 9.0 to 11.5 Mb, were de novo sequenced and the high-quality genomes analyzed. Using whole-genome, ribosomal RNA and marker-gene-concatenate analyses, close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T, versus more remote relationships to P. caribensis DSM 13236T were found. All four fungiphilic strains clustered closely to the two-species cluster. Analyses of average nucleotide identities (ANIm) and tetranucleotide frequencies (TETRA) confirmed the close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T (ANIm = 95.42; TETRA = 0.99784), as compared to the similarities of each one of these strains to P. caribensis DSM 13236T. A species cluster was thus proposed. Furthermore, high similarities of the fungiphilic strains BS001, BS007, BS110 and BS437 with this cluster were found, indicating that these strains also make part of it, being closely linked to P. hospita DSM 17164T (ANIm = 99%; TETRA = 0.99). We propose to coin this cluster the P. hospita species cluster (containing P. hospita DSM 17164T, P. terrae DSM 17804T and strains BS001, BS007, BS110 and BS437), being clearly divergent from the closely related species P. caribiensis (type strain DSM 13236T). Moreover, given their close relatedness to P. hospita DSM 17164T within the cluster, we propose to rename the four fungiphilic strains as members of P. hospita. Analysis of migratory behavior along with fungal growth through soil revealed both P. terrae DSM 17804T and P. hospita DSM 17164T (next to the four fungiphilic strains) to be migration-proficient, whereas P. caribensis DSM 13236T was a relatively poor migrator. Examination of predicted functions across the genomes of the seven investigated strains, next to several selected additional ones, revealed the common presence of features in the P. hospita cluster strains that are potentially important in interactions with soil fungi. Thus, genes encoding specific metabolic functions, biofilm formation (pelABCDEFG, pgaABCD, alginate-related genes), motility/chemotaxis, type-4 pili and diverse secretion systems were found.}, }
@article {pmid32066625, year = {2020}, author = {Ghosh, TS and Rampelli, S and Jeffery, IB and Santoro, A and Neto, M and Capri, M and Giampieri, E and Jennings, A and Candela, M and Turroni, S and Zoetendal, EG and Hermes, GDA and Elodie, C and Meunier, N and Brugere, CM and Pujos-Guillot, E and Berendsen, AM and De Groot, LCPGM and Feskins, EJM and Kaluza, J and Pietruszka, B and Bielak, MJ and Comte, B and Maijo-Ferre, M and Nicoletti, C and De Vos, WM and Fairweather-Tait, S and Cassidy, A and Brigidi, P and Franceschi, C and O'Toole, PW}, title = {Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2019-319654}, pmid = {32066625}, issn = {1468-3288}, abstract = {OBJECTIVE: Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty.<br><br>DESIGN: We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet).<br><br>RESULTS: Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks.<br><br>CONCLUSION: Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.}, }
@article {pmid32063916, year = {2019}, author = {Orr, JN and Neilson, R and Freitag, TE and Roberts, DM and Davies, KG and Blok, VC and Cock, PJA}, title = {Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1763}, doi = {10.3389/fpls.2019.01763}, pmid = {32063916}, issn = {1664-462X}, abstract = {Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the most economically significant plant parasitic nematodes (PPNs). Highly species-specific nematode suppression may be observed in soils containing a sufficiently high density of Pasteuria spp. spores. This suppression is enacted by the bacteria via inhibition of root invasion and sterilization of the nematode host. Molecular methods for the detection of Pasteuria spp. from environmental DNA (eDNA) have been described; however, these methods are limited in both scale and in depth. We report the use of small subunit rRNA gene metabarcoding to profile Pasteuria spp. and nematode communities in parallel. We have investigated Pasteuria spp. population structure in Scottish soils using eDNA from two sources: soil extracted DNA from the second National Soil Inventory of Scotland (NSIS2); and nematode extracted DNA collected from farms in the East Scotland Farm Network (ESFN). We compared the Pasteuria spp. community culture to both nematode community structure and the physiochemical properties of soils. Our results indicate that Pasteuria spp. populations in Scottish soils are broadly dominated by two sequence variants. The first of these aligns with high identity to Pasteuria hartismeri, a species first described parasitizing Meloidogyne ardenensis, a nematode parasite of woody and perennial plants in northern Europe. The second aligns with a Pasteuria-like sequence which was first recovered from a farm near Edinburgh which was found to contain bacterial feeding nematodes and Pratylenchus spp. encumbered by Pasteuria spp. endospores. Further, soil carbon, moisture, bulk density, and pH showed a strong correlation with the Pasteuria spp. community composition. These results indicate that metabarcoding is appropriate for the sensitive, specific, and semi-quantitative profiling of Pasteuria species from eDNA.}, }
@article {pmid32062778, year = {2020}, author = {Nkongolo, KK and Narendrula-Kotha, R}, title = {Advances in monitoring soil microbial community dynamic and function.}, journal = {Journal of applied genetics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s13353-020-00549-5}, pmid = {32062778}, issn = {2190-3883}, support = {CRDP-J- 470535-2014//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.}, }
@article {pmid32062526, year = {2020}, author = {Iacumin, L and Osualdini, M and Bovolenta, S and Boscolo, D and Chiesa, L and Panseri, S and Comi, G}, title = {Microbial, chemico-physical and volatile aromatic compounds characterization of Pitina PGI, a peculiar sausage-like product of North East Italy.}, journal = {Meat science}, volume = {163}, number = {}, pages = {108081}, doi = {10.1016/j.meatsci.2020.108081}, pmid = {32062526}, issn = {1873-4138}, abstract = {Pitina is a fermented sausage-like produced in the mountainous area of the North-East Italy by artisanal plants without the use of both selected starters and casing (Slow Food Presidium). Originally, Pitina has been a way of preserving meat and it is manifactured by meat from ungulates mixed with pork lard, smoked, dryed and ripened. In this study, microbial ecology, physic-chemical parameters, and volatile aromatic compounds of Pitina SR and LR, which differ by the duration of ripening processes, were investigated. Results showed the good hygienic quality. Staphylococcus xylosus and Lactobacillus sakei were responsible for the ripening. Other Coagulase-negative Catalase-positive Cocci (CNCPC) and LAB species were identified: S. equorum, S. warneri, S. succinus and Carnobacterium divergens, Streptococcus equinus, Kocuria rhizophila. Giberella moniliformis and Penicillium turbatum were the only mould species isolated. Strain characterization demonstrated a high genetic variability. Raw meat, environment and ripening conditions seemed to affect strains distribution, which had an impact on the aromatic profile of the product.}, }
@article {pmid32062264, year = {2020}, author = {Stopelli, E and Duyen, VT and Mai, TT and Trang, PTK and Viet, PH and Lightfoot, A and Kipfer, R and Schneider, M and Eiche, E and Kontny, A and Neumann, T and Glodowska, M and Patzner, M and Kappler, A and Kleindienst, S and Rathi, B and Cirpka, O and Bostick, B and Prommer, H and Winkel, LHE and Berg, M}, title = {Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes.}, journal = {The Science of the total environment}, volume = {717}, number = {}, pages = {137143}, doi = {10.1016/j.scitotenv.2020.137143}, pmid = {32062264}, issn = {1879-1026}, abstract = {Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010-2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5-510 μg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 μg/L for the studied period of 2010-2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations.}, }
@article {pmid32061251, year = {2020}, author = {Zhu, X and Campanaro, S and Treu, L and Seshadri, R and Ivanova, N and Kougias, PG and Kyrpides, N and Angelidaki, I}, title = {Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {22}, doi = {10.1186/s40168-019-0780-9}, pmid = {32061251}, issn = {2049-2618}, support = {12-132654//Innovationfonden/ ; }, abstract = {Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.}, }
@article {pmid32060621, year = {2020}, author = {Walter, JM and Coutinho, FH and Leomil, L and Hargreaves, PI and Campeão, ME and Vieira, VV and Silva, BS and Fistarol, GO and Salomon, PS and Sawabe, T and Mino, S and Hosokawa, M and Miyashita, H and Maruyama, F and van Verk, MC and Dutilh, BE and Thompson, CC and Thompson, FL}, title = {Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01480-x}, pmid = {32060621}, issn = {1432-184X}, support = {BIOCOMP//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Universal//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; CNE//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (BR)/ ; }, abstract = {Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.}, }
@article {pmid32060494, year = {2020}, author = {Louca, P and Menni, C and Padmanabhan, S}, title = {Genomic determinants of hypertension with a focus on metabolomics and the gut microbiome.}, journal = {American journal of hypertension}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajh/hpaa022}, pmid = {32060494}, issn = {1941-7225}, abstract = {Epidemiologic and genomic studies have progressively improved our understanding of the causation of hypertension and the complex relationship with diet and environment. The majority of mendelian forms of syndromic hypotension and HTN have all been linked to mutations in genes whose encoded proteins regulate salt-water balance in the kidney, supporting the primacy of the kidneys in BP regulation. There are over 1,477 single nucleotide polymorphisms associated with blood pressure and hypertension and the challenge is establishing a causal role for these variants. Hypertension is a complex multifactorial phenotype and it is likely to be influenced by multiple factors including interactions between diet and lifestyle factors, microbiome and epigenetics. Given the finite genetic variability that is possible in humans, it is likely that incremental gains from single marker analyses have now plateaued and a greater leap in our understanding of the genetic basis of disease will come from integration of other omics and the interacting environmental factors. In this review, we focus on emerging results from the microbiome and metabolomics and discuss how leveraging these findings may facilitate a deeper understanding of the interrelationships between genomics, diet and microbial ecology in humans in the causation of essential hypertension.}, }
@article {pmid32059463, year = {2020}, author = {Costa, OYA and Zerillo, MM and Zühlke, D and Kielak, AM and Pijl, A and Riedel, K and Kuramae, EE}, title = {Responses of AcidobacteriaGranulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, doi = {10.3390/microorganisms8020244}, pmid = {32059463}, issn = {2076-2607}, support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 202496/2015-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.}, }
@article {pmid32056227, year = {2020}, author = {Smirnova, E and Puri, P and Muthiah, MD and Daitya, K and Brown, R and Chalasani, N and Liangpunsakul, S and Shah, VH and Gelow, K and Siddiqui, MS and Boyett, S and Mirshahi, F and Sikaroodi, M and Gillevet, P and Sanyal, AJ}, title = {Fecal microbiome distinguishes alcohol consumption from alcoholic hepatitis but does not discriminate disease severity.}, journal = {Hepatology (Baltimore, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/hep.31178}, pmid = {32056227}, issn = {1527-3350}, abstract = {BACKGROUND AND AIMS: The role of the intestinal microbiome in alcoholic hepatitis is not established. The aims of this study were to: (1) characterize the fecal microbial ecology associated with alcoholic hepatitis, (2) relate microbiome changes to disease severity and (3) infer the functional relevance of shifts in microbial ecology.<br><br>METHODS: The fecal microbiome in patients with moderate or severe alcoholic hepatitis (MAH and SAH) was compared to healthy (HC) and heavy drinking controls (HDC). Microbial taxa were identified by 16S pyrosequencing. Functional metagenomics was performed using PICRUSt. Fecal short chain fatty acids (SCFA) were measured using an LC/MS platform.<br><br>RESULTS: 78 participants (HC, n=24; HDC, n=20; MAH, n=10; SAH, n=24) were studied. Heavy drinking had a distinct signature compared to healthy controls with depletion of Bacteroidetes (46% vs 26%; p=0.01). Alcoholic hepatitis was associated with a distinct microbiome signature compared to heavy drinking controls (AUC=0.826); differential abundance of Ruminococcaceae, Veillonellaceae, Lachnospiraceae, Porphyromonadaceae, and Rikenellaceae families were the key contributors to these differences. The beta diversity was significantly different amongst the groups (PERMANOVA p < 0.001). Severe alcoholic hepatitis was associated with increased Proteobacteria (SAH 14% vs. HDC 7% and SAH vs. HC 2%, p=0.20 and 0.01 respectively). Firmicutes abundance declined from HDC to MAH to SAH (63% vs. 53% vs. 48% respectively, p=0.09 HDC vs. SAH). Microbial taxa did not distinguish between moderate and severe alcoholic hepatitis (PERMANOVA p= 0.785). SCFA producing bacteria (Lachnospiraceae and Ruminococcaceae) were decreased in alcoholic hepatitis, and a similar decrease was observed in fecal short chain fatty acids among alcoholic hepatitis patients.<br><br>CONCLUSIONS: There are distinct changes in fecal microbiome associated with development of but not severity of alcoholic hepatitis.}, }
@article {pmid32055819, year = {2020}, author = {Marlow, JJ and Colocci, I and Jungbluth, SP and Weber, NM and Gartman, A and Kallmeyer, J}, title = {Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaa031}, pmid = {32055819}, issn = {1574-6968}, abstract = {Interactions among microorganisms and their mineralogical substrates govern the structure, function, and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset, and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2, and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities 'as they really are' and explore determinants of metabolic activity across a range of microbiomes.}, }
@article {pmid32055027, year = {2020}, author = {Hatzenpichler, R and Krukenberg, V and Spietz, RL and Jay, ZJ}, title = {Next-generation physiology approaches to study microbiome function at single cell level.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41579-020-0323-1}, pmid = {32055027}, issn = {1740-1534}, abstract = {The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.}, }
@article {pmid32054207, year = {2019}, author = {Park, J and Kim, EB}, title = {Differences in microbiome and virome between cattle and horses in the same farm.}, journal = {Asian-Australasian journal of animal sciences}, volume = {}, number = {}, pages = {}, doi = {10.5713/ajas.19.0267}, pmid = {32054207}, issn = {1011-2367}, abstract = {Objective: The ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal's health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated.<br><br>Methods: Here, we collected feces and dust samples (4 groups. Cattle feces; C_F, Horse feces; H_F, Cattle dust; C_D, and Horse dust; H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing.<br><br>Results: Dust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% - max 42.8%), Firmicutes (19.1% - 24.9%), Bacteroidetes (10.6% - 22.1%), and Actinobacteria (6.1% - 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease (FMD) virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected.<br><br>Conclusions: Our results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.}, }
@article {pmid32052099, year = {2020}, author = {Nakabachi, A and Malenovský, I and Gjonov, I and Hirose, Y}, title = {16S rRNA Sequencing Detected Profftella, Liberibacter, Wolbachia, and Diplorickettsia from Relatives of the Asian Citrus Psyllid.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01491-z}, pmid = {32052099}, issn = {1432-184X}, support = {KAKENHI grant number 26292174//the Japan Society for the Promotion of Science/ ; NA//Tatematsu Foundation/ ; NA//Nagase Science and Technology Foundation/ ; }, abstract = {The Asian citrus psyllid Diaphorina citri (Hemiptera: Psylloidea) is a serious pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria: Rhizobiales), the causative agents of the incurable citrus disease, huanglongbing or greening disease. Diaphorina citri possesses a specialized organ called a bacteriome, which harbors vertically transmitted intracellular mutualists, Ca. Carsonella ruddii (Gammaproteobacteria: Oceanospirillales) and Ca. Profftella armatura (Gammaproteobacteria: Betaproteobacteriales). Whereas Carsonella is a typical nutritional symbiont, Profftella is an unprecedented type of toxin-producing defensive symbiont, unusually sharing organelle-like features with nutritional symbionts. Additionally, many D. citri strains are infected with Wolbachia, which manipulate reproduction in various arthropod hosts. In the present study, in an effort to obtain insights into the evolution of symbioses between Diaphorina and bacteria, microbiomes of psyllids closely related to D. citri were investigated. Bacterial populations of Diaphorina cf. continua and Diaphorina lycii were analyzed using Illumina sequencing of 16S rRNA gene amplicons and compared with data obtained from D. citri. The analysis revealed that all three Diaphorina spp. harbor Profftella as well as Carsonella lineages, implying that Profftella is widespread within the genus Diaphorina. Moreover, the analysis identified Ca. Liberibacter europaeus and Diplorickettsia sp. (Gammaproteobacteria: Diplorickettsiales) in D. cf. continua, and a total of four Wolbachia (Alphaproteobacteria: Rickettsiales) lineages in the three psyllid species. These results provide deeper insights into the interactions among insects, bacteria, and plants, which would eventually help to better manage horticulture.}, }
@article {pmid32051016, year = {2020}, author = {Glendinning, L and Stewart, RD and Pallen, MJ and Watson, KA and Watson, M}, title = {Assembly of hundreds of novel bacterial genomes from the chicken caecum.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {34}, doi = {10.1186/s13059-020-1947-1}, pmid = {32051016}, issn = {1474-760X}, support = {BB/P013759/1, BB/P013732/1, BB/J004235/1, BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1, BBS/E/F/000PR10351/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.<br><br>RESULTS: We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.<br><br>CONCLUSIONS: This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.}, }
@article {pmid32045510, year = {2020}, author = {Boreczek, J and Litwinek, D and Żylińska-Urban, J and Izak, D and Buksa, K and Gawor, J and Gromadka, R and Bardowski, JK and Kowalczyk, M}, title = {Bacterial community dynamics in spontaneous sourdoughs made from wheat, spelt, and rye wholemeal flour.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e1009}, doi = {10.1002/mbo3.1009}, pmid = {32045510}, issn = {2045-8827}, support = {PBS2/B8/12/2014//Narodowe Centrum Badań i Rozwoju/ ; }, abstract = {Sourdough fermentation is a traditional process that is used to improve bread quality. A spontaneous sourdough ecosystem consists of a mixture of flour and water that is fermented by endogenous lactic acid bacteria (LAB) and yeasts. The aim of this study was to identify bacterial diversity during backslopping of spontaneous sourdoughs prepared from wheat, spelt, or rye wholemeal flour. Culture-dependent analyses showed that the number of LAB (109 CFU/ml) was higher by three orders of magnitude than the number of yeasts (106 CFU/ml), irrespective of the flour type. These results were complemented by next-generation sequencing of the 16S rDNA V3 and V4 variable regions. The dominant phylum in all sourdough samples was Firmicutes, which was represented exclusively by the Lactobacillales order. The two remaining and less abundant phyla were Proteobacteria and Bacteroidetes. The culture-independent approach allowed us to detect changes in microbial ecology during the 72-hr fermentation period. Weissella sp. was the most abundant genus after 24 hr of fermentation of the rye sourdough, but as the process progressed, its abundance decreased in favor of the Lactobacillus genus similarly as in wheat and spelt sourdoughs. The Lactobacillus genus was dominant in all sourdoughs after 72 hr, which was consistent with our results obtained using culture-dependent analyses. This work was carried out to determine the microbial biodiversity of sourdoughs that are made from wheat, spelt, and rye wholemeal flour and can be used as a source of strains for specific starter cultures to produce functional bread.}, }
@article {pmid32043958, year = {2020}, author = {Hofmann, K and Huptas, C and Doll, EV and Scherer, S and Wenning, M}, title = {Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.004043}, pmid = {32043958}, issn = {1466-5034}, abstract = {Two strains, WS 5063T and WS 5067, isolated from raw cow's milk and skimmed milk concentrate, could be affiliated as members of the same, hitherto unknown, Pseudomonas species by 16S rRNA and rpoD gene sequences. Multilocus sequence and average nucleotide identity (ANIm) analyses based on draft genome sequences confirmed the discovery of a novel Pseudomonas species. It was most closely related to Pseudomonas synxantha DSM 18928T with an ANIm of 91.4 %. The DNA G+C content of WS 5063T was 60.0 mol %. Phenotypic characterizations showed that the isolates are rod-shaped, motile, catalase- and oxidase-positive, and aerobic. Growth occurred at 4-34 °C and at pH values of pH 5.5-8.0. Both strains showed strong β-haemolysis on blood agar. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant quinone was Q-9 (90 %), but noticeable amounts of Q-8 (9 %) and traces of Q-7 were also detected. Fatty acid profiles were typical for Pseudomonas species and exhibited C16 : 0 as a major component. Based on these results, we conclude that both strains belong to a novel species, for which the name Pseudomonas haemolytica sp. nov. is proposed. The type strain is WS 5063T (=DSM 108987T=LMG 31232T) and an additional strain is WS 5067 (=DSM 108988=LMG 31233).}, }
@article {pmid32043954, year = {2020}, author = {Wenning, M and Breitenwieser, F and Huptas, C and Doll, E and Bächler, B and Schulz, A and Dunkel, A and Hofmann, T and von Neubeck, M and Busse, HJ and Scherer, S}, title = {Brevilactibacter flavus gen. nov., sp. nov., a novel bacterium of the family Propionibacteriaceae isolated from raw milk and dairy products and reclassification of Propioniciclava sinopodophylli as Brevilactibacter sinopodophylli comb. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003909}, pmid = {32043954}, issn = {1466-5034}, abstract = {Eight facultatively anaerobic rod-shaped bacteria were isolated from raw milk and two other dairy products. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates are placed in a distinct lineage within the family Propionibacteriaceae with Propioniciclava sinopodophylli and Propioniciclava tarda as the closest relatives (94.6 and 93.5 % similarity, respectively). The cell-wall peptidoglycan contained meso-diaminopimelic acid, alanine and glutamic acid and was of the A1γ type (meso-DAP-direct). The major cellular fatty acid was anteiso-C15 : 0 and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and three unidentified glycolipids. The quinone system contained predominantly menaquinone MK-9(H4). The G+C content of the genomic DNA of strain VG341T was 67.7 mol%. The whole-cell sugar pattern contained ribose, rhamnose, arabinose and galactose. On the basis of phenotypic and genetic data, eight strains (VG341T, WS4684, WS4769, WS 4882, WS4883, WS4901, WS4902 and WS4904) are proposed to be classified as members of a novel species in a new genus of the family Propionibacteriaceae, for which the name Brevilactibacter flavus gen. nov., sp. nov. is proposed. The type strain is VG341T (=WS4900T=DSM 100885T=LMG 29089T) and seven additional strains are WS4684, WS4769, WS4882, WS4883, WS4901, WS4902 and WS4904. Furthermore, we propose the reclassification of P. sinopodophylli as Brevilactibacter sinopodophylli comb. nov.}, }
@article {pmid32042158, year = {2020}, author = {Zhang, J and Fu, XX and Li, RQ and Zhao, X and Liu, Y and Li, MH and Zwaenepoel, A and Ma, H and Goffinet, B and Guan, YL and Xue, JY and Liao, YY and Wang, QF and Wang, QH and Wang, JY and Zhang, GQ and Wang, ZW and Jia, Y and Wang, MZ and Dong, SS and Yang, JF and Jiao, YN and Guo, YL and Kong, HZ and Lu, AM and Yang, HM and Zhang, SZ and Van de Peer, Y and Liu, ZJ and Chen, ZD}, title = {The hornwort genome and early land plant evolution.}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41477-019-0588-4}, pmid = {32042158}, issn = {2055-0278}, abstract = {Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.}, }
@article {pmid32042128, year = {2020}, author = {VanInsberghe, D and Elsherbini, JA and Varian, B and Poutahidis, T and Erdman, S and Polz, MF}, title = {Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-020-0668-2}, pmid = {32042128}, issn = {2058-5276}, abstract = {Although Clostridium difficile is widely considered an antibiotic- and hospital-associated pathogen, recent evidence indicates that this is an insufficient depiction of the risks and reservoirs. A common thread that links all major risk factors of infection is their association with gastrointestinal disturbances, but this relationship to C. difficile colonization has never been tested directly. Here, we show that disturbances caused by diarrhoeal events trigger susceptibility to C. difficile colonization. Using survey data of the human gut microbiome, we detected C. difficile colonization and blooms in people recovering from food poisoning and Vibrio cholerae infections. Carriers remained colonized for year-long time scales and experienced highly variable patterns of C. difficile abundance, where increased shedding over short periods of 1-2 d interrupted week-long periods in which C. difficile was undetectable. Given that short shedding events were often linked to gastrointestinal disturbances, our results help explain why C. difficile is frequently detected as a co-infecting pathogen in patients with diarrhoea. To directly test the impact of diarrhoea on susceptibility to colonization, we developed a mouse model of variable disturbance intensity, which allowed us to monitor colonization in the absence of disease. As mice exposed to avirulent C. difficile spores ingested increasing quantities of laxatives, more individuals experienced C. difficile blooms. Our results indicate that the likelihood of colonization is highest in the days immediately following acute disturbances, suggesting that this could be an important window during which transmission could be interrupted and the incidence of infection lowered.}, }
@article {pmid32038529, year = {2019}, author = {Lee, JY and Haruta, S and Kato, S and Bernstein, HC and Lindemann, SR and Lee, DY and Fredrickson, JK and Song, HS}, title = {Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {3049}, doi = {10.3389/fmicb.2019.03049}, pmid = {32038529}, issn = {1664-302X}, abstract = {Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients - basic parameters required for implementing the MIIA - are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite.}, }
@article {pmid32036919, year = {2020}, author = {Babaahmadifooladi, M and Jacxsens, L and Van de Wiele, T and Laing, GD}, title = {Gap analysis of nickel bioaccessibility and bioavailability in different food matrices and its impact on the nickel exposure assessment.}, journal = {Food research international (Ottawa, Ont.)}, volume = {129}, number = {}, pages = {108866}, doi = {10.1016/j.foodres.2019.108866}, pmid = {32036919}, issn = {1873-7145}, abstract = {The metal nickel is well known to cause nickel allergy in sensitive humans by prolonged dermal contact to materials releasing (high) amounts of nickel. Oral nickel exposure via water and food intake is of potential concern. Nickel is essential to plants and animals and can be naturally found in food products or contamination may occur across the agro-food chain. This gap analysis is an evaluation of nickel as a potential food safety hazard causing a risk for human health. In the first step, the available data regarding the occurrence of nickel and its contamination in food and drinks have been collected through literature review. Subsequently, a discussion is held on the potential risks associated with this contamination. Elevated nickel concentrations were mostly found in plant-based foods, e.g. legumes and nuts in which nickel of natural origin is expected. However, it was observed that dedicated and systematic screening of foodstuffs for the presence of nickel is currently still lacking. In a next step, published studies on exposure of humans to nickel via foods and drinks were critically evaluated. Not including bioaccessibility and/or bioavailability of the metal may lead to an overestimation of the exposure of the body to nickel via food and drinks. This overestimation may be problematic when the measured nickel level in foods is high and bioaccessibility and/or bioavailability of nickel in these products is low. Therefore, this paper analyzes the outcomes of the existing dietary intake and bioaccessibility/bioavailability studies conducted for nickel. Besides, the available gaps in nickel bioaccessibility and/or bioavailability studies have been clarified in this paper. The reported bioaccessibility and bioavailability percentages for different food and drinks were found to vary between <LOD and 83% and between 0 and 30% respectively. This indicates that of the total nickel contained in the foodstuffs only a fraction can be absorbed by the intestinal epithelium cells. This paper provides a unique critical overview on nickel in the human diet starting from factors affecting its occurrence in food until its absorption by the body.}, }
@article {pmid32036914, year = {2020}, author = {Vossen, E and Goethals, S and De Vrieze, J and Boon, N and Van Hecke, T and De Smet, S}, title = {Red and processed meat consumption within two different dietary patterns: Effect on the colon microbial community and volatile metabolites in pigs.}, journal = {Food research international (Ottawa, Ont.)}, volume = {129}, number = {}, pages = {108793}, doi = {10.1016/j.foodres.2019.108793}, pmid = {32036914}, issn = {1873-7145}, abstract = {Pigs were fed either red and processed meat or chicken meat within either a prudent or a Western dietary pattern for four weeks (2 × 2 full factorial design). The colon microbial community and volatile organic compounds were assessed (either quantified or based on their presence). Results show that Lactobacilli were characteristic for the chicken × prudent dietary pattern treatment and Paraprevotella for the red and processed meat × prudent dietary pattern treatment. Enterobacteriaceae and Desulfovibrio were characteristic for the chicken × Western dietary pattern treatment and Butyrivibrio for the red and processed meat × Western dietary pattern treatment. Campylobacter was characteristic for chicken consumption and Clostridium XIVa for red and processed meat, irrespective of the dietary pattern. Ethyl valerate and 1-methylthio-propane were observed more frequently in pigs fed red and processed meat compared to chicken meat. The prevalence of 3-methylbutanal was >80% for pigs receiving a Western dietary pattern, whereas for pigs fed a prudent dietary pattern the prevalence was <35%. The concentration of butanoic acid was significantly higher when the prudent dietary pattern was given, compared to the Western dietary pattern, but no differences for other short chain fatty acids or protein fermentation products were observed.}, }
@article {pmid32034763, year = {2020}, author = {Rombouts, JL and Kranendonk, EMM and Regueira, A and Weissbrodt, DG and Kleerebezem, R and van Loosdrecht, MCM}, title = {Selecting for lactic acid producing and utilising bacteria in anaerobic enrichment cultures.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.27301}, pmid = {32034763}, issn = {1097-0290}, abstract = {Lactic acid producing bacteria are important in many fermentations, such as the production of biobased plastics. Insight in the competitive advantage of lactic acid bacteria over other fermentative bacteria in a mixed culture enables ecology-based process design and can aid the development of sustainable and energy-efficient bioprocesses. Here we demonstrate the enrichment of lactic acid bacteria in a controlled sequencing batch bioreactor environment using a glucose based medium supplemented with peptides and B vitamins. A mineral medium enrichment operated in parallel was dominated by Ethanoligenens species and fermented glucose to acetate, butyrate and hydrogen. The complex medium enrichment was populated by Lactococcus, Lactobacillus and Megasphaera species and showed a product spectrum of acetate, ethanol, propionate, butyrate and valerate. An intermediate peak of lactate was observed, showing the simultaneous production and consumption of lactate, which is of concern for lactic acid production purposes. This study underlines that the competitive advantage for lactic acid producing bacteria primarily lies in their ability to attain a high biomass specific uptake rate of glucose, which was two times higher for the complex medium enrichment when compared to the mineral medium enrichment. The competitive advantage of lactic acid production in rich media can be explained using a resource allocation theory for microbial growth processes. This article is protected by copyright. All rights reserved.}, }
@article {pmid32034151, year = {2020}, author = {Kitzinger, K and Marchant, HK and Bristow, LA and Herbold, CW and Padilla, CC and Kidane, AT and Littmann, S and Daims, H and Pjevac, P and Stewart, FJ and Wagner, M and Kuypers, MMM}, title = {Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {767}, doi = {10.1038/s41467-020-14542-3}, pmid = {32034151}, issn = {2041-1723}, support = {W 1257//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean.}, }
@article {pmid32031212, year = {2020}, author = {Fenske, GJ and Ghimire, S and Antony, L and Christopher-Hennings, J and Scaria, J}, title = {Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa022}, pmid = {32031212}, issn = {1574-6941}, abstract = {Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contented that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.}, }
@article {pmid32030584, year = {2020}, author = {Mariano, C and Mello, IS and Barros, BM and da Silva, GF and Terezo, AJ and Soares, MA}, title = {Mercury alters the rhizobacterial community in Brazilian wetlands and it can be bioremediated by the plant-bacteria association.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-020-07913-2}, pmid = {32030584}, issn = {1614-7499}, support = {409062/2018-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 568258/2014//Fundação de Amparo à Pesquisa do Estado de Mato Grosso/ ; }, abstract = {This study examined how soil mercury contamination affected the structure and functionality of rhizobacteria communities from Aeschynomene fluminensis and Polygonum acuminatum and how rhizobacteria mediate metal bioremediation. The strains were isolated using culture-dependent methods, identified through 16S rDNA gene sequencing, and characterized with respect to their functional traits related to plant growth promotion and resistance to metals and antibiotics. The bioremediation capacity of the rhizobacteria was determined in greenhouse using corn plants. The isolated bacteria belonged to the phyla Actinobacteria, Deinococcus-Thermus, Firmicutes, and Proteobacteria, with great abundance of the species Microbacterium trichothecenolyticum. The rhizobacteria abundance, richness, and diversity were greater in mercury-contaminated soils. Bacteria isolated from contaminated environments had higher minimum inhibitory concentration values, presented plasmids and the merA gene, and were multi-resistant to metals and antibiotics. Enterobacter sp._C35 and M. trichothecenolyticum_C34 significantly improved (Dunnett's test, p < 0.05) corn plant growth in mercury-contaminated soil. These bacteria helped to reduce up to 87% of the mercury content in the soil, and increased the mercury bioaccumulation factor by up to 94%. Mercury bioremediation mitigated toxicity of the contaminated substrate. Enterobacter sp._C35, Bacillus megaterium_C28, and Bacillus mycoides_C1 stimulated corn plant growth and could be added to biofertilizers produced in research and related industries.}, }
@article {pmid32027305, year = {2020}, author = {Lee, HJ and Whang, KS}, title = {Elioraea rosea sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.004028}, pmid = {32027305}, issn = {1466-5034}, abstract = {A Gram-stain-negative bacterium, designated strain PF-30T, was isolated from floodwater of a paddy field in South Korea. Strain PF-30T was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25-40 °C (optimum, 28 °C), at pH 5.0-9.0 (optimum pH 7.0) and at salinities of 0.5-3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30T belongs to the genus Elioraea, showing highest sequence similarity to Elioraea tepidiphila TU-7T (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae. The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain PF-30T and E. tepidiphila TU-7T yielded an ANI value of 75.1 % and DNA-DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30T was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30T represents a novel species of the genus Elioraea, for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30T (=KACC 19985T=NBRC 113984T).}, }
@article {pmid32025810, year = {2020}, author = {Smichi, N and Messaoudi, Y and Allaf, K and Gargouri, M}, title = {Steam explosion (SE) and instant controlled pressure drop (DIC) as thermo-hydro-mechanical pretreatment methods for bioethanol production.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00449-020-02297-6}, pmid = {32025810}, issn = {1615-7605}, abstract = {Lignocellulosic biomass can be considered as one of the largest sources for the production of renewable biofuels (bioethanol). It involves an enzymatic treatment capable of ensuring the depolymerization of cellulose into fermentable sugars, followed by the production of ethanol by appropriate bacteriological fermentation. Proper destruction of the compact natural structure of the biomass would allow an interesting intensification of the operation. Among the most prominent technical approaches, the steam explosion (SE) is the most famous. However, this high pressure-high temperature process implies too high energy consumption while leading to the generation of many non-fermentable molecules. In recent years, many studies have proposed the use of the Instant Controlled Pressure-Drop (DIC) texturing pretreatment as an effective alternative to SE for ethanol production. Therefore, in this manuscript, we propose to compare and discuss the fundamental principles and experimental results of these two operations, as presented in the relevant literature.}, }
@article {pmid32024862, year = {2020}, author = {Snyder, GT and Matsumoto, R and Suzuki, Y and Kouduka, M and Kakizaki, Y and Zhang, N and Tomaru, H and Sano, Y and Takahata, N and Tanaka, K and Bowden, SA and Imajo, T}, title = {Evidence in the Japan Sea of microdolomite mineralization within gas hydrate microbiomes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1876}, doi = {10.1038/s41598-020-58723-y}, pmid = {32024862}, issn = {2045-2322}, support = {17K05712//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 17K05712//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 17K05712//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 17K05712//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {Over the past 15 years, massive gas hydrate deposits have been studied extensively in Joetsu Basin, Japan Sea, where they are associated primarily with active gas chimney structures. Our research documents the discovery of spheroidal microdolomite aggregates found in association with other impurities inside of these massive gas hydrates. The microdolomites are often conjoined and show dark internal cores occasionally hosting saline fluid inclusions. Bacteroidetes sp. are concentrated on the inner rims of microdolomite grains, where they degrade complex petroleum-macromolecules present as an impurity within yellow methane hydrate. These oils show increasing biodegradation with depth which is consistent with the microbial activity of Bacteroidetes. Further investigation of these microdolomites and their contents can potentially yield insight into the dynamics and microbial ecology of other hydrate localities. If microdolomites are indeed found to be ubiquitous in both present and fossil hydrate settings, the materials preserved within may provide valuable insights into an unusual microhabitat which could have once fostered ancient life.}, }
@article {pmid32023186, year = {2020}, author = {Dhaulaniya, AS and Balan, B and Yadav, A and Jamwal, R and Kelly, S and Cannavan, A and Singh, DK}, title = {Development of an FTIR based chemometric model for the qualitative and quantitative evaluation of cane sugar as an added sugar adulterant in apple fruit juices.}, journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/19440049.2020.1718774}, pmid = {32023186}, issn = {1944-0057}, abstract = {A Fourier Transform Infrared Spectroscopy based chemometric model was evaluated for the rapid identification and estimation of cane sugar as an added sugar adulterant in apple fruit juices. For all the ninety samples, spectra were acquired in the mid-infrared range (4000 cm-1-400 cm-1). The spectral analysis provided information regarding the distinctive variable region, which lies in the range of 1200cm-1 to 900cm-1, designated as fingerprint region for the carbohydrates. A specific peak in the fingerprint region was observed at 997cm-1 in all the adulterated samples and was undetectable in pure samples. Based on different levels of cane sugar adulteration (5, 10, 15, and 20%), principal component analysis showed the clustering of samples and further helped us in compression of data by selecting wavenumbers with maximum variability based on the loading line plot. Supervised classification methods (SIMCA and LDA) were evaluated based on their classification efficiencies for a test set. Though SIMCA showed 100% classification efficiency (Raw data set), LDA was able to classify the test set with an accuracy of only 96.67% (Raw as well as Transformed data set) between pure and 5% adulterated samples. For the quantitative estimation, calibration models were developed using partial least square regression (PLS-R) and principal component regression method (PCR) methods. PLS-1st derivative showed a maximum coefficient of determination (R2) with a value of 0.991 for calibration and 0.992 for prediction. The RMSECV, RMSEP, LOD and LOQ observed for PLS-1st derivative model were 0.75% w/v, 0.61% w/v, 1.28%w/v and 3.88%w/v, respectively. The coefficient of variation as a measure of precision (repeatability) was also determined for all models, and it ranged from 0.23% to 1.83% (interday), and 0.25% to 1.43% (intraday).}, }
@article {pmid32020257, year = {2020}, author = {Wang, F and Cale, JA and Erbilgin, N}, title = {Induced Defenses of a Novel Host Tree Affect the Growth and Interactions of Bark Beetle-Vectored Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01490-0}, pmid = {32020257}, issn = {1432-184X}, abstract = {Mountain pine beetle (MPB) has recently expanded its host range to the novel jack pine forests in Alberta. Invasion success of MPB may depend on the outcome of interactions between its symbiotic fungus Grosmannia clavigera and Ophiostoma ips, a fungal associate of a potential competitor Ips pini. However, how the quality of jack pine phloem could influence interactions between the fungi is unknown. We investigated whether introduced concentrations of host nitrogen and monoterpenes affect the growth of and interaction between the fungi. Nitrogen concentrations did not affect the growth rate of either fungus. In the absence of monoterpenes, the presence of O. ips promoted G. clavigera growth. Monoterpenes either promoted or inhibited the growth of both fungi, and altered the outcome of species interactions from facilitation to no-effect. Overall, these results suggest that jack pine phloem quality and the presence of a niche-sharing fungus could influence MPB development.}, }
@article {pmid32019835, year = {2020}, author = {Rodriguez-Gonzalez, RA and Leung, CY and Chan, BK and Turner, PE and Weitz, JS}, title = {Quantitative Models of Phage-Antibiotic Combination Therapy.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSystems.00756-19}, pmid = {32019835}, issn = {2379-5077}, abstract = {The spread of multidrug-resistant (MDR) bacteria is a global public health crisis. Bacteriophage therapy (or &quot;phage therapy&quot;) constitutes a potential alternative approach to treat MDR infections. However, the effective use of phage therapy may be limited when phage-resistant bacterial mutants evolve and proliferate during treatment. Here, we develop a nonlinear population dynamics model of combination therapy that accounts for the system-level interactions between bacteria, phage, and antibiotics for in vivo application given an immune response against bacteria. We simulate the combination therapy model for two strains of Pseudomonas aeruginosa, one which is phage sensitive (and antibiotic resistant) and one which is antibiotic sensitive (and phage resistant). We find that combination therapy outperforms either phage or antibiotic alone and that therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotics, e.g., ciprofloxacin. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of innate immunity in shaping therapeutic outcomes.IMPORTANCE This work develops and analyzes a novel model of phage-antibiotic combination therapy, specifically adapted to an in vivo context. The objective is to explore the underlying basis for clinical application of combination therapy utilizing bacteriophage that target antibiotic efflux pumps in Pseudomonas aeruginosa In doing so, the paper addresses three key questions. How robust is combination therapy to variation in the resistance profiles of pathogens? What is the role of immune responses in shaping therapeutic outcomes? What levels of phage and antibiotics are necessary for curative success? As we show, combination therapy outperforms either phage or antibiotic alone, and therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotic. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of system-level feedbacks in shaping therapeutic outcomes.}, }
@article {pmid32019791, year = {2020}, author = {Tkacz, A and Bestion, E and Bo, Z and Hortala, M and Poole, PS}, title = {Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, doi = {10.1128/mBio.02785-19}, pmid = {32019791}, issn = {2150-7511}, abstract = {Plant roots influence the soil microbiota via physical interaction, secretion, and plant immunity. However, it is unclear whether the root fraction or soil is more important in determining the structure of the prokaryotic or eukaryotic community and whether this varies between plant species. Furthermore, the leaf (phyllosphere) and root microbiotas have a large overlap; however, it is unclear whether this results from colonization of the phyllosphere by the root microbiota. Soil, rhizosphere, rhizoplane, and root endosphere prokaryote-, eukaryote-, and fungus-specific microbiotas of four plant species were analyzed with high-throughput sequencing. The strengths of factors controlling microbiota structure were determined using permutational multivariate analysis of variance (PERMANOVA) statistics. The origin of the phyllosphere microbiota was investigated using a soil swap experiment. Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root itself more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. A reciprocal soil swap experiment shows that the phyllosphere is colonized from the soil in which the plant is grown.IMPORTANCE Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined, indicating conserved adaptation of microbial communities to plants. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. We observed a remarkable similarity in the structure of a plant's phyllosphere and root microbiotas and show by reciprocal soil swap experiments that both fractions are colonized from the soil in which the plant is grown. Thus, the phyllosphere is continuously colonized by the soil microbiota.}, }
@article {pmid32018979, year = {2020}, author = {Gionchetta, G and Oliva, F and Romaní, AM and Bañeras, L}, title = {Hydrological variations shape diversity and functional responses of streambed microbes.}, journal = {The Science of the total environment}, volume = {714}, number = {}, pages = {136838}, doi = {10.1016/j.scitotenv.2020.136838}, pmid = {32018979}, issn = {1879-1026}, abstract = {Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.}, }
@article {pmid32016609, year = {2020}, author = {Pantigoso, HA and Manter, DK and Vivanco, JM}, title = {Differential Effects of Phosphorus Fertilization on Plant Uptake and Rhizosphere Microbiome of Cultivated and Non-cultivated Potatoes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01486-w}, pmid = {32016609}, issn = {1432-184X}, abstract = {There is evidence that shows that phosphorus (P) fertilization has a moderate effect on the rhizosphere microbial composition of cultivated crops. But how this effect is manifested on wild species of the same crop is not clear. This study compares the impact of phosphorus fertilization with rhizosphere bacterial community composition and its predicted functions, related to P-cycling genes, in both cultivated and non-cultivated potato (Solanum sp.) plants. It was found that the biomass of non-cultivated potatoes was more responsive to P fertilization as compared with cultivated plants. Differences in general bacterial community composition patterns under increasing P amendments were subtle for both potato groups. However, potato genotype significantly influenced community composition with several bacterial families being more abundant in the cultivated plants. In addition, the predicted phosphatases had lower abundances in modern cultivars compared with non-cultivated potatoes. In summary, despite higher accumulation of differentially abundant bacteria in the rhizosphere of cultivated plants, the responsiveness of these plants to increase P levels was lower than in non-cultivated plants.}, }
@article {pmid32014077, year = {2020}, author = {Morand, C and De Roos, B and Garcia-Conesa, MT and Gibney, ER and Landberg, R and Manach, C and Milenkovic, D and Rodriguez-Mateos, A and Van de Wiele, T and Tomas-Barberan, F}, title = {Why interindividual variation in response to consumption of plant food bioactives matters for future personalised nutrition.}, journal = {The Proceedings of the Nutrition Society}, volume = {}, number = {}, pages = {1-11}, doi = {10.1017/S0029665120000014}, pmid = {32014077}, issn = {1475-2719}, abstract = {Food phytochemicals are increasingly considered to play a key role in the cardiometabolic health effects of plant foods. However, the heterogeneity in responsiveness to their intake frequently observed in clinical trials can hinder the beneficial effects of these compounds in specific subpopulations. A range of factors, including genetic background, gut microbiota, age, sex and health status, could be involved in these interindividual variations; however, the current knowledge is limited and fragmented. The European network, European Cooperation in Science and Technology (COST)-POSITIVe, has analysed, in a systematic way, existing knowledge with the aim to better understand the factors responsible for the interindividual variation in response to the consumption of the major families of plant food bioactives, regarding their bioavailability and bioefficacy. If differences in bioavailability, likely reflecting differences in human subjects' genetics or in gut microbiota composition and functionality, are believed to underpin much of the interindividual variability, the key molecular determinants or microbial species remain to be identified. The systematic analysis of published studies conducted to assess the interindividual variation in biomarkers of cardiometabolic risk suggested some factors (such as adiposity and health status) as involved in between-subject variation. However, the contribution of these factors is not demonstrated consistently across the different compounds and biological outcomes and would deserve further investigations. The findings of the network clearly highlight that the human subjects' intervention studies published so far are not adequate to investigate the relevant determinants of the absorption/metabolism and biological responsiveness. They also emphasise the need for a new generation of intervention studies designed to capture this interindividual variation.}, }
@article {pmid32014020, year = {2020}, author = {Woodhams, DC and Bletz, MC and Becker, CG and Bender, HA and Buitrago-Rosas, D and Diebboll, H and Huynh, R and Kearns, PJ and Kueneman, J and Kurosawa, E and LaBumbard, BC and Lyons, C and McNally, K and Schliep, K and Shankar, N and Tokash-Peters, AG and Vences, M and Whetstone, R}, title = {Host-associated microbiomes are predicted by immune system complexity and climate.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {23}, doi = {10.1186/s13059-019-1908-8}, pmid = {32014020}, issn = {1474-760X}, abstract = {BACKGROUND: Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.<br><br>RESULTS: Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.<br><br>CONCLUSIONS: Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.}, }
@article {pmid32012657, year = {2020}, author = {Purushotham, N and Jones, E and Monk, J and Ridgway, H}, title = {Community Structure, Diversity and Potential of Endophytic Bacteria in the Primitive New Zealand Medicinal Plant Pseudowintera colorata.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/plants9020156}, pmid = {32012657}, issn = {2223-7747}, abstract = {Although the importance of the plant microbiome in commercial plant health has been well established, there are limited studies in native medicinal plants. Pseudowintera colorata (horopito) is a native New Zealand medicinal plant recognized for its antimicrobial properties. Denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq analysis of P. colorata plants from ten sites across New Zealand showed that tissue type strongly influenced the diversity and richness of endophytic bacteria (PERMANOVA, P < 0.05). In addition, two OTUs belonging to the genus Pseudomonas (Greengenes ID: 646549 and 138914) were found to be present in >75% of all P. colorata leaf, stem and root samples and were identified as the members of the P. colorata &quot;core endomicrobiome&quot;. Culture-independent analysis was complemented by the recovery of 405 endophytic bacteria from the tissues of P. colorata. Some of these cultured endophytic bacteria (n = 10) showed high antagonism against four different phytopathogenic fungi tested. The influence of endophytic bacteria on plant growth was assessed by inoculating P. colorata seedlings. The mean shoot height of seedlings treated with Bacillus sp. TP1LA1B were longer (1.83×), had higher shoot dry weight (1.8×) and produced more internodes (1.8×) compared to the control.}, }
@article {pmid32010196, year = {2019}, author = {Mascarenhas, R and Ruziska, FM and Moreira, EF and Campos, AB and Loiola, M and Reis, K and Trindade-Silva, AE and Barbosa, FAS and Salles, L and Menezes, R and Veiga, R and Coutinho, FH and Dutilh, BE and Guimarães, PR and Assis, APA and Ara, A and Miranda, JGV and Andrade, RFS and Vilela, B and Meirelles, PM}, title = {Integrating Computational Methods to Investigate the Macroecology of Microbiomes.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1344}, doi = {10.3389/fgene.2019.01344}, pmid = {32010196}, issn = {1664-8021}, abstract = {Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as &quot;everything is everywhere, but the environment selects&quot;) as well as applied ecological problems, such as those posed by human induced global environmental changes.}, }
@article {pmid32006806, year = {2020}, author = {Trebuch, LM and Oyserman, BO and Janssen, M and Wijffels, RH and Vet, LEM and Fernandes, TV}, title = {Impact of hydraulic retention time on community assembly and function of photogranules for wastewater treatment.}, journal = {Water research}, volume = {173}, number = {}, pages = {115506}, doi = {10.1016/j.watres.2020.115506}, pmid = {32006806}, issn = {1879-2448}, abstract = {Photogranules are dense, spherical agglomerates of cyanobacteria, microalgae and non-phototrophic microorganisms that have considerable advantages in terms of harvesting and nutrient removal rates for light driven wastewater treatment processes. This ecosystem is poorly understood in terms of the microbial community structure and the response of the community to changing abiotic conditions. To get a better understanding, we investigated the effect of hydraulic retention time (HRT) on photogranule formation and community assembly over a period of 148 days. Three laboratory bioreactors were inoculated with field samples from various locations in the Netherlands and operated in sequencing batch mode. The bioreactors were operated at four different HRTs (2.00, 1.00, 0.67, 0.33 days), while retaining the same solid retention time of 7 days. A microbial community with excellent settling characteristics (95-99% separation efficiency) was established within 2-5 weeks. The observed nutrient uptake rates ranged from 24 to 90 mgN L-1 day-1 and from 3.1 to 5.4 mgP L-1 day-1 depending on the applied HRT. The transition from single-cell suspension culture to floccular agglomeration to granular sludge was monitored by microscopy and 16S/18S sequencing. In particular, two important variables for driving aggregation and granulation, and for the structural integrity of photogranules were identified: 1. Extracellular polymeric substances (EPS) with high protein to polysaccharide ratio and 2. specific microorganisms. The key players were found to be the cyanobacteria Limnothrix and Cephalothrix, the colony forming photosynthetic eukaryotes within Chlamydomonadaceae, and the biofilm producing bacteria Zoogloea and Thauera. Knowing the makeup of the microbial community and the operational conditions influencing granulation and bioreactor function is crucial for successful operation of photogranular systems.}, }
@article {pmid32001557, year = {2020}, author = {Eichorst, SA and Trojan, D and Huntemann, M and Clum, A and Pillay, M and Palaniappan, K and Varghese, N and Mikhailova, N and Stamatis, D and Reddy, TBK and Daum, C and Goodwin, LA and Shapiro, N and Ivanova, N and Kyrpides, N and Woyke, T and Woebken, D}, title = {One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil.}, journal = {Microbiology resource announcements}, volume = {9}, number = {5}, pages = {}, doi = {10.1128/MRA.01087-19}, pmid = {32001557}, issn = {2576-098X}, abstract = {We report eight genomes from representatives of the phylum Acidobacteria subdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.}, }
@article {pmid32000682, year = {2020}, author = {De Maayer, P and Pillay, T and Coutinho, TA}, title = {Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {100}, doi = {10.1186/s12864-020-6529-9}, pmid = {32000682}, issn = {1471-2164}, abstract = {BACKGROUND: The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized.<br><br>RESULTS: Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~ 3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag-2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria.<br><br>CONCLUSIONS: The flag-2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.}, }
@article {pmid31999996, year = {2020}, author = {Ahmad, JI and Liu, G and van der Wielen, PWJJ and Medema, G and Peter van der Hoek, J}, title = {Effects of cold recovery technology on the microbial drinking water quality in unchlorinated distribution systems.}, journal = {Environmental research}, volume = {183}, number = {}, pages = {109175}, doi = {10.1016/j.envres.2020.109175}, pmid = {31999996}, issn = {1096-0953}, abstract = {Drinking water distribution systems (DWDSs) are used to supply hygienically safe and biologically stable water for human consumption. The potential of thermal energy recovery from drinking water has been explored recently to provide cooling for buildings. Yet, the effects of increased water temperature induced by this &quot;cold recovery&quot; on the water quality in DWDSs are not known. The objective of this study was to investigate the impact of cold recovery from DWDSs on the microbiological quality of drinking water. For this purpose, three pilot distribution systems were operated in parallel for 38 weeks. System 1 has an operational heat exchanger, mimicking the cold recovery system by maintaining the water temperature at 25 °C; system 2 operated with a non-operational heat exchanger and system 3 run without heat exchanger. The results showed no significant effects on drinking water quality: cell numbers and ATP concentrations remained around 3.5 × 105 cells/ml and 4 ng ATP/l, comparable observed operational taxonomic units (OTUs) (~470-490) and similar Shannon indices (7.7-8.9). In the system with cold recovery, a higher relative abundance of Pseudomonas spp. and Chryseobacterium spp. was observed in the drinking water microbial community, but only when the cold recovery induced temperature difference (ΔT) was higher than 9 °C. In the 38 weeks' old biofilm, higher ATP concentration (475 vs. 89 pg/cm2), lower diversity (observed OTUs: 88 vs. ≥200) and a different bacterial community composition (e.g. higher relative abundance of Novosphingobium spp.) were detected, which did not influence water quality. No impacts were observed for the selected opportunisitic pathogens after introducing cold recovery. It is concluded that cold recovery does not affect bacterial water quality. Further investigation for a longer period is commended to understand the dynamic responses of biofilm to the increased temperature caused by cold recovery.}, }
@article {pmid31998352, year = {2019}, author = {Harkes, P and van Steenbrugge, JJM and van den Elsen, SJJ and Suleiman, AKA and de Haan, JJ and Holterman, MHM and Helder, J}, title = {Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1697}, doi = {10.3389/fpls.2019.01697}, pmid = {31998352}, issn = {1664-462X}, abstract = {Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of M. chitwoodi had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the M. chitwoodi decline. A closer look revealed that a local accumulation and activation of Pseudomonas, a genus that includes a number of nematode-suppressive species, paralleled the lower M. chitwoodi densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of e.g. crops and soil management regimes.}, }
@article {pmid31998276, year = {2019}, author = {Eberl, C and Ring, D and Münch, PC and Beutler, M and Basic, M and Slack, EC and Schwarzer, M and Srutkova, D and Lange, A and Frick, JS and Bleich, A and Stecher, B}, title = {Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2999}, doi = {10.3389/fmicb.2019.02999}, pmid = {31998276}, issn = {1664-302X}, abstract = {The Oligo-Mouse-Microbiota (OMM12) is a recently developed synthetic bacterial community for functional microbiome research in mouse models (Brugiroux et al., 2016). To date, the OMM12 model has been established in several germ-free mouse facilities world-wide and is employed to address a growing variety of research questions related to infection biology, mucosal immunology, microbial ecology and host-microbiome metabolic cross-talk. The OMM12 consists of 12 sequenced and publically available strains isolated from mice, representing five bacterial phyla that are naturally abundant in the murine gastrointestinal tract (Lagkouvardos et al., 2016). Under germ-free conditions, the OMM12 colonizes mice stably over multiple generations. Here, we investigated whether stably colonized OMM12 mouse lines could be reproducibly established in different animal facilities. Germ-free C57Bl/6J mice were inoculated with a frozen mixture of the OMM12 strains. Within 2 weeks after application, the OMM12 community reached the same stable composition in all facilities, as determined by fecal microbiome analysis. We show that a second application of the OMM12 strains after 72 h leads to a more stable community composition than a single application. The availability of such protocols for reliable de novo generation of gnotobiotic rodents will certainly contribute to increasing experimental reproducibility in biomedical research.}, }
@article {pmid31998260, year = {2019}, author = {Rath, S and Rud, T and Pieper, DH and Vital, M}, title = {Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2966}, doi = {10.3389/fmicb.2019.02966}, pmid = {31998260}, issn = {1664-302X}, abstract = {Human gut bacteria metabolize dietary components such as choline and carnitine to trimethylamine (TMA) that is subsequently oxidized to trimethylamine-N-oxide (TMAO) by hepatic enzymes. Increased plasma levels of TMAO are associated with the development of cardiovascular and renal disease. In this study, we applied gene-targeted assays in order to quantify (qPCR) and characterize (MiSeq) bacterial genes encoding enzymes responsible for TMA production, namely choline-TMA lyase (CutC), carnitine oxygenase (CntA) and betaine reductase (GrdH) in 89 fecal samples derived from various mammals spanning three dietary groups (carnivores, omnivores and herbivores) and four host orders (Carnivora, Primates, Artiodactyla and Perissodactyla). All samples contained potential TMA-producing bacteria, however, at low abundances (<1.2% of total community). The cutC gene was more abundant in omnivores and carnivores compared with herbivores. CntA was almost absent from herbivores and grdH showed lowest average abundance of all three genes. Bacteria harboring cutC and grdH displayed high diversities where sequence types affiliated with various taxa within Firmicutes dominated, whereas cntA comprised sequences primarily linked to Escherichia. Composition of TMA-forming communities was strongly influenced by diet and host taxonomy and despite their high correlation, both factors contributed uniquely to community structure. Furthermore, Random Forest (RF) models could differentiate between groups at high accuracies. This study gives a comprehensive overview of potential TMA-producing bacteria in the mammalian gut demonstrating that both diet and host taxonomy govern their abundance and composition. It highlights the role of functional redundancy sustaining potential TMA formation in distinct gut environments.}, }
@article {pmid31998259, year = {2019}, author = {Rahi, P and Vaishampayan, P}, title = {Editorial: MALDI-TOF MS Application in Microbial Ecology Studies.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2954}, doi = {10.3389/fmicb.2019.02954}, pmid = {31998259}, issn = {1664-302X}, }
@article {pmid31997534, year = {2020}, author = {Van Gestel, NC and Ducklow, HW and Bååth, E}, title = {Comparing temperature sensitivity of bacterial growth in Antarctic marine water and soil.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.15020}, pmid = {31997534}, issn = {1365-2486}, abstract = {The western Antarctic Peninsula is an extreme low temperature environment that is warming rapidly due to global change. Little is known, however, about the temperature sensitivity of growth of microbial communities in Antarctic soils and in the surrounding oceanic waters. This is the first study that directly compares temperature adaptation of adjacent marine and terrestrial bacteria in a polar environment. The bacterial communities in the ocean were adapted to lower temperatures than those from nearby soil, with cardinal temperatures for growth in the ocean being the lowest so far reported for microbial communities. This was reflected in lower minimum (Tmin) and optimum temperatures (Topt) for growth in water (-17°C and +20°C, respectively) than in soil (-11°C and +27°C), with lower sensitivity to changes in temperature (Q10 ; 0-10°C interval) in Antarctic water (2.7) than in soil (3.9). This is likely due to the more stable low temperature conditions of Antarctic waters than soils, and the fact that maximum in situ temperatures in water are lower than in soils, at least in summer. Importantly, the thermally stable environment of Antarctic marine water makes it feasible to create a single temperature response curve for bacterial communities. This would thus allow for calculations of temperature-corrected growth rates, and thereby quantifying the influence of factors other than temperature on observed growth rates, as well as predicting the effects of future temperature increases on Antarctic marine bacteria.}, }
@article {pmid31996939, year = {2020}, author = {Zhang, Z and Liu, W and Shao, S and Wang, ET and Li, Y}, title = {Diverse Genomic Backgrounds Vs. Highly Conserved Symbiotic Genes in Sesbania-Nodulating Bacteria: Shaping of the Rhizobial Community by Host and Soil Properties.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01489-7}, pmid = {31996939}, issn = {1432-184X}, support = {31600009//National Natural Science Foundation of China/ ; 31800099//National Natural Science Foundation of China/ ; 19273802D//Key Research and Development Program of Hebei province/ ; 2019SYHZ0036//Joint fund of Jilin province and Chinese Academy of Sciences for high-tech industrialization/ ; KFZD-SW-112//Key Deployment Project of Chinese Academy of Sciences/ ; }, abstract = {Aiming at investigating the overall diversity, biogeography, and symbiosis gene evolutionary history of the Sesbania cannabina-nodulating rhizobia in China, a total of 874 rhizobial isolates originating from the root nodules of this plant grown at different sites were characterized and compared with those of some reference strains. All of the S. cannabina-nodulating rhizobia were classified into 16 (geno) species, including seven novel genospecies in the genera Ensifer, Rhizobium, Neorhizobium, and Agrobacterium, with Ensifer sesbaniae and Neorhizobium huautlense as the dominant and universal species. Ten of these species were found to nodulate other leguminous hosts or to lack nodulating abilities and were defined as symbiovar sesbania. Biogeographic patterns were observed, for which pH, TN, AK, and AP were the main determinants. The effects of pH were opposite to those of TN and AK, while AP presented effects independently of TN, AK, and pH. Symbiotic genes of these rhizobia showed a common origin, but nodA evolved faster than nifH. Point mutation is the main driving force in the evolution of both nodA and nifH, and lateral transfer of symbiotic genes might play an important role in the formation of diverse S. cannabina-nodulating rhizobial species. S. cannabina only nodulates with Sesbania rhizobia, demonstrating its severe selection on rhizobial symbiosis genes. Soil pH and physiochemical characteristics could affect rhizobial survival and competitive nodulation. This study provides insight into the community shifts and evolution of rhizobia in relation to their host and soil environments.}, }
@article {pmid31996419, year = {2020}, author = {Ghannam, RB and Schaerer, LG and Butler, TM and Techtmann, SM}, title = {Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSphere.00481-19}, pmid = {31996419}, issn = {2379-5042}, abstract = {We conducted a global characterization of the microbial communities of shipping ports to serve as a novel system to investigate microbial biogeography. The community structures of port microbes from marine and freshwater habitats house relatively similar phyla, despite spanning large spatial scales. As part of this project, we collected 1,218 surface water samples from 604 locations across eight countries and three continents to catalogue a total of 20 shipping ports distributed across the East and West Coast of the United States, Europe, and Asia to represent the largest study of port-associated microbial communities to date. Here, we demonstrated the utility of machine learning to leverage this robust system to characterize microbial biogeography by identifying trends in biodiversity across broad spatial scales. We found that for geographic locations sharing similar environmental conditions, subpopulations from the dominant phyla of these habitats (Actinobacteria, Bacteroidetes, Cyanobacteria, and Proteobacteria) can be used to differentiate 20 geographic locations distributed globally. These results suggest that despite the overwhelming diversity within microbial communities, members of the most abundant and ubiquitous microbial groups in the system can be used to differentiate a geospatial location across global spatial scales. Our study provides insight into how microbes are dispersed spatially and robust methods whereby we can interrogate microbial biogeography.IMPORTANCE Microbes are ubiquitous throughout the world and are highly diverse. Characterizing the extent of variation in the microbial diversity across large geographic spatial scales is a challenge yet can reveal a lot about what biogeography can tell us about microbial populations and their behavior. Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment. Here, we display how supervised machine learning approaches can be useful to understand microbial biodiversity and biogeography using microbes from globally distributed shipping ports. Our findings indicate that the members of globally dominant phyla are important for differentiating locations, which reduces the reliance on rare taxa to probe geography. Further, this study displays how global biogeographic patterning of aquatic microbial communities (and other systems) can be assessed through populations of the highly abundant and ubiquitous taxa that dominant the system.}, }
@article {pmid31996418, year = {2020}, author = {Bartelme, RP and Custer, JM and Dupont, CL and Espinoza, JL and Torralba, M and Khalili, B and Carini, P}, title = {Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSphere.00024-20}, pmid = {31996418}, issn = {2379-5042}, abstract = {The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here, we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted cells extracted from soil into one of two custom-designed defined growth media that differed by 100-fold in the concentration of amino acids and organic carbon. Across the two media, we isolated a total of 133 pure cultures, all of which were classified as Actinobacteria or Alphaproteobacteria The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of Alphaproteobacteria We isolated cultures that were representative of the most abundant phylotype in the soil microbial community (Bradyrhizobium spp.) and representatives of five of the top 10 most abundant Actinobacteria phylotypes, including Nocardioides spp., Mycobacterium spp., and several other phylogenetically divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and that the concentration of substrates in culture medium influences the culturability of specific microbial lineages.IMPORTANCE Isolating environmental microbes and studying their physiology under controlled conditions are essential aspects of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities-the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.}, }
@article {pmid31994719, year = {2020}, author = {Yuan, S and Meng, F}, title = {Ecological insights into the underlying evolutionary patterns of biofilm formation from biological wastewater treatment systems: Red or Black Queen Hypothesis?.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.27289}, pmid = {31994719}, issn = {1097-0290}, abstract = {Interspecies interactions and phylogenetic distances were studied to reveal the underlying evolutionary adaptations of biofilms sourced from wastewater treatment processes. Based on 380 pairwise cocultures of 40 strains from two microbial aggregates (surface-attached and mobile aggregates (flocs)) at two substrate concentrations (LB broth and 0.1x LB broth), interspecies interactions were explored using biofilm classification schemes. There was a strong source-dependence of biofilm development formed by the mono-cultures, i.e., a higher biofilm formation potential for strains from attached aggregates than for those from sludge flocs at both substrate concentrations. Interestingly, the results showed that total biofilm reduction was dominant in the dual-species biofilm sourced from flocs in both LB broth (67.37%) and 0.1x LB broth (64.21%), indicating high interspecific competition in mobile aggregates and the independence of substrate concentrations. However, biofilm reduction was higher (33.68%) than induction (19.37%) for the biofilms formed by surface-attached aggregates in LB broth, while the opposite trend was apparent in 0.1x LB broth, suggesting the occurrence of indeterministic processes for biofilm formation and important roles of substrate concentrations. In addition, the more closely related phylogenetic relationships of cocultures from mobile aggregates was consistent with higher competition compared with those from surface-attached aggregates. Overall, the underlying evolutionary patterns of biofilms formed from mobile aggregates consistently followed the essence of the 'Red Queen Hypothesis', while biofilms developed from surface-attached aggregates were not deterministic. This study advanced our understanding of biofilm-related treatment processes using the principles of microbial ecology. This article is protected by copyright. All rights reserved.}, }
@article {pmid31992626, year = {2020}, author = {Lennon, JT}, title = {Microbial Life Deep Underfoot.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, doi = {10.1128/mBio.03201-19}, pmid = {31992626}, issn = {2150-7511}, abstract = {Soil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored. Brewer et al. (mBio 10:e01318-19, 2019, https://doi.org/10.1128/mBio.01318-19) documented consistent shifts in the composition and genomic attributes of microbial communities as a function of depth in 20 soil pits that spanned a range of ecosystems across North America. The unique microorganisms found in deep soils appear to be adapted to conditions of low energy based on the recovery of genes that code for traits such as internal resource storage, mixotrophy, and dormancy.}, }
@article {pmid31989236, year = {2020}, author = {Zhu, B and Wang, Z and Kanaparthi, D and Kublik, S and Ge, T and Casper, P and Schloter, M and Lueders, T}, title = {Long-Read Amplicon Sequencing of Nitric Oxide Dismutase (nod) Genes Reveal Diverse Oxygenic Denitrifiers in Agricultural Soils and Lake Sediments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01482-0}, pmid = {31989236}, issn = {1432-184X}, support = {616644//FP7 Ideas: European Research Council/ ; }, abstract = {Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 × 106-3.2 × 107 gene copies g-1 soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.}, }
@article {pmid31988316, year = {2020}, author = {Remizovschi, A and Carpa, R and Forray, FL and Chiriac, C and Roba, CA and Beldean-Galea, S and Andrei, AȘ and Szekeres, E and Baricz, A and Lupan, I and Knut, R and Coman, C}, title = {Mud volcanoes and the presence of PAHs.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1253}, doi = {10.1038/s41598-020-58282-2}, pmid = {31988316}, issn = {2045-2322}, abstract = {A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its sediments. Recurrent expulsion of various hydrocarbons consolidates the growth of hydrocarbonoclastic bacterial communities in the areas around MVs. In addition to the widely-known availability of biologically malleable alkanes, MVs can represent hotbeds of polyaromatic hydrocarbons (PAHs), as well - an aspect that has not been previously explored. This study measured the availability of highly recalcitrant PAHs and the isotopic signature of MV sediments both by GC-MS and δ13C analyses. Subsequently, this study highlighted both the occurrence and distribution of putative PAH-degrading bacterial OTUs using a metabarcoding technique. The putative hydrocarbonoclastic taxa incidence are the following: Enterobacteriaceae (31.5%), Methylobacteriaceae (19.9%), Bradyrhizobiaceae (16.9%), Oxalobacteraceae (10.2%), Comamonadaceae (7.6%) and Sphingomonadaceae (5.5%). Cumulatively, the results of this study indicate that MVs represent polyaromatic hydrocarbonoclastic hotbeds, as defined by both natural PAH input and high incidence of putative PAH-degrading bacterial OTUs.}, }
@article {pmid31987702, year = {2020}, author = {Kalita, M and Małek, W and Coutinho, TA}, title = {Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {126056}, doi = {10.1016/j.syapm.2020.126056}, pmid = {31987702}, issn = {1618-0984}, abstract = {In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89T and Bradyrhizobium valentinum LmjM3T. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887T in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89T, Bradyrhizobium valentinum LmjM3T and Bradyrhizobium retamae Ro19T belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.}, }
@article {pmid31985137, year = {2020}, author = {Cramer, N and Fischer, S and Hedtfeld, S and Dorda, M and Tümmler, B}, title = {Intraclonal competitive fitness of longitudinal cystic fibrosis Pseudomonas aeruginosa airway isolates in liquid cultures.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14924}, pmid = {31985137}, issn = {1462-2920}, abstract = {The metabolically versatile Pseudomonas aeruginosa inhabits biotic and abiotic environments including the niche of cystic fibrosis (CF) airways. This study investigated how the adaptation to CF lungs affects the within-clone fitness of P. aeruginosa to grow and persist in liquid cultures in the presence of the clonal ancestors. Longitudinal clonal P. aeruginosa isolates that had been collected from 12 CF donors since the onset of colonization for up to 30 years were subjected to within-clone competition experiments. The relative quantities of individual strains were determined by marker-free amplicon sequencing of multiplex PCR products of strain-specific nucleotide sequence variants, a novel method that is generally applicable to studies in evolutionary genetics and microbial ecology with real-world strain collections. For ten of the twelve examined patient courses, P. aeruginosa isolates of the first years of colonization grew faster in the presence of their clonal progeny than alone. Single growth of individual strains showed no temporal trend with colonization time, but in co-culture the early isolates out-competed their clonal progeny. Irrespective of the genetic make-up of the clone and its genomic microevolution in CF lungs the early isolates expressed fitness traits to win the within-clone competition that were absent in their progeny. This article is protected by copyright. All rights reserved.}, }
@article {pmid31984651, year = {2020}, author = {Xu, H and Wang, X and Feng, W and Liu, Q and Zhou, S and Liu, Q and Cai, L}, title = {The gut microbiota and its interactions with cardiovascular disease.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13524}, pmid = {31984651}, issn = {1751-7915}, support = {81770372//National Natural Science Foundation of China/ ; 81570338//National Natural Science Foundation of China/ ; }, abstract = {The intestine is colonized by a considerable community of microorganisms that cohabits within the host and plays a critical role in maintaining host homeostasis. Recently, accumulating evidence has revealed that the gut microbial ecology plays a pivotal role in the occurrence and development of cardiovascular disease (CVD). Moreover, the effects of imbalances in microbe-host interactions on homeostasis can lead to the progression of CVD. Alterations in the composition of gut flora and disruptions in gut microbial metabolism are implicated in the pathogenesis of CVD. Furthermore, the gut microbiota functions like an endocrine organ that produces bioactive metabolites, including trimethylamine/trimethylamine N-oxide, short-chain fatty acids and bile acids, which are also involved in host health and disease via numerous pathways. Thus, the gut microbiota and its metabolic pathways have attracted growing attention as a therapeutic target for CVD treatment. The fundamental purpose of this review was to summarize recent studies that have illustrated the complex interactions between the gut microbiota, their metabolites and the development of common CVD, as well as the effects of gut dysbiosis on CVD risk factors. Moreover, we systematically discuss the normal physiology of gut microbiota and potential therapeutic strategies targeting gut microbiota to prevent and treat CVD.}, }
@article {pmid31982930, year = {2020}, author = {Chen, YT and Zeng, Y and Wang, HZ and Zheng, D and Kamagata, Y and Narihiro, T and Nobu, MK and Tang, YQ}, title = {Different Interspecies Electron Transfer Patterns during Mesophilic and Thermophilic Syntrophic Propionate Degradation in Chemostats.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01485-x}, pmid = {31982930}, issn = {1432-184X}, support = {2016YFE0127700//Ministry of Science and Technology of the People's Republic of China/ ; 51678378//National Natural Science Foundation of China/ ; 41701295//National Natural Science Foundation of China/ ; 2018M643480//Postdoctoral Research Foundation of China/ ; 2018SCUH0023//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Propionate is one of the major intermediates in anaerobic digestion of organic waste to CO2 and CH4. In methanogenic environments, propionate is degraded through a mutualistic interaction between symbiotic propionate oxidizers and methanogens. Although temperature heavily influences the microbial ecology and performance of methanogenic processes, its effect on syntrophic interaction during propionate degradation remains poorly understood. In this study, metagenomics and metatranscriptomics were employed to compare mesophilic and thermophilic propionate degradation communities. Mesophilic propionate degradation involved multiple syntrophic organisms (Syntrophobacter, Smithella, and Syntrophomonas), pathways, interactions, and preference toward formate-based electron transfer to methanogenic partners (i.e., Methanoculleus). In thermophilic propionate degradation, one syntrophic organism predominated (Pelotomaculum), interspecies H2 transfer played a major role, and phylogenetically and metabolically diverse H2-oxidizing methanogens were present (i.e., Methanoculleus, Methanothermobacter, and Methanomassiliicoccus). This study showed that microbial interactions, metabolic pathways, and niche diversity are distinct between mesophilic and thermophilic microbial communities responsible for syntrophic propionate degradation.}, }
@article {pmid31982929, year = {2020}, author = {Tivey, TR and Parkinson, JE and Mandelare, PE and Adpressa, DA and Peng, W and Dong, X and Mechref, Y and Weis, VM and Loesgen, S}, title = {N-Linked Surface Glycan Biosynthesis, Composition, Inhibition, and Function in Cnidarian-Dinoflagellate Symbiosis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01487-9}, pmid = {31982929}, issn = {1432-184X}, support = {1557804//Division of Integrative Organismal Systems/ ; }, abstract = {The success of symbioses between cnidarian hosts (e.g., corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiont Breviolum minutum (family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content of B. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition of B. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) by B. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success by B. minutum.}, }
@article {pmid31972955, year = {2020}, author = {Lepoutre, A and Faassen, EJ and Zweers, AJ and Lürling, M and Geffard, A and Lance, E}, title = {How the Neurotoxin β-N-Methylamino-l-Alanine Accumulates in Bivalves: Distribution of the Different Accumulation Fractions among Organs.}, journal = {Toxins}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/toxins12020061}, pmid = {31972955}, issn = {2072-6651}, support = {Bourse Eole//Réseau Franco-Néerlandais de l'enseignement supérieur et de la recherche (RFN) and the Nuffic (Netherlands Organization for International Co-operation in Higher Education)./ ; 2015/1/191//Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail/ ; }, abstract = {The environmental neurotoxin β-methylamino-l-alanine (BMAA) may represent a risk for human health. BMAA accumulates in freshwater and marine organisms consumed by humans. However, few data are available about the kinetics of BMAA accumulation and detoxification in exposed organisms, as well as the organ distribution and the fractions in which BMAA is present in tissues (free, soluble bound or precipitated bound cellular fractions). Here, we exposed the bivalve mussel Dreissena polymorpha to 7.5 µg of dissolved BMAA/mussel/3 days for 21 days, followed by 21 days of depuration in clear water. At 1, 3, 8, 14 and 21 days of exposure and depuration, the hemolymph and organs (digestive gland, the gills, the mantle, the gonad and muscles/foot) were sampled. Total BMAA as well as free BMAA, soluble bound and precipitated bound BMAA were quantified by tandem mass spectrometry. Free and soluble bound BMAA spread throughout all tissues from the first day of exposure to the last day of depuration, without a specific target organ. However, precipitated bound BMAA was detected only in muscles and foot from the last day of exposure to day 8 of depuration, at a lower concentration compared to free and soluble bound BMAA. In soft tissues (digestive gland, gonad, gills, mantle and muscles/foot), BMAA mostly accumulated as a free molecule and in the soluble bound fraction, with variations occurring between the two fractions among tissues and over time. The results suggest that the assessment of bivalve contamination by BMAA may require the quantification of total BMAA in whole individuals when possible.}, }
@article {pmid31969867, year = {2019}, author = {Qu, EB and Omelon, CR and Oren, A and Meslier, V and Cowan, DA and Maggs-Kölling, G and DiRuggiero, J}, title = {Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities From Global Deserts.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2952}, pmid = {31969867}, issn = {1664-302X}, abstract = {Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are relatively simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial communities. We conducted a comprehensive survey of endolithic sandstones using high-throughput marker gene sequencing to characterize global patterns of diversity in endolithic microbial communities. We also tested a range of abiotic variables in order to investigate the factors that drive community assembly at various trophic levels. Macroclimate was found to be the primary driver of endolithic community composition, with the most striking difference witnessed between hot and polar deserts. This difference was largely attributable to the specialization of prokaryotic and eukaryotic primary producers to different climate conditions. On a regional scale, microclimate and properties of the rock substrate were found to influence community assembly, although to a lesser degree than global hot versus polar conditions. We found new evidence that the factors driving endolithic community assembly differ between trophic levels. While phototrophic taxa, mostly oxygenic photosynthesizers, were rigorously selected for among different sites, heterotrophic taxa were more cosmopolitan, suggesting that stochasticity plays a larger role in heterotroph assembly. This study is the first to uncover the global drivers of desert endolithic diversity using high-throughput sequencing. We demonstrate that phototrophs and heterotrophs in the endolithic community assemble under different stochastic and deterministic influences, emphasizing the need for studies of microorganisms in context of their functional niche in the community.}, }
@article {pmid31969866, year = {2019}, author = {Hao, X and Zhu, YG and Nybroe, O and Nicolaisen, MH}, title = {The Composition and Phosphorus Cycling Potential of Bacterial Communities Associated With Hyphae of Penicillium in Soil Are Strongly Affected by Soil Origin.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2951}, pmid = {31969866}, issn = {1664-302X}, abstract = {Intimate fungal-bacterial interactions are widespread in nature. However the main drivers for the selection of hyphae-associated bacterial communities and their functional traits in soil systems remain elusive. In the present study, baiting microcosms were used to recover hyphae-associated bacteria from two Penicillium species with different phosphorus-solubilizing capacities in five types of soils. Based on amplicon sequencing of 16S rRNA genes, the composition of bacterial communities associated with Penicillium hyphae differed significantly from the soil communities, showing a lower diversity and less variation in taxonomic structure. Furthermore, soil origin had a significant effect on hyphae-associated community composition, whereas the two fungal species used in this study had no significant overall impact on bacterial community structure, despite their different capacities to solubilize phosphorus. However, discriminative taxa and specific OTUs were enriched in hyphae-associated communities of individual Penicillium species indicating that each hyphosphere represented a unique niche for bacterial colonization. Additionally, an increased potential of phosphorus cycling was found in hyphae-associated communities, especially for the gene phnK involved in phosphonate degradation. Altogether, it was established that the two Penicillium hyphae represent unique niches in which microbiome assemblage and phosphorus cycling potential are mainly driven by soil origin, with less impact made by fungal identity with a divergent capacity to utilize phosphorus.}, }
@article {pmid31968298, year = {2020}, author = {Lu, B and Shen, Z and Zhang, Q and Hu, X and Warren, A and Song, W}, title = {Morphology and molecular analyses of four epibiotic peritrichs on crustacean and polychaete hosts, including descriptions of two new species (Ciliophora, Peritrichia).}, journal = {European journal of protistology}, volume = {73}, number = {}, pages = {125670}, doi = {10.1016/j.ejop.2019.125670}, pmid = {31968298}, issn = {1618-0429}, abstract = {Four epibiotic sessilid peritrichs, i.e., Zoothamnium wilberti n. sp., Baikalonis microdiscus n. sp., Epistylis anastatica (Linnaeus, 1767) Ehrenberg, 1830, and Rhabdostyla commensalisMöbius, 1888, were isolated from one syllid polychaete and three crustacean hosts in Qingdao, China. For each species, specimens were observed both in vivo and following silver staining. Their SSU rDNA was also sequenced for phylogenetic analyses. Zoothamnium wilberti n. sp. is characterized by the appearance of its colony, which is up to 350 μm high, and usually has fewer than 16 zooids, and the dichotomously branched stalk with transverse wrinkles, the conspicuously conical peristomial disc, and infundibular polykinety 3 comprising three isometric ciliary rows. Baikalonis microdiscus n. sp. can be recognized by its barrel-shaped zooid, small peristomial disc, smooth and short stalk, and its unusual infundibular polykinety 3 comprising a long inner row and a short outer row. Two poorly known species, i.e., Epistylis anastatica and Rhabdostyla commensalis, are redescribed and redefined. Phylogenetic analyses reveal that: (i) R. commensalis is closely related to the family Astylozoidae rather than to the morphologically similar Epistylididae; (ii) B. microdiscus n. sp. is sister to the family Scyphidiidae; (iii) E. anastatica groups with vorticellids and ophrydiids, which further supports the polyphyly of the genus Epistylis; and (iv) Z. wilberti n. sp. is nested within the Zoothamniidae, as expected.}, }
@article {pmid31967575, year = {2020}, author = {Probst, AJ and Vaishampayan, P}, title = {Are we There Yet? Understanding Interplanetary Microbial Hitchhikers using Molecular Methods.}, journal = {Current issues in molecular biology}, volume = {38}, number = {}, pages = {33-52}, doi = {10.21775/cimb.038.033}, pmid = {31967575}, issn = {1467-3045}, abstract = {Since the early time of space travel, planetary bodies undergoing chemical or biological evolution have been of particular interest for life detection missions. NASA's and ESA's Planetary Protection offices ensure responsible exploration of the solar system and aim at avoiding inadvertent contamination of celestial bodies with biomolecules or even living organisms. Life forms that have the potential to colonize foreign planetary bodies could be a threat to the integrity of science objectives of life detection missions. While standard requirements for assessing the cleanliness of spacecraft are still based on cultivation approaches, several molecular methods have been applied in the past to elucidate the full breadth of (micro)organisms that can be found on spacecraft and in cleanrooms, where the hardware is assembled. Here, we review molecular assays that have been applied in Planetary Protection research and list their significant advantages and disadvantages. By providing a comprehensive summary of the latest molecular methods yet to be applied in this research area, this article will not only aid in designing technological roadmaps for future Planetary Protection endeavors but also help other disciplines in environmental microbiology that deal with low biomass samples.}, }
@article {pmid31965838, year = {2019}, author = {Moens, F and Duysburgh, C and van den Abbeele, P and Morera, M and Marzorati, M}, title = {Lactobacillus rhamnosus GG and Saccharomyces cerevisiae boulardii exert synergistic antipathogenic activity in vitro against enterotoxigenic Escherichia coli.}, journal = {Beneficial microbes}, volume = {10}, number = {8}, pages = {923-935}, doi = {10.3920/BM2019.0064}, pmid = {31965838}, issn = {1876-2891}, abstract = {Short-term colonic in vitro batch incubations were performed to elucidate the possible synergistic effects of Lactobacillus rhamnosus GG (CNCM-I-4798) and Saccharomyces cerevisiae boulardii (CNCM-I-1079) (associated in Smebiocta/Smectaflora Protect®) on the colonic microbial fermentation process, as well as their antipathogenic activity against enterotoxigenic Escherichia coli (LMG2092) (ETEC). These incubations adequately simulate the native microbiota and environmental conditions of the proximal colon of both adult and toddler donors, including the colonic mucosal layer. Results indicated that both strains were capable of growing together without showing antagonistic effects. Co-cultivation of both strains resulted in increased butyrate (stimulated by L. rhamnosus GG), propionate (stimulated by S. boulardii), and ethanol (produced by S. boulardii) production compared to the control incubations, revealing the additive effect of both strains. After inoculation of ETEC under simulated dysbiotic conditions, a 40 and 46% reduction in the concentration of ETEC was observed upon addition of both strains during the experiments with the adult and toddler donor, respectively. Furthermore, ETEC toxin levels decreased upon S. boulardii inoculation, probably due to proteolytic activity of this strain, with a synergistic effect being observed upon co-cultivation of L. rhamnosus GG and S. boulardii resulting in a reduction of 57 and 46% for the adult and toddler donor, respectively. Altogether, the results suggest that both probiotics together may help microbiota functionality, in both adults and toddlers and under healthy or impaired conditions, which could be of great interest when the colonic microbiota is dysbiotic and therefore sensitive to pathogenic invasion such as during antibiotic treatment.}, }
@article {pmid31965223, year = {2020}, author = {Mina, D and Pereira, JA and Lino-Neto, T and Baptista, P}, title = {Epiphytic and Endophytic Bacteria on Olive Tree Phyllosphere: Exploring Tissue and Cultivar Effect.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01488-8}, pmid = {31965223}, issn = {1432-184X}, support = {PTDC/ASP-PLA/31133/2017//Fundação para a Ciência e a Tecnologia/ ; SFRH-BD-105341/2014//Fundação para a Ciência e a Tecnologia/ ; PRIMA/0002/2018//Horizon 2020 Framework Programme/ ; }, abstract = {Variation on bacterial communities living in the phyllosphere as epiphytes and endophytes has been attributed to plant host effects. However, there is contradictory or inconclusive evidence regarding the effect of plant genetics (below the species' level) and of plant tissue type on phyllosphere bacterial community assembly, in particular when epiphytes and endophytes are considered simultaneously. Here, both surface and internal bacterial communities of two olive (Olea europaea) cultivars were evaluated in twigs and leaves by molecular identification of cultivable isolates, with an attempt to answer these questions. Overall, Proteobacteria, Actinobacteria and Firmicutes were the dominant phyla, being epiphytes more diverse and abundant than endophytes. Host genotype (at cultivar level) had a structuring effect on the composition of bacterial communities and, in a similar way, for both epiphytes and endophytes. Plant organ (leaf vs. twig) control of the bacterial communities was less evident when compared with plant genotype and with a greater influence on epiphytic than on endophytic community structure. Each olive genotype/plant organ was apparently selective towards specific bacterial operational taxonomic units (OTUs), which may lead to specific feedbacks on fitness of plant genotypes. Bacterial recruitment was observed to happen mainly within epiphytes than in endophytes and in leaves as compared with twigs. Such host specificity suggested that the benefits derived from the plant-bacteria interaction should be considered at genetic levels below the species.}, }
@article {pmid31964728, year = {2020}, author = {Carini, P and Delgado-Baquerizo, M and Hinckley, ES and Holland-Moritz, H and Brewer, TE and Rue, G and Vanderburgh, C and McKnight, D and Fierer, N}, title = {Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, doi = {10.1128/mBio.02776-19}, pmid = {31964728}, issn = {2150-7511}, abstract = {Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.}, }
@article {pmid31958594, year = {2020}, author = {Vandekerckhove, TGL and Props, R and Carvajal-Arroyo, JM and Boon, N and Vlaeminck, SE}, title = {Adaptation and characterization of thermophilic anammox in bioreactors.}, journal = {Water research}, volume = {172}, number = {}, pages = {115462}, doi = {10.1016/j.watres.2019.115462}, pmid = {31958594}, issn = {1879-2448}, abstract = {Anammox, the oxidation of ammonium with nitrite, is a key microbial process in the nitrogen cycle. Under mesophilic conditions (below 40 °C), it is widely implemented to remove nitrogen from wastewaters lacking organic carbon. Despite evidence of the presence of anammox bacteria in high-temperature environments, reports on the cultivation of thermophilic anammox bacteria are limited to a short-term experiment of 2 weeks. This study showcases the adaptation of a mesophilic inoculum to thermophilic conditions, and its characterization. First, an attached growth technology was chosen to obtain the process. In an anoxic fixed-bed biofilm bioreactor (FBBR), a slow linear temperature increase from 38 to over 48 °C (0.05-0.07 °C d-1) was imposed to the community over 220 days, after which the reactor was operated at 48 °C for over 200 days. Maximum total nitrogen removal rates reached up to 0.62 g N L-1 d-1. Given this promising performance, a suspended growth system was tested. The obtained enrichment culture served as inoculum for membrane bioreactors (MBR) operated at 50 °C, reaching a maximum total nitrogen removal rate of 1.7 g N L-1 d-1 after 35 days. The biomass in the MBR had a maximum specific anammox activity of 1.1 ± 0.1 g NH4+-N g-1 VSS d-1, and the growth rate was estimated at 0.075-0.19 d-1. The thermophilic cultures displayed nitrogen stoichiometry ratios typical for mesophilic anammox: 0.93-1.42 g NO2--Nremoved g-1 NH4+-Nremoved and 0.16-0.35 g NO3--Nproduced g-1 NH4+-Nremoved. Amplicon and Sanger sequencing of the 16S rRNA genes revealed a disappearance of the original &quot;Ca. Brocadia&quot; and &quot;Ca. Jettenia&quot; taxa, yielding Planctomycetes members with only 94-95% similarity to &quot;Ca. Brocadia anammoxidans&quot; and &quot;Ca. B. caroliniensis&quot;, accounting for 45% of the bacterial FBBR community. The long-term operation of thermophilic anammox reactors and snapshot views on the nitrogen stoichiometry, kinetics and microbial community open up the development path of thermophilic partial nitritation/anammox. A first economic assessment highlighted that treatment of sludge reject water from thermophilic anaerobic digestion of sewage sludge may become attractive.}, }
@article {pmid31955749, year = {2020}, author = {Gontijo, MTP and Silva, JS and Vidigal, PMP and Martin, JGP}, title = {Phylogenetic distribution of the bacteriocin repertoire of lactic acid bacteria species associated with artisanal cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {128}, number = {}, pages = {108783}, doi = {10.1016/j.foodres.2019.108783}, pmid = {31955749}, issn = {1873-7145}, abstract = {The microbiota contributes to artisanal cheese bioprotection and biopreservation through inter and intraspecific competition. This work aimed to investigate the phylogenetic distribution of the repertoire of bacteriocin structural genes of model lactic acid bacteria (LAB) in order to investigate its respective role in the artisanal cheeses microenvironment. A phylogenetic analysis of the rRNA 16S gene from 445 model strains of LAB was conducted using bayesian inference and the repertoire of bacteriocin genes was predicted from these strains by BAGEL software. Bacterial strains were clustered in five monophyletic clades (A, B, C, D and E) with high posterior probability values (PP > 0.99). One bacteriocin structural gene was predicted for 88.5% of the analyzed strains. The majority of the species encoded different classes of bacteriocins. Greater diversity of bacteriocin genes was found for strains included in clade A, comprising Lactococcus lactis, Streptococcus agalactiae, Streptococcus thermophilus, Streptococcus macedonicus, Enterococcus faecalis and Enterococcus faecium. In addition, Lactococcus lactis presented higher diversity of bacteriocin classes, encoding glycocins, lanthipeptides, sactipeptides, cyclic and linear azole-containing peptides, included in bacteriocins class I, besides class II and III. The results suggest that the distribution of bacteriocin structural genes is related to the phylogenetic clades of LAB species, with a higher frequency in some specific clades. Information comprised in this study contributes to comprehend the bacterial competition mechanisms in the artisanal cheese microenvironment.}, }
@article {pmid31955225, year = {2020}, author = {Liu, H and Gao, H and Wu, M and Ma, C and Wu, J and Ye, X}, title = {Distribution Characteristics of Bacterial Communities and Hydrocarbon Degradation Dynamics During the Remediation of Petroleum-Contaminated Soil by Enhancing Moisture Content.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01476-7}, pmid = {31955225}, issn = {1432-184X}, support = {No. 21577109//National Natural Science Foundation of China/ ; }, abstract = {Microorganisms are the driver of petroleum hydrocarbon degradation in soil micro-ecological systems. However, the distribution characteristics of microbial communities and hydrocarbon degradation dynamics during the remediation of petroleum-contaminated soil by enhancing moisture content are not clear. In this study, polymerase chain reaction and high-throughput sequencing of soil microbial DNA were applied to investigate the compositions of microorganisms and alpha diversity in the oil-polluted soil, and the hydrocarbon removal also being analyzed using ultrasonic extraction and gravimetric method in a laboratory simulated ex-situ experiment. Results showed the distribution of petroleum hydrocarbon degrading microorganisms in the petroleum-contaminated loessal soil mainly was Proteobacteria phylum (96.26%)-Gamma-proteobacteria class (90.03%)-Pseudomonadales order (89.98%)-Pseudomonadaceae family (89.96%)-Pseudomonas sp. (87.22%). After 15% moisture content treatment, Actinobacteria, Proteobacteria, and Firmicutes still were the predominant phyla, but their relative abundances changed greatly. Also Bacillus sp. and Promicromonospora sp. became the predominant genera. Maintaining 15% moisture content increased the relative abundance of Firmicutes phylum and Bacillus sp. As the moisture-treated time increases, the uniformity and the richness of the soil bacterial community were decreased and increased respectively; the relative abundance of Pseudomonas sp. increased. Petroleum hydrocarbon degradation by enhancing soil moisture accorded with the pseudo-first-order reaction kinetic model (correlation coefficient of 0.81; half-life of 56 weeks). The richness of Firmicutes phylum and Bacillus sp. may be a main reason for promoting the removal of 18% petroleum hydrocarbons responded to 15% moisture treatment. Our results provided some beneficial microbiological information of oil-contaminated soil and will promote the exploration of remediation by changing soil moisture content for increasing petroleum hydrocarbon degradation efficiency.}, }
@article {pmid31954761, year = {2020}, author = {Mongui, A and Lozano, GL and Handelsman, J and Restrepo, S and Junca, H}, title = {Design and validation of a transposon that promotes expression of genes in episomal DNA.}, journal = {Journal of biotechnology}, volume = {310}, number = {}, pages = {1-5}, doi = {10.1016/j.jbiotec.2020.01.007}, pmid = {31954761}, issn = {1873-4863}, abstract = {Functional metagenomics, or the cloning and expression of DNA isolated directly from environmental samples, represents a source of novel compounds with biotechnological potential. However, attempts to identify such compounds in metagenomic libraries are generally inefficient in part due to lack of expression of heterologous DNA. In this research, the TnC_T7 transposon was developed to supply transcriptional machinery during functional analysis of metagenomic libraries. TnC_T7 contains bidirectional T7 promoters, the gene encoding the T7 RNA polymerase (T7RNAP), and a kanamycin resistance gene. The T7 RNA polymerase gene is regulated by the inducible arabinose promoter (PBAD), thereby facilitating inducible expression of genes adjacent to the randomly integrating transposon. The high processivity of T7RNAP should make this tool particularly useful for obtaining gene expression in long inserts. TnC_T7 functionality was validated by conducting in vitro transposition of pKR-C12 or fosmid pF076_GFPmut3*, carrying metagenomic DNA from soil. We identified transposon insertions that enhanced GFP expression in both vectors, including insertions in which the promoter delivered by the transposon was located as far as 8.7 kb from the GFP gene, indicating the power of the high processivity of the T7 polymerase. The results gathered in this research demonstrate the potential of TnC_T7 to enhance gene expression in functional metagenomic studies.}, }
@article {pmid31954367, year = {2020}, author = {Giri, S and Shitut, S and Kost, C}, title = {Harnessing ecological and evolutionary principles to guide the design of microbial production consortia.}, journal = {Current opinion in biotechnology}, volume = {62}, number = {}, pages = {228-238}, doi = {10.1016/j.copbio.2019.12.012}, pmid = {31954367}, issn = {1879-0429}, abstract = {Bacteria are widely used for commercially producing biomolecules. However, attempts to rationally design production strains and optimize cultivation conditions are frequently counteracted by the emergence of mutants with reduced production characteristics that decrease overall process yield. The reason why these mutants arise is likely because of a mismatch between the ecological conditions under which bacteria evolved in nature and the situation they experience in an industrial setting. Thus, there is a great potential for improving biotechnological production processes by implementing eco-evolutionary knowledge. However, this is often limited by a lack of effective communication between process engineers and microbial ecologists/evolutionary biologists. Here, we highlight recent findings in the field of microbial ecology and evolution and suggest implementation of this knowledge can significantly enhance microbial bioproduction.}, }
@article {pmid31952848, year = {2020}, author = {Krishnamoorthy, S and Coetzee, V and Kruger, J and Potgieter, H and Buys, EM}, title = {Dysbiosis Signatures of Fecal Microbiota in South African Infants with Respiratory, Gastrointestinal, and Other Diseases.}, journal = {The Journal of pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jpeds.2019.11.029}, pmid = {31952848}, issn = {1097-6833}, abstract = {OBJECTIVE: To determine the association between the fecal microbiota diversity of the infants with different disease conditions, and vitamin A supplementation, antibiotic, and deworming therapies.<br><br>STUDY DESIGN: In this case-control study, the bacterial community variations and the potential pathogens were identified through 16S ribosomal RNA gene-based amplicon sequencing and quantitative insights into microbial ecology pipeline in fecal samples. The participants were South African infants (mean age, 16 ± 8 months; 17 male and 17 female) hospitalized and diagnosed with gastrointestinal, respiratory, and other diseases.<br><br>RESULTS: The top phyla of the infants with respiratory disease were Proteobacteria, followed by Firmicutes, which were equally abundant in gastrointestinal disease. A significant difference in Shannon (alpha) diversity index (95% CI, 2.6-4.4; P = .008), among the microbiota of the fecal samples categorized by disease conditions, was observed. In beta diversity analysis of fecal microbiota, remarkable variations were found within the groups of deworming therapy (95% CI, 0.40-0.90; P = .033), disease conditions (95% CI, 0.44-0.86; P < .012) through unweighted and antibiotic therapy (95% CI, 0.20-0.75; P = .007), vitamin A intake (95% CI, 0.10-0.80; P < .033) and disease conditions (95% CI, 0.10-0.79; P = .006) through weighted UniFrac distances. The candidate pathogen associated with the disease groups were identified through analysis of the composition of microbiomes analysis.<br><br>CONCLUSIONS: This study provides preliminary evidence for the fecal microbiome-derived dysbiosis signature and pathobiome concept that may be observed in young children during illness.}, }
@article {pmid31952472, year = {2020}, author = {Feng, J and Wang, C and Lei, J and Yang, Y and Yan, Q and Zhou, X and Tao, X and Ning, D and Yuan, MM and Qin, Y and Shi, ZJ and Guo, X and He, Z and Van Nostrand, JD and Wu, L and Bracho-Garillo, RG and Penton, CR and Cole, JR and Konstantinidis, KT and Luo, Y and Schuur, EAG and Tiedje, JM and Zhou, J}, title = {Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {3}, pmid = {31952472}, issn = {2049-2618}, support = {DE-SC0004601//the US Department of Energy, Office of Science, Genomic Science Program/ ; DE-SC0010715//the US Department of Energy, Office of Science, Genomic Science Program/ ; 41430856//National Science Foundation of China/ ; 41877048//National Science Foundation of China/ ; 41825016//National Science Foundation of China/ ; }, abstract = {BACKGROUND: It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern that decomposition of soil organic carbon (SOC) previously stored in this region, which accounts for about 50% of the world's SOC storage, will cause positive feedback that accelerates climate warming. We have previously shown that short-term warming (1.5 years) stimulates rapid, microbe-mediated decomposition of tundra soil carbon without affecting the composition of the soil microbial community (based on the depth of 42684 sequence reads of 16S rRNA gene amplicons per 3 g of soil sample).<br><br>RESULTS: We show that longer-term (5 years) experimental winter warming at the same site altered microbial communities (p < 0.040). Thaw depth correlated the strongest with community assembly and interaction networks, implying that warming-accelerated tundra thaw fundamentally restructured the microbial communities. Both carbon decomposition and methanogenesis genes increased in relative abundance under warming, and their functional structures strongly correlated (R2 > 0.725, p < 0.001) with ecosystem respiration or CH4 flux.<br><br>CONCLUSIONS: Our results demonstrate that microbial responses associated with carbon cycling could lead to positive feedbacks that accelerate SOC decomposition in tundra regions, which is alarming because SOC loss is unlikely to subside owing to changes in microbial community composition. Video Abstract.}, }
@article {pmid31951572, year = {2020}, author = {Li, Z and Van de Peer, Y}, title = {&quot;Winter Is Coming&quot;: How did Polyploid Plants Survive?.}, journal = {Molecular plant}, volume = {13}, number = {1}, pages = {4-5}, doi = {10.1016/j.molp.2019.12.003}, pmid = {31951572}, issn = {1752-9867}, }
@article {pmid31951190, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003973}, pmid = {31951190}, issn = {1466-5034}, abstract = {A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5-1.9 µm, and was able to grow at 10-37 °C (optimum, 28-30 °C), at pH 4.5-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2-92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2-83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn-Gly2-d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae, for which the name Segeticoccusrhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccusrhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).}, }
@article {pmid31950228, year = {2020}, author = {Guhr, A and Kircher, S}, title = {Drought-Induced Stress Priming in Two Distinct Filamentous Saprotrophic Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01481-w}, pmid = {31950228}, issn = {1432-184X}, support = {DFG-GU 1818/1-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Sessile organisms constantly face environmental fluctuations and especially drought is a common stressor. One adaptive mechanism is &quot;stress priming,&quot; the ability to cope with a severe stress (&quot;triggering&quot;) by retaining information from a previous mild stress event (&quot;priming&quot;). While plants have been extensively investigated for drought-induced stress priming, no information is available for saprotrophic filamentous fungi, which are highly important for nutrient cycles. Here, we investigated the potential for drought-induced stress priming of one strain each of two ubiquitous species, Neurospora crassa and Penicillium chrysogenum. A batch experiment with 4 treatments was conducted on a sandy soil: exposure to priming and/or triggering as well as non-stressed controls. A priming stress was caused by desiccation to pF 4. The samples were then rewetted and after 1-, 7-, or 14-days of recovery triggered (pF 6). After triggering, fungal biomass, respiration, and β-glucosidase activity were quantified. P. chrysogenum showed positive stress priming effects. After 1 day of recovery, biomass as well as β-glucosidase activity and respiration were 0.5 to 5 times higher during triggering. Effects on biomass and activity decreased with prolonged recovery but lasted for 7 days and minor effects were still detectable after 14 days. Without triggering, stress priming had a temporary negative impact on biomass but this reversed after 14 days. For N. crassa, no stress priming effect was observed on the tested variables. The potential for drought-induced stress priming seems to be species specific with potentially high impact on composition and activity of fungal communities considering the expected increase of drought events.}, }
@article {pmid31948971, year = {2020}, author = {Korotetskiy, IS and Joubert, M and Magabotha, SM and Jumagaziyeva, AB and Shilov, SV and Suldina, NA and Kenesheva, ST and Yssel, A and Reva, ON and Ilin, AI}, title = {Complete Genome Sequence of Collection Strain Acinetobacter baumannii ATCC BAA-1790, Used as a Model To Study the Antibiotic Resistance Reversion Induced by Iodine-Containing Complexes.}, journal = {Microbiology resource announcements}, volume = {9}, number = {3}, pages = {}, doi = {10.1128/MRA.01467-19}, pmid = {31948971}, issn = {2576-098X}, abstract = {The strain Acinetobacter baumannii ATCC BAA-1790 was sequenced as a model for nosocomial multidrug-resistant infections. Long-read PacBio sequencing revealed a circular chromosome of 3,963,235 bp with two horizontally transferred genomic islands and a 67,023-bp plasmid. Multiple antibiotic resistance genes and genome methylation patterns were identified.}, }
@article {pmid31947979, year = {2020}, author = {Purkamo, L and Kietäväinen, R and Nuppunen-Puputti, M and Bomberg, M and Cousins, C}, title = {Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context.}, journal = {Life (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/life10010002}, pmid = {31947979}, issn = {2075-1729}, support = {2016-2018//Jenny ja Antti Wihurin Rahasto/ ; RENGAS//KYT2018/ ; BIKES//KYT22/ ; C.Cousins//Royal Society of Edinburgh/ ; }, abstract = {The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.}, }
@article {pmid31943686, year = {2020}, author = {Guégan, M and Tran Van, V and Martin, E and Minard, G and Tran, FH and Fel, B and Hay, AE and Simon, L and Barakat, M and Potier, P and Haichar, FEZ and Valiente Moro, C}, title = {Who is eating fructose within the Aedes albopictus gut microbiota?.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14915}, pmid = {31943686}, issn = {1462-2920}, support = {//EC2CO CNRS/ ; ANR-13-EBID-0007-01//ERA-NET BiodivERsA/ ; FWF I-1437//ERA-NET BiodivERsA/ ; DFG KL 2087/6//ERA-NET BiodivERsA/ ; }, abstract = {The Asian tiger mosquito Aedes albopictus is a major public health concern because of its invasive success and its ability to transmit pathogens. Given the low availability of treatments against mosquito-borne diseases, vector control remains the most suitable strategy. The methods used thus far are becoming less effective, but recent strategies have emerged from the study of mosquito-associated microorganisms. Although the role of the microbiota in insect biology does not require further proof, much remains to be deciphered in mosquitoes, especially the contribution of the microbiota to host nutrient metabolism. Mosquitoes feed on plant nectar, composed of mostly fructose. We used stable isotope probing to identify bacteria and fungi assimilating fructose within the gut of Ae. albopictus. Mosquitoes were fed a 13 C-labelled fructose solution for 24 h. Differences in the active microbial community according to the sex of mosquitoes were highlighted. The bacterium Lelliottia and the fungi Cladosporium and Aspergillus dominated the active microbiota in males, whereas the bacterium Ampullimonas and the yeast Cyberlindnera were the most active in females. This study is the first to investigate trophic interactions between Ae. albopictus and its microbiota, thus underscoring the importance of the microbial component in nectar feeding in mosquitoes.}, }
@article {pmid31942799, year = {2020}, author = {Cakmak, I and Marzorati, M and Van den Abbeele, P and Hora, K and Holwerda, HT and Yazici, MA and Savasli, E and Neri, J and Du Laing, G}, title = {Fate and Bioaccessibility of Iodine in Food Prepared from Agronomically Biofortified Wheat and Rice and Impact of Cofertilization with Zinc and Selenium.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.9b05912}, pmid = {31942799}, issn = {1520-5118}, abstract = {Enrichment of food crops with iodine is an option to alleviate dietary deficiencies. Therefore, foliar iodine fertilizer was applied on wheat and rice, in the presence and absence of the other micronutrients zinc and selenium. This treatment increased the concentration of iodine, as well as zinc and selenium, in the staple grains. Subsequently, potential iodine losses during preparation of foodstuffs with the enriched grains were studied. Oven-heating did not affect the iodine content in bread. Extraction of bran from flour lowered the iodine in white bread compared to wholegrain bread, but it was still markedly higher compared to the control. During subsequent in vitro gastrointestinal digestion, a higher percentage of iodine was released from foods based on extracted flour (82-92%) compared to wholegrain foods (50-76%). The foliar fertilization of wheat was found to be adequate to alleviate iodine deficiency in a population with a moderate to high intake of bread.}, }
@article {pmid31942666, year = {2020}, author = {Morrison, ES and Thomas, P and Ogram, A and Kahveci, T and Turner, BL and Chanton, JP}, title = {Characterization of Bacterial and Fungal Communities Reveals Novel Consortia in Tropical Oligotrophic Peatlands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01483-z}, pmid = {31942666}, issn = {1432-184X}, support = {DEB 0841596//National Science Foundation/ ; }, abstract = {Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH4 and CO2 gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.}, }
@article {pmid31942051, year = {2020}, author = {Hampton, HG and Watson, BNJ and Fineran, PC}, title = {The arms race between bacteria and their phage foes.}, journal = {Nature}, volume = {577}, number = {7790}, pages = {327-336}, doi = {10.1038/s41586-019-1894-8}, pmid = {31942051}, issn = {1476-4687}, abstract = {Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.}, }
@article {pmid31941815, year = {2020}, author = {De Rudder, C and Calatayud Arroyo, M and Lebeer, S and Van de Wiele, T}, title = {Dual and Triple Epithelial Coculture Model Systems with Donor-Derived Microbiota and THP-1 Macrophages To Mimic Host-Microbe Interactions in the Human Sinonasal Cavities.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSphere.00916-19}, pmid = {31941815}, issn = {2379-5042}, abstract = {The epithelium of the human sinonasal cavities is colonized by a diverse microbial community, modulating epithelial development and immune priming and playing a role in respiratory disease. Here, we present a novel in vitro approach enabling a 3-day coculture of differentiated Calu-3 respiratory epithelial cells with a donor-derived bacterial community, a commensal species (Lactobacillus sakei), or a pathobiont (Staphylococcus aureus). We also assessed how the incorporation of macrophage-like cells could have a steering effect on both epithelial cells and the microbial community. Inoculation of donor-derived microbiota in our experimental setup did not pose cytotoxic stress on the epithelial cell layers, as demonstrated by unaltered cytokine and lactate dehydrogenase release compared to a sterile control. Epithelial integrity of the differentiated Calu-3 cells was maintained as well, with no differences in transepithelial electrical resistance observed between coculture with donor-derived microbiota and a sterile control. Transition of nasal microbiota from in vivo to in vitro conditions maintained phylogenetic richness, and yet a decrease in phylogenetic and phenotypic diversity was noted. Additional inclusion and coculture of THP-1-derived macrophages did not alter phylogenetic diversity, and yet donor-independent shifts toward higher Moraxella and Mycoplasma abundance were observed, while phenotypic diversity was also increased. Our results demonstrate that coculture of differentiated airway epithelial cells with a healthy donor-derived nasal community is a viable strategy to mimic host-microbe interactions in the human upper respiratory tract. Importantly, including an immune component allowed us to study host-microbe interactions in the upper respiratory tract more in depth.IMPORTANCE Despite the relevance of the resident microbiota in sinonasal health and disease and the need for cross talk between immune and epithelial cells in the upper respiratory tract, these parameters have not been combined in a single in vitro model system. We have developed a coculture system of differentiated respiratory epithelium and natural nasal microbiota and incorporated an immune component. As indicated by absence of cytotoxicity and stable cytokine profiles and epithelial integrity, nasal microbiota from human origin appeared to be well tolerated by host cells, while microbial community composition remained representative for that of the human (sino)nasal cavity. Importantly, the introduction of macrophage-like cells enabled us to obtain a differential readout from the epithelial cells dependent on the donor microbial background to which the cells were exposed. We conclude that both model systems offer the means to investigate host-microbe interactions in the upper respiratory tract in a more representative way.}, }
@article {pmid31940957, year = {2020}, author = {Xu, Y and Shen, Z and Gentekaki, E and Xu, J and Yi, Z}, title = {Comparative Transcriptome Analyses during the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis erythrina (Alveolata, Ciliophora).}, journal = {Microorganisms}, volume = {8}, number = {1}, pages = {}, doi = {10.3390/microorganisms8010108}, pmid = {31940957}, issn = {2076-2607}, support = {2018SDKJ0406-4//Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; 31772440//National Natural Science Foundation of China/ ; 31430077//National Natural Science Foundation of China/ ; 31970486//National Natural Science Foundation of China/ ; GDOE2019A23//Guangdong MEPP Fund/ ; }, abstract = {Studies focusing on molecular mechanisms of cell cycles have been lagging in unicellular eukaryotes compared to other groups. Ciliates, a group of unicellular eukaryotes, have complex cell division cycles characterized by multiple events. During their vegetative cell cycle, ciliates undergo macronuclear amitosis, micronuclear mitosis, stomatogenesis and somatic cortex morphogenesis, and cytokinesis. Herein, we used the hypotrich ciliate Pseudokeronopsis erythrina, whose morphogenesis has been well studied, to examine molecular mechanisms of ciliate vegetative cell cycles. Single-cell transcriptomes of the growth (G) and cell division (D) stages were compared. The results showed that (i) More than 2051 significantly differentially expressed genes (DEGs) were detected, among which 1545 were up-regulated, while 256 were down-regulated at the D stage. Of these, 11 randomly picked DEGs were validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR); (ii) Enriched DEGs during the D stage of the vegetative cell cycle of P. erythrina were involved in development, cortex modifications, and several organelle-related biological processes, showing correspondence of molecular evidence to morphogenetic changes for the first time; (iii) Several individual components of molecular mechanisms of ciliate vegetative division, the sexual cell cycle and cellular regeneration overlap; and (iv) The P. erythrina cell cycle and division have the same essential components as other eukaryotes, including cyclin-dependent kinases (CDKs), cyclins, and genes closely related to cell proliferation, indicating the conserved nature of this biological process. Further studies are needed focusing on detailed inventory and gene interactions that regulate specific ciliated cell-phase events.}, }
@article {pmid31937947, year = {2020}, author = {Amaral-Zettler, LA and Zettler, ER and Mincer, TJ}, title = {Ecology of the plastisphere.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41579-019-0308-0}, pmid = {31937947}, issn = {1740-1534}, abstract = {The plastisphere, which comprises the microbial community on plastic debris, rivals that of the built environment in spanning multiple biomes on Earth. Although human-derived debris has been entering the ocean for thousands of years, microplastics now numerically dominate marine debris and are primarily colonized by microbial and other microscopic life. The realization that this novel substrate in the marine environment can facilitate microbial dispersal and affect all aquatic ecosystems has intensified interest in the microbial ecology and evolution of this biotope. Whether a 'core' plastisphere community exists that is specific to plastic is currently a topic of intense investigation. This Review provides an overview of the microbial ecology of the plastisphere in the context of its diversity and function, as well as suggesting areas for further research.}, }
@article {pmid31937679, year = {2020}, author = {Weissman, JL and Johnson, PLF}, title = {Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSystems.00752-19}, pmid = {31937679}, issn = {2379-5077}, abstract = {A diversity of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity to bacteria and archaea through recording &quot;memories&quot; of past viral infections. Recently, many novel CRISPR-associated proteins have been discovered via computational studies, but those studies relied on biased and incomplete databases of assembled genomes. We avoided these biases and applied a network theory approach to search for novel CRISPR-associated genes by leveraging subtle ecological cooccurrence patterns identified from environmental metagenomes. We validated our method using existing annotations and discovered 32 novel CRISPR-associated gene families. These genes span a range of putative functions, with many potentially regulating the response to infection.IMPORTANCE Every branch on the tree of life, including microbial life, faces the threat of viral pathogens. Over the course of billions of years of coevolution, prokaryotes have evolved a great diversity of strategies to defend against viral infections. One of these is the CRISPR adaptive immune system, which allows microbes to &quot;remember&quot; past infections in order to better fight them in the future. There has been much interest among molecular biologists in CRISPR immunity because this system can be repurposed as a tool for precise genome editing. Recently, a number of comparative genomics approaches have been used to detect novel CRISPR-associated genes in databases of genomes with great success, potentially leading to the development of new genome-editing tools. Here, we developed novel methods to search for these distinct classes of genes directly in environmental samples (&quot;metagenomes&quot;), thus capturing a more complete picture of the natural diversity of CRISPR-associated genes.}, }
@article {pmid31937676, year = {2020}, author = {Sedlacek, CJ and Giguere, AT and Dobie, MD and Mellbye, BL and Ferrell, RV and Woebken, D and Sayavedra-Soto, LA and Bottomley, PJ and Daims, H and Wagner, M and Pjevac, P}, title = {Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, doi = {10.1128/mSystems.00562-19}, pmid = {31937676}, issn = {2379-5077}, abstract = {Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea's sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria.IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.}, }
@article {pmid31935341, year = {2020}, author = {Bophela, KN and Petersen, Y and Bull, CT and Coutinho, TA}, title = {Identification of Pseudomonas Isolates Associated With Bacterial Canker of Stone Fruit Trees in the Western Cape, South Africa.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS05191102RE}, doi = {10.1094/PDIS-05-19-1102-RE}, pmid = {31935341}, issn = {0191-2917}, abstract = {Bacterial canker is a common bacterial disease of stone fruit trees. The causal agents responsible for the disease include several pathovars in Pseudomonas syringae sensu lato and newly described Pseudomonas species. Pseudomonad strains were isolated from symptomatic stone fruit trees, namely apricot, peach, and plum trees cultivated in spatially separated orchards in the Western Cape. A polyphasic approach was used to identify and characterize these strains. Using a multilocus sequence typing approach of four housekeeping loci, namely cts, gapA, gyrB, and rpoD, the pseudomonad strains were delineated into two phylogenetic groups within P. syringae sensu lato: P. syringae sensu stricto and Pseudomonas viridiflava. These results were further supported by LOPAT diagnostic assays and analysis of clades in the rep-PCR dendrogram. The pseudomonad strains were pathogenic on both apricot and plum seedlings, indicative of a lack of host specificity between Pseudomonas strains infecting Prunus spp. This is a first report of P. viridiflava isolated from plum trees showing symptoms of bacterial canker. P. viridiflava is considered to be an opportunistic pathogen that causes foliar diseases of vegetable crops, fruit trees, and aromatic herbs, and thus the isolation of pathogenic P. viridiflava from twigs of plum trees showing symptoms of bacterial canker suggests that this bacterial species is a potentially emerging stem canker pathogen of stone fruit trees in South Africa.}, }
@article {pmid31935110, year = {2020}, author = {El Hage, R and Hernandez-Sanabria, E and Calatayud Arroyo, M and Van De Wiele, T}, title = {Supplementation of a propionate-producing consortium improves markers of insulin resistance in an in vitro model of gut-liver axis.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpendo.00523.2019}, pmid = {31935110}, issn = {1522-1555}, abstract = {Gut-liver crosstalk is an important determinant of human health with profound effects on energy homeostasis. While gut microbes produce a huge range of metabolites, specific compounds such as short chain fatty acids (SCFA) can enter the portal circulation and reach the liver, a central organ involved in glucose homeostasis and diabetes control. Propionate is a major SCFA involved in activation of intestinal gluconeogenesis (IGN), thereby regulating food intake, enhancing insulin sensitivity and leading to metabolic homeostasis. Although microbiome modulating strategies may target the increased microbial production of propionate, it is not clear whether such effect spreads through to the hepatic cellular level. Here, we designed a propionate-producing consortium using a selection of commensal gut bacteria, and we investigated how their delivered metabolites impact an in vitro enterohepatic model of insulin resistance. Glycogen storage on hepatocyte-like cells and inflammatory markers associated with insulin resistance were evaluated to understand the role of gut metabolites on gut-liver crosstalk in a simulated scenario of insulin resistance. The metabolites produced by our consortium increased glycogen synthesis by approximately 57% and decreased pro-inflammatory markers such as IL-8 by 12%, thus elucidating the positive effect of our consortium on metabolic function and low-grade inflammation. Our results suggest that microbiota-derived products can be a promising multipurpose strategy to modulate energy homeostasis, with potential ability to assist in managing metabolic diseases due to their adaptability.}, }
@article {pmid31932882, year = {2020}, author = {Cleary, DFR and Polónia, ARM and Reijnen, BT and Berumen, ML and de Voogd, NJ}, title = {Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01465-w}, pmid = {31932882}, issn = {1432-184X}, support = {PTDC/AAC-AMB/115304/2009//FCT/ ; SFRH/BPD/117563/2016//FCT/ ; }, abstract = {In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.}, }
@article {pmid31932881, year = {2020}, author = {Ruiz-Rodríguez, M and Scheifler, M and Sanchez-Brosseau, S and Magnanou, E and West, N and Suzuki, M and Duperron, S and Desdevises, Y}, title = {Host Species and Body Site Explain the Variation in the Microbiota Associated to Wild Sympatric Mediterranean Teleost Fishes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01484-y}, pmid = {31932881}, issn = {1432-184X}, support = {SU-16-R-EMR-22-MICROFISH//Université Sorbonne Paris Cité/ ; }, abstract = {Microorganisms are an important component in shaping the evolution of hosts and as such, the study of bacterial communities with molecular techniques is shedding light on the complexity of symbioses between bacteria and vertebrates. Teleost fish are a heterogeneous group that live in a wide variety of habitats, and thus a good model group to investigate symbiotic interactions and their influence on host biology and ecology. Here we describe the microbiota of thirteen teleostean species sharing the same environment in the Mediterranean Sea and compare bacterial communities among different species and body sites (external mucus, skin, gills, and intestine). Our results show that Proteobacteria is the dominant phylum present in fish and water. However, the prevalence of other bacterial taxa differs between fish and the surrounding water. Significant differences in bacterial diversity are observed among fish species and body sites, with higher diversity found in the external mucus. No effect of sampling time nor species individual was found. The identification of indicator bacterial taxa further supports that each body site harbors its own characteristic bacterial community. These results improve current knowledge and understanding of symbiotic relationships among bacteria and their fish hosts in the wild since the majority of previous studies focused on captive individuals.}, }
@article {pmid31929046, year = {2020}, author = {Obata, O and Salar-Garcia, MJ and Greenman, J and Kurt, H and Chandran, K and Ieropoulos, I}, title = {Development of efficient electroactive biofilm in urine-fed microbial fuel cell cascades for bioelectricity generation.}, journal = {Journal of environmental management}, volume = {258}, number = {}, pages = {109992}, doi = {10.1016/j.jenvman.2019.109992}, pmid = {31929046}, issn = {1095-8630}, mesh = {*Bioelectric Energy Sources ; Biofilms ; Electricity ; Electrodes ; Sewage ; }, abstract = {The Microbial fuel cell (MFC) technology harnesses the potential of some naturally occurring bacteria for electricity generation. Digested sludge is commonly used as the inoculum to initiate the process. There are, however, health hazards and practical issues associated with the use of digested sludge depending on its origin as well as the location for system deployment. This work reports the development of an efficient electroactive bacterial community within ceramic-based MFCs fed with human urine in the absence of sludge inoculum. The results show the development of a uniform bacterial community with power output levels equal to or higher than those generated from MFCs inoculated with sludge. In this case, the power generation begins within 2 days of the experimental set-up, compared to about 5 days in some sludge-inoculated MFCs, thus significantly reducing the start-up time. The metagenomics analysis of the successfully formed electroactive biofilm (EAB) shows significant shifts between the microbial ecology of the feeding material (fresh urine) and the developed anodic biofilm. A total of 21 bacteria genera were detected in the urine feedstock whilst up to 35 different genera were recorded in the developed biofilm. Members of Pseudomonas (18%) and Anaerolineaceae (17%) dominate the bacterial community of the fresh urine feed while members of Burkholderiaceae (up to 50%) and Tissierella (up to 29%) dominate the anodic EAB. These results highlight a significant shift in the bacterial community of the feedstock towards a selection and adaptation required for the various electrochemical reactions essential for survival through power generation.}, }
@article {pmid31927597, year = {2020}, author = {Sun, F and Wang, C and Chen, H and Zheng, Z}, title = {Metagenomic Analysis of the Effect of Enteromorpha prolifera Bloom on Microbial Community and Function in Aquaculture Environment.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-019-01862-x}, pmid = {31927597}, issn = {1432-0991}, support = {2017A020216008//Guangdong Science and Technology Department/ ; 2016I1002//Fujian Provincial Department of Science and Technology/ ; 2017T3010//Fujian Provincial Department of Science and Technology/ ; }, abstract = {Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.}, }
@article {pmid31926392, year = {2019}, author = {Lepoutre, A and Hervieux, J and Faassen, EJ and Zweers, AJ and Lurling, M and Geffard, A and Lance, E}, title = {Usability of the bivalves Dreissena polymorpha and Anodonta anatina for a biosurvey of the neurotoxin BMAA in freshwater ecosystems.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {259}, number = {}, pages = {113885}, doi = {10.1016/j.envpol.2019.113885}, pmid = {31926392}, issn = {1873-6424}, abstract = {The environmental neurotoxin β-methylamino-L-alanine (BMAA) may represent a risk for human health in case of chronic exposure or after short-term exposure during embryo development. BMAA accumulates in freshwater and marine organisms consumed by humans. It is produced by marine and freshwater phytoplankton species, but the range of producers remains unknown. Therefore, analysing the phytoplankton composition is not sufficient to inform about the risk of freshwater contamination by BMAA. Filter-feeders mussels have accumulation capacities and therefore appear to be relevant to monitor various pollutants in aquatic ecosystems. We investigated the suitability of the freshwater mussels Dreissena polymorpha and Anodonta anatina for monitoring BMAA in water. Both species were exposed to 1, 10, and 50 μg of dissolved BMAA/L daily for 21 days, followed by 42 days of depuration in clean water. On days 0, 1, 7, 14, and 21 of exposure and 1, 7, 14, 21 and 42 of depuration, whole D. polymorpha and digestive glands of A. anatina were sampled, and the total BMAA concentration was measured. D. polymorpha accumulated BMAA earlier (from day 1 at all concentrations) and at higher tissue concentrations than A. anatina, which accumulated BMAA from day 14 when exposed to 10 μg BMAA/L and from day 7 when exposed to 50 μg BMAA/L. As BMAA accumulation by D. polymorpha was time and concentration-dependent, with a significant elimination during the depuration period, this species may be able to reflect the levels and dynamics of water contamination by dissolved BMAA. The species A. anatina could be used for monitoring water concentrations above 10 μg BMAA/L.}, }
@article {pmid31926010, year = {2020}, author = {Cesare, AD and Eckert, EM and Cottin, C and Bouchez, A and Callieri, C and Cortesini, M and Lami, A and Corno, G}, title = {The vertical distribution of tetA and intI1 in a deep lake is rather due to sedimentation than to resuspension.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa002}, pmid = {31926010}, issn = {1574-6941}, abstract = {Lakes are exposed to anthropogenic pollution including the release of allochthonous bacteria into their waters. Antibiotic resistance genes (ARGs) stabilize in bacterial communities of temperate lakes, and these environments act as long-term reservoirs of ARGs. Still, it is not clear if the stabilization of the ARGs is caused by a periodical introduction, or by other factors regulated by dynamics within the water column. Here we observed the dynamics of the tetracycline resistance gene (tetA) and of the class 1 integron integrase gene intI1 a proxy of anthropogenic pollution in the water column and in the sediments of subalpine Lake Maggiore, together with several chemical, physical and microbiological variables. Both genes resulted more abundant within the bacterial community of the sediment compared to the water column and the water-sediment interface. Only at the inset of thermal stratification they reached quantifiable abundances in all the water layers, too. Moreover, the bacterial communities of the water-sediment interface were more similar to deep waters than to the sediments. These results suggest that the vertical distribution of tetA and intI1 is mainly due to the deposition of bacteria from the surface water to the sediment, while their resuspension from the sediment is less important.}, }
@article {pmid31925848, year = {2020}, author = {Dove, NC and Safford, HD and Bohlman, GN and Estes, BL and Hart, SC}, title = {High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1002/eap.2072}, pmid = {31925848}, issn = {1051-0761}, abstract = {During the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long-term, belowground implications of altered, ecologically novel fire regimes, especially on soil biological processes. To better understand the long-term implications of ecologically novel, high-severity fire, we used a 44-y high-severity fire chronosequence in the Sierra Nevada where forests were historically adapted to frequent, low-severity fire, but were fire suppressed for at least 70 years. High-severity fire in the Sierra Nevada resulted in a long-term (44 + y) decrease (>50%, p < 0.05) in soil extracellular enzyme activities, basal microbial respiration (56-72%, p < 0.05), and organic carbon (>50%, p < 0.05) in the upper 5 cm compared to sites that had not been burned for at least 115 y. However, nitrogen (N) processes were only affected in the most-recent fire site (4 y post-fire). Net nitrification increased by over 600% in the most recent fire site (p < 0.001), but returned to similar levels as the unburned control in the 13-y site. Contrary to previous studies, we did not find a consistent effect of plant cover type on soil biogeochemical processes in mid-successional (10-50 y) forest soils. Rather, the 44-y reduction in soil organic carbon (C) quantity correlated positively with dampened C cycling processes. Our results show the drastic and long-term implication of ecologically novel, high-severity fire on soil biogeochemistry and underscore the need for long-term fire ecological experiments.}, }
@article {pmid31925212, year = {2019}, author = {Krych, Ł and Castro-Mejía, JL and Forero-Junco, LM and Moesby, DN and Mikkelsen, MB and Rasmussen, MA and Sykulski, M and Nielsen, DS}, title = {DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq.}, journal = {Communications biology}, volume = {2}, number = {1}, pages = {369}, doi = {10.1038/s42003-019-0617-x}, pmid = {31925212}, issn = {2399-3642}, abstract = {Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.}, }
@article {pmid31924857, year = {2018}, author = {Rampelli, S and Guenther, K and Turroni, S and Wolters, M and Veidebaum, T and Kourides, Y and Molnár, D and Lissner, L and Benitez-Paez, A and Sanz, Y and Fraterman, A and Michels, N and Brigidi, P and Candela, M and Ahrens, W}, title = {Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity.}, journal = {Communications biology}, volume = {1}, number = {1}, pages = {222}, doi = {10.1038/s42003-018-0221-5}, pmid = {31924857}, issn = {2399-3642}, abstract = {It is widely accepted that the intestinal microbiome is connected to obesity, as key mediator of the diet impact on the host metabolic and immunological status. To investigate whether the individual gut microbiome has a potential in predicting the onset and progression of diseases, here we characterized the faecal microbiota of 70 children in a two-time point prospective study, within a four-year window. All children had normal weight at the beginning of this study, but 36 of them gained excessive weight at the subsequent check-up. Microbiome data were analysed together with the hosts' diet information, physical activity, and inflammatory parameters. We find that the gut microbiota structures were stratified into a discrete number of groups, characterized by different biodiversity that correlates with inflammatory markers and dietary habits, regardless of age, gender, and body weight. Collectively, our data underscore the importance of the microbiome-host-diet configuration as a possible predictor of obesity.}, }
@article {pmid31924617, year = {2020}, author = {Bai, C and Cai, J and Zhou, L and Jiang, X and Hu, Y and Dai, J and Shao, K and Tang, X and Yang, X and Gao, G}, title = {Geographic Patterns of Bacterioplankton among Lakes of the Middle and Lower Reaches of the Yangtze River Basin, China.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02423-19}, pmid = {31924617}, issn = {1098-5336}, abstract = {The revolution of molecular techniques has revealed that the composition of natural bacterial communities normally includes a few abundant taxa and many rare taxa. Unraveling the mechanisms underlying the spatial assembly process of both abundant and rare bacterial taxa had become a central goal in microbial ecology. Here we used high-throughput sequencing to explore geographic patterns and the relative importance of ecological processes in the assembly of abundant and rare bacterial subcommunities from 25 lakes across the middle and lower reaches of Yangtze River basin (MLYB, located in southeast China), where most of the lakes are interconnected by river networks. We found a similar biogeographic pattern of abundant and rare subcommunities which could significantly separate between the two lake groups that were far from each other, while could not separate among the nearby lakes. Both abundant and rare bacteria followed a strong distance-decay relationship. These findings suggest that the interconnectivity between lakes homogenizes the bacterial communities in local areas, and the abundant and rare taxa therein may be affected by the same ecological process. In addition, based on the measured environmental variables, the deterministic processes explain a small fraction of variation within both abundant and rare subcommunities. While both neutral and null model revealed a high stochasticity ratio for the spatial distribution patterns of both abundant and rare taxa. These findings indicate that the stochastic processes exhibited a greater influence on both abundant and rare bacterial subcommunities assembly among interconnected lakes.Importance The Middle and Lower Yangtze Plain is a typical floodplain, in which many lakes will connect with each other, especially in the wet season. More importantly, with the frequent change of regional water level in the wet season, there is a mutual hydrodynamic exchange among these lakes. The microbial biogeography among these interconnected lakes is still poorly understood. This study aims to unravel the mechanisms underlying the assembly process of abundant and rare bacteria among the interconnected lakes in the Middle and Lower Yangtze Plain. Our findings will provide a deeper understanding of the biogeographic patterns of rare and abundant bacterial taxa and their determined processes among interconnected aquatic habitats.}, }
@article {pmid31924214, year = {2020}, author = {Shuai, Y and Ma, Z and Liu, W and Yu, T and Yan, C and Jiang, H and Tian, S and Xu, T and Shu, Y}, title = {TEAD4 modulated LncRNA MNX1-AS1 contributes to gastric cancer progression partly through suppressing BTG2 and activating BCL2.}, journal = {Molecular cancer}, volume = {19}, number = {1}, pages = {6}, pmid = {31924214}, issn = {1476-4598}, support = {71013Y2029//Innovation Fund for Outstanding Doctoral Candidates of Peking University Health Science/ ; 81672896//National Natural Science Foundation of China/ ; 81602071//Young Scientists Fund/ ; }, abstract = {BACKGROUND: Gastric cancer (GC) is the third leading cause of cancer-related mortality globally. Long noncoding RNAs (lncRNAs) are dysregulated in obvious malignancies including GC and exploring the regulatory mechanisms underlying their expression is an attractive research area. However, these molecular mechanisms require further clarification, especially upstream mechanisms.<br><br>METHODS: LncRNA MNX1-AS1 expression in GC tissue samples was investigated via microarray analysis and further determined in a cohort of GC tissues via quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays. Cell proliferation and flow cytometry assays were performed to confirm the roles of MNX1-AS1 in GC proliferation, cell cycle regulation, and apoptosis. The influence of MNX1-AS1 on GC cell migration and invasion was explored with Transwell assays. A xenograft tumour model was established to verify the effects of MNX1-AS1 on in vivo tumourigenesis. The TEAD4-involved upstream regulatory mechanism of MNX1-AS1 was explored through ChIP and luciferase reporter assays. The mechanistic model of MNX1-AS1 in regulating gene expression was further detected by subcellular fractionation, FISH, RIP, ChIP and luciferase reporter assays.<br><br>RESULTS: It was found that MNX1-AS1 displayed obvious upregulation in GC tissue samples and cell lines, and ectopic expression of MNX1-AS1 predicted poor clinical outcomes for patients with GC. Overexpressed MNX1-AS1 expression promoted proliferation, migration and invasion of GC cells markedly, whereas decreased MNX1-AS1 expression elicited the opposite effects. Consistent with the in vitro results, MNX1-AS1 depletion effectively inhibited the growth of xenograft tumour in vivo. Mechanistically, TEAD4 directly bound the promoter region of MNX1-AS1 and stimulated the transcription of MNX1-AS1. Furthermore, MNX1-AS1 can sponge miR-6785-5p to upregulate the expression of BCL2 in GC cells. Meanwhile, MNX1-AS1 suppressed the transcription of BTG2 by recruiting polycomb repressive complex 2 to BTG2 promoter regions.<br><br>CONCLUSIONS: Our findings demonstrate that MNX1-AS1 may be able to serve as a prognostic indicator in GC patients and that TEAD4-activatd MNX1-AS1 can promote GC progression through EZH2/BTG2 and miR-6785-5p/BCL2 axes, implicating it as a novel and potent target for the treatment of GC.}, }
@article {pmid31924126, year = {2020}, author = {Agudelo-Ochoa, GM and Valdés-Duque, BE and Giraldo-Giraldo, NA and Jaillier-Ramírez, AM and Giraldo-Villa, A and Acevedo-Castaño, I and Yepes-Molina, MA and Barbosa-Barbosa, J and Benítez-Paéz, A}, title = {Gut microbiota profiles in critically ill patients, potential biomarkers and risk variables for sepsis.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/19490976.2019.1707610}, pmid = {31924126}, issn = {1949-0984}, abstract = {Critically ill patients are physiologically unstable and recent studies indicate that the intestinal microbiota could be involved in the health decline of such patients during ICU stays. This study aims to assess the intestinal microbiota in critically ill patients with and without sepsis and to determine its impact on outcome variables, such as medical complications, ICU stay time, and mortality. A multi-center study was conducted with a total of 250 peri-rectal swabs obtained from 155 patients upon admission and during ICU stays. Intestinal microbiota was assessed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Linear mixed models were used to integrate microbiota data with more than 40 clinical and demographic variables to detect covariates and minimize the effect of confounding factors. We found that the microbiota of ICU patients with sepsis has an increased abundance of microbes tightly associated with inflammation, such as Parabacteroides, Fusobacterium and Bilophila species. Female sex and aging would represent an increased risk for sepsis possibly because of some of their microbiota features. We also evidenced a remarkable loss of microbial diversity, during the ICU stay. Concomitantly, we detected that the abundance of pathogenic species, such as Enterococcus spp., was differentially increased in sepsis patients who died, indicating these species as potential biomarkers for monitoring during ICU stay. We concluded that particular intestinal microbiota signatures could predict sepsis development in ICU patients. We propose potential biomarkers for evaluation in the clinical management of ICU patients.}, }
@article {pmid31924109, year = {2020}, author = {Triplett, J and Ellis, D and Braddock, A and Roberts, E and Ingram, K and Perez, E and Short, A and Brown, D and Hutzley, V and Webb, C and Soto, A and Chan, V}, title = {Temporal and region-specific effects of sleep fragmentation on gut microbiota and intestinal morphology in Sprague Dawley rats.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/19490976.2019.1701352}, pmid = {31924109}, issn = {1949-0984}, abstract = {Sleep is a fundamental biological process, that when repeatedly disrupted, can result in severe health consequences. Recent studies suggest that both sleep fragmentation (SF) and dysbiosis of the gut microbiome can lead to metabolic disorders, though the underlying mechanisms are largely unclear. To better understand the consequences of SF, we investigated the effects of acute (6 days) and chronic (6 weeks) SF on rats by examining taxonomic profiles of microbiota in the distal ileum, cecum and proximal colon, as well as assessing structural and functional integrity of the gastrointestinal barrier. We further assayed the impact of SF on a host function by evaluating inflammation and immune response. Both acute and chronic SF induced microbial dysbiosis, more dramatically in the distal ileum (compared to other two regions studied), as noted by significant perturbations in alpha- and beta-diversity; though, specific microbial populations were significantly altered throughout each of the three regions. Furthermore, chronic SF resulted in increased crypt depth in the distal ileum and an increase in the number of villi lining both the cecum and proximal colon. Additional changes were noted with chronic SF, including: decreased microbial adhesion and penetration in the distal ileum and cecum, elevation in serum levels of the cytokine KC/GRO, and depressed levels of corticotropin. Importantly, our data show that perturbations to microbial ecology and intestinal morphology intensify in response to prolonged SF and these changes are habitat specific. Together, these results reveal consequences to gut microbiota homeostasis and host response following acute and chronic SF in rats.}, }
@article {pmid31922946, year = {2020}, author = {Studholme, DJ and Wicker, E and Abrare, SM and Aspin, A and Bogdanove, A and Broders, K and Dubrow, Z and Grant, M and Jones, JB and Karamura, G and Lang, J and Leach, J and Mahuku, G and Nakato, GV and Coutinho, T and Smith, J and Bull, CT}, title = {Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {PHYTO03190098LE}, doi = {10.1094/PHYTO-03-19-0098-LE}, pmid = {31922946}, issn = {0031-949X}, abstract = {We present an amended description of the bacterial species Xanthomonas vasicola to include the causative agent of banana Xanthomonas wilt, as well as strains that cause disease on Areca palm, Tripsacum grass, sugarcane, and maize. Genome-sequence data reveal that these strains all share more than 98% average nucleotide with each other and with the type strain. Our analyses and proposals should help to resolve the taxonomic confusion that surrounds some of these pathogens and help to prevent future use of invalid names.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.}, }
@article {pmid31922546, year = {2020}, author = {Morris, MM and Frixione, NJ and Burkert, AC and Dinsdale, EA and Vannette, RL}, title = {Microbial abundance, composition, and function in nectar are shaped by flower visitor identity.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa003}, pmid = {31922546}, issn = {1574-6941}, abstract = {Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics, and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacteria, among visitor treatments. Visitation increased microbial abundance, but robbing resulting in 10x higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism, and specialized transporters. Gene differences were mirrored in function: robbed nectar contained 25% more monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.}, }
@article {pmid31922045, year = {2020}, author = {Chakraborty, A and DasGupta, CK and Bhadury, P}, title = {Diversity of Betaproteobacteria revealed by novel primers suggests their role in arsenic cycling.}, journal = {Heliyon}, volume = {6}, number = {1}, pages = {e03089}, pmid = {31922045}, issn = {2405-8440}, abstract = {High arsenic concentration in groundwater is a severe environmental problem affecting human health, particularly in countries of South and South-East Asia. The Bengal Delta Plain (BDP) distributed within India and Bangladesh is a major arsenic-affected region where groundwater is the primary source of drinking water. Previous studies have indicated that members of the bacterial class Betaproteobacteria constitute a major fraction of the microbial community in many of the aquifers within this region. Bacteria belonging to this class are known to be involved in redox cycling of arsenic as well as other metals such iron and manganese, thereby impacting arsenic mobilization and immobilization. While microbial diversity in arsenic-contaminated environments is generally assessed using universal 16S rRNA gene primers, targeted evaluation of Betaproteobacteria diversity remains poorly constrained. In this study, bacterial diversity was investigated in the groundwater from two shallow aquifers (West Bengal, India) based on 16S rRNA gene clone libraries and sequencing using a custom-designed pair of primers specific to Betaproteobacteria. Specificity of the primers was confirmed in silico as well as by the absence of PCR amplification of other bacterial classes. Four major families (Burkholderiaceae, Comamonadaceae, Gallionellaceae and Rhodocyclaceae) were detected among which members of Burkholderiaceae represented 59% and 71% of the total community in each aquifer. The four OTUs (operational taxonomic units; 97% sequence identity) within Burkholderiaceae were close phylogenetic relatives of bacteria within the genus Burkholderia known to solubilize phosphate minerals. Additionally, the OTUs belonging to Gallionellaceae were closely related to the members of the genera Gallionella and Sideroxydans, known to oxidize iron under microaerophilic conditions. These results suggest that members of Betaproteobacteria can potentially influence iron and phosphorus cycling which can influence biogeochemistry in arsenic-contaminated aquifers of the BDP.}, }
@article {pmid31921433, year = {2020}, author = {Klaps, J and Lievens, B and Álvarez-Pérez, S}, title = {Towards a better understanding of the role of nectar-inhabiting yeasts in plant-animal interactions.}, journal = {Fungal biology and biotechnology}, volume = {7}, number = {}, pages = {1}, pmid = {31921433}, issn = {2054-3085}, abstract = {Flowers offer a wide variety of substrates suitable for fungal growth. However, the mycological study of flowers has only recently begun to be systematically addressed from an ecological point of view. Most research on the topic carried out during the last decade has focused on studying the prevalence and diversity of flower-inhabiting yeasts, describing new species retrieved from floral parts and animal pollinators, and the use of select nectar yeasts as model systems to test ecological hypotheses. In this primer article, we summarize the current state of the art in floral nectar mycology and provide an overview of some research areas that, in our view, still require further attention, such as the influence of fungal volatile organic compounds on the foraging behavior of pollinators and other floral visitors, the analysis of the direct and indirect effects of nectar-inhabiting fungi on the fitness of plants and animals, and the nature and consequences of fungal-bacterial interactions taking place within flowers.}, }
@article {pmid31921095, year = {2019}, author = {Hounmanou, YMG and Leekitcharoenphon, P and Hendriksen, RS and Dougnon, TV and Mdegela, RH and Olsen, JE and Dalsgaard, A}, title = {Corrigendum: Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2974}, doi = {10.3389/fmicb.2019.02974}, pmid = {31921095}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.00901.].}, }
@article {pmid31921014, year = {2019}, author = {Calabrese, F and Voloshynovska, I and Musat, F and Thullner, M and Schlömann, M and Richnow, HH and Lambrecht, J and Müller, S and Wick, LY and Musat, N and Stryhanyuk, H}, title = {Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2814}, pmid = {31921014}, issn = {1664-302X}, abstract = {Phenotypic heterogeneity within microbial populations arises even when the cells are exposed to putatively constant and homogeneous conditions. The outcome of this phenomenon can affect the whole function of the population, resulting in, for example, new &quot;adapted&quot; metabolic strategies and impacting its fitness at given environmental conditions. Accounting for phenotypic heterogeneity becomes thus necessary, due to its relevance in medical and applied microbiology as well as in environmental processes. Still, a comprehensive evaluation of this phenomenon requires a common and unique method of quantitation, which allows for the comparison between different studies carried out with different approaches. Consequently, in this study, two widely applicable indices for quantitation of heterogeneity were developed. The heterogeneity coefficient (HC) is valid when the population follows unimodal activity, while the differentiation tendency index (DTI) accounts for heterogeneity implying outbreak of subpopulations and multimodal activity. We demonstrated the applicability of HC and DTI for heterogeneity quantitation on stable isotope probing with nanoscale secondary ion mass spectrometry (SIP-nanoSIMS), flow cytometry, and optical microscopy datasets. The HC was found to provide a more accurate and precise measure of heterogeneity, being at the same time consistent with the coefficient of variation (CV) applied so far. The DTI is able to describe the differentiation in single-cell activity within monoclonal populations resolving subpopulations with low cell abundance, individual cells with similar phenotypic features (e.g., isotopic content close to natural abundance, as detected with nanoSIMS). The developed quantitation approach allows for a better understanding on the impact and the implications of phenotypic heterogeneity in environmental, medical and applied microbiology, microbial ecology, cell biology, and biotechnology.}, }
@article {pmid31915852, year = {2020}, author = {Baños, I and Montero, MF and Benavides, M and Arístegui, J}, title = {INT Toxicity over Natural Bacterial Assemblages from Surface Oligotrophic Waters: Implications for the Assessment of Respiratory Activity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01479-4}, pmid = {31915852}, issn = {1432-184X}, support = {BES-2016- 078407//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; CTM2015-69392-C3-1-R//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, abstract = {Plankton community respiration (R) is a major component of the carbon flux in aquatic ecosystems. However, current methods to measure actual respiration from oxygen consumption at relevant spatial scales are not sensitive enough in oligotrophic environments where respiration rates are very low. To overcome this drawback, more sensitive indirect enzymatic approaches are commonly used as R proxies. The in vivo electron transport system (ETSvivo) assay, which measures the reduction of (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl tetrazolium chloride salt, INT) to INT-formazan in the presence of natural substrate levels, was recently proposed as an indirect reliable estimation of R for natural plankton communities. However, under in vivo conditions, formazan salts could be toxic to the cells. Here, we test the toxicity of 0.2 mM of final INT concentration, widely used for ETSvivo assays, on natural bacterial assemblages collected in coastal and oceanic waters off Gran Canaria (Canary Islands, subtropical North Atlantic), in eight independent experiments. After 0.5 h of incubation, a significant but variable decline in cell viability (14-49%) was observed in all samples inoculated with INT. Moreover, INT also inhibited leucine uptake in less than 90 min of incubation. In the light of these results, we argue that enzymatic respiratory rates obtained with the ETSvivo method need to be interpreted with caution to derive R in oceanic regions where bacteria largely contribute to community respiration. Moreover, the variable toxicity on bacterial assemblages observed in our experiments questions the use of a single R/ETSvivo relationship as a universal proxy for regional studies.}, }
@article {pmid31915217, year = {2020}, author = {Schnizlein, MK and Vendrov, KC and Edwards, SJ and Martens, EC and Young, VB}, title = {Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31915217}, issn = {2379-5042}, abstract = {Dietary fiber provides a variety of microbiota-mediated benefits ranging from anti-inflammatory metabolites to pathogen colonization resistance. A healthy gut microbiota protects against Clostridioides difficile colonization. Manipulation of these microbes through diet may increase colonization resistance to improve clinical outcomes. The primary objective of this study was to identify how the dietary fiber xanthan gum affects the microbiota and C. difficile colonization. We added 5% xanthan gum to the diet of C57BL/6 mice and examined its effect on the microbiota through 16S rRNA gene amplicon sequencing and short-chain fatty acid analysis. Following either cefoperazone or an antibiotic cocktail administration, we challenged mice with C. difficile and measured colonization by monitoring the CFU. Xanthan gum administration is associated with increases in fiber-degrading taxa and short-chain fatty acid concentrations. However, by maintaining both the diversity and absolute abundance of the microbiota during antibiotic treatment, the protective effects of xanthan gum administration on the microbiota were more prominent than the enrichment of these fiber-degrading taxa. As a result, mice that were on the xanthan gum diet experienced limited to no C. difficile colonization. Xanthan gum administration alters mouse susceptibility to C. difficile colonization by maintaining the microbiota during antibiotic treatment. While antibiotic-xanthan gum interactions are not well understood, xanthan gum has previously been used to bind drugs and alter their pharmacokinetics. Thus, xanthan gum may alter the activity of the oral antibiotics used to make the microbiota susceptible. Future research should further characterize how this and other common dietary fibers interact with drugs.IMPORTANCE A healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens. Clostridioides difficile capitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance to C. difficile colonization by either supplementing with bacteria that promote resistance or a diet to enrich for those already present in the gut. In this study, we describe an interaction between xanthan gum, a human dietary additive, and the microbiota resulting in an altered gut environment that is protective against C. difficile colonization.}, }
@article {pmid31911465, year = {2020}, author = {Li, P and Li, W and Dumbrell, AJ and Liu, M and Li, G and Wu, M and Jiang, C and Li, Z}, title = {Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31911465}, issn = {2379-5077}, abstract = {Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, &quot;everything is everywhere, but the environment selects,&quot; although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths.IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.}, }
@article {pmid31909618, year = {2020}, author = {Van den Abbeele, P and Moens, F and Pignataro, G and Schnurr, J and Ribecco, C and Gramenzi, A and Marzorati, M}, title = {Yeast-Derived Formulations Are Differentially Fermented by the Canine and Feline Microbiome As Assessed in a Novel In Vitro Colonic Fermentation Model.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.9b05085}, pmid = {31909618}, issn = {1520-5118}, abstract = {The current study evaluated the effect of five yeast-derived formulations (T1-T5) on microbial metabolism and composition of the canine and feline gut microbiota using a novel in vitro colonic incubation approach. This novel in vitro model allowed for growth of the entire spectrum of dog- and cat-derived bacteria from the inoculum, thus offering an excellent platform to evaluate effects of nutritional interventions on the gut microbiota. Further, yeast-derived ingredients differentially increased production of acetate, propionate, butyrate, ammonium, and branched short-chain fatty acids, with T5 and T1 consistently stimulating propionate and butyrate, respectively. 16S-targeted Illumina sequencing coupled with flow cytometry provided unprecedented high-resolution quantitative insights in canine and feline microbiota modulation by yeast-derived ingredients, revealing that effects on propionate production were related to Prevotellaceae, Tannerellaceae, Bacteroidaceae, and Veillonellaceae members, while effects on butyrate production were related to Erysipelotrichaceae, Lachnospiraceae, Ruminococcaceae, and Fusobacteriaceae. Overall, these findings strengthen the health-promoting potential of yeast-derived ingredients.}, }
@article {pmid31897988, year = {2020}, author = {Zhang, D and Luther, AK and Clauwaert, P and Ciccioli, P and Ronsse, F}, title = {Assessment of carbon recovery from solid organic wastes by supercritical water oxidation for a regenerative life support system.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-019-07527-3}, pmid = {31897988}, issn = {1614-7499}, support = {201406350071//China Sponsorship Council/ ; 4000113452/15/NL/AT//European Space Agency/ ; DOZA/DDC/AM/DL/171b-2015//Universiteit Gent/ ; }, abstract = {The carbon recovery from organic space waste by supercritical water oxidation (SCWO) was studied to support resource recovery in a regenerative life support system. Resource recovery is of utmost importance in such systems which only have a limited total amount of mass. However, the practical waste treatment strategies for solid space wastes employed today are only storing and disposal without further recovery. This work assesses the performance of SCWO at recovering organic wastes as CO2 and water, to discuss the superiority of SCWO over most present strategies, and to evaluate the different SCWO reactor systems for space application. Experiments were carried out with a batch and a continuous reactor at different reaction conditions. The liquid and gas products distribution were analyzed to understand the conversion of organics in SCWO. Up to 97% and 93% of the feed carbon were recovered as CO2 in the continuous and the batch reactor, respectively. Residual carbon was mostly found as soluble organics in the effluent. Compared with the batch reactor, the continuous reactor system demonstrated a ten times higher capacity within the same reactor volume, while the batch reactor system was capable of handling feeds that contained particulate matter though suffering from poor heat integration (hence low-energy efficiency) and inter-batch variability. It was concluded that SCWO could be a promising technology to treat solid wastes for space applications. A continuous reactor would be more suitable for a regenerative life support system.}, }
@article {pmid31897570, year = {2020}, author = {Donati, I and Cellini, A and Sangiorgio, D and Vanneste, JL and Scortichini, M and Balestra, GM and Spinelli, F}, title = {Pseudomonas syringae pv. actinidiae: Ecology, Infection Dynamics and Disease Epidemiology.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01459-8}, pmid = {31897570}, issn = {1432-184X}, support = {613678//Seventh Framework Programme/ ; }, abstract = {Since 2008, the kiwifruit industry has been devastated by a pandemic outbreak of Pseudomonas syringae pv. actinidiae (Psa), the causal agent of bacterial canker. This disease has become the most significant limiting factor in kiwifruit production. Psa colonizes different organs of the host plant, causing a specific symptomatology on each of them. In addition, the systemic invasion of the plant may quickly lead to plant death. Despite the massive risk that this disease poses to the kiwifruit industry, studies focusing on Psa ecology have been sporadic, and a comprehensive description of the disease epidemiology is still missing. Optimal environmental conditions for infection, dispersal and survival in the environment, or the mechanisms of penetration and colonization of host tissues have not been fully elucidated yet. The present work aims to provide a synthesis of the current knowledge, and a deeper understanding of the epidemiology of kiwifruit bacterial canker based on new experimental data. The pathogen may survive in the environment or overwinter in dormant tissues and be dispersed by wind or rain. Psa was observed in association with several plant structures (stomata, trichomes, lenticels) and wounds, which could represent entry points for apoplast infection. Environmental conditions also affect the bacterial colonization, with lower optimum values of temperature and humidity for epiphytic than for endophytic growth, and disease incidence requiring a combination of mild temperature and leaf wetness. By providing information on Psa ecology, these data sets may contribute to plan efficient control strategies for kiwifruit bacterial canker.}, }
@article {pmid31897569, year = {2020}, author = {Floc'h, JB and Hamel, C and Harker, KN and St-Arnaud, M}, title = {Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01475-8}, pmid = {31897569}, issn = {1432-184X}, abstract = {Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.}, }
@article {pmid31896790, year = {2020}, author = {Op De Beeck, M and Troein, C and Siregar, S and Gentile, L and Abbondanza, G and Peterson, C and Persson, P and Tunlid, A}, title = {Regulation of fungal decomposition at single-cell level.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0583-9}, pmid = {31896790}, issn = {1751-7370}, support = {2017-04261//Vetenskapsrådet (Swedish Research Council)/ ; 2016-04561//Vetenskapsrådet (Swedish Research Council)/ ; 2017-04261//Vetenskapsrådet (Swedish Research Council)/ ; 2016-04561//Vetenskapsrådet (Swedish Research Council)/ ; 2017-04261//Vetenskapsrådet (Swedish Research Council)/ ; 2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, abstract = {Filamentous fungi play a key role as decomposers in Earth's nutrient cycles. In soils, substrates are heterogeneously distributed in microenvironments. Hence, individual hyphae of a mycelium may experience very different environmental conditions simultaneously. In the current work, we investigated how fungi cope with local environmental variations at single-cell level. We developed a method based on infrared spectroscopy that allows the direct, in-situ chemical imaging of the decomposition activity of individual hyphal tips. Colonies of the ectomycorrhizal Basidiomycete Paxillus involutus were grown on liquid media, while parts of colonies were allowed to colonize lignin patches. Oxidative decomposition of lignin by individual hyphae growing under different conditions was followed for a period of seven days. We identified two sub-populations of hyphal tips: one with low decomposition activity and one with much higher activity. Active cells secreted more extracellular polymeric substances and oxidized lignin more strongly. The ratio of active to inactive hyphae strongly depended on the environmental conditions in lignin patches, but was further mediated by the decomposition activity of entire mycelia. Phenotypic heterogeneity occurring between genetically identical hyphal tips may be an important strategy for filamentous fungi to cope with heterogeneous and constantly changing soil environments.}, }
@article {pmid31896018, year = {2019}, author = {Yuan, W and Tian, T and Yang, Q and Riaz, L}, title = {Transfer potentials of antibiotic resistance genes in Escherichia spp. strains from different sources.}, journal = {Chemosphere}, volume = {246}, number = {}, pages = {125736}, doi = {10.1016/j.chemosphere.2019.125736}, pmid = {31896018}, issn = {1879-1298}, abstract = {Multidrug-resistant Escherichia coli and antibiotic-resistance genes (ARGs) present a danger to public health. However, information on the dissemination potentials of antibiotic resistance among bacteria from different environments is lacking. We isolated multiple antibiotic-resistant Escherichia spp. from animal farms, hospitals, and municipal wastewater-treatment plants (MWWTPs) using culture-based methods, and carried out resistance phenotype and gene analyses. Thirty-five isolates of multiple antibiotic-resistant Escherichia spp. were further screened to detect 61 ARGs, 18 mobile genetic elements (MGEs), and gene cassettes. The isolates from livestock manure and MWWTPs showed greater diversity in plasmid profiling than hospital wastewater. Each Escherichia sp. carried 21-26 ARGs and 8-12 MGEs. In addition, 11 gene cassettes were detected in 34 Escherichia isolates, with greater diversity in livestock manure and MWWTPs than in hospital wastewater. The results indicated that the potential for ARG transfer was higher in livestock manure and MWWTPs compared with human clinical sources, possibly related to the high occurrence of both residual antibiotics and heavy metals in these environments.}, }
@article {pmid31894632, year = {2020}, author = {Baricz, A and Chiriac, CM and Andrei, AȘ and Bulzu, PA and Levei, EA and Cadar, O and Battes, KP and Cîmpean, M and Șenilă, M and Cristea, A and Muntean, V and Alexe, M and Coman, C and Szekeres, EK and Sicora, CI and Ionescu, A and Blain, D and O'Neill, WK and Edwards, J and Hallsworth, JE and Banciu, HL}, title = {Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14909}, pmid = {31894632}, issn = {1462-2920}, support = {//Department of Agriculture, Environment and Rural Affairs (DAERA), Northern Ireland/ ; NE/E016804/1//Natural Environment Research Council (NERC, UK)/ ; PN-II-ID-PCE-2011-3-0546//Romanian National Authority for Scientific Research (CNCS-UEFISCDI)/ ; PN-III-P4-ID-PCE-2016-0303//Romanian National Authority for Scientific Research (CNCS-UEFISCDI)/ ; //STAR-UBB Advanced Fellowship-Intern (Babeş-Bolyai University)/ ; //European Union - European Social Fund (ESF) - Operational Programme II - Cohesion Policy2014-2020/ ; }, abstract = {Ursu Lake is located in the Middle Miocene salt deposit of Central Romania. It is stratified, and the water column has three distinct water masses: an upper freshwater-to-moderately saline stratum (0-3 m), an intermediate stratum exhibiting a steep halocline (3-3.5 m), and a lower hypersaline stratum (4 m and below) that is euxinic (i.e. anoxic and sulphidic). Recent studies have characterized the lake's microbial taxonomy and given rise to intriguing ecological questions. Here, we explore whether the communities are dynamic or stable in relation to taxonomic composition, geochemistry, biophysics, and ecophysiological functions during the annual cycle. We found: (i) seasonally fluctuating, light-dependent communities in the upper layer (≥0.987-0.990 water-activity), a stable but phylogenetically diverse population of heterotrophs in the hypersaline stratum (water activities down to 0.762) and a persistent plate of green sulphur bacteria that connects these two (0.958-0.956 water activity) at 3-3.5 to 4 m; (ii) communities that might be involved in carbon- and sulphur-cycling between and within the lake's three main water masses; (iii) uncultured lineages including Acetothermia (OP1), Cloacimonetes (WWE1), Marinimicrobia (SAR406), Omnitrophicaeota (OP3), Parcubacteria (OD1) and other Candidate Phyla Radiation bacteria, and SR1 in the hypersaline stratum (likely involved in the anaerobic steps of carbon- and sulphur-cycling); and (iv) that species richness and habitat stability are associated with high redox-potentials. Ursu Lake has a unique and complex ecology, at the same time exhibiting dynamic fluctuations and stability, and can be used as a modern analogue for ancient euxinic water bodies and comparator system for other stratified hypersaline systems.}, }
@article {pmid31891451, year = {2020}, author = {Cosetta, CM and Wolfe, BE}, title = {Deconstructing and Reconstructing Cheese Rind Microbiomes for Experiments in Microbial Ecology and Evolution.}, journal = {Current protocols in microbiology}, volume = {56}, number = {1}, pages = {e95}, doi = {10.1002/cpmc.95}, pmid = {31891451}, issn = {1934-8533}, support = {1715553//National Science Foundation/ ; }, abstract = {Cheese rind microbiomes are useful model systems for identifying the mechanisms that control microbiome diversity. Here, we describe the methods we have optimized to first deconstruct in situ cheese rind microbiome diversity and then reconstruct that diversity in laboratory environments to conduct controlled microbiome manipulations. Most cheese rind microbial species, including bacteria, yeasts, and filamentous fungi, can be easily cultured using standard lab media. Colony morphologies of taxa are diverse and can often be used to distinguish taxa at the phylum and sometimes even genus level. Through the use of cheese curd agar medium, thousands of unique community combinations or microbial interactions can be assessed. Transcriptomic experiments and transposon mutagenesis screens can pinpoint mechanisms of interactions between microbial species. Our general approach of creating a tractable synthetic microbial community from cheese can be easily applied to other fermented foods to develop other model microbiomes. © 2019 by John Wiley &amp; Sons, Inc. Basic Protocol 1: Isolation of cheese rind microbial communities Support Protocol 1: Preparation of plate count agar with milk and salt Basic Protocol 2: Identification of cheese rind bacterial and fungal isolates using 16S and ITS sequences Basic Protocol 3: Preparation of experimental glycerol stocks of yeasts and bacteria Basic Protocol 4: Preparation of experimental glycerol stocks of filamentous fungi Basic Protocol 5: Reconstruction of cheese rind microbial communities in vitro Support Protocol 2: Preparation of lyophilized and powdered cheese curd Support Protocol 3: Preparation of 10% cheese curd agar plates and tubes Basic Protocol 6: Interaction screens using responding lawns Support Protocol 4: Preparation of liquid 2% cheese curd Basic Protocol 7: Experimental evolution Basic Protocol 8: Measuring community function: pH/acidification Basic Protocol 9: Measuring community function: Pigment production Basic Protocol 10: RNA sequencing of cheese rind biofilms.}, }
@article {pmid31889749, year = {2019}, author = {Philips, CA and Phadke, N and Ganesan, K and Rajesh, S and Padsalgi, G and Ahamed, R and John, SK and Valiathan, GC and Augustine, P}, title = {Gut Microbiota in Alcoholic Hepatitis is Disparate from Those in Acute Alcoholic Pancreatitis and Biliary Disease.}, journal = {Journal of clinical and experimental hepatology}, volume = {9}, number = {6}, pages = {690-698}, pmid = {31889749}, issn = {0973-6883}, abstract = {Background: Alcoholic hepatitis (AH) is associated with gut dysbiosis. Comparative gut microbial profiles of acute alcoholic pancreatitis (AAP) and acute biliary disease (ABD) are not demonstrated. We aimed to compare gut microbiota of AH, AAP, and ABD patients with each other and with their respective healthy controls (HCs).<br><br>Methods: From December 2016 to September 2017, consecutive patients with AH, AAP, and ABD (acute cholecystitis, acute biliary pancreatitis, and choledocholithiasis with cholangitis) were included in the study. Qualitative and functional stool microbiota comparative analysis was performed between groups, with AH as the reference comparator.<br><br>Results: Of 3564, 882, and 224 patients with liver disease, pancreatic disease, and biliary disease, respectively, after exclusion, 29 patients with AH and 7 patients each with AAP and ABD and their corresponding HCs were included in the study analysis. The alpha diversity between patients with AH and AAP was found to be significantly different. Significant relative abundance (RA) of Acinetobacter and Moraxella was noted among patients with AAP. Enterobacter, Atopobium, Synergistia, and Devosia were significantly higher in patients with ABD compared to patients with AH, in whom Faecalibacterium and Megamonas were higher. Functional pathways associated with carbohydrate metabolism, phenylpropanoid biosynthesis, and ethylbenzene degradation were significantly higher in AAP when compared to AH. Fatty acid and inositol phosphate metabolism and dioxin degradation were significantly upregulated in patients with ABD while lipid and fatty acid biosynthetic pathways and pathways associated with immune processes were upregulated in patients with AH.<br><br>Conclusions: Differential gut dysbiosis is evident in both patients with AH, AAP, and ABD and also in comparison to HCs. The differential microbiota among patients with AH and AAP maybe important in promotion and progression of liver or pancreatic disease among alcohol users and may be a potential therapeutic target, which needs to be confirmed in larger multicenter studies.}, }
@article {pmid31889414, year = {2019}, author = {García-Timermans, C and Rubbens, P and Heyse, J and Kerckhof, FM and Props, R and Skirtach, AG and Waegeman, W and Boon, N}, title = {Discriminating Bacterial Phenotypes at the Population and Single-Cell Level: A Comparison of Flow Cytometry and Raman Spectroscopy Fingerprinting.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cyto.a.23952}, pmid = {31889414}, issn = {1552-4930}, support = {01IO3618//Bijzonder Onderzoeksfonds/ ; BAS094-18//Bijzonder Onderzoeksfonds/ ; BOF14/IOP/003//Bijzonder Onderzoeksfonds/ ; BOF15/GOA/006//Bijzonder Onderzoeksfonds/ ; BOFDOC2015000601//Bijzonder Onderzoeksfonds/ ; BOFSTA2015000501//Bijzonder Onderzoeksfonds/ ; 3G020119//Flemish Fund for Scientific Research/ ; FWO-Vlaanderen 1S80618N//Flemish Fund for Scientific Research/ ; G043219//Flemish Fund for Scientific Research/ ; //Qindao Beibao Marine Science &amp; Technology Co. Ltd./ ; //Qingdao West-coast economic new area, China/ ; }, abstract = {Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical tools are available, such as flow cytometry and Raman spectroscopy, which describe optical properties of the individual cell. In this work, we compare Raman spectroscopy and flow cytometry to study phenotypic heterogeneity in bacterial populations. The growth stages of three replicate Escherichia coli populations were characterized using both technologies. Our findings show that flow cytometry detects and quantifies shifts in phenotypic heterogeneity at the population level due to its high-throughput nature. Raman spectroscopy, on the other hand, offers a much higher resolution at the single-cell level (i.e., more biochemical information is recorded). Therefore, it can identify distinct phenotypic populations when coupled with analyses tailored toward single-cell data. In addition, it provides information about biomolecules that are present, which can be linked to cell functionality. We propose a computational workflow to distinguish between bacterial phenotypic populations using Raman spectroscopy and validated this approach with an external data set. We recommend using flow cytometry to quantify phenotypic heterogeneity at the population level, and Raman spectroscopy to perform a more in-depth analysis of heterogeneity at the single-cell level. © 2019 International Society for Advancement of Cytometry.}, }
@article {pmid31887587, year = {2019}, author = {van Dorst, J and Wilkins, D and King, CK and Spedding, T and Hince, G and Zhang, E and Crane, S and Ferrari, B}, title = {Applying microbial indicators of hydrocarbon toxicity to contaminated sites undergoing bioremediation on subantarctic Macquarie Island.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {259}, number = {}, pages = {113780}, doi = {10.1016/j.envpol.2019.113780}, pmid = {31887587}, issn = {1873-6424}, abstract = {Microorganisms are useful biological indicators of toxicity and play a key role in the functioning of healthy soils. In this study, we investigated the residual toxicity of hydrocarbons in aged contaminated soils and determined the extent of microbial community recovery during in-situ bioremediation at subantarctic Macquarie Island. Previously identified microbial indicators of hydrocarbon toxicity were used to understand interactions between hydrocarbon concentrations, soil physicochemical parameters and the microbial community. Despite the complexity of the field sites, which included active fuel storage areas with high levels of soil heterogeneity, multiple spill events and variable fuel sources, we observed consistent microbial community traits associated with exposure to high concentrations of hydrocarbons. These included; reductions in alpha diversity, inhibition of nitrification potential and a reduction in the ratio of oligotrophic to copiotrophic species. These observed responses and the sensitivity of microbial communities in the field, were comparable to sensitivity estimates obtained in a previous lab-based mesocosm study with hydrocarbon spiked soils. This study provides a valuable and often missing link between the quite disparate conditions of controlled lab-based spiking experiments and the complexity presented by 'real-world' contaminated field sites.}, }
@article {pmid31887546, year = {2019}, author = {Carney, RL and Brown, MV and Siboni, N and Raina, JB and Kahlke, T and Mitrovic, SM and Seymour, JR}, title = {Highly heterogeneous temporal dynamics in the abundance and diversity of the emerging pathogens Arcobacter at an urban beach.}, journal = {Water research}, volume = {171}, number = {}, pages = {115405}, doi = {10.1016/j.watres.2019.115405}, pmid = {31887546}, issn = {1879-2448}, abstract = {While the significance of Arcobacter in clinical settings grows, the ecological dynamics of potentially pathogenic Arcobacter in coastal marine environments remains unclear. In this study, we monitored the temporal dynamics of Arcobacter at an urban beach subject to significant stormwater input and wet weather sewer overflows (WWSO). Weekly monitoring of bacterial communities over 24 months using 16S rRNA amplicon sequencing revealed large, intermittent peaks in the relative abundance of Arcobacter. Quantitative PCR was subsequently employed to track absolute abundance of Arcobacter 23S rRNA gene copies, revealing peaks in abundance reaching up to 108 gene copies L-1, with these increases statistically correlated with stormwater and WWSO intrusion. Notably, peaks in Arcobacter abundance were poorly correlated with enterococci plate counts, and remained elevated for one week following heavy rainfall. Using oligotyping we discriminated single nucleotide variants (SNVs) within the Arcobacter population, revealing 10 distinct clusters of SNVs that we defined as Arcobacter &quot;ecotypes&quot;, with each displaying distinct temporal dynamics. The most abundant ecotype during stormwater and modelled WWSO events displayed 16S rRNA sequence similarity to A. cryaerophilius, a species previously implicated in human illness. Our findings highlight the diverse environmental drivers of Arcobacter abundance within coastal settings and point to a potentially important, yet overlooked exposure risk of these potential pathogens to humans.}, }
@article {pmid31885873, year = {2019}, author = {Pareek, S and Kurakawa, T and Das, B and Motooka, D and Nakaya, S and Rongsen-Chandola, T and Goyal, N and Kayama, H and Dodd, D and Okumura, R and Maeda, Y and Fujimoto, K and Nii, T and Ogawa, T and Iida, T and Bhandari, N and Kida, T and Nakamura, S and Nair, GB and Takeda, K}, title = {Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {}, pages = {37}, pmid = {31885873}, issn = {2055-5008}, support = {K08 DK110335/DK/NIDDK NIH HHS/United States ; }, abstract = {The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.}, }
@article {pmid31885375, year = {2019}, author = {Wein, T and Stücker, FT and Hülter, NF and Dagan, T}, title = {Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {154}, pages = {}, doi = {10.3791/60749}, pmid = {31885375}, issn = {1940-087X}, abstract = {Plasmids play a major role in microbial ecology and evolution as vehicles of lateral gene transfer and reservoirs of accessory gene functions in microbial populations. This is especially the case under rapidly changing environments such as fluctuating antibiotics exposure. We recently showed that plasmids maintain antibiotic resistance genes in Escherichia coli without positive selection for the plasmid presence. Here we describe an experimental system that allows following both the plasmid genotype and phenotype in long-term evolution experiments. We use molecular techniques to design a model plasmid that is subsequently introduced to an experimental evolution batch system approach in an E. coli host. We follow the plasmid frequency over time by applying replica plating of the E. coli populations while quantifying the antibiotic resistance persistence. In addition, we monitor the conformation of plasmids in host cells by analyzing the extent of plasmid multimer formation by plasmid nicking and agarose gel electrophoresis. Such an approach allows us to visualize not only the genome size of evolving plasmids but also their topological conformation-a factor highly important for plasmid inheritance. Our system combines molecular strategies with traditional microbiology approaches and provides a set-up to follow plasmids in bacterial populations over a long time. The presented approach can be applied to study a wide range of mobile genetic elements in the future.}, }
@article {pmid31881501, year = {2020}, author = {Favere, J and Buysschaert, B and Boon, N and De Gusseme, B}, title = {Online microbial fingerprinting for quality management of drinking water: Full-scale event detection.}, journal = {Water research}, volume = {170}, number = {}, pages = {115353}, doi = {10.1016/j.watres.2019.115353}, pmid = {31881501}, issn = {1879-2448}, mesh = {Bacteria ; *Drinking Water ; Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Microbial regrowth during drinking water distribution can result in a variety of problems such as a deviating taste and odor, and may even pose a risk to public health. Frequent monitoring is essential to anticipate events of biological instability, and relevant microbial parameters for operational control of biostability of drinking water should be developed. Here, online flow cytometry and derived biological metrics were used to assess the biological stability of a full-scale drinking water tower during normal and disturbed flow regime. Pronounced operational events, such as switching from drinking water source, and seasonal changes, were detected in the total cell counts, and regrowth was observed despite the short hydraulic residence time of 6-8 h. Based on the flow cytometric fingerprints, the Bray-Curtis dissimilarity was calculated and was developed as unambiguous parameter to indicate or warn for changing microbial drinking water quality during operational events. In the studied water tower, drastic microbial water quality changes were reflected in the Bray-Curtis dissimilarity, which demonstrates its use as an indicator to follow-up and detect microbial quality changes in practice. Hence, the Bray-Curtis dissimilarity can be used in an online setup as a straightforward parameter during full-scale operation of drinking water distribution, and combined with the cell concentration, it serves as an early-warning system for biological instability.}, }
@article {pmid31878322, year = {2019}, author = {Sahu, SK and Liu, M and Yssel, A and Kariba, R and Muthemba, S and Jiang, S and Song, B and Hendre, PS and Muchugi, A and Jamnadass, R and Kao, SM and Featherston, J and Zerega, NJC and Xu, X and Yang, H and Deynze, AV and Peer, YV and Liu, X and Liu, H}, title = {Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis).}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/genes11010027}, pmid = {31878322}, issn = {2073-4425}, abstract = {Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.}, }
@article {pmid31873774, year = {2019}, author = {Velasco-González, I and Sanchez-Jimenez, A and Singer, D and Murciano, A and Díez-Hermano, S and Lara, E and Martín-Cereceda, M}, title = {Correction to: Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01478-5}, pmid = {31873774}, issn = {1432-184X}, abstract = {The original version of this article contained an erratum of omission in the Acknowledgments section.}, }
@article {pmid31873773, year = {2019}, author = {Poret-Peterson, AT and Sayed, N and Glyzewski, N and Forbes, H and González-Orta, ET and Kluepfel, DA}, title = {Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01477-6}, pmid = {31873773}, issn = {1432-184X}, support = {2032-22000-016-00D//Agricultural Research Service/ ; }, abstract = {Anaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.e., release of volatile organic compounds) and abiotic (i.e., lowered pH, release of metal ions) factors. In this study, we examined how the soil microbiome changes over time in response to ASD initiated with rice bran, tomato pomace, or red grape pomace as amendments using growth chamber mesocosms that replicate ASD-induced field soil redox conditions. Within 2 days, the soil microbiome rapidly shifted from a diverse assemblage of taxa to being dominated by members of the Firmicutes for all ASD treatments, whereas control mesocosms maintained diverse and more evenly distributed communities. Rice bran and tomato pomace amendments resulted in microbial communities with similar compositions and trajectories that were different from red grape pomace communities. Quantitative PCR showed nitrogenase gene abundances were higher in ASD communities and tended to increase over time, suggesting the potential for altering soil nitrogen availability. These results highlight the need for temporal and functional studies to understand how pathogen suppressive microbial communities assemble and function in ASD-treated soils.}, }
@article {pmid31872949, year = {2019}, author = {Harrison, JG and Calder, WJ and Shastry, V and Buerkle, CA}, title = {Dirichlet-multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13128}, pmid = {31872949}, issn = {1755-0998}, support = {EPS-1655726//National Science Foundation/ ; //University of Wyoming/ ; }, abstract = {Molecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modelled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features in an underlying Dirichlet distribution. These distributions together form a hierarchical model for relative abundances among replicates and sampling groups. This type of Dirichlet-multinomial modelling (DMM) has been described previously, but its benefits and limitations are largely untested. With simulated data, we quantified the ability of DMM to detect differences in proportions between treatment and control groups, and compared the efficacy of three computational methods to implement DMM-Hamiltonian Monte Carlo (HMC), variational inference (VI), and Gibbs Markov chain Monte Carlo. We report that DMM was better able to detect shifts in relative abundances than analogous analytical tools, while identifying an acceptably low number of false positives. Among methods for implementing DMM, HMC provided the most accurate estimates of relative abundances, and VI was the most computationally efficient. The sensitivity of DMM was exemplified through analysis of previously published data describing lung microbiomes. We report that DMM identified several potentially pathogenic, bacterial taxa as more abundant in the lungs of children who aspirated foreign material during swallowing; these differences went undetected with different statistical approaches. Our results suggest that DMM has strong potential as a statistical method to guide inference in molecular ecology.}, }
@article {pmid31872380, year = {2019}, author = {Mohr, T and Aliyu, H and Biebinger, L and Gödert, R and Hornberger, A and Cowan, D and de Maayer, P and Neumann, A}, title = {Effects of different operating parameters on hydrogen production by Parageobacillus thermoglucosidasius DSM 6285.}, journal = {AMB Express}, volume = {9}, number = {1}, pages = {207}, pmid = {31872380}, issn = {2191-0855}, support = {031B0180//Bundesministerium für Bildung und Forschung/ ; 109137//National Research Foundation/ ; }, abstract = {Hydrogen gas represents a promising alternative energy source to dwindling fossil fuel reserves, as it carries the highest energy per unit mass and its combustion results in the release of water vapour as only byproduct. The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius is able to produce hydrogen via the water-gas shift reaction catalyzed by a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Here we have evaluated the effects of several operating parameters on hydrogen production, including different growth temperatures, pre-culture ages and inoculum sizes, as well as different pHs and concentrations of nickel and iron in the fermentation medium. All of the tested parameters were observed to have a substantive effect on both hydrogen yield and (specific) production rates. A final experiment incorporating the best scenario for each tested parameter showed a marked increase in the H2 production rate compared to each individual parameter. The optimised parameters serve as a strong basis for improved hydrogen production with a view of commercialisation of this process.}, }
@article {pmid31870202, year = {2019}, author = {Erber, AC and Cetin, H and Berry, D and Schernhammer, ES}, title = {The role of gut microbiota, butyrate and proton pump inhibitors in amyotrophic lateral sclerosis: a systematic review.}, journal = {The International journal of neuroscience}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/00207454.2019.1702549}, pmid = {31870202}, issn = {1563-5279}, abstract = {Aim of the study: We conducted a systematic review on existing literature in humans and animals, linking the gut microbiome with amyotrophic lateral sclerosis (ALS). Additionally, we sought to explore the role of the bacterially produced metabolite butyrate as well as of proton pump inhibitors (PPIs) in these associations.Materials and methods: Following PRISMA guidelines for systematic literature reviews, four databases (Medline, Scopus, Embase and Web of Science) were searched and screened by two independent reviewers against defined inclusion criteria. Six studies in humans and six animal studies were identified, summarized and reviewed.Results: Overall, the evidence accrued to date is supportive of changes in the gut microbiome being associated with ALS risk, and potentially progression, though observational studies are small (describing a total of 145 patients with ALS across all published studies), and not entirely conclusive.Conclusions: With emerging studies beginning to apply metagenome sequencing, more clarity regarding the importance and promise of the gut microbiome in ALS can be expected. Future studies may also help establish the therapeutic potential of butyrate, and the role of PPIs in these associations.}, }
@article {pmid31867834, year = {2019}, author = {Kuenen, JG}, title = {Anammox and beyond.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14904}, pmid = {31867834}, issn = {1462-2920}, abstract = {When looking back and wonder how we did it, I became even more aware of how my wanderings in microbiology are all linked, from the start of my PhD with Hans Veldkamp on sulphur-oxidizing bacteria in chemostats. My interests broadened from obligate chemolithoautotrophic bacteria to facultative organisms and the question about the ecological niches of these different metabolic types. The sulphide oxidizing bacteria also may be used to produce elemental sulphur, which can easily be removed from wastewater. This fitted in a long-standing collaboration with Dimitry Sorokin on the ecophysiology and application of alkaliphilic sulphur bacteria. Then came the denitrifying sulphur-oxidizing bacteria and their application to remove sulphide from wastewater, which lead to our interest in nitrate, nitrite and ammonium removal in general. The big surprise was the serendipitous discovery of the 'anammox'-process, whereby ammonium is anaerobically oxidized to dinitrogen gas with nitrite as electron acceptor. The early days of our anammox research are the main focus of this article, which describes the struggle of growing and identifying the most peculiar bacteria we ever came across. A specialized organelle, the anammoxosome was shown to be responsible for the key ammonium oxidation, whereby a rocket fuel, hydrazine, turned out to be an intermediate. Soon after we became aware that anammox is everywhere and in the marine environment makes up a major portion of the nitrogen cycle. The intense scientific collaboration with Mike Jetten and Mark van Loosdrecht and colleagues led to our further understanding and application of this fascinating process, which is briefly summarized in this article. My broader interest in environmental microbiology and microbial ecology has been a regularly returning theme, taking me all over the world to great collaborations lasting to this very day.}, }
@article {pmid31867463, year = {2019}, author = {Oliveira, M and Rodrigues, CM and Teixeira, P}, title = {Microbiological quality of raw berries and their products: A focus on foodborne pathogens.}, journal = {Heliyon}, volume = {5}, number = {12}, pages = {e02992}, pmid = {31867463}, issn = {2405-8440}, abstract = {Berry samples (n = 316; strawberries, raspberries, blackberries and blueberries) obtained from a fruit processing plant were examined regarding bacteriological quality and their potential public health risk. Three types of berry products were analysed including raw material, product from the mixing step and final product. Escherichia coli, Salmonella spp., Listeria monocytogenes, Bacillus cereus, sulphite-reducing clostridia spores and coagulase-positive staphylococci were the parameters investigated. Salmonella enterica serovar Braenderup and L. monocytogenes were isolated from one fruit sample of raw material each. Two samples harboured E. coli between 0.7 and 0.9 log cfu g-1, not exceeding the hygienic criteria. Coagulase-positive staphylococci were not detected in the studied samples; however, coagulase-negative staphylococci (CNS) were isolated from a small proportion of samples mainly raspberries. Presumptive B. cereus were isolated from a relatively large proportion of the samples, raspberries and blackberries being the most contaminated fruits. The absence of pathogenic microorganisms in the final product as well as the low prevalence of presumptive B. cereus and CNS indicates proper implementation of good manufacturing and hygiene practices (GMPs/GHPs) by the food industry. Nevertheless, the results indicate that the raw material examined may contain pathogenic bacteria and thereby represent a risk to consumers regarding the manifestation of foodborne diseases.}, }
@article {pmid31866955, year = {2019}, author = {Li, Z and Yao, Q and Guo, X and Crits-Christoph, A and Mayes, MA and Iv, WJH and Lebeis, SL and Banfield, JF and Hurst, GB and Hettich, RL and Pan, C}, title = {Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2706}, pmid = {31866955}, issn = {1664-302X}, abstract = {Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.}, }
@article {pmid31863131, year = {2019}, author = {Wang, ZB and Sun, YY and Li, Y and Chen, XL and Wang, P and Ding, HT and Chen, B and Zhang, XY and Song, XY and Wang, M and McMinn, A and Zhang, YZ and Qin, QL}, title = {Significant Bacterial Distance-Decay Relationship in Continuous, Well-Connected Southern Ocean Surface Water.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01472-x}, pmid = {31863131}, issn = {1432-184X}, support = {2018YFC1406706//National Key R&amp;D Program of China/ ; U1706207//National Science Foundation of China/ ; 2017ASTCP-OS14//AoShan Talents Cultivation Program/ ; 2009TS079//Taishan Scholars Program of Shandong Province/ ; 2016WLJH36//Young Scholars Program of Shandong University/ ; }, abstract = {Recently, an increasing number of studies have focused on the biogeographic distribution of marine microorganisms. However, the extent to which geographic distance can affect marine microbial communities is still unclear, especially for the microbial communities in well-connected surface seawaters. In this study, the bacterial community compositions of 21 surface seawater samples, that were distributed over a distance of 7800 km, were surveyed to investigate how bacterial community similarity changes with increasing geographical distance. Proteobacteria and Bacteroidetes were the dominant bacterial phyla, with Proteobacteria accounting for 52.6-92.5% and Bacteroidetes comprising 3.5-46.9% of the bacterial communities. A significant bacterial distance-decay relationship was observed in the well-connected Southern Ocean surface seawater. The number of pairwise shared operational taxonomic units (OTUs), and community similarities tended to decrease with increasing geographic distance. Calculation of the similarity indices with all, abundant or rare OTUs did not affect the observed distance-decay relationship. Spatial distance can largely explain the observed bacterial community variation. This study shows that even in well-connected surface waters, bacterial distance-decay patterns can be found as long as the geographical distance is great enough. The biogeographic patterns should then be present for marine microorganisms considering the large size and complexity of the marine ecosystem.}, }
@article {pmid31860060, year = {2020}, author = {Cavichiolli de Oliveira, N and Cônsoli, FL}, title = {Beyond host regulation: Changes in gut microbiome of permissive and non-permissive hosts following parasitization by the wasp Cotesia flavipes.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz206}, pmid = {31860060}, issn = {1574-6941}, abstract = {Koinobiont parasitoids regulate the physiology of their hosts, possibly interfering with the host gut microbiota and ultimately impacting parasitoid development. We used the parasitoid Cotesia flavipes to investigate if the regulation of the host would also affect the host gut microbiota. We also wondered if the effects of parasitization on the gut microbiota would depend on the host-parasitoid association by testing the permissive Diatraea saccharalis and the non-permissive Spodoptera frugiperda hosts. We determined the structure and potential functional contribution of the gut microbiota of the fore-midgut and hindgut of the hosts at different stages of development of the immature parasitoid. The abundance and diversity of operational taxonomic units of the anteromedial (fore-midgut) gut and posterior (hindgut) region from larvae of the analyzed hosts were affected by parasitization. Changes in the gut microbiota induced by parasitization altered the potential functional contribution of the gut microbiota associated with both hosts. Our data also indicated that the mechanism by which C. flavipes interferes with the gut microbiota of the host does not require a host-parasitoid coevolutionary history. Changes observed in the potential contribution of the gut microbiota of parasitized hosts impact the host's nutritional quality, and could favor host exploitation by C. flavipes.}, }
@article {pmid31858913, year = {2019}, author = {Basilua, JM and Pochart, P}, title = {Cotrimoxazole Prophylaxis Is Not Associated with a Higher occurrence of Atazanavir Treatment Failure: analysis of Worldwide Pharmacovigilance Data.}, journal = {Infectious disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/1871526520666191220112416}, pmid = {31858913}, issn = {2212-3989}, abstract = {BACKGROUND: Cotrimoxazole is the main antibiotic used in HIV-infected patients for the prophylaxis of opportunistic infections. This antibiotic is prescribed in patients receiving antiretroviral agents (ART) such as Atazanavir (ATV), a protease inhibitor used with other ART classes. The objective of this study was to compare HIV treatment failure (HIVTF) in HIV-infected patients treated concomitantly with ATV and cotrimoxazole to those of patients treated only with ATV.<br><br>MATERIALS AND METHODS: This is a comparative analysis of the safety data of HIVTF available with ATV in the WHO International Pharmacovigilance database &quot;VigiBase®&quot;. We used the SMQ (Standardized MedDRA Querie) to identify all the terms corresponding to HIVTF. We presented results as a percentage or an adjusted Reporting Odds Ratio (aROR) with a 95% confidence interval (95% CI).<br><br>RESULTS: A total of 116 cases of HIVTF (2.2%) were reported with ATV among the 5196 individual case safety reports (ICSR) included in the analysis. The proportion of HIV-infected patients who presented ATV treatment failure (ATVTF) was lower (2.6%, 3/116) when cotrimoxazole was concomitant (aROR was 0.5 with a 95%CI from 0.2 to 1.7). Only 10 of 273 ICSRs (3.7%) were reported from Africa concerning the use of cotrimoxazole prophylaxis concomitantly with ATV.<br><br>CONCLUSION: This study did not show a higher occurrence of ATVTF when cotrimoxazole was concomitant. These results reinforce the place of concomitant use of ATV with cotrimoxazole in the management of HIV treatment.}, }
@article {pmid31854329, year = {2019}, author = {Hewson, I}, title = {Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson.}, journal = {Diseases of aquatic organisms}, volume = {137}, number = {2}, pages = {109-124}, doi = {10.3354/dao03432}, pmid = {31854329}, issn = {0177-5103}, mesh = {Animals ; Bias ; *Microbiota ; }, abstract = {The accessibility of high-throughput DNA sequencing technologies has attracted the application of comparative microbial analyses to study diseases. These studies present a window into host microbiome diversity and composition that can be used to address ecological theory in the context of host biology and behavior. Recently, comparative microbiome studies have been used to study non-vertebrate aquatic diseases to elucidate microorganisms potentially involved in disease processes or in disease prevention. These investigations suffer from many well-described biases, especially prior to sequence analyses, that could lead to misleading conclusions. Microbiome-focused studies of aquatic metazoan diseases provide valuable documentation of microbial ecology, although, they are only a starting point for establishing disease etiology, which demands quantitative validation through targeted approaches. The microbiome approach to understanding disease is most useful after laboratory diagnostics guided by pathology have failed to identify a causative agent. This opinion piece presents several technical pitfalls which may affect wider interpretation of microbe-host interactions through comparative microbial community analyses and provides recommendations, based on studies in non-aquatic systems, for incorporation into future aquatic disease research.}, }
@article {pmid31853069, year = {2020}, author = {Zhang, L and Chen, F and Zhang, X and Li, Z and Zhao, Y and Lohaus, R and Chang, X and Dong, W and Ho, SYW and Liu, X and Song, A and Chen, J and Guo, W and Wang, Z and Zhuang, Y and Wang, H and Chen, X and Hu, J and Liu, Y and Qin, Y and Wang, K and Dong, S and Liu, Y and Zhang, S and Yu, X and Wu, Q and Wang, L and Yan, X and Jiao, Y and Kong, H and Zhou, X and Yu, C and Chen, Y and Li, F and Wang, J and Chen, W and Chen, X and Jia, Q and Zhang, C and Jiang, Y and Zhang, W and Liu, G and Fu, J and Chen, F and Ma, H and Van de Peer, Y and Tang, H}, title = {The water lily genome and the early evolution of flowering plants.}, journal = {Nature}, volume = {577}, number = {7788}, pages = {79-84}, doi = {10.1038/s41586-019-1852-5}, pmid = {31853069}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, abstract = {Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1-3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.}, }
@article {pmid31849864, year = {2019}, author = {Bains, M and Laney, C and Wolfe, AE and Orr, M and Waschek, JA and Ericsson, AC and Dorsam, GP}, title = {Vasoactive Intestinal Peptide Deficiency Is Associated With Altered Gut Microbiota Communities in Male and Female C57BL/6 Mice.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2689}, pmid = {31849864}, issn = {1664-302X}, abstract = {Vasoactive intestinal peptide (VIP) is crucial for gastrointestinal tract (GIT) health. VIP sustains GIT homeostasis through maintenance of the intestinal epithelial barrier and acts as a potent anti-inflammatory mediator that contributes to gut bacterial tolerance. Based on these biological functions by VIP, we hypothesized that its deficiency would alter gut microbial ecology. To this end, fecal samples from male and female VIP+/+, VIP+/-, and VIP-/- littermates (n = 47) were collected and 16S rRNA sequencing was conducted. Our data revealed significant changes in bacterial composition, biodiversity, and weight loss from VIP-/- mice compared to VIP+/+ and VIP+/- littermates, irrespective of sex. The gut bacteria compositional changes observed in VIP-/- mice was consistent with gut microbial structure changes reported for certain inflammatory and autoimmune disorders. Moreover, predicted functional changes by PICRUSt software suggested an energy surplus within the altered microbiota from VIP-/- mice. These data support that VIP plays an important role in maintaining microbiota balance, biodiversity, and GIT function, and its genetic removal results in significant gut microbiota restructuring and weight loss.}, }
@article {pmid31849848, year = {2019}, author = {Madigan, AP and Egidi, E and Bedon, F and Franks, AE and Plummer, KM}, title = {Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2616}, pmid = {31849848}, issn = {1664-302X}, abstract = {An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg-1 soil) or salt (4 or 7 g kg-1 soil) and treated with melatonin (0.2 and 4 mg kg-1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.}, }
@article {pmid31848649, year = {2019}, author = {Somers, DJ and Strock, KE and Saros, JE}, title = {Environmental Controls on Microbial Diversity in Arctic Lakes of West Greenland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01474-9}, pmid = {31848649}, issn = {1432-184X}, support = {1203434//Arctic System Science program of the US National Science Foundation/ ; SFR161//Center for Sustainability Education at Dickinson College/ ; }, abstract = {We assessed the microbial community structure of six arctic lakes in West Greenland and investigated relationships to lake physical and chemical characteristics. Lakes from the ice sheet region exhibited the highest species richness, while inland and plateau lakes had lower observed taxonomical diversity. Lake habitat differentiation during summer stratification appeared to alter within lake microbial community composition in only a subset of lakes, while lake variability across regions was a consistent driver of microbial community composition in these arctic lakes. Principal coordinate analysis revealed differentiation of communities along two axes: each reflecting differences in morphometric (lake surface area), geographic (latitude and distance from the ice sheet), physical lake variables (water clarity), and lakewater chemistry (dissolved organic carbon [DOC], dissolved oxygen [DO], total nitrogen [TN], and conductivity). Understanding these relationships between environmental variables and microbial communities is especially important as heterotrophic microorganisms are key to organic matter decomposition, nutrient cycling, and carbon flow through nutrient poor aquatic environments in the Arctic.}, }
@article {pmid31846683, year = {2019}, author = {Moccia, KM and Lebeis, SL}, title = {Microbial Ecology: How to Fight the Establishment.}, journal = {Current biology : CB}, volume = {29}, number = {24}, pages = {R1320-R1323}, doi = {10.1016/j.cub.2019.10.067}, pmid = {31846683}, issn = {1879-0445}, abstract = {Creating microbial consortia capable of consistently producing desired qualities requires a detailed understanding of community interactions. A new paper demonstrates the role of historical contingency in Arabidopsis thaliana leaf-microbiome formation using an adaptable experimental approach, which could be applied to other host organisms.}, }
@article {pmid31845419, year = {2019}, author = {Bakker, A and Siegel, JA and Mendell, MJ and Prussin, AJ and Marr, LC and Peccia, J}, title = {Bacterial and fungal ecology on air conditioning cooling coils is influenced by climate and building factors.}, journal = {Indoor air}, volume = {}, number = {}, pages = {}, doi = {10.1111/ina.12632}, pmid = {31845419}, issn = {1600-0668}, support = {G-2015-14134//Alfred P. Sloan Foundation/ ; CBET-1438103//National Science Foundation/ ; }, abstract = {The presence of biofilms on the cooling coils of commercial air conditioning (AC) units can significantly reduce the heat transfer efficiency of the coils and may lead to the aerosolization of microbes into occupied spaces of a building. We investigated how climate and AC operation influence the ecology of microbial communities on AC coils. Forty large-scale commercial ACs were considered with representation from warm-humid and hot-dry climates. Both bacterial and fungal ecologies, including richness and taxa, on the cooling coil surfaces were significantly impacted by outdoor climate, through differences in dew point that result in increased moisture (condensate) on coils, and by the minimum efficiency reporting value (MERV 8 vs MERV 14) of building air filters. Based on targeted qPCR and sequence analysis, low efficiency upstream filters (MERV 8) were associated with a greater abundance of pathogenic bacteria and medically relevant fungi. As the implementation of air conditioning continues to grow worldwide, better understanding of the factors impacting microbial growth and ecology on cooling coils should enable more rational approaches for biofilm control and ultimately result in reduced energy consumption and healthier buildings.}, }
@article {pmid31844910, year = {2019}, author = {Bridier, A and Piard, JC and Briandet, R and Bouchez, T}, title = {Emergence of a Synergistic Diversity as a Response to Competition in Pseudomonas putida Biofilms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01470-z}, pmid = {31844910}, issn = {1432-184X}, support = {SYSCOMM project DISCO, ANR-09-SYSC-003//French National Research Agency (ANR)/ ; }, abstract = {Genetic diversification through the emergence of variants is one of the known mechanisms enabling the adaptation of bacterial communities. We focused in this work on the adaptation of the model strain Pseudomonas putida KT2440 in association with another P. putida strain (PCL1480) recently isolated from soil to investigate the potential role of bacterial interactions in the diversification process. On the basis of colony morphology, three variants of P. putida KT2440 were obtained from co-culture after 168 h of growth whereas no variant was identified from the axenic KT2440 biofilm. The variants exhibited distinct phenotypes and produced biofilms with specific architecture in comparison with the ancestor. The variants better competed with the P. putida PCL1480 strain in the dual-strain biofilms after 24 h of co-culture in comparison with the ancestor. Moreover, the synergistic interaction of KT2440 ancestor and the variants led to an improved biofilm production and to higher competitive ability versus the PCL1480 strain, highlighting the key role of diversification in the adaptation of P. putida KT2440 in the mixed community. Whole genome sequencing revealed mutations in polysaccharides biosynthesis protein, membrane transporter, or lipoprotein signal peptidase genes in variants.}, }
@article {pmid31844283, year = {2019}, author = {Wang, S and Li, L and Li, H and Sahu, SK and Wang, H and Xu, Y and Xian, W and Song, B and Liang, H and Cheng, S and Chang, Y and Song, Y and Çebi, Z and Wittek, S and Reder, T and Peterson, M and Yang, H and Wang, J and Melkonian, B and Van de Peer, Y and Xu, X and Wong, GK and Melkonian, M and Liu, H and Liu, X}, title = {Genomes of early-diverging streptophyte algae shed light on plant terrestrialization.}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41477-019-0560-3}, pmid = {31844283}, issn = {2055-0278}, abstract = {Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.}, }
@article {pmid31838570, year = {2019}, author = {Li, XD and Chen, YH and Liu, C and Hong, J and Deng, H and Yu, DJ}, title = {Eutrophication and Related Antibiotic Resistance of Enterococci in the Minjiang River, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01464-x}, pmid = {31838570}, issn = {1432-184X}, support = {2016YFD0501310//State Key Development Program during the 13th Five-Year Plan period of China/ ; 31272606//National Natural Science Foundation of China/ ; 31602106//National Natural Science Foundation of China/ ; 2017J01598//Natural Science Foundation of Fujian Province/ ; }, abstract = {Antimicrobial resistance (AMR) in the aquatic environment has received increasing attention in recent years, and growing eutrophication problems may contribute to AMR in aquatic ecosystems. To evaluate whether and how eutrophication affects AMR, 40 surface water samples were collected from the Minjiang River, Fujian Province, China. Total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (CODMn) were measured as eutrophication factors. Additionally, enterococci species were isolated and their resistance to six common antibiotics was tested. Eutrophication generally showed a trend of increasing with the flow direction of the Minjiang River, with 25 sites (62.5%) having a TN/TP value over the Redfield value (16:1), which indicated that eutrophication in this region was of phosphorus limitation. High nutrition sites were in or near urban areas. Poor quality water was found in the middle and lower reaches of the Minjiang River system. The resistance frequency of 40 enterococci isolates to the six antibiotics tested was as follows: oxytetracycline > erythromycin > ciprofloxacin > chloramphenicol > ampicillin > vancomycin (70, 50, 17.5, 12.5, 2.5, 0%), and the multi-resistant rate reached 50% with eight resistance phenotypes. AMR also increased along the direction of water flow downstream, and most of the sites with the highest AMR were in or near urban areas, as was true for nutrition levels. Positive correlations between AMR and eutrophication factors (TN, TP, and CODMn) were identified using the Pearson's correlation coefficient, and TN/TP generally was negatively related to AMR. These results indicated that eutrophication may induce or selective for resistance of water-borne pathogens to antibiotics, with a high resistance level and a wide resistance spectrum.}, }
@article {pmid31838363, year = {2020}, author = {Chun, SJ and Cui, Y and Lee, JJ and Choi, IC and Oh, HM and Ahn, CY}, title = {Network analysis reveals succession of Microcystis genotypes accompanying distinctive microbial modules with recurrent patterns.}, journal = {Water research}, volume = {170}, number = {}, pages = {115326}, doi = {10.1016/j.watres.2019.115326}, pmid = {31838363}, issn = {1879-2448}, mesh = {*Cyanobacteria ; Genotype ; *Microcystis ; RNA, Ribosomal, 16S ; Republic of Korea ; }, abstract = {Every member of the ecological community is connected via a network of vital and complex relationships, called the web of life. To elucidate the ecological network and interactions among producers, consumers, and decomposers in the Daechung Reservoir, Korea, during cyanobacterial harmful algal blooms (cyanoHAB), especially those involving Microcystis, we investigated the diversity and compositions of the cyanobacterial (16S rRNA gene), including the genotypes of Microcystis (cpcBA-IGS gene), non-cyanobacterial (16S), and eukaryotic (18S) communities through high-throughput sequencing. Microcystis blooms were divided into the Summer Major Bloom and Autumn Minor Bloom with different dominant genotypes of Microcystis. Network analysis demonstrated that the modules involved in the different phases of the Microcystis blooms were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups at all sampling stations. In addition, the non-cyanobacterial components of each Group were classified, while the same Group showed similarity across all stations, suggesting that Microcystis and other microbes were highly interdependent and organized into cyanoHAB-related module units. Importantly, the Microcystis genotype-based sub-network uncovered that Pirellula, Pseudanabaena, and Vampirovibrionales preferred to interact with specific Microcystis genotypes in the Summer Major Bloom than with other genotypes in the Autumn Minor Bloom, while the copepod Skistodiaptomus exhibited the opposite pattern. In conclusion, the transition patterns of cyanoHAB-related modules and their key components could be crucial in the succession of Microcystis genotypes and to enhance the understanding of microbial ecology in an aquatic environment.}, }
@article {pmid31838145, year = {2019}, author = {Mickalide, H and Kuehn, S}, title = {Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community.}, journal = {Cell systems}, volume = {9}, number = {6}, pages = {521-533.e10}, doi = {10.1016/j.cels.2019.11.004}, pmid = {31838145}, issn = {2405-4720}, abstract = {The composition of an ecosystem is thought to be important for determining its resistance to invasion. Studies of natural ecosystems, from plant to microbial communities, have found that more diverse communities are more resistant to invasion. In some cases, more diverse communities resist invasion by more completely consuming the resources necessary for the invader. We show that Escherichia coli can successfully invade cultures of the alga Chlamydomonas reinhardtii (phototroph) or the ciliate Tetrahymena thermophila (predator) but cannot invade a community where both are present. The invasion resistance of the algae-ciliate community arises from a higher-order interaction between species (interaction modification) that is unrelated to resource consumption. We show that the mode of this interaction is the algal inhibition of bacterial aggregation, which leaves bacteria vulnerable to predation. This mode requires both the algae and the ciliate to be present and provides an example of invasion resistance through an interaction modification.}, }
@article {pmid31837971, year = {2020}, author = {Böllmann, J and Martienssen, M}, title = {Comparison of different media for the detection of denitrifying and nitrate reducing bacteria in mesotrophic aquatic environments by the most probable number method.}, journal = {Journal of microbiological methods}, volume = {168}, number = {}, pages = {105808}, doi = {10.1016/j.mimet.2019.105808}, pmid = {31837971}, issn = {1872-8359}, abstract = {The cultivation based characterization of microbial communities and the quantification of certain functional bacterial groups is still an essential part of microbiology and microbial ecology. For plate count methods meanwhile low strength media are recommended, since they cover a broader range of different species and result in higher counts compared to established high strength media. For liquid media, as they are used for most probable number (MPN) quantifications, comparisons between high and low strength media are rare. In this study we compare the performance of different high and low strength media for the MPN quantification of nitrate reducing and denitrifying bacteria in two different fresh water environments. We also calculated the cell specific turnover rates of several denitrifying cultures previously enriched in high and low strength media from three different fresh water environments and a waste water treatment plant. For fresh water samples, our results indicate that high strength media detect higher MPN of denitrifying bacteria and in equal MPN of nitrate reducing bacteria compared to low strength media, which is in contrary to plate count techniques. For sediment samples, high and low strength media performed equal. The cell specific turnover rate was independent from the enrichment media and the media of the performance test. The cause of the lower denitrifyer MPN in low strength media remains, however, unclear. The results are important for further MPN quantifications of bacteria in nutrient poor environments and for calculations of nitrogen turnover rates by kinetical models using the number of metabolic active cells as one parameter.}, }
@article {pmid31836929, year = {2019}, author = {Nyirabuhoro, P and Liu, M and Xiao, P and Liu, L and Yu, Z and Wang, L and Yang, J}, title = {Seasonal Variability of Conditionally Rare Taxa in the Water Column Bacterioplankton Community of Subtropical Reservoirs in China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01458-9}, pmid = {31836929}, issn = {1432-184X}, support = {91851104//National Natural Science Foundation of China/ ; 31500372//National Natural Science Foundation of China/ ; KFJ-SW-YW036//Program of Field Station Alliance, Chinese Academy of Sciences/ ; 2019J02016//Natural Science Foundation of Fujian Province/ ; }, abstract = {Conditionally rare bacteria are ubiquitous and perhaps the most diverse of microbial lifeforms, but their temporal dynamics remain largely unknown. High-throughput and deep sequencing of the 16S rRNA gene has allowed us to identify and compare the conditionally rare taxa with other bacterioplankton subcommunities. In this study, we examined the effect of season, water depth, and ecological processes on the fluctuations of bacterial subcommunities (including abundant, conditionally rare, moderate, and rare taxa) from three subtropical reservoirs in China. We discovered that the conditionally rare taxa (CRT) made up 49.7 to 71.8% of the bacterioplankton community richness, and they accounted for 70.6 to 84.4% of the temporal changes in the community composition. Beta-diversity analysis revealed strong seasonal succession patterns among all bacterioplankton subcommunities, suggesting abundant, conditionally rare, moderate, and rare taxa subcommunities have comparable environmental sensitivity. The dominant phyla of CRT were Proteobacteria, Actinobacteria, and Bacteroidetes, whose variations were strongly correlated with environmental variables. Both deterministic and stochastic processes showed strong effect on bacterioplankton community assembly, with deterministic patterns more pronounced for CRT subcommunity. The difference in bacterial community composition was strongly linked with seasonal change rather than water depth. The seasonal patterns of CRT expand our understanding of underlying mechanisms for bacterial community structure and composition. This implies their importance in the function and stability of freshwater ecosystem after environmental disturbance.}, }
@article {pmid31836376, year = {2019}, author = {Ntagia, E and Fiset, E and Truong Cong Hong, L and Vaiopoulou, E and Rabaey, K}, title = {Electrochemical treatment of industrial sulfidic spent caustic streams for sulfide removal and caustic recovery.}, journal = {Journal of hazardous materials}, volume = {}, number = {}, pages = {121770}, doi = {10.1016/j.jhazmat.2019.121770}, pmid = {31836376}, issn = {1873-3336}, abstract = {Alkaline spent caustic streams (SCS) produced in the petrochemical and chemical manufacturing industry, contain high concentrations of reactive sulfide (HS-) and caustic soda (NaOH). Common treatment methods entail high operational costs while not recovering the possible resources that SCS contain. Here we studied the electrochemical treatment of SCS from a chemical manufacturing industry in an electrolysis cell, aiming at anodic HS- removal and cathodic NaOH, devoid of sulfide, recovery. Using a synthetic SCS we first evaluated the HS- oxidation product distribution over time, as well as the HS- removal and the NaOH recovery, as a function of current density. In a second step, we investigated the operational aspects of such treatment for the industrial SCS, under 300 A m-2 fixed current density. In an electrolysis cell receiving 205 ± 60 g S L-1 d-1 HS- over 20 days of continuous operation, HS- was removed with a 38.0 ± 7.7 % removal and ∼80 % coulombic efficiency, with a concomitant recovery of a ∼12 wt.% NaOH solution. The low cell voltage obtained (1.75 ± 0.12 V), resulted in low energy requirements of 3.7 ± 0.6 kW h kg-1 S and 6.3 ± 0.4 kW h kg-1 NaOH and suggests techno-economic viability of this process.}, }
@article {pmid31835452, year = {2019}, author = {Cancello, R and Turroni, S and Rampelli, S and Cattaldo, S and Candela, M and Cattani, L and Mai, S and Vietti, R and Scacchi, M and Brigidi, P and Invitti, C}, title = {Effect of Short-Term Dietary Intervention and Probiotic Mix Supplementation on the Gut Microbiota of Elderly Obese Women.}, journal = {Nutrients}, volume = {11}, number = {12}, pages = {}, pmid = {31835452}, issn = {2072-6643}, support = {RICCOR number: 2015_12_15_03//Ministero della Salute/ ; }, abstract = {Accumulating literature is providing evidence that the gut microbiota is involved in metabolic disorders, but the question of how to effectively modulate it to restore homeostasis, especially in the elderly, is still under debate. In this study, we profiled the intestinal microbiota of 20 elderly obese women (EO) at the baseline (T0), after 15 days of hypocaloric Mediterranean diet administered as part of a nutritional-metabolic rehabilitation program for obesity (T1), and after a further 15 days of the same diet supplemented with a probiotic mix (T2). Fecal samples were characterized by Illumina MiSeq sequencing of the 16S rRNA gene. The EO microbiota showed the typical alterations found in obesity, namely, an increase in potential pro-inflammatory components (i.e., Collinsella) and a decrease in health-promoting, short-chain fatty acid producers (i.e., Lachnospiraceae and Ruminococcaceae members), with a tendency to reduced biodiversity. After 15 days of the rehabilitation program, weight decreased by (2.7 ± 1.5)% and the gut microbiota dysbiosis was partially reversed, with a decline of Collinsella and an increase in leanness-related taxa. During the next 15 days of diet and probiotics, weight dropped further by (1.2 ± 1.1)%, markers of oxidative stress improved, and Akkermansia, a mucin degrader with beneficial effects on host metabolism, increased significantly. These findings support the relevant role of a correct dietetic approach, even in the short term, to modulate the EO gut microbiota towards a metabolic health-related configuration, counteracting the increased risk of morbidity in these patients.}, }
@article {pmid31835036, year = {2019}, author = {Pachiadaki, MG and Brown, JM and Brown, J and Bezuidt, O and Berube, PM and Biller, SJ and Poulton, NJ and Burkart, MD and La Clair, JJ and Chisholm, SW and Stepanauskas, R}, title = {Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.}, journal = {Cell}, volume = {179}, number = {7}, pages = {1623-1635.e11}, doi = {10.1016/j.cell.2019.11.017}, pmid = {31835036}, issn = {1097-4172}, support = {R21 AI134037/AI/NIAID NIH HHS/United States ; }, abstract = {Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.}, }
@article {pmid31832698, year = {2019}, author = {Huang, CL and Sarkar, R and Hsu, TW and Yang, CF and Chien, CH and Chang, WC and Chiang, TY}, title = {Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01467-8}, pmid = {31832698}, issn = {1432-184X}, support = {106-2621-B-006-001-MY3//Ministry of Science and Technology, Taiwan/ ; }, abstract = {Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.}, }
@article {pmid31831078, year = {2019}, author = {Ricci, F and Rossetto Marcelino, V and Blackall, LL and Kühl, M and Medina, M and Verbruggen, H}, title = {Beneath the surface: community assembly and functions of the coral skeleton microbiome.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {159}, pmid = {31831078}, issn = {2049-2618}, abstract = {Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.}, }
@article {pmid31828390, year = {2019}, author = {Vick, SHW and Greenfield, P and Willows, RD and Tetu, SG and Midgley, DJ and Paulsen, IT}, title = {Subsurface Stappia: Success Through Defence, Specialisation and Putative Pressure-Dependent Carbon Fixation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01471-y}, pmid = {31828390}, issn = {1432-184X}, abstract = {Diverse microbial communities living in subsurface coal seams are responsible for important geochemical processes including the movement of carbon between the geosphere, biosphere and atmosphere. Microbial conversion of the organic matter in coal to methane involves a complex assemblage of bacteria and archaea working in syntrophic relationships. Despite the importance and value of this microbial process, very few of the microbial taxa have defined metabolic or ecological roles in these environments. Additionally, the genomic features mediating life in this chemically reduced, energy poor, deep subsurface environment are not well characterised. Here we describe the isolation and genomic and catabolic characterisation of three alphaproteobacterial Stappia indica species from three coal basins across Australia. S. indica genomes from coal seams were compared with those from closely related S. indica isolated from diverse surface waters, revealing a coal seam-specific suite of genes associated with life in the subsurface. These genes are linked to processes including viral defence, secondary metabolite production, polyamine metabolism, polypeptide uptake membrane transporters and putative energy neutral pressure-dependent CO2 fixation. This indicates that subsurface Stappia have diverse metabolisms for biomass recycling and pressure-dependent CO2 fixation and require a suite of defensive and competitive strategies relative to their surface-dwelling relatives.}, }
@article {pmid31828389, year = {2019}, author = {Gnanasekaran, G and Lim, JY and Hwang, I}, title = {Disappearance of Quorum Sensing in Burkholderia glumae During Experimental Evolution.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01445-0}, pmid = {31828389}, issn = {1432-184X}, support = {Grant 2010-0018280//National Research Foundation of Korea/ ; }, abstract = {The plant pathogen Burkholderia glumae uses quorum sensing (QS) that allows bacteria to share information and alter gene expression on the basis of cell density. The wild-type strain of B. glumae produces quorum-sensing signals (autoinducers) to detect their community and upregulate QS-dependent genes across the population for performing social and group behaviors. The model organism B. glumae was selected to investigate adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses by using experimental evolution. The wild-type B. glumae virulent strain showed genotypic changes during regular subculture due to oxygen limitation. The laboratory-evolved clones failed to produce the signaling molecule of C8-HSL/C6-HSL for activation of the quorum-sensing system. Further, the laboratory-evolved clones failed to produce catalase and oxalate for protecting themselves from the toxic environment at stationary phase and phytotoxins (toxoflavin) for infecting rice grain, respectively. The laboratory-evolved clones were completely sequenced and compared with the wild-type. Sequencing analysis of the evolved clones revealed that mutations in QS-responsible genes (iclR), sensor genes (shk, mcp), and signaling genes (luxR) were responsible for quorum-sensing activity failure. The experimental results and sequencing analysis revealed quorum-sensing process failure in the laboratory-evolved clones. In conclusion, the wild-type B. glumae strain was often exposed to oxidative stress during regular subculture and evolved as an avirulent strain (quorum-sensing mutant) by losing the phenotypic and genotypic characteristics.}, }
@article {pmid31828388, year = {2019}, author = {Brambilla, S and Soto, G and Odorizzi, A and Arolfo, V and McCormick, W and Primo, E and Giordano, W and Jozefkowicz, C and Ayub, N}, title = {Spontaneous Mutations in the Nitrate Reductase Gene napC Drive the Emergence of Eco-friendly Low-N2O-Emitting Alfalfa Rhizobia in Regions with Different Climates.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01473-w}, pmid = {31828388}, issn = {1432-184X}, support = {FVT-39//Fondo de Valorización Tecnológica/ ; PICT-2017-0674//Fondo para la Investigación Científica y Tecnológica/ ; }, abstract = {We have recently shown that commercial alfalfa inoculants (e.g., Sinorhizobium meliloti B399), which are closely related to the denitrifier model strain Sinorhizobium meliloti 1021, have conserved nitrate, nitrite, and nitric oxide reductases associated with the production of the greenhouse gas nitrous oxide (N2O) from nitrate but lost the N2O reductase related to the degradation of N2O to gas nitrogen. Here, we screened a library of nitrogen-fixing alfalfa symbionts originating from different ecoregions and containing N2O reductase genes and identified novel rhizobia (Sinorhizobium meliloti INTA1-6) exhibiting exceptionally low N2O emissions. To understand the genetic basis of this novel eco-friendly phenotype, we sequenced and analyzed the genomes of these strains, focusing on their denitrification genes, and found mutations only in the nitrate reductase structural gene napC. The evolutionary analysis supported that, in these natural strains, the denitrification genes were inherited by vertical transfer and that their defective nitrate reductase napC alleles emerged by independent spontaneous mutations. In silico analyses showed that mutations in this gene occurred in ssDNA loop structures with high negative free energy (-ΔG) and that the resulting mutated stem-loop structures exhibited increased stability, suggesting the occurrence of transcription-associated mutation events. In vivo assays supported that at least one of these ssDNA sites is a mutational hot spot under denitrification conditions. Similar benefits from nitrogen fixation were observed when plants were inoculated with the commercial inoculant B399 and strains INTA4-6, suggesting that the low-N2O-emitting rhizobia can be an ecological alternative to the current inoculants without resigning economic profitability.}, }
@article {pmid31827386, year = {2019}, author = {Zheng, P and Wang, C and Zhang, X and Gong, J}, title = {Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2019}, number = {}, pages = {5108012}, pmid = {31827386}, issn = {1472-3654}, abstract = {Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.}, }
@article {pmid31827245, year = {2019}, author = {Hiraoka, S and Hirai, M and Matsui, Y and Makabe, A and Minegishi, H and Tsuda, M and Juliarni,  and Rastelli, E and Danovaro, R and Corinaldesi, C and Kitahashi, T and Tasumi, E and Nishizawa, M and Takai, K and Nomaki, H and Nunoura, T}, title = {Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0564-z}, pmid = {31827245}, issn = {1751-7370}, support = {JP18H06080//Japan Society for the Promotion of Science London (JSPS London)/ ; }, abstract = {Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.}, }
@article {pmid31826981, year = {2019}, author = {Klufa, J and Bauer, T and Hanson, B and Herbold, C and Starkl, P and Lichtenberger, B and Srutkova, D and Schulz, D and Vujic, I and Mohr, T and Rappersberger, K and Bodenmiller, B and Kozakova, H and Knapp, S and Loy, A and Sibilia, M}, title = {Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy.}, journal = {Science translational medicine}, volume = {11}, number = {522}, pages = {}, doi = {10.1126/scitranslmed.aax2693}, pmid = {31826981}, issn = {1946-6242}, support = {P 27129/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Epidermal growth factor receptor (EGFR)-targeted anticancer therapy induces stigmatizing skin toxicities affecting patients' quality of life and therapy adherence. The lack of mechanistic details underlying these adverse events hampers their management. We found that EGFR/ERK signaling is required in LRIG1-positive stem cells during de novo hair eruption to secure barrier integrity and prevent the invasion of commensal microbiota and inflammatory skin disease. EGFR-deficient epidermis is permissive for microbiota outgrowth and displays an atopic-like TH2-dominated signature. The opening of the follicular ostia during hair eruption allows invasion of commensal microbiota into the hair follicle, initiating an additional TH1 and TH17 response culminating in chronic folliculitis. Restoration of epidermal ERK signaling via prophylactic FGF7 treatment or transgenic SOS expression rescues the barrier defect in the absence of EGFR, highlighting a therapeutic anchor point. These data reveal that commensal skin microbiota provoke atopic-like inflammatory skin diseases by invading into the follicular opening of erupting hair.}, }
@article {pmid31824766, year = {2019}, author = {Carruthers, LV and Moses, A and Adriko, M and Faust, CL and Tukahebwa, EM and Hall, LJ and Ranford-Cartwright, LC and Lamberton, PHL}, title = {The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e8133}, pmid = {31824766}, issn = {2167-8359}, abstract = {Background: Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions.<br><br>Methods: Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0-32 h. Metataxonomic profiling was used to profile samples, targeting the V1-V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software.<br><br>Results: Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0-32 h) used. Stool heterogeneity yielded no apparent microbiome differences.<br><br>Conclusions: Stool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout.}, }
@article {pmid31824462, year = {2019}, author = {Liu, D and Zhang, P and Chen, D and Howell, K}, title = {From the Vineyard to the Winery: How Microbial Ecology Drives Regional Distinctiveness of Wine.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2679}, pmid = {31824462}, issn = {1664-302X}, abstract = {Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.}, }
@article {pmid31823065, year = {2019}, author = {Schultz, J and Rosado, AS}, title = {Extreme environments: a source of biosurfactants for biotechnological applications.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-019-01151-2}, pmid = {31823065}, issn = {1433-4909}, abstract = {The surfactant industry moves billions of dollars a year and consists of chemically synthesized molecules usually derived from petroleum. Surfactant is a versatile molecule that is widely used in different industrial areas, with an emphasis on the petroleum, biomedical and detergent industries. Recently, interest in environmentally friendly surfactants that are resistant to extreme conditions has increased because of consumers' appeal for sustainable products and industrial processes that often require these characteristics. With this context, the need arises to search for surfactants produced by microorganisms coming from extreme environments and to mine their unique biotechnological potential. The production of biosurfactants is still incipient and presents challenges regarding economic viability due to the high costs of cultivation, production, recovery and purification. Advances can be made by exploring the extreme biosphere and bioinformatics tools. This review focuses on biosurfactants produced by microorganisms from different extreme environments, presenting a complete overview of what information is available in the literature, including the advances, challenges and future perspectives, as well as showing the possible applications of extreme biosurfactants.}, }
@article {pmid31822601, year = {2019}, author = {Sogin, EM and Puskás, E and Dubilier, N and Liebeke, M}, title = {Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography-Mass Spectrometry.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31822601}, issn = {2379-5077}, abstract = {Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats limits the nontargeted analyses of the ocean exometabolome using mass spectrometry (MS). Current methods require salt removal prior to sample measurements, which can alter the molecular composition of the metabolome and limit the types of compounds detected by MS. To overcome these limitations, we developed a gas chromatography MS (GC-MS) method that avoids sample altering during salt removal and that detects metabolites down to nanomolar concentrations from less than 1 ml of seawater. We applied our method (SeaMet) to explore marine metabolomes in vitro and in vivo First, we measured the production and consumption of metabolites during the culture of a heterotrophic bacterium, Marinobacter adhaerens Our approach revealed successional uptake of amino acids, while sugars were not consumed. These results show that exocellular metabolomics provides insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered high concentrations of sugars and fatty acids, compounds predicted to play a key role for the abundant and diverse microbial communities in coral reef and mangrove sediments. Our data demonstrate that SeaMet advances marine metabolomics by enabling a nontargeted and quantitative analysis of marine metabolites, thus providing new insights into nutrient cycles in the oceans.IMPORTANCE Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other &quot;omics&quot; (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats.}, }
@article {pmid31821931, year = {2020}, author = {Sun, H and Mei, R and Zhang, XX and Ren, H and Liu, WT and Ye, L}, title = {Bacterial enrichment in highly-selective acetate-fed bioreactors and its application in rapid biofilm formation.}, journal = {Water research}, volume = {170}, number = {}, pages = {115359}, doi = {10.1016/j.watres.2019.115359}, pmid = {31821931}, issn = {1879-2448}, mesh = {Acetates ; Bacteria ; Biofilms ; *Bioreactors ; RNA, Ribosomal, 16S ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {In this study, we systematically investigated the bacterial community dynamics in highly-selective (strong hydraulic selection pressure and high organic loading rate) bioreactors with acetate as the sole carbon source. 16S rRNA gene high-throughput sequencing and metagenomic sequencing results showed that phenolics-degrading bacteria (PDB), which were mainly Acinetobacter species, in the newly-formed aerobic granules could account for >70% of the total bacteria. Near full-length 16S rRNA gene sequences obtained by cloning suggest that the PDB are potentially novel species because they are distantly related to known Acinetobacter species. However, these PDB only temporarily appeared in the early stage of the granule formation and their abundance quickly decreased along the reactor operation. To retain these PDB, we demonstrated that the newly-formed aerobic granules could accelerate biofilm formation in moving bed biofilm reactors (MBBRs), and the biofilm carriers showed gradually-increased phenol degradation performance in the MBBRs. While, the bacterial community in biofilm significantly changed during the operation process of the MBBRs and the community structure became more complicated than that in the aerobic granules. Collectively, this study provides new insights into the microbial ecology of sludge granulation and biofilm formation process in the wastewater treatment systems for remediating phenolic matters.}, }
@article {pmid31820074, year = {2019}, author = {Tong, Q and Hu, ZF and Du, XP and Bie, J and Wang, HB}, title = {Effects of Seasonal Hibernation on the Similarities Between the Skin Microbiota and Gut Microbiota of an Amphibian (Rana dybowskii).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01466-9}, pmid = {31820074}, issn = {1432-184X}, abstract = {Both the gut and skin microbiotas have important functions for amphibians. The gut microbiota plays an important role in both the health and evolution of the host species, whereas the role of skin microbiota in disease resistance is particularly important for amphibians. Many studies have examined the effects of environmental factors on the skin and gut microbiotas, but no study has yet explored the similarities between the skin and gut microbiotas. In this study, the gut and skin microbiotas of Rana dybowskii in summer and winter were investigated via high-throughput Illumina sequencing. The results showed that the alpha diversity of gut and skin microbiotas decreased significantly from summer to winter. In both seasons, the microbial composition and structure differed significantly between the gut and skin, and the similarities between these microbiotas differed between seasons. The pairwise distances between the gut and skin microbiotas were greater in winter than in summer. The ratio of core OTUs and shared OTUs to the sum of the OTUs in the gut and skin microbiotas in summer was significantly higher than that in winter. The similarities between the gut and skin microbiotas are important for understanding amphibian ecology and life history.}, }
@article {pmid31820073, year = {2019}, author = {Arai, H and Lin, SR and Nakai, M and Kunimi, Y and Inoue, MN}, title = {Closely Related Male-Killing and Nonmale-Killing Wolbachia Strains in the Oriental Tea Tortrix Homona magnanima.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01469-6}, pmid = {31820073}, issn = {1432-184X}, abstract = {Wolbachia are inherited intracellular bacteria that cause male-specific death in some arthropods, called male-killing. To date, three Wolbachia strains have been identified in the oriental tea tortrix Homona magnanima (Tortricidae, Lepidoptera); however, none of these caused male-killing in the Japanese population. Here, we describe a male-killing Wolbachia strain in Taiwanese H. magnanima. From field-collected H. magnanima, two female-biased host lines were established, and antibiotic treatments revealed Wolbachia (wHm-t) as the causative agent of male-killing. The wsp and MLST genes in wHm-t are identical to corresponding genes in the nonmale-killing strain wHm-c from the Japanese population, implying a close relationship of the two strains. Crossing the Japanese and Taiwanese H. magnanima revealed that Wolbachia genotype rather than the host genetic background was responsible for the presence of the male-killing phenotype. Quantitative PCR analyses revealed that the density of wHm-t was higher than that of other Wolbachia strains in H. magnanima, including wHm-c. The densities of wHm-t were also heterogeneous between host lines. Notably, wHm-t in the low-density and high-density lines carried identical wsp and MLST genes but had distinct lethal patterns. Furthermore, over 90% of field-collected lines of H. magnanima in Taiwan were infected with wHm-t, although not all host lines harboring wHm-t showed male-killing. The host lines that showed male-killing harbored a high density of Wolbachia compared to the host lines that did not show male-killing. Thus, the differences in the phenotypes appear to be dependent on biological and genetic characteristics of closely related Wolbachia strains.}, }
@article {pmid31820072, year = {2019}, author = {Basili, D and Lutfi, E and Falcinelli, S and Balbuena-Pecino, S and Navarro, I and Bertolucci, C and Capilla, E and Carnevali, O}, title = {Photoperiod Manipulation Affects Transcriptional Profile of Genes Related to Lipid Metabolism and Apoptosis in Zebrafish (Danio rerio) Larvae: Potential Roles of Gut Microbiota.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01468-7}, pmid = {31820072}, issn = {1432-184X}, support = {AGL2014-57974-R//Ministerio de Economía y Competitividad/ ; AGL2014-57974-R//Ministerio de Economía y Competitividad/ ; AGL2017-89436-R//Ministerio de Economía y Competitividad/ ; AGL2017-89436-R//Ministerio de Economía y Competitividad/ ; FA2015//Università Politecnica delle Marche/ ; FAR2018//Università degli Studi di Ferrara/ ; FIR2018//Università degli Studi di Ferrara/ ; }, abstract = {Gut microbiota plays a fundamental role in maintaining host's health by controlling a wide range of physiological processes. Administration of probiotics and manipulation of photoperiod have been suggested as modulators of microbial composition and are currently undergoing an extensive research in aquaculture as a way to improve health and quality of harvested fish. However, our understanding regarding their effects on physiological processes is still limited. In the present study we investigated whether manipulation of photoperiod and/or probiotic administration was able to alter microbial composition in zebrafish larvae at hatching stage. Our findings show that probiotic does not elicit effects while photoperiod manipulation has a significant impact on microbiota composition. Moreover, we successfully predicted lipid biosynthesis and apoptosis to be modulated by microbial communities undergoing continuous darkness. Interestingly, expression levels of caspase 3 gene (casp3) and lipid-related genes (hnf4a, npc1l1, pparγ, srebf1, agpat4 and fitm2) were found to be significantly overexpressed in dark-exposed larvae, suggesting an increase in the occurrence of apoptotic processes and a lipid metabolism impairment, respectively (p < 0.05). Our results provide the evidence that microbial communities in zebrafish at early life stages are not modulated by a short administration of probiotics and highlight the significant effect that dark photoperiod elicits on zebrafish microbiota and potentially on health.}, }
@article {pmid31819142, year = {2019}, author = {Costa, JH and Wassano, CI and Angolini, CFF and Scherlach, K and Hertweck, C and Pacheco Fill, T}, title = {Antifungal potential of secondary metabolites involved in the interaction between citrus pathogens.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18647}, pmid = {31819142}, issn = {2045-2322}, support = {SFB 1127 ChemBioSys//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Numerous postharvest diseases have been reported that cause substantial losses of citrus fruits worldwide. Penicillium digitatum is responsible for up to 90% of production losses, and represent a problem for worldwide economy. In order to control phytopathogens, chemical fungicides have been extensively used. Yet, the use of some artificial fungicides cause concerns about environmental risks and fungal resistance. Therefore, studies focusing on new approaches, such as the use of natural products, are getting attention. Co-culture strategy can be applied to discover new bioactive compounds and to understand microbial ecology. Mass Spectrometry Imaging (MSI) was used to screen for potential antifungal metabolites involved in the interaction between Penicillium digitatum and Penicillium citrinum. MSI revealed a chemical warfare between the fungi: two tetrapeptides, deoxycitrinadin A, citrinadin A, chrysogenamide A and tryptoquialanines are produced in the fungi confrontation zone. Antimicrobial assays confirmed the antifungal activity of the investigated metabolites. Also, tryptoquialanines inhibited sporulation of P. citrinum. The fungal metabolites reported here were never described as antimicrobials until this date, demonstrating that co-cultures involving phytopathogens that compete for the same host is a positive strategy to discover new antifungal agents. However, the use of these natural products on the environment, as a safer strategy, needs further investigation. This paper aimed to contribute to the protection of agriculture, considering health and ecological risks.}, }
@article {pmid31817158, year = {2019}, author = {D'Amico, F and Biagi, E and Rampelli, S and Fiori, J and Zama, D and Soverini, M and Barone, M and Leardini, D and Muratore, E and Prete, A and Gotti, R and Pession, A and Masetti, R and Brigidi, P and Turroni, S and Candela, M}, title = {Enteral Nutrition in Pediatric Patients Undergoing Hematopoietic SCT Promotes the Recovery of Gut Microbiome Homeostasis.}, journal = {Nutrients}, volume = {11}, number = {12}, pages = {}, pmid = {31817158}, issn = {2072-6643}, support = {GR-2013-02357136//Ministero della Salute/ ; }, abstract = {Hematopoietic stem cell transplantation (HSCT) is the first-line immunotherapy to treat several hematologic disorders, although it can be associated with many complications reducing the survival rate, such as acute graft-versus-host disease (aGvHD) and infections. Given the fundamental role of the gut microbiome (GM) for host health, it is not surprising that a suboptimal path of GM recovery following HSCT may compromise immune homeostasis and/or increase the risk of opportunistic infections, with an ultimate impact in terms of aGvHD onset. Traditionally, the first nutritional approach in post-HSCT patients is parenteral nutrition (PN), which is associated with several clinical adverse effects, supporting enteral nutrition (EN) as a preferential alternative. The aim of the study was to evaluate the impact of EN vs. PN on the trajectory of compositional and functional GM recovery in pediatric patients undergoing HSCT. The GM structure and short-chain fatty acid (SCFA) production profiles were analyzed longitudinally in twenty pediatric patients receiving HSCT-of which, ten were fed post-transplant with EN and ten with total PN. According to our findings, we observed the prompt recovery of a structural and functional eubiotic GM layout post-HSCT only in EN subjects, thus possibly reducing the risk of systemic infections and GvHD onset.}, }
@article {pmid31816089, year = {2019}, author = {Linsmith, G and Rombauts, S and Montanari, S and Deng, CH and Celton, JM and Guérif, P and Liu, C and Lohaus, R and Zurn, JD and Cestaro, A and Bassil, NV and Bakker, LV and Schijlen, E and Gardiner, SE and Lespinasse, Y and Durel, CE and Velasco, R and Neale, DB and Chagné, D and Van de Peer, Y and Troggio, M and Bianco, L}, title = {Pseudo-chromosome-length genome assembly of a double haploid &quot;Bartlett&quot; pear (Pyrus communis L.).}, journal = {GigaScience}, volume = {8}, number = {12}, pages = {}, pmid = {31816089}, issn = {2047-217X}, abstract = {BACKGROUND: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same &quot;Bartlett&quot; reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis.<br><br>FINDINGS: A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.<br><br>CONCLUSIONS: We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.}, }
@article {pmid31813647, year = {2020}, author = {Sutherland, WJ and Dias, MP and Dicks, LV and Doran, H and Entwistle, AC and Fleishman, E and Gibbons, DW and Hails, R and Hughes, AC and Hughes, J and Kelman, R and Le Roux, X and LeAnstey, B and Lickorish, FA and Maggs, L and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Spalding, MD and Tonneijck, FH and Wentworth, J and Thornton, A}, title = {A Horizon Scan of Emerging Global Biological Conservation Issues for 2020.}, journal = {Trends in ecology &amp; evolution}, volume = {35}, number = {1}, pages = {81-90}, doi = {10.1016/j.tree.2019.10.010}, pmid = {31813647}, issn = {1872-8383}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; Forecasting ; Forests ; }, abstract = {In this horizon scan, we highlight 15 emerging issues of potential relevance to global conservation in 2020. Seven relate to potentially extensive changes in vegetation or ecological systems. These changes are either relatively new, for example, conversion of kelp forests to simpler macroalgal systems, or may occur in the future, for example, as a result of the derivation of nanocelluose from wood or the rapid expansion of small hydropower schemes. Other topics highlight potential changes in national legislation that may have global effect on international agreements. Our panel of 23 scientists and practitioners selected these issues using a modified version of the Delphi technique from a long-list of 89 potential topics.}, }
@article {pmid31813285, year = {2019}, author = {Ritter, MR and Tempesta de, OM and Makimori, RY and Sereia, AL and Simionato, AS and Chierrito, D and Galdino, AF and Gonçalves de, OA and Brentan da, SD and Novello, CR and Cristina de, MD and Benedito Prado, DF and João Carlos Palazzo de, M}, title = {Dimeric glycosylated flavan-3-ol and antimicrobial in vitro evaluation of Trichilia catigua extracts.}, journal = {Natural product research}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/14786419.2019.1698569}, pmid = {31813285}, issn = {1478-6427}, abstract = {Trichilia catigua is a tree known as &quot;catuaba&quot;, widely distributed in Brazil. Studies carried out with T. catigua barks suggest that plant has antidepressant, antidiabetic, antimicrobial, antioxidant, antiviral, and preventive against brain damage. The aim of this work was to isolate and characterise compounds from the semipurified fraction of T. catigua barks, and to conduct microbiological screening against bacteria and fungi. The crude extract (CE) of &quot;catuaba&quot; was produced by turbo extraction with acetone-water, and later, partitioned to yield ethyl-acetate (EAF) and aqueous (AqF) fractions. From AqF the new catechin-3-O-α-L-rhamnoside-(4α→8)-epicatechin was isolated, identified, and described here for the first time. Regarding antimicrobial activity, the extracts presented impressive results, mainly for Vancomycin Resistant Enterococcus faecium (VREfm) with MIC of 156.5 μg/mL. The results suggest that extract of T. catigua could potentially be used as an adjuvant to treatment and is a promising candidate for the development of new antimicrobial drugs.}, }
@article {pmid31812391, year = {2020}, author = {Rowles, LS and Hossain, AI and Aggarwal, S and Kirisits, MJ and Saleh, NB}, title = {Water quality and associated microbial ecology in selected Alaska Native communities: Challenges in off-the-grid water supplies.}, journal = {The Science of the total environment}, volume = {711}, number = {}, pages = {134450}, doi = {10.1016/j.scitotenv.2019.134450}, pmid = {31812391}, issn = {1879-1026}, abstract = {The availability of safe water for potable purposes in Alaska Native communities is limited due to naturally occurring metals and contaminants released from anthropogenic activities, such as drilling and mining. The impacts of climate change are magnified in the arctic and sub-arctic regions and thus have the potential to mobilize contaminants and exacerbate the water contamination problem. Alaska Native communities are vulnerable to such changes in their water quality because of their remote location and limited access to resources. This study initiates an assessment of water quality, including its microbial ecology, in off-the-grid Alaskan water supplies (i.e., primarily groundwater wells). In particular, water quality data were collected from nine communities (22 ground water wells). Water quality analyses included basic water quality parameters, a suite of metals relevant to human health, and microbial community composition. Results revealed location-specific elevated arsenic concentrations based on the underlying geological formation, particularly in the areas located in the geological formation of the McHugh Complex. Diverse microbial communities were observed, and the grouping appeared to be based on elevation. These findings present evidence of compromised water quality in an understudied area in the United States. The results from this study should be considered as a snapshot in time, which highlight the importance for further systematic studies in similar off-the-grid communities.}, }
@article {pmid31812098, year = {2020}, author = {Neckovic, A and van Oorschot, RAH and Szkuta, B and Durdle, A}, title = {Investigation of direct and indirect transfer of microbiomes between individuals.}, journal = {Forensic science international. Genetics}, volume = {45}, number = {}, pages = {102212}, doi = {10.1016/j.fsigen.2019.102212}, pmid = {31812098}, issn = {1878-0326}, abstract = {The human microbiome encompasses the fungi, bacteria and viruses that live on, within, and immediately surrounding the body. Microbiomes have potential utility in forensic science as an evidentiary tool to link or exclude persons of interest associated with criminal activities. Research has shown the microbiome is individualised, and that personal microbial signatures can be recovered from surfaces such as phones, shoes and fabrics. Before the human microbiome may be used as an investigative tool, further research is required to investigate the utility and potential limitations surrounding microbial profiling. This includes the detectability of microbial transfer between individuals or items, the associated risks (such as contamination events) and the applicability of microbial profiling for forensic purposes. This research aimed to identify whether an individual's distinguishable microbiome could be transferred to another individual and onto substrates, and vice versa. Paper, cotton, and glass surfaces were chosen to represent a range of substrate matrices. The study involved six participants placed into three pairs; participants took part in two modes of transfer. Transfer Mode 1 involved the pair shaking hands, followed by rubbing a substrate in their right hand. Transfer Mode 2 involved individuals rubbing a substrate in their left hand, swapping substrates with their partner and then rubbing the swapped substrate in their left hand. 16S rRNA sequencing was performed on the extracted microbial DNA from participant and substrate samples. Quantitative Insights into Microbial Ecology 2 (QIIME 2) was used for sequence quality control and beta (between-sample) diversity analyses and taxonomic assignment. Principal Coordinate Analysis (PCoA) based on Jaccard distances was visualised through Emperor software to determine the phylogenetic similarity of bacterial communities between participants and among participant pairs. Statistical testing through PERMANOVA revealed significant differences in the Jaccard distances between each participant pair (P < 0.001), highlighting not only the potential distinguishability of skin microbiomes among individuals, but also the clustering effect observed between participant pairs due to the potential transfer of hand-associated microbiomes between individuals. The study demonstrated that transfer of the human skin microbiome had occurred between all participant pairs, regardless of substrate type or mode of transfer.}, }
@article {pmid31811330, year = {2019}, author = {Wang, L and Xing, P and Li, H and Zhou, L and Wu, QL}, title = {Distinct Intra-lake Heterogeneity of Diazotrophs in a Deep Oligotrophic Mountain Lake.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01461-0}, pmid = {31811330}, issn = {1432-184X}, support = {31730013//National Natural Science Foundation of China (CN)/ ; 41621002//National Natural Science Foundation of China (CN)/ ; QYZDJ-SSW-DQC030//the Key Research Program of Frontier Science, CAS/ ; }, abstract = {To date, little is known about the diazotrophs in freshwater ecosystems. In this study, we examined the diversity, abundance, and distribution of the diazotrophic community in the deep oligotrophic Lake Fuxian using high-throughput sequencing and quantitative polymerase chain reaction of nifH genes. Our results showed that the diazotrophs in Lake Fuxian were diverse and were distributed among Proteobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, and other unclassified environmental sequences. For the first time, it is found that Bacteroidetes and Planctomycetes harbor diazotrophs in freshwater ecosystems. The diazotrophic community compositions were significantly different between the littoral and pelagic zones in the surface layer, and they also changed dramatically along the vertical profile. High diazotrophic abundance and diversity were mostly observed in the surface littoral zone, and overall, a significant relationship between nifH gene richness and abundance was observed. The water turbidity, nitrite, and phosphorus were the most important factors explaining the spatial changes in diversity and abundances of this important functional group. The two most dominant operational taxonomic units belonging to Betaroproteobacteria and Planctomycetes demonstrated opposite distribution patterns in abundance that were driven by non-overlapping environmental factors. This study is by far the first to uncover the high diversity and intra-lake heterogeneity of diazotrophs in a freshwater lake and illuminate the controlling factors. It provides the probability of the co-occurrence of N2 fixation and N-loss in particles.}, }
@article {pmid31811036, year = {2019}, author = {Hinger, I and Ansorge, R and Mussmann, M and Romano, S}, title = {Phylogenomic analyses of the widespread marine heterotroph Pseudovibrio suggest distinct evolutionary trajectories and a novel genus Polycladidabacter gen. nov.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02395-19}, pmid = {31811036}, issn = {1098-5336}, abstract = {Bacteria belonging to the Pseudovibrio genus are widespread, metabolically versatile, and able to thrive as both free-living and host-associated organisms. Although more than 50 genomes are available, a comprehensive comparative genomics study to resolve taxonomic inconsistencies is currently missing. We analyzed all available genomes and used 552 core genes to perform a robust phylogenomic reconstruction. This in-depth analysis revealed the divergence of two monophyletic basal lineages of strains isolated from polyclad flatworm hosts, namely Pseudovibrio hongkongensis and Pseudovibrio stylochi. These strains have reduced genomes, lack sulfur-related metabolisms and major biosynthetic gene clusters, and their environmental distribution appears to be tightly associated with invertebrate hosts. We show experimentally that the divergent strains are unable to utilize various sulfur compounds that in contrast can be utilized by the type strain Pseudovibrio denitrificans. Our analyses suggest that the lineage leading to these two strains has been subject to relaxed purifying selection resulting in great gene loss. Overall genome relatedness indices (OGRI) indicate substantial differences between the divergent strains and the rest of the genus. While 16S rRNA gene analyses do not support the establishment of a different genus for the divergent strains, their substantial genomic, phylogenomic, and physiological differences strongly suggest a divergent evolutionary trajectory and the need for their reclassification. Therefore, we propose the novel genus, Polycladidabacter gen. nov.Importance The genus Pseudovibrio is commonly associated with marine invertebrates, which are essential for ocean health and marine nutrient cycling. Traditionally, the phylogeny of the genus has been based on 16S rRNA gene analysis. The use of the 16S rRNA gene or any other single marker gene for robust phylogenetic placement has recently been questioned. We used a large set of marker genes from all available Pseudovibrio genomes for in-depth phylogenomic analyses. We identified divergent monophyletic basal lineages within the Pseudovibrio genus, including two strains isolated from polyclad flatworms. These strains showed reduced sulfur metabolisms and biosynthetic capacities. The phylogenomic analyses revealed distinct evolutionary trajectories and ecological adaptations that differentiate the divergent strains from the other Pseudovibrio members and suggest that they fall into a novel genus. Our data show the importance of widening the use of phylogenomics for better understanding bacterial physiology, phylogeny and evolution.}, }
@article {pmid31811031, year = {2019}, author = {Song, Y and Jiang, CY and Liang, ZL and Wang, BJ and Jiang, Y and Yin, Y and Zhu, HZ and Qin, YL and Cheng, RX and Liu, ZP and Liu, Y and Jin, T and Corvini, PF and Rabaey, K and Wang, AJ and Liu, SJ}, title = {Casimicrobium huifangae gen. nov. sp. nov., a ubiquitous &quot;most-wanted&quot; core bacterial taxon from municipal wastewater treatment plants.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02209-19}, pmid = {31811031}, issn = {1098-5336}, abstract = {Microorganisms in wastewater treatment plants (WWTPs) play a key role in the removal of pollutants from municipal and industrial wastewaters. A recent study estimated that activated sludge from global municipal WWTPs harbors 1-2×109 microbial species, the majority of which have not yet been cultivated and twenty-eight core taxa were identified as &quot;most-wanted&quot; ones [Nat. Microbiol. 4 (7): 1183-1195, 2019]. Cultivation and characterization of the &quot;most-wanted&quot; core bacteria are critical to understand their genetic, physiological, phylogenetic and ecological traits, as well as to improve the performance of WWTPs. In this study, we isolated a bacterial strain, designated SJ-1, who represents a novel cluster within β-Proteobacteria and corresponds to OTU_16 within the 28 core taxa in the &quot;most-wanted&quot; list. Strain SJ-1 was identified and nominated as Casimicrobium huifangae gen. nov. sp. nov. of a novel family CasimicrobiaceaeC. huifangae is ubiquitously distributed and is metabolically versatile. In addition to mineralizing various carbon sources (including carbohydrates, aromatic compounds and short chain fatty acids), C. huifangae is capable of nitrate reduction and phosphorus accumulation. The population of C. huifangae accounted for more than 1% in that of the activated sludge microbiome from Qinghe WWTP, which showed seasonal dynamic changes. Co-occurrence analysis suggested that C. huifangae was an important module hub in the bacterial network of Qinghe WWTP.Importance Activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and exploring their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome and it potentially plays an important role in municipal wastewater treatment plants.}, }
@article {pmid31810817, year = {2019}, author = {Estrella, MJ and Fontana, MF and Cumpa Velásquez, LM and Torres Tejerizo, GA and Diambra, L and Hansen, LH and Pistorio, M and Sannazzaro, AI}, title = {Mesorhizobium intechi sp. nov. isolated from nodules of Lotus tenuis in soils of the Flooding Pampa, Argentina.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {126044}, doi = {10.1016/j.syapm.2019.126044}, pmid = {31810817}, issn = {1618-0984}, abstract = {Three symbiotic nitrogen-fixing bacteria (BD68T, BD66 and BD73) isolated from root nodules of Lotus tenuis in lowland soils of the Flooding Pampa (Argentina), previously classified as members of the Mesorhizobium genus, were characterized in this study. Phylogenetic analysis of their 16S rRNA gene sequences showed a close relationship to M. japonicum MAFF 303099T, M. erdmanii USDA 3471T, M. carmichaelinearum ICMP 18942T, M. opportunistum WSM 2975T and M. jarvisii ATCC 33699T, with sequence identities of 99.72%-100%. Multilocus sequence analysis of other housekeeping genes revealed that the three isolates belonged to a phylogenetically distinct clade within the genus Mesorhizobium. Strain BD68T was designated as the group representative and its genome was fully sequenced. The average nucleotide identity and in silico DNA-DNA hybridization comparisons between BD68T and the most related type strains showed values below the accepted threshold for species discrimination. Phenotypic and chemotaxonomic features were also studied. Based on these results, BD68T, BD66 and BD73 could be considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium intechi sp. nov. is hereby proposed. The type strain of this species is BD68T (=CECT 9304T=LMG 30179T).}, }
@article {pmid31807860, year = {2019}, author = {Zhao, J and Li, G and Lu, W and Huang, S and Zhang, Z}, title = {Dominant and Subordinate Relationship Formed by Repeated Social Encounters Alters Gut Microbiota in Greater Long-Tailed Hamsters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01462-z}, pmid = {31807860}, issn = {1432-184X}, support = {No. XDB11050300//&quot;Strategic Priority Research Program&quot; of the Chinese Academy of Sciences/ ; No. 152111KYSB20160089//International Partnership Program of Chinese Academy of Sciences/ ; No.152111KYSB20150023//External Cooperation Program of BIC, Chinese Academy of Sciences/ ; }, abstract = {Social stress can dramatically influence the health of animals via communication between gut microbiota and the HPA system. However, this effect has been rarely investigated among different social ranked animals after chronic repeated social encounters. In this study, we evaluated changes and differences in microbiota among control, dominant, and subordinate male greater long-tailed hamsters (Tscherskia triton) over 28 successive days of repeated social encounter. Our results indicated that as compared with the control group, short-term repeated social encounters significantly altered fecal microbiota of subordinate hamsters, while chronic repeated social encounters altered colonic mucosa-associated microbiota of both dominant and subordinate hamsters. Fecal microbiota showed a transition in composition and diversity on day 2 for the subordinate group but on day 4 for the control and dominant groups under repeated encounters. Compared with their baseline, genus Lactobacillus increased in both dominant and subordinate groups, while genus Bifidobacterium increased in the subordinate group and genus Adlercreutzia increased in the dominant group. Our results suggest that chronic repeated social encounter can alter diversity and composition of gut microbiota of hamsters in both feces and colonic mucosa, but the latter performed better in reflecting the effects of chronic stress on microbiota in this species. Future studies should focus on elucidating how these microbiota alterations may affect animal behavior and fitness.}, }
@article {pmid31806445, year = {2019}, author = {Qi, Y and Ossowicki, A and Yang, X and Huerta Lwanga, E and Dini-Andreote, F and Geissen, V and Garbeva, P}, title = {Effects of plastic mulch film residues on wheat rhizosphere and soil properties.}, journal = {Journal of hazardous materials}, volume = {}, number = {}, pages = {121711}, doi = {10.1016/j.jhazmat.2019.121711}, pmid = {31806445}, issn = {1873-3336}, abstract = {Plastic residues could accumulate in soils as a consequence of using plastic mulching, which results in a serious environmental concern for agroecosystems. As an alternative, biodegradable plastic films stand as promising products to minimize plastic debris accumulation and reduce soil pollution. However, the effects of residues from traditional and biodegradable plastic films on the soil-plant system are not well studied. In this study, we used a controlled pot experiment to investigate the effects of macro- and micro- sized residues of low-density polyethylene and biodegradable plastic mulch films on the rhizosphere bacterial communities, rhizosphere volatile profiles and soil chemical properties. Interestingly, we identified significant effects of biodegradable plastic residues on the rhizosphere bacterial communities and on the blend of volatiles emitted in the rhizosphere. For example, in treatments with biodegradable plastics, bacteria genera like Bacillus and Variovorax were present in higher relative abundances and volatile compounds like dodecanal were exclusively produced in treatment with biodegradable microplastics. Furthermore, significant differences in soil pH, electrical conductivity and C:N ratio were observed across treatments. Our study provides evidence for both biotic and abiotic impacts of plastic residues on the soil-plant system, suggesting the urgent need for more research examining their environmental impacts on agroecosystems.}, }
@article {pmid31803164, year = {2019}, author = {Yang, Y and Ashworth, AJ and Willett, C and Cook, K and Upadhyay, A and Owens, PR and Ricke, SC and DeBruyn, JM and Moore, PA}, title = {Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2639}, doi = {10.3389/fmicb.2019.02639}, pmid = {31803164}, issn = {1664-302X}, abstract = {Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.}, }
@article {pmid31803161, year = {2019}, author = {Banerji, A and Jahne, M and Herrmann, M and Brinkman, N and Keely, S}, title = {Bringing Community Ecology to Bear on the Issue of Antimicrobial Resistance.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2626}, pmid = {31803161}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a global concern, pertaining not only to human health but also to the health of industry and the environment. AMR research has traditionally focused on genetic exchange mechanisms and abiotic environmental constraints, leaving important aspects of microbial ecology unresolved. The genetic and ecological aspects of AMR, however, not only contribute separately to the problem but also are interrelated. For example, mutualistic associations among microbes such as biofilms can both serve as a barrier to antibiotic penetration and a breeding ground for horizontal exchange of antimicrobial resistance genes (ARGs). In this review, we elucidate how species interactions promote and impede the establishment, maintenance, and spread of ARGs and indicate how management initiatives might benefit from leveraging the principles and tools of community ecology to better understand and manipulate the processes underlying AMR.}, }
@article {pmid31802728, year = {2020}, author = {Fix, J and Chandrashekhar, K and Perez, J and Bucardo, F and Hudgens, MG and Yuan, L and Twitchell, E and Azcarate-Peril, MA and Vilchez, S and Becker-Dreps, S}, title = {Association between Gut Microbiome Composition and Rotavirus Vaccine Response among Nicaraguan Infants.}, journal = {The American journal of tropical medicine and hygiene}, volume = {102}, number = {1}, pages = {213-219}, pmid = {31802728}, issn = {1476-1645}, abstract = {Rotavirus is the leading cause of childhood deaths due to diarrhea. Although existing oral rotavirus vaccines are highly efficacious in high-income countries, these vaccines have been demonstrated to have decreased efficacy in low- and middle-income countries. A possible explanation for decreased efficacy is the impact of gut microbiota on the enteric immune system's response to vaccination. We analyzed the gut microbiome of 50 children enrolled in a prospective study evaluating response to oral pentavalent rotavirus vaccination (RV5) to assess associations between relative abundance of bacterial taxa and seroconversion following vaccination. Stool samples were taken before the first RV5 dose, and microbiome composition characterized using 16S rRNA amplicon sequencing and Quantitative Insights Into Microbial Ecology software. Relative abundance of bacterial taxa between seroconverters following the first RV5 dose, those with ≥ 4-fold increase in rotavirus-specific IgA titers, and nonseroconverters were compared using the Wilcoxon-Mann-Whitney test. We identified no significant differences in microbiome composition between infants who did and did not respond to vaccination. Infants who responded to vaccination tended to have higher abundance of Proteobacteria and Eggerthella, whereas those who did not respond had higher abundance of Fusobacteria and Enterobacteriaceae; however, these differences were not statistically significant following a multiple comparison correction. This study suggests a limited impact of gut microbial taxa on response to oral rotavirus vaccination among infants; however, additional research is needed to improve our understanding of the impact of gut microbiome on vaccine response, toward a goal of improving vaccine efficacy and rotavirus prevention.}, }
@article {pmid31802185, year = {2019}, author = {Walker, DM and Hill, AJ and Albecker, MA and McCoy, MW and Grisnik, M and Romer, A and Grajal-Puche, A and Camp, C and Kelehear, C and Wooten, J and Rheubert, J and Graham, SP}, title = {Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01456-x}, pmid = {31802185}, issn = {1432-184X}, abstract = {A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.}, }
@article {pmid31802184, year = {2019}, author = {Xu, S and Jiang, L and Qiao, G and Chen, J}, title = {The Bacterial Flora Associated with the Polyphagous Aphid Aphis gossypii Glover (Hemiptera: Aphididae) Is Strongly Affected by Host Plants.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01435-2}, pmid = {31802184}, issn = {1432-184X}, support = {2016YFE0203100//National Key R &amp; D Program of China/ ; XDA19050303//Strategic Priority Research Program A of the Chinese Academy of Sciences/ ; 31620103916//National Natural Science Foundation of China/ ; 31430078//National Natural Science Foundation of China/ ; }, abstract = {Aphids live in symbiosis with a variety of bacteria, including the obligate symbiont Buchnera aphidicola and diverse facultative symbionts. The symbiotic associations for one aphid species, especially for polyphagous species, often differ across populations. In the present study, by using high-throughput 16S rRNA sequencing, we surveyed in detail the microbiota in natural populations of the cotton aphid Aphis gossypii in China and assessed differences in bacterial diversity with respect to host plant and geography. The microbial community of A. gossypii was dominated by a few heritable symbionts. Arsenophonus was the most dominant secondary symbiont, and Spiroplasma was detected for the first time. Statistical tests and ordination analyses showed that host plants rather than geography seemed to have shaped the associated symbiont composition. Special symbiont communities inhabited the Cucurbitaceae-feeding populations, which supported the ecological specialization of A. gossypii on cucurbits from the viewpoint of symbiotic bacteria. Correlation analysis suggested antagonistic interactions between Buchnera and coexisting secondary symbionts and more complicated interactions between different secondary symbionts. Our findings lend further support to an important role of the host plant in structuring symbiont communities of polyphagous aphids and will improve our understanding of the interactions among phytophagous insects, symbionts, and environments.}, }
@article {pmid31798545, year = {2019}, author = {Harth-Chu, EN and Alves, LA and Theobaldo, JD and Salomão, MF and Höfling, JF and King, WF and Smith, DJ and Mattos-Graner, RO}, title = {PcsB Expression Diversity Influences on Streptococcus mitis Phenotypes Associated With Host Persistence and Virulence.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2567}, doi = {10.3389/fmicb.2019.02567}, pmid = {31798545}, issn = {1664-302X}, abstract = {S. mitis is an abundant member of the commensal microbiota of the oral cavity and pharynx, which has the potential to promote systemic infections. By analyzing a collection of S. mitis strains isolated from the oral cavity at commensal states or from systemic infections (blood strains), we established that S. mitis ubiquitously express the surface immunodominant protein, PcsB (also called GbpB), required for binding to sucrose-derived exopolysaccharides (EPS). Immuno dot blot assays with anti-PcsB antibodies and RT-qPCR transcription analyses revealed strain-specific profiles of PcsB production associated with diversity in pcsB transcriptional activities. Additionally, blood strains showed significantly higher levels of PcsB expression compared to commensal isolates. Because Streptococcus mutans co-colonizes S. mitis dental biofilms, and secretes glucosyltransferases (GtfB/C/D) for the synthesis of highly insoluble EPS from sucrose, profiles of S. mitis binding to EPS, biofilm formation and evasion of the complement system were assessed in sucrose-containing BHI medium supplemented or not with filter-sterilized S. mutans culture supernatants. These analyses showed significant S. mitis binding to EPS and biofilm formation in the presence of S. mutans supernatants supplemented with sucrose, compared to BHI or BHI-sucrose medium. In addition, these phenotypes were abolished if strains were grown in culture supernatants of a gtfBCD-defective S. mutans mutant. Importantly, GtfB/C/D-associated phenotypes were enhanced in high PcsB-expressing strains, compared to low PcsB producers. Increased PcsB expression was further correlated with increased resistance to deposition of C3b/iC3b of the complement system after exposure to human serum, when strains were previously grown in the presence of S. mutans supernatants. Finally, analyses of PcsB polymorphisms and bioinformatic prediction of epitopes with significant binding to MHC class II alleles revealed that blood isolates harbor PcsB polymorphisms in its functionally conserved CHAP-domain, suggesting antigenic variation. These findings reveal important roles of PcsB in S. mitis-host interactions under commensal and pathogenic states, highlighting the need for studies to elucidate mechanisms regulating PcsB expression in this species.}, }
@article {pmid31798544, year = {2019}, author = {Gallardo-Navarro, ÓA and Santillán, M}, title = {Three-Way Interactions in an Artificial Community of Bacterial Strains Directly Isolated From the Environment and Their Effect on the System Population Dynamics.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2555}, doi = {10.3389/fmicb.2019.02555}, pmid = {31798544}, issn = {1664-302X}, abstract = {This work is motivated by previous studies that have analyzed the population ecology of a collection of culturable thermoresistant bacteria, isolated from the Churince lagoon in Cuatro Cienegas, Mexico. In particular, it is aimed at testing a hypothesis from a modeling study, which states that antagonistic and sensitive bacteria co-exist thanks to resistant bacteria that protect sensitive ones by forming physical barriers. We selected three different bacterial strains from the referred collection: one antagonistic, one sensitive, and one resistant, and studied the population dynamics of mixed colonies. Our results show that, although the proposed protective mechanism does not work in this case, the resistant strain confers some kind of protection to sensitive bacteria. Further modeling and experimental results suggest that the presence of resistant bacteria indirectly improves the probability that patches of sensitive bacteria grow in a mixed colony. More precisely, our results suggest that by making antagonistic bacteria produce and secrete an antagonistic substance (with the concomitant metabolic cost and growth rate reduction), resistant bacteria increase the likelihood that sensitive bacteria locally outcompete antagonistic ones.}, }
@article {pmid31796996, year = {2019}, author = {Velasco-González, I and Sanchez-Jimenez, A and Singer, D and Murciano, A and Díez-Hermano, S and Lara, E and Martín-Cereceda, M}, title = {Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01463-y}, pmid = {31796996}, issn = {1432-184X}, support = {CGL2013-40851-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; SNF 31003A_143960//Swiss Re Foundation/ ; }, abstract = {Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.}, }
@article {pmid31796995, year = {2019}, author = {González-Serrano, F and Pérez-Cobas, AE and Rosas, T and Baixeras, J and Latorre, A and Moya, A}, title = {The Gut Microbiota Composition of the Moth Brithys crini Reflects Insect Metamorphosis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01460-1}, pmid = {31796995}, issn = {1432-184X}, support = {SAF2015-65878-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; BFU2015-64322-C2-1-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; Prometeo/2018/A/133//Conselleria d'Educació, Investigació, Cultura i Esport/ ; Co-finance//Interreg/ ; PGC2018-099344-B-100//Agencia Estatal de Investigación/ ; }, abstract = {Lepidoptera is a highly diverse insect order with major importance in agriculture as many species are considered pests. The role of the gut microbiota in insect physiology is still poorly understood, despite the research undertaken in recent years. Furthermore, Lepidoptera are holometabolous insects and few studies have addressed the influence of the changes taking place on the gut microbiome composition and diversity during metamorphosis, especially in monophagous species. The V3-V4 region of the 16S rRNA gene was sequenced to investigate the microbiota composition and diversity of the monophagous moth Brithys crini during three different life stages: egg, larvae (midgut and hindgut), and adult (gut). Our results showed that the microbiota composition of B. crini was stage specific, indicating that the developmental stage is a main factor affecting the gut microbiome in composition and potential functions. Moreover, the diversity of the gut microbiome reflected the developmental process, since a drop in diversity occurred between the larval and the adult phase, when the intestine is completely renewed. In spite of the changes in the gut microbiota during metamorphosis, 29 genera were conserved throughout the three developmental stages, mainly belonging to the Proteobacteria phylum, which define the core microbiome of B. crini. These genera seem to contribute to host physiology by participating in food digestion, nutrition, and detoxification mechanisms.}, }
@article {pmid31791792, year = {2020}, author = {Nguyen, LN and Commault, AS and Kahlke, T and Ralph, PJ and Semblante, GU and Johir, MAH and Nghiem, LD}, title = {Genome sequencing as a new window into the microbial community of membrane bioreactors - A critical review.}, journal = {The Science of the total environment}, volume = {704}, number = {}, pages = {135279}, doi = {10.1016/j.scitotenv.2019.135279}, pmid = {31791792}, issn = {1879-1026}, abstract = {Recent developed sequencing techniques have resulted in a new and unprecedented way to study biological wastewater treatment, in which most organisms are uncultivable. This review provides (i) an insight on state-of-the-art sequencing techniques and their limitations; (ii) a critical assessment of the microbial community in biological reactor and biofouling layer in a membrane bioreactor (MBR). The data from high-throughput sequencing has been used to infer microbial growth conditions and metabolisms of microorganisms present in MBRs at the time of sampling. These data shed new insight to two fundamental questions about a microbial community in the MBR process namely the microbial composition (who are they?) and the functions of each specific microbial assemblage (what are their function?). The results to date also highlight the complexity of the microbial community growing on MBRs. Environmental conditions are dynamic and diverse, and can influence the diversity and structural dynamics of any given microbial community for wastewater treatment. The benefits of understanding the structure of microbial communities on three major aspects of the MBR process (i.e. nutrient removal, biofouling control, and micropollutant removal) were symmetrically delineated. This review also indicates that the deployment of microbial community analysis for a practical engineering context, in terms of process design and system optimization, can be further realized.}, }
@article {pmid31791487, year = {2020}, author = {Mathews, ER and Wood, JL and Phillips, D and Billington, N and Barnett, D and Franks, AE}, title = {Town-scale microbial sewer community and H2S emissions response to common chemical and biological dosing treatments.}, journal = {Journal of environmental sciences (China)}, volume = {87}, number = {}, pages = {133-148}, doi = {10.1016/j.jes.2019.06.011}, pmid = {31791487}, issn = {1001-0742}, mesh = {Hydrogen Sulfide/*analysis/chemistry ; Hydrogen-Ion Concentration ; Microbiota ; Sewage/chemistry/microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Controlling hydrogen sulfide (H2S) odors and emissions using a single, effective treatment across a town-scale sewer network is a challenge faced by many water utilities. Implementation of a sewer diversion provided the opportunity to compare the effectiveness of magnesium hydroxide (Mg(OH)2) and two biological dosing compounds (Bioproducts A and B), with different modes of action (MOA), in a field-test across a large sewer network. Mg(OH)2 increases sewer pH allowing suppression of H2S release into the sewer environment while Bioproduct A acts to disrupt microbial communication through quorum sensing (QS), reducing biofilm integrity. Bioproduct B reduces H2S odors by scouring the sewer of fats, oils and grease (FOGs), which provide adhesion points for the microbial biofilm. Results revealed that only Mg(OH)2 altered the microbial community structure and reduced H2S emissions in a live sewer system, whilst Bioproducts A and B did not reduce H2S emissions or have an observable effect on the composition of the microbial community at the dosed site. Study results recommend in situ testing of dosing treatments before implementation across an operational system.}, }
@article {pmid31790889, year = {2020}, author = {Yan, L and Herrmann, M and Kampe, B and Lehmann, R and Totsche, KU and Küsel, K}, title = {Environmental selection shapes the formation of near-surface groundwater microbiomes.}, journal = {Water research}, volume = {170}, number = {}, pages = {115341}, doi = {10.1016/j.watres.2019.115341}, pmid = {31790889}, issn = {1879-2448}, mesh = {Bacteria ; *Groundwater ; *Microbiota ; }, abstract = {Hydrodynamics drives both stochastic and deterministic community assembly in aquatic habitats, by translocating microbes across geographic barriers and generating changes in selective pressures. Thus, heterogeneity of hydrogeological settings and episodic surface inputs from recharge areas might play important roles in shaping and maintaining groundwater microbial communities. Here we took advantage of the Hainich Critical Zone Exploratory to disentangle mechanisms of groundwater microbiome differentiation via a three-year observation in a setting of mixed carbonate-siliciclastic alternations along a hillslope transect. Variation partitioning of all data elucidated significant roles of hydrochemistry (35.0%) and spatial distance (18.6%) but not of time in shaping groundwater microbiomes. Groundwater was dominated by rare species (99.6% of OTUs), accounting for 25.9% of total reads, whereas only 26 OTUs were identified as core species. The proximity to the recharge area gave prominence to high microbial diversity coinciding with high surface inputs. In downstream direction, the abundance of rare OTUs decreased whereas core OTUs abundance increased up to 47% suggesting increasing selection stress with a higher competition cost for colonization. In general, environmental selection was the key mechanism driving the spatial differentiation of groundwater microbiomes, with N-compounds and dissolved oxygen as the major determinants, but it was more prominent in the upper aquifer with low flow velocity. Across the lower aquifer with higher flow velocity, stochastic processes appeared to be additionally important for community assembly. Overall, this study highlights the impact of surface and subsurface conditions, as well as flow regime and related habitat accessibility, on groundwater microbiomes assembly.}, }
@article {pmid31790419, year = {2019}, author = {Díaz-Riaño, J and Posada, L and Acosta, IC and Ruíz-Pérez, C and García-Castillo, C and Reyes, A and Zambrano, MM}, title = {Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0221540}, pmid = {31790419}, issn = {1932-6203}, abstract = {Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the immediate radiation response of D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions.}, }
@article {pmid31788934, year = {2019}, author = {Hannula, SE and Ma, HK and Pérez-Jaramillo, JE and Pineda, A and Bezemer, TM}, title = {Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14882}, pmid = {31788934}, issn = {1462-2920}, support = {865.14.006//Netherlands Organization for Scientific Research NWO VICI/ ; 870.15.080//Netherlands Organization for Scientific Research NWO VICI/ ; }, abstract = {Interactions between plants and soil microbes are important for plant growth and resistance. Through plant-soil-feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant-soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant-induced changes in soil microbiomes on the growth of the commercially important cut-flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next-generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species-specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.}, }
@article {pmid31787951, year = {2019}, author = {Pelikan, C and Jaussi, M and Wasmund, K and Seidenkrantz, MS and Pearce, C and Kuzyk, ZZA and Herbold, CW and Røy, H and Kjeldsen, KU and Loy, A}, title = {Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2558}, doi = {10.3389/fmicb.2019.02558}, pmid = {31787951}, issn = {1664-302X}, abstract = {Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had &quot;young&quot; sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.}, }
@article {pmid31786395, year = {2020}, author = {Xu, R and Zhang, S and Meng, F}, title = {Large-sized planktonic bioaggregates possess high biofilm formation potentials: Bacterial succession and assembly in the biofilm metacommunity.}, journal = {Water research}, volume = {170}, number = {}, pages = {115307}, doi = {10.1016/j.watres.2019.115307}, pmid = {31786395}, issn = {1879-2448}, mesh = {Bacteria ; Biofilms ; Calcium Hydroxide ; *Extracellular Polymeric Substance Matrix ; Hydroxyapatites ; Phylogeny ; *Plankton ; Silicates ; }, abstract = {Wanted and unwanted surface-attached growth of bacteria is ubiquitous in natural and engineered settings. Normally, attachment of planktonic cells to media surfaces initiates biofilm formation and fundamentally regulates biofilm assembly processes. Here, culturing biofilm with planktonic sludge as source community, we found distinct succession profiles of biofilm communities sourced from the size-fractionated sludge flocs (<25; 25-120; >120 μm). Null model analyses revealed that deterministic process dominated in biofilm community assemblies but decreased with decreasing floc size. Additionally, the relative importance of environmental selection increased with increasing floc size of the source sludge, whereas homogenizing dispersal and ecological drift followed opposite trends. Phylogenetic molecular ecological networks (pMENs) indicated that species interactions were intensive in biofilm microbiota developed from large-sized flocs (>120 μm), as evidenced by the low modularity and harmonic geodesic distance and the high average degree. Intriguingly, the keystone taxa in these biofilm ecological networks were controlled by distinct interaction patterns but all showed strong habitat characteristics (e.g., facultative anaerobic, motile, hydrophobic and involved in extracellular polymeric substance metabolism), corroborating the crucial roles of environmental filtering in structuring biofilm community. Taken together, our findings highlight the role of planktonic floc properties in biofilm community assembly and advance our understanding of microbial ecology in biofilm-based systems.}, }
@article {pmid31785367, year = {2019}, author = {Wilson, JM and Platts-Mills, TAE}, title = {α-Gal and other recent findings that have informed our understanding of anaphylaxis.}, journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.anai.2019.11.024}, pmid = {31785367}, issn = {1534-4436}, abstract = {OBJECTIVE: To summarize the current understanding of anaphylaxis, with an emphasis on major findings that have been reported within the last 10 years.<br><br>DATA SOURCES: Queries relating to anaphylaxis, immunoglobulin E (IgE), and mast cells were conducted with PubMed and Google Scholar, searching for primary articles and review papers.<br><br>STUDY SELECTIONS: We focused on articles written in English and which were reported in major allergy and immunology journals.<br><br>RESULTS: Anaphylaxis represents an extreme manifestation of a form of allergic immunity that appears to have evolved to protect against &quot;toxic&quot; threats that present at skin and mucosal barriers. The factors that have contributed to a rise in anaphylaxis are increasingly appreciated to relate to changes in hygiene and microbial ecology that have occurred with industrialization. Induction of allergen-specific IgG4 is often part of the allergic response and is associated with protection against anaphylaxis. The recognition of the α-Gal syndrome suggests that carbohydrates can be epitopes that are relevant to anaphylaxis and that IgE-mediated reactions do not always occur &quot;immediately.&quot;<br><br>CONCLUSION: Our understanding of anaphylaxis has advanced significantly over the past 10 years. It is anticipated that ongoing research will build on this foundation to further advance our knowledge of anaphylaxis and also translate into clinically meaningful therapies.}, }
@article {pmid31784839, year = {2019}, author = {Chen, J and He, Y and Wang, J and Huang, M and Guo, C}, title = {Dynamics of nitrogen transformation and bacterial community with different aeration depths in malodorous river.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {12}, pages = {196}, pmid = {31784839}, issn = {1573-0972}, support = {41877477//National Natural Science Foundation of China/ ; 16ZR1408800//Natural Science Foundation of Shanghai/ ; 16PJD023//Shanghai Pujiang Talent Program/ ; 18DZ1203806//Shanghai Science and Technology Development Foundation/ ; 1701K005//Research Funds of The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control/ ; }, mesh = {Bacteria/classification/genetics/*metabolism ; China ; Geologic Sediments/microbiology ; Microbiota/*physiology ; Nitrogen/*metabolism ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Rivers/*chemistry/*microbiology ; Sulfur/metabolism ; }, abstract = {In this research, the dynamics of nitrogen transformation and bacterial community in malodorous river were investigated with different aeration depths. Computational flow dynamics (CFD) and Reynolds number (Re) were specially used to characterize the hydrodynamics condition under different aeration depths. The results indicated that aeration depth had vital impact on nitrogen transformation and bacterial community structure. It was found that a range of aeration depth (0.20-0.45 m above sediment-water interface) facilitated the removal of NH4+-N and TN with Re ranging between 6211 and 8930. Proteobacteria took over Firmicutes to become the predominant phylum (36-78%) under aeration, and the main subdivisions of γ-, β- and δ-Proteobacteria also varied greatly with different aeration depths. Interestingly, there was a marked shift of the inferentially identified dominant functional role within Proteobacteria from organic-matter degradation to nitrogen metabolism and then to sulfur metabolism as well as the coupling of nitrogen and sulfur with the increase of disturbance. The redundancy analysis (RDA) further confirmed the importance of aeration disturbance in shaping bacterial community. These findings help to gain improved understanding of endogenous N-behavior and aquatic microbial ecology, and underline the need for integrating the hydrodynamics factors with microbial community.}, }
@article {pmid31781077, year = {2019}, author = {Glamoclija, M and Ramirez, S and Sirisena, K and Widanagamage, I}, title = {Subsurface Microbial Ecology at Sediment-Groundwater Interface in Sulfate-Rich Playa; White Sands National Monument, New Mexico.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2595}, pmid = {31781077}, issn = {1664-302X}, abstract = {The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.}, }
@article {pmid31781072, year = {2019}, author = {Zhang, Z and Li, D and Xu, W and Tang, R and Li, L}, title = {Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2576}, pmid = {31781072}, issn = {1664-302X}, abstract = {Fish are the most widespread aquaculture species and maintain complex associations with microbial consortiums. However, the ecology of these associations present in multiple microhabitats in fish remains elusive, especially on the microbial assembly in fish external (skin and gill) and internal (stomach and intestine) niches, and the relationship with the rearing environment. To understand host dependence and niche differentiation of organ-specific microbiome signatures using a 16S rRNA gene-based sequencing technique, we systematically provided characterizations of a comparative framework relevant to the microbiome of stomach, regional intestine, skin, and gill in two important farmed fish species, herbivorous grass carp (Ctenopharyngodon idella) and carnivorous southern catfish (Silurus meridionalis), and of the rearing water. The different feeding habits of grass carp and southern catfish showed a significant separation of microbial community structure, with great compositional differences across body sites within each species. Site-driven divergences relied on host species: the same types of microhabitats between grass carp and southern catfish harbored differential microbiome. Additionally, body sites had remarkably distinct communities and displayed lower alpha diversity compared to rearing water. Unexpectedly, the stomach of southern catfish had the highest microbial diversity in the digestive tract of the two co-cultured fish species. For external sites within each species, a higher diversity occurred in gill of grass carp and in skin of southern catfish. Our results unveil different topographical microbiome signatures of the co-cultured species, indicating host selection in individual-level microbial assemblages and niche differentiation at the organ scale. This work represents a foundation for understanding the comprehensive microbial ecology of cohabiting farmed fish, suggesting potential applications associated with fish microbiome that urgently needs to be assessed in polycultured operations in aquaculture.}, }
@article {pmid31780680, year = {2019}, author = {Vivero, RJ and Villegas-Plazas, M and Cadavid-Restrepo, GE and Herrera, CXM and Uribe, SI and Junca, H}, title = {Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17746}, pmid = {31780680}, issn = {2045-2322}, abstract = {Phlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.}, }
@article {pmid31780241, year = {2020}, author = {Lavergne, C and Bovio-Winkler, P and Etchebehere, C and García-Gen, S}, title = {Towards centralized biogas plants: Co-digestion of sewage sludge and pig manure maintains process performance and active microbiome diversity.}, journal = {Bioresource technology}, volume = {297}, number = {}, pages = {122442}, doi = {10.1016/j.biortech.2019.122442}, pmid = {31780241}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Biofuels ; Bioreactors ; Manure ; Methane ; *Microbiota ; RNA, Ribosomal, 16S ; *Sewage ; Swine ; }, abstract = {The aim of this study is to assess the performance of anaerobic digestion against co-digestion systems during the start-up stages based on key process parameters and biological indicators. Two parallel experiments treating sewage sludge alone or co-digested with low concentration of pig manure (8% vol., 2-3% in COD basis) were carried out in two lab-scale CSTR at mesophilic conditions. Same inoculant and organic loading rate sequences were applied for two consecutive runs of 79 and 90 days. According to the removal efficiencies achieved, no significant differences were encountered amongst mono-digestion and co-digestion. This observation was reinforced with the analysis of the total/active microbiome, sequencing 16S rRNA genes and transcripts. The addition of a co-substrate at low concentration had a negligible effect on the total/active microbial communities; they evolved following the same pattern. This might be an advantage in order to upgrade existing wastewater treatment plants to become centralized biogas facilities.}, }
@article {pmid31779402, year = {2019}, author = {Taylor, AW and Harris, DM}, title = {Optimized commercial desktop cutter technique for rapid-prototyping of microfluidic devices and application to Taylor dispersion.}, journal = {The Review of scientific instruments}, volume = {90}, number = {11}, pages = {116102}, doi = {10.1063/1.5123130}, pmid = {31779402}, issn = {1089-7623}, abstract = {Microfluidics provides a platform for efficient and transportable microanalysis, catalyzing advancements in fields such as biochemistry, materials science, and microbial ecology. While the analysis is cost-effective, standard device fabrication techniques are disproportionately expensive and specialized. A commercially available desktop cutting plotter provides an accessible method for rapidly fabricating microfluidic devices at extremely low costs. The optimized technique described in the present work enables fabrication of microchannels with dimensions as small as ∼100 μm. Straightness of channel walls is comparable to other common fabrication techniques but achieved here at a fraction of the cost and fabrication time. Solute dispersion experiments are performed using the rapidly prototyped channels to measure the effective dispersion coefficient in laminar flow through rectangular channels. The results of these experiments compare favorably to predictions from classical Taylor-Aris dispersion theory. This note provides all necessary tools for researchers and educators to seamlessly apply the desktop cutter fabrication technique. Materials list, fabrication instructions, and detailed channel characterization results are available in the supplementary material.}, }
@article {pmid31771976, year = {2019}, author = {Janzon, A and Goodrich, JK and Koren, O and ,  and Waters, JL and Ley, RE}, title = {Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31771976}, issn = {2379-5077}, abstract = {Interactions between the gut microbiome and immunoglobulin A (IgA) in the gut during infancy are important for future health. IgM and IgG are also present in the gut; however, their interactions with the microbiome in the developing infant remain to be characterized. Using stool samples sampled 15 times in infancy from 32 healthy subjects at 4 locations in 3 countries, we characterized patterns of microbiome development in relation to fecal levels of IgA, IgG, and IgM. For 8 infants from a single location, we used fluorescence-activated cell sorting of microbial cells from stool by Ig-coating status over 18 months. We used 16S rRNA gene profiling on full and sorted microbiomes to assess patterns of antibody coating in relation to age and other factors. All antibodies decreased in concentration with age but were augmented by breastmilk feeding regardless of infant age. Levels of IgA correlated with relative abundances of operational taxonomic units (OTUs) belonging to the Bifidobacteria and Enterobacteriaceae, which dominated the early microbiome, and IgG levels correlated with Haemophilus The diversity of Ig-coated microbiota was influenced by breastfeeding and age. IgA and IgM coated the same microbiota, which reflected the overall diversity of the microbiome, while IgG targeted a different subset. Blautia generally evaded antibody coating, while members of the Bifidobacteria and Enterobacteriaceae were high in IgA/M. IgA/M displayed similar dynamics, generally coating the microbiome proportionally, and were influenced by breastfeeding status. IgG only coated a small fraction of the commensal microbiota and differed from the proportion targeted by IgA and IgM.IMPORTANCE Antibodies are secreted into the gut and attach to roughly half of the trillions of bacterial cells present. When babies are born, the breastmilk supplies these antibodies until the baby's own immune system takes over this task after a few weeks. The vast majority of these antibodies are IgA, but two other types, IgG and IgM, are also present in the gut. Here, we ask if these three different antibody types target different types of bacteria in the infant gut as the infant develops from birth to 18 months old and how patterns of antibody coating of bacteria change with age. In this study of healthy infant samples over time, we found that IgA and IgM coat the same bacteria, which are generally representative of the diversity present, with a few exceptions that were more or less antibody coated than expected. IgG coated a separate suite of bacteria. These results provide a better understanding of how these antibodies interact with the developing infant gut microbiome.}, }
@article {pmid31769802, year = {2020}, author = {Jiménez, DJ and Wang, Y and Chaib de Mares, M and Cortes-Tolalpa, L and Mertens, JA and Hector, RE and Lin, J and Johnson, J and Lipzen, A and Barry, K and Mondo, SJ and Grigoriev, IV and Nichols, NN and van Elsas, JD}, title = {Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {1}, pages = {}, doi = {10.1093/femsec/fiz186}, pmid = {31769802}, issn = {1574-6941}, abstract = {Coniochaeta species are versatile ascomycetes that have great capacity to deconstruct lignocellulose. Here, we explore the transcriptome of Coniochaeta sp. strain 2T2.1 from wheat straw-driven cultures with the fungus growing alone or as a member of a synthetic microbial consortium with Sphingobacterium multivorum w15 and Citrobacter freundii so4. The differential expression profiles of carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation by 2T2.1 during the initial 24 hours of incubation. Within the tripartite consortium, 63 transcripts of strain 2T2.1 were differentially expressed at this time point. The presence of the two bacteria significantly upregulated the expression of one galactose oxidase, one GH79-like enzyme, one multidrug transporter, one laccase-like protein (AA1 family) and two bilirubin oxidases, suggesting that inter-kingdom interactions (e.g. amensalism) take place within this microbial consortium. Overexpression of multicopper oxidases indicated that strain 2T2.1 may be involved in lignin depolymerization (a trait of enzymatic synergism), while S. multivorum and C. freundii have the metabolic potential to deconstruct arabinoxylan. Under the conditions applied, 2T2.1 appears to be a better degrader of wheat straw when the two bacteria are absent. This conclusion is supported by the observed suppression of its (hemi)cellulolytic arsenal and lower degradation percentages within the microbial consortium.}, }
@article {pmid31768533, year = {2020}, author = {Duysburgh, C and Ossieur, WP and De Paepe, K and Van den Abbeele, P and Vichez-Vargas, R and Vital, M and Pieper, DH and Van de Wiele, T and Hesta, M and Possemiers, S and Marzorati, M}, title = {Development and validation of the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME)1.}, journal = {Journal of animal science}, volume = {98}, number = {1}, pages = {}, doi = {10.1093/jas/skz357}, pmid = {31768533}, issn = {1525-3163}, abstract = {Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon. This semi-continuous gastrointestinal tract model allowed a long-term, region-dependent, and pH-controlled simulation of the colon-associated microbial community of dogs. Upon reaching a functional steady state, the simulated canine microbial community composition proved to be representative of the in vivo situation. Indeed, the predominant bacterial phyla present in the in vitro proximal and distal colon corresponded with the main bacterial phyla detected in the fecal material of the dogs, resulting in an average community composition along the simulated canine gastrointestinal tract of 50.5% Firmicutes, 34.5% Bacteroidetes, 7.4% Fusobacteria, 4.9% Actinobacteria, and 2.7% Proteobacteria. A parallel in vivo-in vitro comparison assessing the effects of fructooligosaccharides (FOS) on the canine microbial community composition showed a consistent stimulation of Lactobacillus concentrations in the in vivo fecal samples as well as in the in vitro canine gut model. Furthermore, the in vitro platform provided additional insights about the prebiotic effect of FOS supplementation of dogs, such as a reduced abundance of Megamonas spp. which are only present in very low abundance in in vivo fecal samples, indicating an interesting application potential of the developed canine in vitro model in research related to gastrointestinal health of dogs.}, }
@article {pmid31766265, year = {2019}, author = {Sun, Z and Yu, Z and Wang, B}, title = {Perilla frutescens Leaf Alters the Rumen Microbial Community of Lactating Dairy Cows.}, journal = {Microorganisms}, volume = {7}, number = {11}, pages = {}, pmid = {31766265}, issn = {2076-2607}, support = {31902181//National Natural Science Foundation of China/ ; }, abstract = {Perilla frutescens (L.) Britt., an annual herbaceous plant, has antibacterial, anti-inflammation, and antioxidant properties. To understand the effects of P. frutescens leaf on the ruminal microbial ecology of cattle, Illumina MiSeq 16S rRNA sequencing technology was used. Fourteen cows were used in a randomized complete block design trial. Two diets were fed to these cattle: a control diet (CON); and CON supplemented with 300 g/d P. frutescens leaf (PFL) per cow. Ruminal fluid was sampled at the end of the experiment for microbial DNA extraction. Overall, our findings revealed that supplementation with PFL could increase ruminal fluid pH value. The ruminal bacterial community of cattle was dominated by Bacteroidetes, Firmicutes, and Proteobacteria. The addition of PFL had a positive effect on Firmicutes, Actinobacteria, and Spirochaetes, but had no effect on Bacteroidetes and Proteobacteria compared with the CON. The supplementation with PFL significantly increased the abundance of Marvinbryantia, Acetitomaculum, Ruminococcusgauvreauii, Eubacteriumcoprostanoligenes, Selenomonas_1, Pseudoscardovia, norank_f__Muribaculaceae, and Sharpea, and decreased the abundance of Treponema_2 compared to CON. Eubacterium coprostanoligenes, and norank_f__Muribaculaceae were positively correlated with ruminal pH value. It was found that norank_f__Muribaculaceae and Acetitomaculum were positively correlated with milk yield, indicating that these different genera are PFL associated bacteria. This study suggests that PFL supplementation could increase the ruminal pH value and induce shifts in the ruminal bacterial composition.}, }
@article {pmid31763752, year = {2019}, author = {Zanne, AE and Abarenkov, K and Afkhami, ME and Aguilar-Trigueros, CA and Bates, S and Bhatnagar, JM and Busby, PE and Christian, N and Cornwell, WK and Crowther, TW and Flores-Moreno, H and Floudas, D and Gazis, R and Hibbett, D and Kennedy, P and Lindner, DL and Maynard, DS and Milo, AM and Nilsson, RH and Powell, J and Schildhauer, M and Schilling, J and Treseder, KK}, title = {Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.12570}, pmid = {31763752}, issn = {1469-185X}, support = {1623040//Division of Environmental Biology/ ; 1655759//Division of Environmental Biology/ ; //National Science Foundation/ ; }, abstract = {Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.}, }
@article {pmid31763477, year = {2019}, author = {Anderson, OR}, title = {Atmospheric respiratory CO2 efflux by aquatic suspended particle-bound microbial communities: A laboratory experimental study.}, journal = {Heliyon}, volume = {5}, number = {11}, pages = {e02816}, pmid = {31763477}, issn = {2405-8440}, abstract = {Natural sources of atmospheric CO2 are of increasing interest as possible contributors to global climate warming. This study documents the amount of respiratory CO2 contributed by microbial communities associated with suspended particulates in aquatic water columns. Microcosms containing three different sources of water (pond freshwater, NY East River estuary and Hudson River estuary) were used to experimentally determine the atmospheric respiratory CO2 released from particle-associated microbes. Two different approaches were used. In the first, finely powdered dried cereal leaves (alfalfa) were added to each of the three microcosms as a consistent source of particulate organic matter (POM). In the second, only Hudson River estuary water samples were used with natural densities of POM. Respiration rates associated with two sizes of particles were assessed: 1) ≥ 200 μm and 2) ≥ 50 μm but less than 200 μm. The total respiration rate for the three microcosms with cereal leaf POM ranged from 5.09 to 14.87 μmol CO2 min-1 L-1. Of this, the amount contributed by larger particulates was in the range of 55-63%; and for smaller particulates ranged from 18 to 32 %. Data for microcosms containing water from the Hudson River estuary, with natural particulates, was as follows: total respiration ranged from ∼3 μmol CO2 min-1 L-1 to ∼3.73 μmol CO2 min-1 L-1. Larger particulates contributed approximately 40% of total respiration, and that of smaller particulates was substantially less (4-5% of total). Overall, these results indicate that microbial communities associated with particulates in the water column (especially larger particulates) may contribute substantial amounts of CO2 to the atmosphere.}, }
@article {pmid31759643, year = {2020}, author = {Wen, D and Ordonez, D and McKenna, A and Chang, NB}, title = {Fate and transport processes of nitrogen in biosorption activated media for stormwater treatment at varying field conditions of a roadside linear ditch.}, journal = {Environmental research}, volume = {181}, number = {}, pages = {108915}, doi = {10.1016/j.envres.2019.108915}, pmid = {31759643}, issn = {1096-0953}, abstract = {Roadside drainage networks can result in changes to watershed hydrology and water quality. By acting as hydrological links between urban development, agricultural fields, and natural streams, roadside ditches may be modified by filling in some green sorption media to control nitrogen pollution. Biosorption activated media (BAM), one of the green sorption media, are composed of sand, tire crumb, and clay, which can remove nitrogen from stormwater and groundwater through integrated hydrological, chemophysical, and microbial processes. The fate and transport processes of interest are complicated by internal microbial processes including ammonification, nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), each of which is controlled by different microbial species in addition to some varying field conditions. In this study, BAM was tested in a suite of columns to address site-specific physical, chemical and biological concerns driven by in situ traffic compaction, carbon availability, and animal impact (such as gopher turtles, moles, and ants) all of which impose different impacts on nitrogen fate and transport processes that may be signified by changing dissolved organic nitrogen species (DONs). The traffic compaction condition resulted in the most suitable hydraulic retention time in the hydrological process, which is beneficial for the assimilation of DONs in a long-term carbon rich environment due to biofilm expansion. Denitrifiers were the most predominant microbial population and the microbial species of DNRA were the second most predominant one in all three field conditions. However, the relationship of denitrifiers and DNRA in BAM can be shifted from commensalism to competition or even inhibition after carbon addition in microbial ecology.}, }
@article {pmid31758237, year = {2020}, author = {Wang, Y and Xie, Q and Zhang, Y and Ma, W and Ning, K and Xiang, JY and Cui, J and Xiang, H}, title = {Combination of probiotics with different functions alleviate DSS-induced colitis by regulating intestinal microbiota, IL-10, and barrier function.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {1}, pages = {335-349}, doi = {10.1007/s00253-019-10259-6}, pmid = {31758237}, issn = {1432-0614}, support = {20180201078YY//Science and Technology Development Planning of Jilin/ ; }, abstract = {The potential of probiotics for treating ulcerative colitis (UC) has attracted increasing attention. However, more studies are still needed to guide physicians on the proper selection and use of probiotics. Here, we propose that combination of multiple probiotics with different functions can reduce intestinal inflammation. In this study, the effects of probiotics (Lactobacillus reuteri, Bacillus coagulans, Bifidobacterium longum, and Clostridium butyricum) on the physiology and histopathology of colon were evaluated in a dextran sulfate sodium (DSS)-induced colitis mouse model. The combined species, as well as the species individually, were tested and compared with sulfasalazine (SASP) and two Chinese herbal therapies. Results show that the functions of the four probiotic strains were different in regulating intestinal immunity and barrier function. The four-species probiotic cocktail was more effective than the species individually and anti-inflammatory drugs in repairing the dysbiosis of mucosal microbial ecology and reducing intestinal inflammation. The multi-strain probiotic mixture increased the proportion of beneficial bacteria and decreased the proportion of pro-inflammatory bacteria in the colonic mucosa. In addition, probiotic mixture significantly enhanced the expression of IL-10 and intestinal barrier function. These results suggest that a combination of multiple probiotics with different functions has synergistic effects and can restore the balance of interactions between microorganisms and immunological niches.}, }
@article {pmid31757825, year = {2020}, author = {Frankel-Bricker, J and Buerki, S and Feris, KP and White, MM}, title = {Influences of a Prolific Gut Fungus (Zancudomyces culisetae) on Larval and Adult Mosquito (Aedes aegypti)-Associated Microbiota.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {3}, pages = {}, doi = {10.1128/AEM.02334-19}, pmid = {31757825}, issn = {1098-5336}, abstract = {Adult mosquitoes inherit a bacterial community from larvae via transstadial transmission, an understudied process that may influence host-microbe interactions. Microbes contribute to important host life history traits, and analyzing transmitted microbial communities, the interrelationship between larval and adult-associated microbiota, and factors influencing host-microbe relationships provides targets for research. During its larval stage, the yellow fever mosquito (Aedes aegypti) hosts the trichomycete gut fungus Zancudomyces culisetae, and fungal colonization coincides with environmental perturbations in the digestive tract microecosystem. Natural populations are differentially exposed to fungi, thereby potentially harboring distinct microbiota and experiencing disparate host-microbe interactions. This study's objectives were to characterize larval and initial adult microbiomes, investigate variation in diversity and distribution of microbial communities across individuals, and assess whether larval fungal colonization impacted microbiomes at these developmental stages. Laboratory-based fungal infestation assays, sequencing of 16S rRNA gene amplicons, and bacterial load quantification protocols revealed that initial adult microbiomes varied in diversity and distribution. Larval fungal colonization had downstream effects on initial adult microbiomes, significantly reducing microbial community variation, shifting relative abundances of certain bacterial families, and influencing transstadial transmission outcomes of particular genera. Further, abundances of several families consistently decreased in adults relative to levels in larvae, possibly reflecting impacts of host development on specific bacterial taxa. These findings demonstrated that a prolific gut fungus impacted mosquito-associated microbiota at two developmental stages in an insect connected with global human health.IMPORTANCE Mosquitoes are widespread vectors of numerous human pathogens and harbor microbiota known to affect host phenotypic traits. However, little research has directly investigated how bacterial communities associated with larvae and adults are connected. We characterized whole-body bacterial communities in mosquito larvae preceding pupation and in newly emerged adults, and investigated whether a significant biotic factor, fungal colonization of the larval hindgut, impacted these microbiomes. Results showed that fungal colonization reduced microbial community variation across individuals and differentially impacted the outcomes of transstadial transmission for certain bacterial genera, revealing downstream effects of the fungus on initial adult microbiomes. The importance of our research is in providing a thorough comparative analysis of whole-body microbiota harbored in larvae and adults of the yellow fever mosquito (Aedes aegypti) and in demonstrating the important role a widespread gut fungus played in a host-associated microbiome.}, }
@article {pmid31757758, year = {2019}, author = {Garin-Fernandez, A and Wichels, A}, title = {Looking for the hidden: Characterization of lysogenic phages in potential pathogenic Vibrio species from the North Sea.}, journal = {Marine genomics}, volume = {}, number = {}, pages = {100725}, doi = {10.1016/j.margen.2019.100725}, pmid = {31757758}, issn = {1876-7478}, abstract = {The incidence of potentially pathogenic Vibrio species in the marine environment around Europe, is correlated with the increase of surface seawater temperature. Despite their importance, little is known about the trigger factors of potential outbreak-causing strains in this region. As prophages may compose a major reservoir of virulence traits in marine ecosystems, this study aims to identify and characterize the genomes of lysogenic Vibrio phages exemplarily from the North Sea. Therefore, 31 isolates from potentially pathogenic Vibrio species from the North Sea were screened for inducible prophages with mitomycin C. From them, one V. cholerae isolate and 40% V. parahaemolyticus isolates carried inducible prophages. Three lysogenic phages were selected for genomic characterization. The phage vB_VpaM_VP-3212 (unclassified Myoviridae) has a genome with a length of 36.81 Kbp and 55 CDS were identified. This lysogenic phage of V. parahaemolyticus contains genes related to replicative transposition mechanism, such as transposase and mobile elements similar to Mu-like viruses. The phage vB_VpaP_VP-3220 (Podoviridae, unclassified Nona33virus) has a genome length of 58,14 Kbp and contains 63 CDS. This V. parahaemolyticus phage probably uses a headful (pac) packaging replication mechanism. The phage vB_VchM_VP-3213 (unclassified Myoviridae) has a genome with a length of 41 Kbp and 63 CDS were identified, including integrase and Xer system for lysogenic recombination. This lysogenic phage of V. cholerae has similar genomic features as lambdoid phages. Although no pathogenicity genes were identified, their similarity among other phage genomes indicates that these phages can affect the development of pathogenic Vibrio strains in marine environments.}, }
@article {pmid31757204, year = {2019}, author = {Patuzzi, I and Baruzzo, G and Losasso, C and Ricci, A and Di Camillo, B}, title = {metaSPARSim: a 16S rRNA gene sequencing count data simulator.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 9}, pages = {416}, pmid = {31757204}, issn = {1471-2105}, support = {-//Università degli Studi di Padova/ ; }, mesh = {Animals ; Computer Simulation ; DNA, Ribosomal/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; *Metagenomics ; RNA, Ribosomal, 16S/*genetics ; *Software ; }, abstract = {BACKGROUND: In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable popularity of this technique, an exiguous number of specific tools are currently available for proper 16S rDNA-seq count data preprocessing and simulation. Indeed, the great majority of tools have been developed adapting methodologies previously used for bulk RNA-seq data, with poor assessment of their applicability in the metagenomics field. For such tools and the few ones specifically developed for 16S rDNA-seq data, performance assessment is challenging, mainly due to the complex nature of the data and the lack of realistic simulation models. In fact, to the best of our knowledge, no software thought for data simulation are available to directly obtain synthetic 16S rDNA-seq count tables that properly model heavy sparsity and compositionality typical of these data.<br><br>RESULTS: In this paper we present metaSPARSim, a sparse count matrix simulator intended for usage in development of 16S rDNA-seq metagenomic data processing pipelines. metaSPARSim implements a new generative process that models the sequencing process with a Multivariate Hypergeometric distribution in order to realistically simulate 16S rDNA-seq count table, resembling real experimental data compositionality and sparsity. It provides ready-to-use count matrices and comes with the possibility to reproduce different pre-coded scenarios and to estimate simulation parameters from real experimental data. The tool is made available at http://sysbiobig.dei.unipd.it/?q=Software#metaSPARSimand https://gitlab.com/sysbiobig/metasparsim.<br><br>CONCLUSION: metaSPARSim is able to generate count matrices resembling real 16S rDNA-seq data. The availability of count data simulators is extremely valuable both for methods developers, for which a ground truth for tools validation is needed, and for users who want to assess state of the art analysis tools for choosing the most accurate one. Thus, we believe that metaSPARSim is a valuable tool for researchers involved in developing, testing and using robust and reliable data analysis methods in the context of 16S rRNA gene sequencing.}, }
@article {pmid31757073, year = {2019}, author = {Yssel, AEJ and Kao, SM and Van de Peer, Y and Sterck, L}, title = {ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes.}, journal = {Genes}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/genes10120950}, pmid = {31757073}, issn = {2073-4425}, abstract = {ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to &quot;public&quot; or &quot;restricted&quot; mode; anonymous users can browse public genomes but cannot make any changes. Aside from providing a user-&amp;nbsp;friendly interface to view genome annotations, the platform also includes tools and information (such as gene expression evidence) that enables authorized users to edit and validate genome annotations. The ORCAE-AOCC platform will enable various stakeholders from around the world to coordinate their efforts to annotate and study underutilized crops.}, }
@article {pmid31756853, year = {2019}, author = {Suleiman, AKA and Harkes, P and van den Elsen, S and Holterman, M and Korthals, GW and Helder, J and Kuramae, EE}, title = {Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare).}, journal = {The Science of the total environment}, volume = {695}, number = {}, pages = {133885}, doi = {10.1016/j.scitotenv.2019.133885}, pmid = {31756853}, issn = {1879-1026}, mesh = {Agriculture ; Bacteria ; Biota ; Ecosystem ; Eukaryota ; Fertilizers ; Food Chain ; Fungi ; *Hordeum ; *Rhizosphere ; Soil ; *Soil Microbiology ; }, abstract = {Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.}, }
@article {pmid31756842, year = {2019}, author = {Hylling, O and Nikbakht Fini, M and Ellegaard-Jensen, L and Muff, J and Madsen, HT and Aamand, J and Hansen, LH}, title = {A novel hybrid concept for implementation in drinking water treatment targets micropollutant removal by combining membrane filtration with biodegradation.}, journal = {The Science of the total environment}, volume = {694}, number = {}, pages = {133710}, doi = {10.1016/j.scitotenv.2019.133710}, pmid = {31756842}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; Drinking Water/*chemistry ; *Filtration ; Water Pollutants, Chemical/*analysis ; Water Purification/*methods ; }, abstract = {Groundwater extracted for drinking water production is commonly treated by aeration and sand filtration. However, this simple treatment is typically unable to remove pesticide residues. As a solution, bioaugmentation of sand filter units (i.e., the addition of specific degrader strains) has been proposed as an alternative &quot;green&quot; technology for targeted pesticide removal. However, the introduced degraders are challenged by (i) micropollutant levels of target residue, (ii) the oligotrophic environment and (iii) competition and predation by the native microorganisms, leading to loss of population and degradation potential. To overcome these challenges, we propose the introduction of a novel hybrid treatment step to the overall treatment process in which reverse osmosis filtration and biodegradation are combined to remove a target micropollutant. Here, the reverse osmosis produces a concentrated retentate that will act as a feed to a dedicated biofilter unit, intended to promote biodegradation potential and stability of an introduced degrader. Subsequently, the purified retentate will be re-mixed with the permeate from reverse osmosis, for re-mineralization and downstream consumption. In our study, we investigated the effect of reverse osmosis retentates on the degradation potential of an introduced degrader. This paper provides the first promising results of this hybrid concept using the 2,6-dichlorobenzamide (BAM)-degrading bacteria Aminobacter sp. MSH1 in batch experiments, spiked with radiolabeled BAM. The results showed an increased degradation potential of MSH1 in retentate waters versus untreated water. Colony-forming units and qPCR showed a stable MSH1 population, despite higher concentrations of salts and metals, and increased growth of native bacteria.}, }
@article {pmid31756831, year = {2019}, author = {Iqbal, A and Shang, Z and Rehman, MLU and Ju, M and Rehman, MMU and Rafiq, MK and Ayub, N and Bai, Y}, title = {Pattern of microbial community composition and functional gene repertoire associated with methane emission from Zoige wetlands, China-A review.}, journal = {The Science of the total environment}, volume = {694}, number = {}, pages = {133675}, doi = {10.1016/j.scitotenv.2019.133675}, pmid = {31756831}, issn = {1879-1026}, mesh = {China ; Methane/*metabolism ; *Microbiota ; *Soil Microbiology ; *Wetlands ; }, abstract = {The Hindu-Kush Himalaya region extends over 4 million km2 across the eight countries. Knowingly, the Qinghai-Tibetan Plateau (QTP) is considered the principal altitudinal permafrost constituent on earth and is deemed as the third 'pole'. Among which, the Zoige wetlands are located in the northeastern boundary of QTP, wrapping a total area of 6180 km2 with an average altitude of 3500 m. This entire region is the hotspot for methane emission since the last decade. Given the importance of methane emission, many studies have focused on the effect of environmental fluctuations on the overall methane profile and, more recently on the methanogenic community structure. The current review summarizes recent advancements of the methanogenic community and methane profile and outlines a framework for better understanding of the microbial ecology of the Zoige wetlands, China. Moreover, as microorganisms are indispensable to biogeochemical cycles, especially for methane, they are believed to be the best indicators to identify the condition of wetlands. Hence, we suggest that, underpinning the microbial profile could help understand the status of a wetland.}, }
@article {pmid31754744, year = {2019}, author = {Rajagopala, SV and Singh, H and Yu, Y and Zabokrtsky, KB and Torralba, MG and Moncera, KJ and Frank, B and Pieper, R and Sender, L and Nelson, KE}, title = {Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01448-x}, pmid = {31754744}, issn = {1432-184X}, abstract = {Prophylactic or therapeutic antibiotic use along with chemotherapy treatment potentially has a long-standing adverse effect on the resident gut microbiota. We have established a case-control cohort of 32 pediatric and adolescent acute lymphoblastic leukemia (ALL) patients and 25 healthy siblings (sibling controls) to assess the effect of chemotherapy as well as antibiotic prophylaxis on the gut microbiota. We observe that the microbiota diversity and richness of the ALL group is significantly lower than that of the control group at diagnosis and during chemotherapy. The microbiota diversity is even lower in antibiotics-exposed ALL patients. Although the gut microbial diversity tends to stabilize after 1-year post-chemotherapy, their abundances were altered because of chemotherapy and prophylactic antibiotic treatments. Specifically, the abundances of mucolytic gram-positive anaerobic bacteria, including Ruminococcus gnavus and Ruminococcus torques, tended to increase during the chemotherapy regimen and continued to be elevated 1 year beyond the initiation of chemotherapy. This dysbiosis may contribute to the development of gastrointestinal complications in ALL children following chemotherapy. These findings set the stage to further understand the role of the gut microbiome dynamics in ALL patients and their potential role in alleviating some of the adverse side effects of chemotherapy and antibiotics use in immunocompromised children.}, }
@article {pmid31753627, year = {2020}, author = {Vázquez-Blanco, R and Arias-Estévez, M and Bååth, E and Fernández-Calviño, D}, title = {Comparison of Cu salts and commercial Cu based fungicides on toxicity towards microorganisms in soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {257}, number = {}, pages = {113585}, doi = {10.1016/j.envpol.2019.113585}, pmid = {31753627}, issn = {1873-6424}, abstract = {Microbial responses to Cu pollution as a function of Cu sources (Cu salts and commercial Cu fungicides) were assessed in a soil using basal soil respiration, and bacterial and fungal community growth, as endpoints. The soil was amended with different concentrations (0-32 mmol Cu kg-1) of Cu nitrate, Cu sulfate, Bordeaux mixture and 3 types of Cu oxychloride. Cu salts decreased soil pH, while this was not found with the other Cu sources. This difference in soil pH effects caused differences in the respiration, bacterial growth and fungal growth response. Basal soil respiration was negatively affected by Cu addition when the soil was spiked with Cu salts, but almost unaffected by commercial Cu fungicides. Bacterial growth was significantly and negatively affected by Cu addition for all the Cu sources, but Cu toxicity was higher for Cu salts than for commercial Cu fungicides. Fungal growth response was also different for Cu salts and commercial Cu fungicides, but only in the long-term. High Cu amendments using Cu salts stimulated fungal growth, whereas for commercial Cu fungicides, these concentrations inhibited fungal growth. Thus, the use of products similar to those used in commercial fungicides is a recommended practice for Cu risk assessments in soil.}, }
@article {pmid31750314, year = {2019}, author = {Gupta, VVSR and Zhang, B and Penton, CR and Yu, J and Tiedje, JM}, title = {Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil.}, journal = {Frontiers in molecular biosciences}, volume = {6}, number = {}, pages = {115}, pmid = {31750314}, issn = {2296-889X}, abstract = {Summer-growing perennial grasses such as Panicum coloratum L. cv. Bambatsi (Bambatsi panic), Chloris gayana Kunth cv. Katambora (Rhodes grass) and Digitaria eriantha Steud. cv. Premier (Premier digit grass) growing in the poor fertility sandy soils in the Mediterranean regions of southern Australia and western Australia mainly depend upon soil N and biological N inputs through diazotrophic (free living or associative) N fixation. We investigated the community composition and diversity (nifH-amplicon sequencing), abundance (qPCR) and functional capacity (15N incubation assay) of the endophytic diazotrophic community in the below and above ground plant parts of field grown and unfertilized grasses. Results showed a diverse and abundant diazotrophic community inside plant both above and below-ground and there was a distinct diazotrophic assemblage in the different plant parts in all the three grasses. There was a limited difference in the diversity between leaves, stems and roots except that Panicum grass roots harbored greater species richness. Nitrogen fixation potentials ranged between 0.24 and 5.9 mg N kg-1 day-1 and N fixation capacity was found in both the above and below ground plant parts. Results confirmed previous reports of plant species-based variation and that Alpha-Proteobacteria were the dominant group of nifH-harboring taxa both in the belowground and aboveground parts of the three grass species. Results also showed a well-structured nifH-harboring community in all plant parts, an example for a functional endophytic community. Overall, the variation in the number and identity of module hubs and connectors among the different plant parts suggests that co-occurrence patterns within the nifH-harboring community specific to individual compartments and local environments of the niches within each plant part may dictate the overall composition of diazotrophs within a plant.}, }
@article {pmid31749830, year = {2019}, author = {Guo, J and Quensen, JF and Sun, Y and Wang, Q and Brown, CT and Cole, JR and Tiedje, JM}, title = {Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {957}, pmid = {31749830}, issn = {1664-8021}, abstract = {Shotgun metagenomics has greatly advanced our understanding of microbial communities over the last decade. Metagenomic analyses often include assembly and genome binning, computationally daunting tasks especially for big data from complex environments such as soil and sediments. In many studies, however, only a subset of genes and pathways involved in specific functions are of interest; thus, it is not necessary to attempt global assembly. In addition, methods that target genes can be computationally more efficient and produce more accurate assembly by leveraging rich databases, especially for those genes that are of broad interest such as those involved in biogeochemical cycles, biodegradation, and antibiotic resistance or used as phylogenetic markers. Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, SAT-Assembler, HMM-GRASPx, GenSeed-HMM, and MEGAN. We tested these tools using two datasets with known genomes, a synthetic community of artificial reads derived from the genomes of 17 bacteria, shotgun sequence data from a mock community with 48 bacteria and 16 archaea genomes, and a large soil shotgun metagenomic dataset. We compared assemblies of a universal single copy gene (rplB) and two N cycle genes (nifH and nirK). We measured their computational efficiency, sensitivity, specificity, and chimera rate and found Xander and MegaGTA, which both use a probabilistic graph structure to model the genes, have the best overall performance with all three datasets, although MEGAN, a reference matching assembler, had better sensitivity with synthetic and mock community members chosen from its reference collection. Also, Xander and MegaGTA are the only tools that include post-assembly scripts tuned for common molecular ecology and diversity analyses. Additionally, we provide a mathematical model for estimating the probability of assembling targeted genes in a metagenome for estimating required sequencing depth.}, }
@article {pmid31749167, year = {2019}, author = {Ferlian, O and Thakur, MP and Castañeda González, A and San Emeterio, LM and Marr, S and da Silva Rocha, B and Eisenhauer, N}, title = {Soil chemistry turned upside down: a meta-analysis of invasive earthworm effects on soil chemical properties.}, journal = {Ecology}, volume = {}, number = {}, pages = {e02936}, doi = {10.1002/ecy.2936}, pmid = {31749167}, issn = {1939-9170}, support = {TH 2307/1-1//German Research Foundation/ ; FZT 118//German Research Foundation/ ; 677232//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program/ ; }, abstract = {Recent studies have shown that invasive earthworms can dramatically reduce native biodiversity, both above and below the ground. However, we still lack a synthetic understanding of the underlying mechanisms behind these changes, such as whether earthworm effects on soil chemical properties drive such relationships. Here, we investigated the effects of invasive earthworms on soil chemical properties (pH, water content, and the stocks and fluxes of carbon, nitrogen, and phosphorus) by conducting a meta-analysis. Invasive earthworms generally increased soil pH, indicating that the removal of organic layers and the upward transport of more base-rich mineral soil caused a shift in soil pH. Moreover, earthworms significantly decreased soil water content, suggesting that the burrowing activities of earthworms may have increased water infiltration of and/or increased evapotranspiration from soil. Notably, invasive earthworms had opposing effects on organic and mineral soil for carbon and nitrogen stocks, with decreases in organic, and increases in mineral soil. Nitrogen fluxes were higher in mineral soil, whereas fluxes in organic soil were not significantly affected by the presence of invasive earthworms, indicating that earthworms mobilize and redistribute nutrients among soil layers and increase overall nitrogen loss from the soil. Invasive earthworm effects on element stocks increased with ecological group richness only in organic soil. Earthworms further decreased ammonium stocks with negligible effects on nitrate stocks in organic soil, whereas they increased nitrate stocks but not ammonium stocks in mineral soil. Notably, all of these results were consistent across forest and grassland ecosystems underlining the generality of our findings. However, we found some significant differences between studies that were conducted in the field (observational and experimental settings) and in the lab, such as that the effects on soil pH decreased from field to lab settings, calling for a careful interpretation of lab findings. Our meta-analysis provides strong empirical evidence that earthworm invasion may lead to substantial changes in soil chemical properties and element cycling in soil. Furthermore, our results can help explain the dramatic effects of invasive earthworms on native biodiversity, for example, shifts towards the dominance of grass species over herbaceous ones, as shown by recent meta-analyses.}, }
@article {pmid31748246, year = {2019}, author = {Tomkovich, S and Lesniak, NA and Li, Y and Bishop, L and Fitzgerald, MJ and Schloss, PD}, title = {The Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine Model.}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31748246}, issn = {2379-5042}, support = {U01 AI124255/AI/NIAID NIH HHS/United States ; }, abstract = {Proton pump inhibitor (PPI) use has been associated with microbiota alterations and susceptibility to Clostridioides difficile infections (CDIs) in humans. We assessed how PPI treatment alters the fecal microbiota and whether treatment promotes CDIs in a mouse model. Mice receiving a PPI treatment were gavaged with 40 mg of omeprazole per kg of body weight during a 7-day pretreatment phase, the day of C. difficile challenge, and the following 9 days. We found that mice treated with omeprazole were not colonized by C. difficile When omeprazole treatment was combined with a single clindamycin treatment, one cage of mice remained resistant to C. difficile colonization, while the other cage was colonized. Treating mice with only clindamycin followed by challenge resulted in C. difficile colonization. 16S rRNA gene sequencing analysis revealed that omeprazole had minimal impact on the structure of the murine microbiota throughout the 16 days of omeprazole exposure. These results suggest that omeprazole treatment alone is not sufficient to disrupt microbiota resistance to C. difficile infection in mice that are normally resistant in the absence of antibiotic treatment.IMPORTANCE Antibiotics are the primary risk factor for Clostridioides difficile infections (CDIs), but other factors may also increase a person's risk. In epidemiological studies, proton pump inhibitor (PPI) use has been associated with CDI incidence and recurrence. PPIs have also been associated with alterations in the human intestinal microbiota in observational and interventional studies. We evaluated the effects of the PPI omeprazole on the structure of the murine intestinal microbiota and its ability to disrupt colonization resistance to C. difficile We found omeprazole treatment had minimal impact on the murine fecal microbiota and did not promote C. difficile colonization. Further studies are needed to determine whether other factors contribute to the association between PPIs and CDIs seen in humans or whether aspects of murine physiology may limit its utility to test these types of hypotheses.}, }
@article {pmid31743949, year = {2020}, author = {Weber, L and González-Díaz, P and Armenteros, M and Ferrer, VM and Bretos, F and Bartels, E and Santoro, AE and Apprill, A}, title = {Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys.}, journal = {Environmental microbiology}, volume = {22}, number = {1}, pages = {499-519}, pmid = {31743949}, issn = {1462-2920}, support = {//Dalio Foundation/ ; 1736288//Division of Ocean Sciences/ ; //National Science Foundation/ ; //Cuban Center for Inspection and Environmental Control/ ; }, abstract = {There are a few baseline reef-systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected 'crown jewel' offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta-diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.}, }
@article {pmid31742865, year = {2019}, author = {Geesink, P and Wegner, CE and Probst, AJ and Herrmann, M and Dam, HT and Kaster, AK and Küsel, K}, title = {Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14865}, pmid = {31742865}, issn = {1462-2920}, support = {2016 FGI 0024//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; CRC 1076//Collaborative Research Centre AquaDiva/ ; ANR-10-INBS-09//France Génomique and French Bioinformatics Institute/ ; ANR-11-INBS-0013//France Génomique and French Bioinformatics Institute/ ; //LABGeM (CEA/Genoscope &amp; CNRS UMR8030)/ ; SAS-2015-HKI-LWC//Leibniz Research Cluster InfectoOptics/ ; //Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen/ ; 41-5507-2016//Strategy and Innovation Grant from the Free State of Thuringia/ ; //Agence Nationale pour la Recherche/ ; //Deutsche Forschungsgemeinschaft/ ; //Friedrich Schiller University Jena/ ; }, abstract = {Subsurface ecosystems like groundwater harbour diverse microbial communities, including small-sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates (Cand. Roizmanbacterium ADI133) from oligotrophic groundwater using mini-metagenomics and monitored its spatio-temporal distribution using 16S rRNA gene analyses. A Roizmanbacteria-specific quantitative PCR assay allowed us to track its abundance over the course of 1 year within eight groundwater wells along a 5.4 km hillslope transect, where Roizmanbacteria reached maximum relative abundances of 2.3%. In-depth genomic analyses suggested that Cand. Roizmanbacterium ADI133 is a lactic acid fermenter, potentially able to utilize a range of complex carbon substrates, including cellulose. We hypothesize that it attaches to host cells using a trimeric autotransporter adhesin and inhibits their cell wall biosynthesis using a toxin-antitoxin system. Network analyses based on correlating Cand. Roizmanbacterium ADI133 abundances with amplicon sequencing-derived microbial community profiles suggested one potential host organism, classified as a member of the class Thermodesulfovibrionia (Nitrospirae). By providing lactate as an electron donor Cand. Roizmanbacterium ADI133 potentially mediates the transfer of carbon to other microorganisms and thereby is an important connector in the microbial community.}, }
@article {pmid31741310, year = {2019}, author = {Alves, KJ and da Silva, MCP and Cotta, SR and Ottoni, JR and van Elsas, JD and de Oliveira, VM and Andreote, FD}, title = {Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, doi = {10.1007/s42770-019-00162-7}, pmid = {31741310}, issn = {1678-4405}, support = {Finance Code 001.//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.}, }
@article {pmid31741007, year = {2019}, author = {Hayek, M and Baraquet, C and Lami, R and Blache, Y and Molmeret, M}, title = {The Marine Bacterium Shewanella woodyi Produces C8-HSL to Regulate Bioluminescence.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01454-z}, pmid = {31741007}, issn = {1432-184X}, abstract = {Quorum sensing (QS), a cell-to-cell communication system involved in the synchronization of bacterial behavior in a cell-density-dependent manner has been shown to control phenotypes such as luminescence, virulence, and biofilm formation. The marine strain, Shewanella woodyi MS32 has been identified as a luminous bacterium. Very little information is known on this bacterium, in particular if its luminescence and biofilm formation are controlled by QS. In this study, we have demonstrated that S. woodyi MS32 emits luminescence in planktonic and sessile conditions. The putative QS regulatory genes homologous to luxI and luxR identified in the S. woodyi MS32 genome, named swoI and swoR, are divergently transcribed and are not genetically linked to the lux operon in contrast with its closest parent Shewanella hanedai and with Aliivibrio fischeri. Interestingly, the phylogenetic analysis based on the SwoI and SwoR sequences shows that a separate horizontal gene transfer (HGT) occurred for the regulatory genes and for the lux operon. Functional analyses demonstrate that the swoI and swoR mutants were non-luminescent. Expression of lux genes was impaired in the QS regulatory mutants. N-octanoyl-L-homoserine lactone (C8-HSL) identified using liquid chromatography mass spectrometry in the wild-type strain (but not in ΔswoI) can induce S. woodyi luminescence. No significant difference has been detected between the wild-type and mutants on adhesion and biofilm formation in the conditions tested. Therefore, we have demonstrated that the luxCDABEG genes of S. woodyi MS32 are involved in luminescence emission and that the swoR/swoI genes, originated from a separate HGT, regulate luminescence through C8-HSL production.}, }
@article {pmid31737577, year = {2019}, author = {Khan, S and Voordouw, MJ and Hill, JE}, title = {Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {374}, pmid = {31737577}, issn = {2235-2988}, abstract = {Gardnerella spp. are hallmarks of bacterial vaginosis, a clinically significant dysbiosis of the vaginal microbiome. Gardnerella has four subgroups (A, B, C, and D) based on cpn60 sequences. Multiple subgroups are often detected in individual women, and interactions between these subgroups are expected to influence their population dynamics and associated clinical signs and symptoms of bacterial vaginosis. In the present study, contact-independent and contact-dependent interactions between the four Gardnerella subgroups were investigated in vitro. The cell free supernatants of mono- and co-cultures had no effect on growth rates of the Gardnerella subgroups suggesting that there are no contact-independent interactions (and no contest competition). For contact-dependent interactions, mixed communities of 2, 3, or 4 subgroups were created and the initial (0 h) and final population sizes (48 h) were quantified using subgroup-specific PCR. Compared to the null hypothesis of neutral interactions, most (69.3%) of the mixed communities exhibited competition. Competition reduced the growth rates of subgroups A, B, and C. In contrast, the growth rate of subgroup D increased in the presence of the other subgroups. All subgroups were able to form biofilm alone and in mixed communities. Our study suggests that there is scramble competition among Gardnerella subgroups, which likely contributes to the observed distributions of Gardnerella spp. in vaginal microbiomes and the formation of the multispecies biofilms characteristic of bacterial vaginosis.}, }
@article {pmid31737020, year = {2019}, author = {Del Frari, G and Gobbi, A and Aggerbeck, MR and Oliveira, H and Hansen, LH and Ferreira, RB}, title = {Fungicides and the Grapevine Wood Mycobiome: A Case Study on Tracheomycotic Ascomycete Phaeomoniella chlamydospora Reveals Potential for Two Novel Control Strategies.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1405}, pmid = {31737020}, issn = {1664-462X}, abstract = {Phaeomoniella chlamydospora is a tracheomycotic fungus that colonizes the xylem of grapevines (Vitis vinifera L.), causing wood discoloration, brown wood streaking, gummosis, and wood necrosis, which negatively affect the overall health, productivity, and life span of vines. Current control strategies to prevent or cope with P. chlamydospora infections are frequently ineffective. Moreover, it is unclear how fungicides commonly applied in vineyards against downy and powdery mildew agents affect the wood mycobiome, including wood pathogens such as P. chlamydospora. In this study, we used next-generation sequencing to assess the effects of foliar spray of grapevines with inorganic (copper oxychloride and sulfur), synthetic (penconazole and fosetyl-aluminum), and natural (Blad) fungicides currently used against the downy and powdery mildews. The subjects of our investigation were (i) the resident wood mycobiome, (ii) the early colonization by a consortium of fungal wood endophytes (ACEA1), (iii) the wood colonization success of P. chlamydospora, and (iv) the in planta interaction between P. chlamydospora and ACEA1, under greenhouse conditions, in rooted grapevine cuttings of cv. Cabernet Sauvignon. The data obtained suggest that the resident mycobiome is affected by different fungicide treatments. In addition, the early colonization success of the endophytes composing ACEA1 varied in response to fungicides, with relative abundances of some taxa being overrepresented or underrepresented when compared with the control. The wood colonization by P. chlamydospora comported significant changes in the mycobiome composition, and in addition, it was greatly affected by the foliar spray with Blad, which decreased the relative abundance of this pathogen 12-fold (4.9%) when compared with the control (60.7%) and other treatments. The presence of the pathogen also decreased considerably when co-inoculated into the plant with ACEA1, reaching relative abundances between 13.9% and 2.0%, depending on the fungicide treatment applied. This study shows that fungicides sprayed to prevent infections of powdery and downy mildews have an effect on non-target fungi that colonize the endosphere of grapevines. We suggest two potential control strategies to fight P. chlamydospora, namely, the foliar spray with Blad and the use of ACEA1. Further studies to confirm these results are required.}, }
@article {pmid31736494, year = {2019}, author = {Villela, HDM and Vilela, CLS and Assis, JM and Varona, N and Burke, C and Coil, DA and Eisen, JA and Peixoto, RS}, title = {Prospecting Microbial Strains for Bioremediation and Probiotics Development for Metaorganism Research and Preservation.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {152}, pages = {}, doi = {10.3791/60238}, pmid = {31736494}, issn = {1940-087X}, abstract = {Pollution affects all biomes. Marine environments have been particularly impacted, especially coral reefs, one of the most sensitive ecosystems on Earth. Globally, 4.5 billion people are economically dependent on the sea, where most of their livelihood is provided by coral reefs. Corals are of great importance and therefore their extinction leads to catastrophic consequences. There are several possible solutions to remediate marine pollutants and local contamination, including bioremediation. Bioremediation is the capacity of organisms to degrade contaminants. The approach presents several advantages, such as sustainability, relatively low cost, and the fact that it can be applied in different ecosystems, causing minimal impacts to the environment. As an extra advantage, the manipulation of endogenous microbiomes, including putative beneficial microorganisms for corals (pBMCs), may have probiotic effects for marine animals. In this context, the use of the two approaches, bioremediation and pBMC inoculation combined, could be promising. This strategy would promote the degradation of specific pollutants that can be harmful to corals and other metaorganisms while also increasing host resistance and resilience to deal with pollution and other threats. This method focuses on the selection of pBMCs to degrade two contaminants: the synthetic estrogen 17a-ethinylestradiol (EE2) and crude oil. Both have been reported to negatively impact marine animals, including corals, and humans. The protocol describes how to isolate and test bacteria capable of degrading the specific contaminants, followed by a description of how to detect some putative beneficial characteristics of these associated microbes to their coral host. The methodologies described here are relatively cheap, easy to perform, and highly adaptable. Almost any kind of soluble target compound can be used instead of EE2 and oil.}, }
@article {pmid31736217, year = {2020}, author = {Paver, SF and Newton, RJ and Coleman, ML}, title = {Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry.}, journal = {Environmental microbiology}, volume = {22}, number = {1}, pages = {433-446}, pmid = {31736217}, issn = {1462-2920}, support = {OCE-1830011//Division of Ocean Sciences/ ; NA14OAR170095//Illinois-Indiana Sea Grant/ ; //UChicago Women's Board/ ; }, abstract = {The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI-B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI-C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.}, }
@article {pmid31734636, year = {2019}, author = {Sikder, MNA and Xu, H}, title = {Seasonal variations in colonization dynamics of periphytic protozoa in coastal waters of the Yellow Sea, northern China.}, journal = {European journal of protistology}, volume = {72}, number = {}, pages = {125643}, doi = {10.1016/j.ejop.2019.125643}, pmid = {31734636}, issn = {1618-0429}, abstract = {The colonization features of periphytic protozoa have proved to be a useful tool for indicating water quality status in aquatic ecosystems. In order to reveal the seasonal variations in colonization dynamics of the protozoa, a 1-year baseline survey was carried out in coastal waters of the Yellow Sea, northern China. Using glass slides as artificial substrates, a total of 240 slides were collected at a depth of 1 m in four seasons after colonization periods of 3, 7, 10, 14, 21, and 28 days. A total of 122 ciliate species were identified with 21 dominant species. The colonization dynamics of the protozoa were well fitted to the MacArthur-Wilson and logistic models in all four seasons (P < 0.05). However, the equilibrium species numbers (Seq), colonization rates (G), and the time to 90% Seq (T90%) represented a clear seasonal variability: (1) more or less similar levels in spring and autumn (Seq = 29/23; G = 0.301/0.296; T90%=7.650/7.779); (2) with a significant difference in summer and winter (Seq = 32/121; G = 0.708/0.005; T90% = 3.252/479.705). Multivariate approaches demonstrated that the exposure time for the species composition and community structure of the protozoa to an equilibrium period were 10-14 days in spring and autumn, but less and more time periods were needed in summer and winter, respectively. Based on the results, we suggest that the colonization dynamics of periphytic protozoa were different within four seasons, and an optimal sampling strategy for monitoring surveys should be modified during different seasons in marine ecosystems.}, }
@article {pmid31734395, year = {2020}, author = {Clauwaert, P and De Paepe, J and Jiang, F and Alonso-Fariñas, B and Vaiopoulou, E and Verliefde, A and Rabaey, K}, title = {Electrochemical tap water softening: A zero chemical input approach.}, journal = {Water research}, volume = {169}, number = {}, pages = {115263}, doi = {10.1016/j.watres.2019.115263}, pmid = {31734395}, issn = {1879-2448}, mesh = {Electrodes ; Ion Exchange ; *Water Purification ; *Water Softening ; }, abstract = {Electrochemical water softening was proposed as a sustainable alternative for ion exchange softening, avoiding the input of salt to drinking water and the production of a concentrated brine. Here we demonstrated two novel modes of operation combining an electrochemical cell with a fluidized bed crystallizer. The first approach relied on an electrochemical cell consisting of an anode and cathode separated by a cation or anion exchange membrane. The feed water was first directed into a crystallizer where it was blended with alkaline cathode effluent. The effluent of the crystallizer, softened water, was in part recirculated to the cathode to generate alkalinity, in part to the anode compartment, where the pH was again decreased. Average removal efficiencies for calcium and magnesium of 75-86% and 7-21% respectively, could be sustainably reached, at a specific energy consumption of 7.0-10.1 kWh kg-1 CaCO3 (0.86-1.39 kWh m-3 water). This configuration allowed reagent-free water softening, albeit with an effluent with a pH between 3.0 and 3.6. In a second mode of operation, the process influent to soften was also directed to the crystallizer and recirculated over the cathode, which was separated from the anode using an anion exchange membrane. In this mode of operation, the cathode effluent was sent through the crystallizing unit, and the anode compartment was operated in closed-loop. Average calcium and magnesium removal efficiencies of 73-78% and 40-44% were obtained at specific energy consumptions of 5.8-7.5 kWh kg-1 CaCO3 (0.77-0.88 kWh m-3 water). Although the softened water had an elevated pH (∼9.4), the advantage of this configuration is concomitant removal of anions and the formation of acids/disinfectant in the anode compartment. Both methods of operation thus showed reagent-free water softening at a relatively low specific energy consumption. These novel methods of softening could be used in remote locations where access to chemicals or discharge of ion exchange brines proves to be difficult, or in case addition of chemicals for softening is unwanted. Further research is needed to further decrease the specific energy consumption during long-term operation.}, }
@article {pmid31732938, year = {2019}, author = {Dutzan, N and Abusleme, L}, title = {T Helper 17 Cells as Pathogenic Drivers of Periodontitis.}, journal = {Advances in experimental medicine and biology}, volume = {1197}, number = {}, pages = {107-117}, doi = {10.1007/978-3-030-28524-1_9}, pmid = {31732938}, issn = {0065-2598}, mesh = {Animals ; Cell Differentiation ; Disease Models, Animal ; Humans ; Inflammation ; Interleukin-17/immunology ; *Periodontitis/physiopathology ; *Th17 Cells/cytology/immunology ; }, abstract = {T helper 17 (Th17) cells were first described as a T helper subset involved in the pathogenesis of experimental autoimmune inflammation. Since then, these cells have been described as orchestrators of immunopathology in several human inflammatory conditions including psoriasis, rheumatoid arthritis, and inflammatory bowel disease. More recently, the crucial role of Th17 cells in the regulation of immunity and protection of barrier sites has been unveiled. In the present work, we review the available evidence regarding Th17 cells in health and disease with a focus on the oral mucosa and their role in periodontitis pathogenesis. Recent mechanistic studies in animal models have demonstrated that interleukin-17A (IL-17A) and Th17 cells are critical mediators for alveolar bone destruction during periodontal inflammation. Observations in a cohort of patients with naturally occurring impaired Th17 cell differentiation supported these findings. However, interventional studies are needed to conclusively implicate Th17 cells in the immunopathogenesis of human alveolar bone and tissue destruction that characterize periodontitis.}, }
@article {pmid31732575, year = {2020}, author = {Custer, GF and van Diepen, LTA and Stump, WL}, title = {Structural and Functional Dynamics of Soil Microbes following Spruce Beetle Infestation.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {3}, pages = {}, doi = {10.1128/AEM.01984-19}, pmid = {31732575}, issn = {1098-5336}, abstract = {As the range of bark beetles expands into new forests and woodlands, the need to understand their effects on multiple trophic levels becomes increasingly important. To date, much attention has been paid to the aboveground processes affected by bark beetle infestation, with a focus on photoautotrophs and ecosystem level processes. However, indirect effects of bark beetle on belowground processes, especially the structure and function of soil microbiota remains largely a black box. Our study examined the impacts of bark beetle-induced tree mortality on soil microbial community structure and function using high-throughput sequencing of the soil bacterial and fungal communities and measurements of extracellular enzyme activities. The results suggest bark beetle infestation affected edaphic conditions through increased soil water content, pH, electrical conductivity, and carbon/nitrogen ratio and altered bulk and rhizosphere soil microbial community structure and function. Finally, increased enzymatic activity suggests heightened microbial decomposition following bark beetle infestation. With this increase in enzymatic activity, nutrients trapped in organic substrates may become accessible to seedlings and potentially alter the trajectory of forest regeneration. Our results indicate the need for incorporation of microbial processes into ecosystem level models.IMPORTANCE Belowground impacts of bark beetle infestation have not been explored as thoroughly as their aboveground counterparts. In order to accurately model impacts of bark beetle-induced tree mortality on carbon and nutrient cycling and forest regeneration, the intricacies of soil microbial communities must be examined. In this study, we investigated the structure and function of soil bacterial and fungal communities following bark beetle infestation. Our results show bark beetle infestation to impact soil conditions, as well as soil microbial community structure and function.}, }
@article {pmid31732073, year = {2019}, author = {Lee, M and Song, JH and Park, JM and Chang, JY}, title = {Bacterial diversity in Korean temple kimchi fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {126}, number = {}, pages = {108592}, doi = {10.1016/j.foodres.2019.108592}, pmid = {31732073}, issn = {1873-7145}, abstract = {Kimchi is manufactured using salted vegetables and various seasonings, including garlic, scallion, and jeotgal (fermented seafood). However, similar to vegan diets, Korean temple food does not contain animal products (meat- and seafood-free) and is restricted to five pungent herbs: garlic, scallion, leek, onions, and chives. In this study, we investigated the fermentation characteristics of 25 kimchi samples from traditional Korean temples or commercial sources using Illumina MiSeq sequencing. The initial pH of the kimchi samples ranged from 5.05 to 5.95 and the bacterial diversity-index showed a significantly high value in temple-style kimchi. Moreover, differences in microbial community were significantly reflected in kimchi types using non-metric multidimensional scaling plots and analysis of similarity. Additionally, the distribution patterns of the core bacterial genera differed according to kimchi type, especially during early phases of fermentation. These findings offer novel insights into the microbial ecology and quality characteristics of kimchi lacking vital ingredients, which are generally reported based on the origin of the microorganisms.}, }
@article {pmid31731161, year = {2020}, author = {Ma, W and Li, J and Gao, Y and Xing, F and Sun, S and Zhang, T and Zhu, X and Chen, C and Li, Z}, title = {Responses of soil extracellular enzyme activities and microbial community properties to interaction between nitrogen addition and increased precipitation in a semi-arid grassland ecosystem.}, journal = {The Science of the total environment}, volume = {703}, number = {}, pages = {134691}, doi = {10.1016/j.scitotenv.2019.134691}, pmid = {31731161}, issn = {1879-1026}, abstract = {Both atmospheric nitrogen (N) deposition and precipitation can strongly impact below-ground biogeochemical processes. Soil extracellular enzymes activities (EEAs) and microorganisms are considered as the key agents in ecosystem nutrient cycling. However, how the interaction between increasing N deposition and precipitation may affect soil EEAs and microbes remain poorly understood. In a 5-year field experiment in a meadow steppe in northern China, we tested the effects of N addition (N0, 0; N1, 5; N2, 10 g N m-2 yr-1) and increased precipitation (W0, ambient precipitation; W1, increase of 15% ambient precipitation; W2, increase of 30% ambient precipitation) on soil EEAs, microbial and chemical properties. Results showed that their interaction significantly affected all hydrolase activities, except for β-1,4-xylosidase (βX). Furthermore, increased precipitation and N addition interactively affected bacterial gene copies (P ≤ 0.05), and increased precipitation comparatively had a stronger effects. The results on the combination of N addition and increased precipitation showed that increased precipitation alleviated the positive effects of N addition on soil EEAs. This implies that the effects of either treatment alone on grassland biogeochemical processes may be alleviated by their simultaneous occurrence. Our results suggested that soil EEAs were mainly controlled by the content of N and phosphorus (P), and the ratio of C: N and C: P. Therefore, soil element content and stoichiometry could better explain the responses of EEAs to global changes. Moreover, soil microbial communities were mainly controlled by soil P content. Overall, our study highlights that the interaction between N deposition and precipitation may play a vital role in predicting the responses of soil enzyme activities to global changes in grassland ecosystems.}, }
@article {pmid31730850, year = {2019}, author = {Salazar, G and Paoli, L and Alberti, A and Huerta-Cepas, J and Ruscheweyh, HJ and Cuenca, M and Field, CM and Coelho, LP and Cruaud, C and Engelen, S and Gregory, AC and Labadie, K and Marec, C and Pelletier, E and Royo-Llonch, M and Roux, S and Sánchez, P and Uehara, H and Zayed, AA and Zeller, G and Carmichael, M and Dimier, C and Ferland, J and Kandels, S and Picheral, M and Pisarev, S and Poulain, J and ,  and Acinas, SG and Babin, M and Bork, P and Bowler, C and de Vargas, C and Guidi, L and Hingamp, P and Iudicone, D and Karp-Boss, L and Karsenti, E and Ogata, H and Pesant, S and Speich, S and Sullivan, MB and Wincker, P and Sunagawa, S}, title = {Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.}, journal = {Cell}, volume = {179}, number = {5}, pages = {1068-1083.e21}, pmid = {31730850}, issn = {1097-4172}, abstract = {Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.}, }
@article {pmid31730030, year = {2019}, author = {Hofmann, K and Huptas, C and Doll, EV and Scherer, S and Wenning, M}, title = {Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003851}, pmid = {31730030}, issn = {1466-5034}, abstract = {A polyphasic approach was used to investigate the taxonomic status of two bacterial strains, WS 5072T and WS 5092, isolated from skimmed milk concentrate and raw cow's milk. The 16S rRNA and rpoD gene sequences affiliated the strains to the same, hitherto unknown, Pseudomonas species. Further examinations of the draft genomes based on multilocus sequence analysis and average nucleotide identity confirmed the presence of a novel Pseudomonas species. It was most closely related to Pseudomonas fragi DSM 3456T with 86.3 % ANIm. The DNA G+C content of strain WS 5072T was 56.3 mol%. Cells were aerobic, Gram-negative, catalase and oxidase positive, rod-shaped and motile. Growth occurred at 4-34 °C, pH 5.5-8.0 and with salt concentrations of up to 7 %. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The dominating quinone was Q-9 with 94 %, with noticeable amounts of Q-8 (5 %) and traces of Q-7 and Q-10. Fatty acid profiles showed a composition common for Pseudomonas with the major component C16 : 0. Based on these results, the novel species Pseudomonas saxonica sp. nov. is proposed, with the type strain WS 5072T (=DSM 108989T=LMG 31234T) and the additional strain WS 5092 (=DSM 108990=LMG 31235).}, }
@article {pmid31728602, year = {2019}, author = {Quero, GM and Celussi, M and Relitti, F and Kovačević, V and Del Negro, P and Luna, GM}, title = {Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01451-2}, pmid = {31728602}, issn = {1432-184X}, abstract = {The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.}, }
@article {pmid31728601, year = {2019}, author = {Chen, H and Wang, L and Wang, X and Wang, X and Liu, H and Yin, Y}, title = {Distribution and Strain Diversity of Immunoregulating Segmented Filamentous Bacteria in Human Intestinal Lavage Samples.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01441-4}, pmid = {31728601}, issn = {1432-184X}, abstract = {Segmented filamentous bacteria (SFB) are well known for their functions in the immunoregulation of hosts including the promotion of Th17 cell differentiation, B cell maturation, and immune system development. However, most analyses of SFB have focused on animal models, and thus, investigation of SFB prevalence in humans and their roles in human immunoregulation and health is needed. Although little is known overall of SFB prevalence in humans, they are characteristically abundant in animals during weaning. In this study, SFB-like bacteria were detected in ileal lavage samples from human children that were aged between 1 to 17 years old by scanning electron microscopy (SEM) analysis, and their insertion into the mucosa was also observed. In addition, the expression of SFB flagellin at the human bacterial interface was observed by immunohistochemistry (IHC) and western blot. Moreover, two pairs of primers specific for SFB, but targeting different genes, were used to detect SFB in human intestinal lavage samples. These analyses indicated that SFB were present in over 50% of patient ileal samples independent of age. High-throughput gene sequencing indicated that different SFB strains were detected among samples. Between nine and 23 SFB flagellin gene operational taxonomic units were identified. In addition to evaluating the prevalence of SFB in human samples, correlations between SFB presence and chief complaints of clinical symptoms were evaluated, as well as the relationship between SFB and patient serum immunoglobulin concentrations. SFB prevalence was significantly higher in hematochezia patients (68%) than in abdominal pain (56.10%) and diarrhea (43.75%) patients. Furthermore, the concentrations of serum IgA, IgM, and IgE, were similar between SFB-positive and SFB-negative patient groups, although IgG concentrations were significantly higher in the SFB-negative group.}, }
@article {pmid31728526, year = {2020}, author = {Corrêa, FB and Saraiva, JP and Stadler, PF and da Rocha, UN}, title = {TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.}, journal = {Nucleic acids research}, volume = {48}, number = {D1}, pages = {D626-D632}, doi = {10.1093/nar/gkz994}, pmid = {31728526}, issn = {1362-4962}, abstract = {Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.}, }
@article {pmid31728072, year = {2019}, author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, MR and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and ,  and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J}, title = {Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2579}, doi = {10.1038/s41564-019-0617-0}, pmid = {31728072}, issn = {2058-5276}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid31727695, year = {2019}, author = {Aremu, BR and Prigent-Combaret, C and Babalola, OO}, title = {Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16.}, journal = {Microbiology resource announcements}, volume = {8}, number = {46}, pages = {}, pmid = {31727695}, issn = {2576-098X}, abstract = {Here, we report the draft genome sequence of the endophytic Bacillus velezensis strain ZeaDK315Endo16, isolated from DK315 maize from Lyon, France. B. velezensis ZeaDK315Endo16 exhibits a suppressive ability toward Fusarium graminearum, a widely known threat to maize production and quality.}, }
@article {pmid31727118, year = {2019}, author = {Werner, J and Géron, A and Kerssemakers, J and Matallana-Surget, S}, title = {mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {21}, pmid = {31727118}, issn = {1745-6150}, abstract = {Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPies' workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/. REVIEWER: This article was reviewed by Dr. Wilson Wen Bin Goh.}, }
@article {pmid31726596, year = {2020}, author = {Boada, E and Santos-Clotas, E and Bertran, S and Cabrera-Codony, A and Martín, MJ and Bañeras, L and Gich, F}, title = {Potential use of Methylibium sp. as a biodegradation tool in organosilicon and volatile compounds removal for biogas upgrading.}, journal = {Chemosphere}, volume = {240}, number = {}, pages = {124908}, doi = {10.1016/j.chemosphere.2019.124908}, pmid = {31726596}, issn = {1879-1298}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Biofuels/*analysis ; Bioreactors/*microbiology ; Burkholderiales/*growth &amp; development ; Organosilicon Compounds/*analysis ; Volatile Organic Compounds/*analysis ; Water Purification/methods ; }, abstract = {Organosilicon compounds are the most undesirable compounds for the energy recovery of biogas. These compounds are still resistant to biodegradation when biotechnologies are considered for biogas purification. Herein we isolated 52 bacterial species from anaerobic batch enrichment cultures (BEC) saturated with D4 and from an anaerobic lab-scale biotrickling filter (BTF) fed with a gas flow containing D4 as unique carbon source. Among those Methylibium sp. and Pseudomonas aeruginosa showed the highest capacity to remove D4 (53.04% ± 0.03 and 24.42% ± 0.02, respectively). Contrarily, co-culture evaluation treatment for the biodegradation of siloxanes together with volatile organic compounds removed a lower concentration of D4 compared to toluene and limonene, which were completely removed. Remarkably, the siloxane D5 proved to be more biodegradable than D4. Substrates removal values achieved by Methylibium sp. suggested that this bacterial isolate could be used in biological removal technologies of siloxanes.}, }
@article {pmid31726031, year = {2019}, author = {Rolhion, N and Chassaing, B and Nahori, MA and de Bodt, J and Moura, A and Lecuit, M and Dussurget, O and Bérard, M and Marzorati, M and Fehlner-Peach, H and Littman, DR and Gewirtz, AT and Van de Wiele, T and Cossart, P}, title = {A Listeria monocytogenes Bacteriocin Can Target the Commensal Prevotella copri and Modulate Intestinal Infection.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {5}, pages = {691-701.e5}, pmid = {31726031}, issn = {1934-6069}, support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {Understanding the role of the microbiota components in either preventing or favoring enteric infections is critical. Here, we report the discovery of a Listeria bacteriocin, Lmo2776, which limits Listeria intestinal colonization. Oral infection of conventional mice with a Δlmo2776 mutant leads to a thinner intestinal mucus layer and higher Listeria loads both in the intestinal content and deeper tissues compared to WT Listeria. This latter difference is microbiota dependent, as it is not observed in germ-free mice. Strikingly, it is phenocopied by pre-colonization of germ-free mice before Listeria infection with Prevotella copri, an abundant gut-commensal bacteria, but not with the other commensals tested. We further show that Lmo2776 targets P. copri and reduces its abundance. Together, these data unveil a role for P.copri in exacerbating intestinal infection, highlighting that pathogens such as Listeria may selectively deplete microbiota bacterial species to avoid excessive inflammation.}, }
@article {pmid31723261, year = {2019}, author = {Schada von Borzyskowski, L and Severi, F and Krüger, K and Hermann, L and Gilardet, A and Sippel, F and Pommerenke, B and Claus, P and Cortina, NS and Glatter, T and Zauner, S and Zarzycki, J and Fuchs, BM and Bremer, E and Maier, UG and Amann, RI and Erb, TJ}, title = {Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle.}, journal = {Nature}, volume = {575}, number = {7783}, pages = {500-504}, doi = {10.1038/s41586-019-1748-4}, pmid = {31723261}, issn = {1476-4687}, abstract = {One of the most abundant sources of organic carbon in the ocean is glycolate, the secretion of which by marine phytoplankton results in an estimated annual flux of one petagram of glycolate in marine environments1. Although it is generally accepted that glycolate is oxidized to glyoxylate by marine bacteria2-4, the further fate of this C2 metabolite is not well understood. Here we show that ubiquitous marine Proteobacteria are able to assimilate glyoxylate via the β-hydroxyaspartate cycle (BHAC) that was originally proposed 56 years ago5. We elucidate the biochemistry of the BHAC and describe the structure of its key enzymes, including a previously unknown primary imine reductase. Overall, the BHAC enables the direct production of oxaloacetate from glyoxylate through only four enzymatic steps, representing-to our knowledge-the most efficient glyoxylate assimilation route described to date. Analysis of marine metagenomes shows that the BHAC is globally distributed and on average 20-fold more abundant than the glycerate pathway, the only other known pathway for net glyoxylate assimilation. In a field study of a phytoplankton bloom, we show that glycolate is present in high nanomolar concentrations and taken up by prokaryotes at rates that allow a full turnover of the glycolate pool within one week. During the bloom, genes that encode BHAC key enzymes are present in up to 1.5% of the bacterial community and actively transcribed, supporting the role of the BHAC in glycolate assimilation and suggesting a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.}, }
@article {pmid31722990, year = {2019}, author = {Dominguez-Mirazo, M and Jin, R and Weitz, JS}, title = {Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in &quot;Candidatus Liberibacter asiaticus&quot;.}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31722990}, issn = {2379-5042}, abstract = {Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen &quot;Candidatus Liberibacter asiaticus&quot; is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of &quot;Ca. Liberibacter asiaticus&quot; has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available &quot;Ca. Liberibacter asiaticus&quot; genomes and are classified into three prophage types. Here, we reexamined all 15 &quot;Ca. Liberibacter asiaticus&quot; genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the &quot;Ca. Liberibacter asiaticus&quot; genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 &quot;Ca. Liberibacter asiaticus&quot; strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and &quot;Ca. Liberibacter asiaticus&quot; pathogenicity.IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is &quot;Candidatus Liberibacter asiaticus.&quot; Prior work using mapping-based approaches identified prophage-like sequences in some &quot;Ca. Liberibacter asiaticus&quot; genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in &quot;Ca. Liberibacter asiaticus&quot; from 16 to 33 and identified at least one prophage-like sequence in all &quot;Ca. Liberibacter asiaticus&quot; strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage-expanding the number of prophage types in &quot;Ca. Liberibacter asiaticus&quot; from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of &quot;Ca. Liberibacter asiaticus.&quot;}, }
@article {pmid31721471, year = {2020}, author = {Tyc, O and Putra, R and Gols, R and Harvey, JA and Garbeva, P}, title = {The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom.}, journal = {MicrobiologyOpen}, volume = {9}, number = {1}, pages = {e00954}, pmid = {31721471}, issn = {2045-8827}, support = {864.11.015//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {Endophytic bacteria are known for their ability in promoting plant growth and defense against biotic and abiotic stress. However, very little is known about the microbial endophytes living in the spermosphere. Here, we isolated bacteria from the seeds of five different populations of wild cabbage (Brassica oleracea L) that grow within 15 km of each other along the Dorset coast in the UK. The seeds of each plant population contained a unique microbiome. Sequencing of the 16S rRNA genes revealed that these bacteria belong to three different phyla (Actinobacteria, Firmicutes, and Proteobacteria). Isolated endophytic bacteria were grown in monocultures or mixtures and the effects of bacterial volatile organic compounds (VOCs) on the growth and development on B. oleracea and on resistance against a insect herbivore was evaluated. Our results reveal that the VOCs emitted by the endophytic bacteria had a profound effect on plant development but only a minor effect on resistance against an herbivore of B. oleracea. Plants exposed to bacterial VOCs showed faster seed germination and seedling development. Furthermore, seed endophytic bacteria exhibited activity via volatiles against the plant pathogen F. culmorum. Hence, our results illustrate the ecological importance of the bacterial seed microbiome for host plant health and development.}, }
@article {pmid31721347, year = {2019}, author = {Scheepers, M and Spielmann, J and Boulanger, M and Carnol, M and Bosman, B and De Pauw, E and Goormaghtigh, E and Motte, P and Hanikenne, M}, title = {Intertwined metal homeostasis, oxidative and biotic stress responses in the Arabidopsis frd3 mutant.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.14610}, pmid = {31721347}, issn = {1365-313X}, support = {FRFC-2.4583.08, PDR-T.0206.13 and CDR J.0009.17//Fonds De La Recherche Scientifique - FNRS/ ; NA//Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture/ ; }, abstract = {FRD3 (FERRIC REDUCTASE DEFECTIVE 3) plays a major role in iron (Fe) and zinc (Zn) homeostasis in Arabidopsis. It transports citrate, which enables metal distribution in the plant. An frd3 mutant is dwarf and chlorotic and displays a constitutive Fe-deficiency response and strongly altered metal distribution in tissues. Here, we have examined the interaction between Fe and Zn homeostasis in an frd3 mutant exposed to varying Zn supply. Detailed phenotyping using transcriptomic, ionomic, histochemical and spectroscopic approaches revealed the full complexity of the frd3 mutant phenotype, which resulted from altered transition metal homeostasis, manganese toxicity, and oxidative and biotic stress responses. The cell wall played a key role in these processes, as a site for Fe and hydrogen peroxide accumulation, and displayed modified structure in the mutant. Finally, we showed that Zn excess interfered with these mechanisms and partially restored root growth of the mutant, without reverting the Fe-deficiency response. In conclusion, the frd3 mutant molecular phenotype is more complex than previously described and illustrates how the response to metal imbalance depends on multiple signaling pathways.}, }
@article {pmid31721121, year = {2020}, author = {Kreth, J and Abdelrahman, YM and Merritt, J}, title = {Multiplex Imaging of Polymicrobial Communities-Murine Models to Study Oral Microbiome Interactions.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2081}, number = {}, pages = {107-126}, doi = {10.1007/978-1-4939-9940-8_8}, pmid = {31721121}, issn = {1940-6029}, abstract = {Similar to other mucosal surfaces of the body, the oral cavity hosts a diverse microbial flora that live in polymicrobial biofilm communities. It is the ecology of these communities that are the primary determinants of oral health (symbiosis) or disease (dysbiosis). As such, both symbiosis and dysbiosis are inherently polymicrobial phenomena. In an effort to facilitate studies of polymicrobial communities within rodent models, we developed a suite of synthetic luciferases suitable for multiplexed in situ analyses of microbial ecology and specific gene expression. Using this approach, it is feasible to noninvasively measure multiple luciferase signals in vivo with both spatial and temporal resolution. In the following chapter, we describe the relevant details and protocols used to establish a biophotonic imaging platform for the study of experimental polymicrobial oral biofilms and abscesses in mice. The protocols described here are specifically tailored for use with oral streptococci, but the general strategies are adaptable for a wide range of polymicrobial infection studies using other species.}, }
@article {pmid31720799, year = {2019}, author = {Thomas, P and Shaik, SP}, title = {Molecular Profiling on Surface-Disinfected Tomato Seeds Reveals High Diversity of Cultivation-Recalcitrant Endophytic Bacteria with Low Shares of Spore-Forming Firmicutes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01440-5}, pmid = {31720799}, issn = {1432-184X}, support = {AMAAS Project//National Bureau of Agriculturally Important Microorganisms/ ; }, abstract = {Seeds are known to harbor diverse microorganisms offering protective effects on them with the prospects of quick root colonization at germination, selective recruitment as endophytes, and possible vertical transmission. The study was undertaken to assess the gross seed-internal bacterial community in tomato and to confirm if spore-forming Firmicutes constituted major seed endophytes adopting cultivation versus molecular approach on surface-sterilized seeds. Testing the initial seed wash solutions of &quot;Arka Vikas&quot; and &quot;Arka Abha&quot; cultivars showed > 1000 bacterial cfu per dry seed, largely Bacillus spp. Tissue homogenates from surface-disinfected seeds did not show any cultivable bacteria on enriched media for 1-2 weeks, while 16S rRNA V3-V4 taxonomic profiling revealed a huge bacterial diversity (10-16 phyla per cultivar). Proteobacteria formed the dominant phylum (65.7-69.6% OTUs) followed by Firmicutes, Actinobacteria, Bacteroidetes, and a notable share of Euryarchaeota (1.1-3.1%). Five more phyla appeared common to both cultivars in minor shares (Acidobacteria, Planctomycetes, Chloroflexi, Spirochaetes, Verrucomicrobia) with the ten phyla together constituting 99.6-99.9% OTUs. Class level and family level, the cultivars displayed elevated bacterial diversity, but similar taxonomic profiles. Arka Vikas and Arka Abha showed 114 and 107 genera, respectively, with 63 common genera constituting 96-97% OTUs. Psychrobacter formed the dominant genus. Bacillus and related genera constituted only negligible OTU share (0.16-0.28%). KEGG functional analysis showed metabolism as the major bacterial community role. One-month-old in vitro seedlings showed the activation of some originally uncultivable bacteria uninfluenced by the OTU share. The study reveals a high diversity of cultivation-recalcitrant endophytic bacteria prevailing in tomato seeds with possible vertical transmission and significant roles in plant biology.}, }
@article {pmid31720759, year = {2019}, author = {Liu, L and Wang, S and Chen, J}, title = {Hysteretic response of Microbial Eukaryotic Communities to Gradually Decreased Nutrient Concentrations in Eutrophic Water.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01457-w}, pmid = {31720759}, issn = {1432-184X}, support = {FZHJ15//Oceans and Fisheries Bureau of Fuzhou, China/ ; 31500372//National Natural Science Foundation of China/ ; 31971469//National Natural Science Foundation of China/ ; XRC-17024//Special Foundation for Yong Scientists of Fuzhou University/ ; }, abstract = {External environments to microbial eukaryotic communities often change gradually with time. However, whether the responses of microbial eukaryotic communities to these gradually changed environments are continuous or hysteretic and the mechanisms underlying these responses are largely unknown. Here, we used a microcosm to investigate the temporal variation of microbial eukaryotic communities with the gradually decreased nutrient concentrations (nitrogen and phosphorus). We found the differences of microbial eukaryotic community composition and species richness between the control and treatment groups were low during the days 0 to 12, although the nutrient concentrations decreased rapidly during this period in treatment group. However, these differences were clear during the days 14 to 18, although the nutrient concentrations decreased slowly during this period in treatment group. The mechanisms for these results are that the strong homogenous selection (perhaps due to the biotic factors) during the days 8 to 10 in treatment group might enhance the stability of microbial eukaryotic communities. However, the continuously decreased nutrient concentrations weakened the homogenous selection and promoted the strength of environmental filtering, and therefore resulted in the distinct change of microbial eukaryotic communities during the days 14 to 18 in treatment group. Fungi, Chlorophyta and Chrysophyta which associated with the nutrient removal played important roles in this hysteretic change of microbial eukaryotic communities. Overall, our findings suggest that disentangling the non-linear response of communities to gradual environmental changes is essential for understanding ecosystem restoration and degradation in future.}, }
@article {pmid31719226, year = {2019}, author = {DAS, B and Nair, GB}, title = {Homeostasis and dysbiosis of the gut microbiome in health and disease.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719226}, issn = {0973-7138}, abstract = {The human gastrointestinal tract (GIT) harbors taxonomically and functionally complex microbial ecosystem. The composition of the microbial species in the GIT ecosystem varies among individuals and throughout development. Both environmental factors as well as host genetics influence the composition and homeostasis of GIT microbiome. Intrinsic GIT microbiome can be characterized in terms of diversity, richness, dynamics and resilience. In healthy individual, microbial communities maintain homeostatic equilibrium and are resistant against perturbations. The resilience and resistance to perturbations of the GIT microbial ecosystem are robust but not absolute. Several factors can affect the homeostatic equilibrium of GIT microbiome and lead to dysbiotic microbiome configuration. Taxonomic and/or functional dysbiosis in the GIT microbiome is associated with numerous health disorders like inflammatory bowel disease (IBD), malnutrition, metabolic disorders, asthma and neurodegenerative diseases. In this review, we discuss our current understanding of homeostasis and dysbiosis of the microbial ecology in the human gut and health disorders that are associated with the microbiome dysbiosis.}, }
@article {pmid31719222, year = {2019}, author = {Senapati, T and Kothidar, A and Banerjee, SK and DAS, B}, title = {Insights into the gastrointestinal tract microbiomes of Indian population.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719222}, issn = {0973-7138}, abstract = {Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.}, }
@article {pmid31717367, year = {2019}, author = {An, B and Sam, C and Dries, V and Ruben, S and Christel, V and Mik, VB and Bart, L and Leen, VC}, title = {Comparison of Six Commercial Meat Starter Cultures for the Fermentation of Yellow Mealworm (Tenebrio molitor) Paste.}, journal = {Microorganisms}, volume = {7}, number = {11}, pages = {}, pmid = {31717367}, issn = {2076-2607}, abstract = {In this study, six commercial meat starters, each consisting of a pure strain of a lactic acid-fermenting bacterium (including Lactococcus lactis, Lactobacillus curvatus, L. farciminis, L. plantarum, L. sakei, and Pediococcus acidilactici), were tested for their ability to ferment a paste produced from the yellow mealworm (Tenebrio molitor). During fermentation, microbial counts, pH, and the bacterial community composition were determined. In addition, UPLC-MS was applied to monitor the consumption of glucose and the production of glutamic (Glu) and aspartic (Asp) acid. All tested starters were able to ferment the mealworm paste, judged by a pH reduction from 6.68 to 4.60-4.95 within 72 h. Illumina amplicon sequencing showed that all starters were able to colonize the substrate eciently. Moreover, the introduction of the starter cultures led to the disappearance of Bacillus and Clostridium species, which were the dominant microorganisms in un-inoculated samples. Of the six cultures tested, Lactobacillus farciminis was most promising as its application resulted in the largest increase (±25 mg/100 g of paste) in the content of free glutamic and aspartic acid. These amino acids are responsible for the appreciated umami flavour in fermented food products and might stimulate the acceptance of insects and their consumption.}, }
@article {pmid31715086, year = {2019}, author = {Saiman, L}, title = {Improving outcomes of infections in cystic fibrosis in the era of CFTR modulator therapy.}, journal = {Pediatric pulmonology}, volume = {54 Suppl 3}, number = {}, pages = {S18-S26}, doi = {10.1002/ppul.24522}, pmid = {31715086}, issn = {1099-0496}, abstract = {Currently, available single and dual-combination cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies have favorably altered the life course of individuals with cystic fibrosis (CF) by decreasing morbidities and increasing survival. However, even with CFTR modulator use, questions and challenges remain to optimize the management of lung infections. This review (a) identifies these ongoing challenges and discusses the current understanding of the potential impact of CFTR modulator therapy on infections; (b) describes ongoing research to optimize detection, diagnosis, and treatment of CF microorganisms; and (c) discusses strategies to develop new anti-infective therapies. The CF Foundation has launched the Infection Research Initiative to fund research that will improve our understanding of the complex microbial ecology within the CF lung, improve detection of CF pathogens, optimize current treatment, including long-term chronic therapies, and develop new anti-infective therapies. Ongoing clinical trials to determine the optimal duration of treatment of pulmonary exacerbations and to diagnose and treat nontuberculous mycobacteria represent clinical research paradigms that could be used to answer other complex treatment questions. The anti-infective pipeline includes both existing anti-infective and non-anti-infective agents, many of which are proposed to have unique mechanisms of action in CF. Future studies plan to evaluate short- and long-term clinical effectiveness and impact on infections, of the next generation of CFTR modulator therapy, the highly effective triple-combination therapy, for individuals with CF, homozygous or heterozygous for F508del.}, }
@article {pmid31712738, year = {2020}, author = {De Paepe, K and Verspreet, J and Courtin, CM and Van de Wiele, T}, title = {Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {584-596}, pmid = {31712738}, issn = {1751-7370}, support = {IWT130028//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {The human gut can be viewed as a flow-through system with a short residence time, a high turnover rate and a spatial gradient of physiological conditions. As a consequence, the gut microbiota is exposed to highly fluctuating environmental determinants presented by the host and diet. Here, we assessed the fermentation and colonisation of insoluble wheat bran by faecal microbiota of three individuals at an unprecedented sampling intensity. Time-resolved 16S rRNA gene amplicon sequencing, revealed a dynamic microbial community, characterised by abrupt shifts in composition, delimiting states with a more constant community, giving rise to a succession of bacterial taxa alternately dominating the community over a 72 h timespan. Early stages were dominated by Enterobacteriaceae and Fusobacterium species, growing on the carbohydrate-low, protein rich medium to which wheat bran was supplemented. The onset of wheat bran fermentation, marked by a spike in short chain fatty acid production with an increasing butyrate proportion and an increased endo-1,4-β-xylanase activity, corresponded to donor-dependent proportional increases of Bacteroides ovatus/stercoris, Prevotella copri and Firmicutes species, which were strongly enriched in the bran-attached community. Literature and database searches provided novel insights into the metabolic and growth characteristics underlying the observed succession and colonisation, illustrating the potency of a time-resolved analysis to increase our understanding of gut microbiota dynamics upon dietary modulations.}, }
@article {pmid31712278, year = {2020}, author = {Bencivenga-Barry, NA and Lim, B and Herrera, CM and Trent, MS and Goodman, AL}, title = {Genetic Manipulation of Wild Human Gut Bacteroides.}, journal = {Journal of bacteriology}, volume = {202}, number = {3}, pages = {}, doi = {10.1128/JB.00544-19}, pmid = {31712278}, issn = {1098-5530}, support = {R35 GM118159/GM/NIGMS NIH HHS/United States ; R01 AI129940/AI/NIAID NIH HHS/United States ; R01 DK114793/DK/NIDDK NIH HHS/United States ; R01 AI076322/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; R01 AI138576/AI/NIAID NIH HHS/United States ; }, abstract = {Bacteroides is one of the most prominent genera in the human gut microbiome, and study of this bacterial group provides insights into gut microbial ecology and pathogenesis. In this report, we introduce a negative selection system for rapid and efficient allelic exchange in wild Bacteroides species that does not require any alterations to the genetic background or a nutritionally defined culture medium. In this approach, dual antibacterial effectors normally delivered via type VI secretion are targeted to the bacterial periplasm under the control of tightly regulated anhydrotetracycline (aTC)-inducible promoters. Introduction of aTC selects for recombination events producing the desired genetic modification, and the dual effector design allows for broad applicability across strains that may have immunity to one counterselection effector. We demonstrate the utility of this approach across 21 human gut Bacteroides isolates representing diverse species, including strains isolated directly from human donors. We use this system to establish that antimicrobial peptide resistance in Bacteroides vulgatus is determined by the product of a gene that is not included in the genomes of previously genetically tractable members of the human gut microbiome.IMPORTANCE Human gut Bacteroides species exhibit strain-level differences in their physiology, ecology, and impact on human health and disease. However, existing approaches for genetic manipulation generally require construction of genetically modified parental strains for each microbe of interest or defined medium formulations. In this report, we introduce a robust and efficient strategy for targeted genetic manipulation of diverse wild-type Bacteroides species from the human gut. This system enables genetic investigation of members of human and animal microbiomes beyond existing model organisms.}, }
@article {pmid31710600, year = {2019}, author = {Wilkins, LGE and Leray, M and O'Dea, A and Yuen, B and Peixoto, RS and Pereira, TJ and Bik, HM and Coil, DA and Duffy, JE and Herre, EA and Lessios, HA and Lucey, NM and Mejia, LC and Rasher, DB and Sharp, KH and Sogin, EM and Thacker, RW and Vega Thurber, R and Wcislo, WT and Wilbanks, EG and Eisen, JA}, title = {Host-associated microbiomes drive structure and function of marine ecosystems.}, journal = {PLoS biology}, volume = {17}, number = {11}, pages = {e3000533}, doi = {10.1371/journal.pbio.3000533}, pmid = {31710600}, issn = {1545-7885}, abstract = {The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.}, }
@article {pmid31710301, year = {2019}, author = {Bai, J and Jhaney, I and Wells, J}, title = {Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study.}, journal = {JMIR medical informatics}, volume = {7}, number = {4}, pages = {e14667}, pmid = {31710301}, issn = {2291-9694}, abstract = {BACKGROUND: Cloud computing for microbiome data sets can significantly increase working efficiencies and expedite the translation of research findings into clinical practice. The Amazon Web Services (AWS) cloud provides an invaluable option for microbiome data storage, computation, and analysis.<br><br>OBJECTIVE: The goals of this study were to develop a microbiome data analysis pipeline by using AWS cloud and to conduct a proof-of-concept test for microbiome data storage, processing, and analysis.<br><br>METHODS: A multidisciplinary team was formed to develop and test a reproducible microbiome data analysis pipeline with multiple AWS cloud services that could be used for storage, computation, and data analysis. The microbiome data analysis pipeline developed in AWS was tested by using two data sets: 19 vaginal microbiome samples and 50 gut microbiome samples.<br><br>RESULTS: Using AWS features, we developed a microbiome data analysis pipeline that included Amazon Simple Storage Service for microbiome sequence storage, Linux Elastic Compute Cloud (EC2) instances (ie, servers) for data computation and analysis, and security keys to create and manage the use of encryption for the pipeline. Bioinformatics and statistical tools (ie, Quantitative Insights Into Microbial Ecology 2 and RStudio) were installed within the Linux EC2 instances to run microbiome statistical analysis. The microbiome data analysis pipeline was performed through command-line interfaces within the Linux operating system or in the Mac operating system. Using this new pipeline, we were able to successfully process and analyze 50 gut microbiome samples within 4 hours at a very low cost (a c4.4xlarge EC2 instance costs $0.80 per hour). Gut microbiome findings regarding diversity, taxonomy, and abundance analyses were easily shared within our research team.<br><br>CONCLUSIONS: Building a microbiome data analysis pipeline with AWS cloud is feasible. This pipeline is highly reliable, computationally powerful, and cost effective. Our AWS-based microbiome analysis pipeline provides an efficient tool to conduct microbiome data analysis.}, }
@article {pmid31709856, year = {2019}, author = {Joshipura, K and Muñoz-Torres, F and Fernández-Santiago, J and Patel, RP and Lopez-Candales, A}, title = {Over-the-counter mouthwash use, nitric oxide and hypertension risk.}, journal = {Blood pressure}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/08037051.2019.1680270}, pmid = {31709856}, issn = {1651-1999}, support = {R01 DE020111/DE/NIDCR NIH HHS/United States ; }, abstract = {Purpose: Mouthwash is used by a large population. Short-term clinical trials have shown that antibacterial mouthwash deplete oral nitrate-reducing bacteria, and decrease systemic nitric oxide bioavailability. Our previous publication from the San Juan Overweight Adults Longitudinal Study (SOALS) was the first to show frequent over-the-counter mouthwash use was independently associated with increased risk of prediabetes/diabetes. This manuscript evaluates whether over-the-counter mouthwash was associated with increased risk of hypertension.Materials and methods: SOALS recruited 40-65 year old overweight/obese individuals; baseline evaluations started in 2011 and the 3-year follow-up exam was completed by 2016. From the 1028 participants (76%) who completed follow-up, we excluded people with reported physician diagnosis of hypertension or systolic or diastolic BP at or above the hypertension cut-offs (n = 481), missing smoking (n = 1), missing physical activity (n = 1) and missing alcohol intake (n = 5) at baseline; 540 participants were included. The primary exposure was mouthwash use twice daily or more. The primary outcome for this manuscript is self-reported physician-diagnosed hypertension over the follow-up. We used Poisson regression controlling for age, sex, smoking, physical activity, waist circumference, alcohol intake, systolic blood pressure, pre-diabetes/diabetes status and cardiac medication use. We additionally evaluated other mouthwash use categorizations.Results: Twelve percent (66/540) developed hypertension over follow-up. People who used mouthwash twice/day or more had higher incidence of hypertension compared to less frequent users (Incidence Rate Ratio = 1.85; 95% Confidence Interval: 1.17, 2.94), and compared to non-users (IRR = 2.17; 95% CI: 1.27, 3.71). Several additional potential confounders evaluated did not impact these associations. Associations persisted among never smokers. Additional outcomes including BP assessed at a single study visit did not show associations.Conclusion: In this study, frequent regular use of over-the-counter mouthwash was associated with increased risk of hypertension, independent of major risk factors for hypertension and several other potential confounders.}, }
@article {pmid31709616, year = {2019}, author = {Crone, S and Vives-Flórez, M and Kvich, L and Saunders, AM and Malone, M and Nicolaisen, MH and Martínez-García, E and Rojas-Acosta, C and Catalina Gomez-Puerto, M and Calum, H and Whiteley, M and Kolter, R and Bjarnsholt, T}, title = {The environmental occurrence of Pseudomonas aeruginosa.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {}, number = {}, pages = {}, doi = {10.1111/apm.13010}, pmid = {31709616}, issn = {1600-0463}, abstract = {Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports have questioned whether or not this description is true, we undertook a rigorous study using three methods to investigate the occurrence of P. aeruginosa: We investigated environmental samples, analyzed 16S rRNA data, and undertook a systematic review and meta-analysis of published data. The environmental sample screening identified P. aeruginosa as significantly associated with hydrocarbon and pesticide-contaminated environments and feces, as compared to uncontaminated environments in which its prevalence was relatively low. The 16S rRNA data analysis showed that P. aeruginosa sequences were present in all habitats but were most abundant in samples from human and animals. Similarly, the meta-analysis revealed that samples obtained from environments with intense human contact had a higher prevalence of P. aeruginosa compared to those with less human contact. Thus, we found a clear tendency of P. aeruginosa to be present in places closely linked with human activity. Although P. aeruginosa may be ubiquitous in nature, it is usually scarce in pristine environments. Thus, we suggest that P. aeruginosa should be described as a bacterium largely found in locations associated with human activity.}, }
@article {pmid31708901, year = {2019}, author = {Navarro, MOP and Simionato, AS and Pérez, JCB and Barazetti, AR and Emiliano, J and Niekawa, ETG and Andreata, MFL and Modolon, F and Dealis, ML and Araújo, EJA and Carlos, TM and Scarpelim, OJ and da Silva, DB and Chryssafidis, AL and Bruheim, P and Andrade, G}, title = {Fluopsin C for Treating Multidrug-Resistant Infections: In vitro Activity Against Clinically Important Strains and in vivo Efficacy Against Carbapenemase-Producing Klebsiella pneumoniae.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2431}, pmid = {31708901}, issn = {1664-302X}, abstract = {The increasing emergence of multidrug-resistant (MDR) organisms in hospital infections is causing a global public health crisis. The development of drugs with effective antibiotic action against such agents is of the highest priority. In the present study, the action of Fluopsin C against MDR clinical isolates was evaluated under in vitro and in vivo conditions. Fluopsin C was produced in cell suspension culture of Pseudomonas aeruginosa LV strain, purified by liquid adsorption chromatography and identified by mass spectrometric analysis. Bioactivity, bacterial resistance development risk against clinically important pathogenic strains and toxicity in mammalian cell were initially determined by in vitro models. In vivo toxicity was evaluated in Tenebrio molitor larvae and mice. The therapeutic efficacy of intravenous Fluopsin C administration was evaluated in a murine model of Klebsiella pneumoniae (KPC) acute sepsis, using six different treatments. The in vitro results indicated MIC and MBC below 2 μg/mL and low bacterial resistance development frequency. Electron microscopy showed that Fluopsin C may have altered the exopolysaccharide matrix and caused disruption of the cell wall of MDR bacteria. Best therapeutic results were achieved in mice treated with a single dose of 2 mg/kg and in mice treated with two doses of 1 mg/kg, 8 h apart. Furthermore, acute and chronic histopathological studies demonstrated absent nephrotoxicity and moderate hepatotoxicity. The results demonstrated the efficacy of Fluopsin C against MDR organisms in in vitro and in vivo models, and hence it can be a novel therapeutic agent for the control of severe MDR infections.}, }
@article {pmid31708885, year = {2019}, author = {Géron, A and Werner, J and Wattiez, R and Lebaron, P and Matallana-Surget, S}, title = {Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2395}, pmid = {31708885}, issn = {1664-302X}, abstract = {Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.}, }
@article {pmid31708883, year = {2019}, author = {Del Campo, J and Heger, TJ and Rodríguez-Martínez, R and Worden, AZ and Richards, TA and Massana, R and Keeling, PJ}, title = {Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2373}, pmid = {31708883}, issn = {1664-302X}, abstract = {Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including the causing agents of toxoplasmosis and malaria, and emergent diseases like cryptosporidiosis or babesiosis. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys, and our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of apicomplexan sequences. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.}, }
@article {pmid31708882, year = {2019}, author = {Smyth, EM and Chattopadhyay, S and Babik, K and Reid, M and Chopyk, J and Malayil, L and Kulkarni, P and Hittle, LE and Clark, PI and Sapkota, AR and Mongodin, EF}, title = {The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2371}, pmid = {31708882}, issn = {1664-302X}, abstract = {Despite their potential importance with regard to tobacco-related health outcomes, as well as their hypothesized role in the production of tobacco-specific N-nitrosamines, bacterial constituents of tobacco products lack characterization. Specifically, to our knowledge, there has been no comprehensive characterization of the effects of storage conditions on the bacterial communities associated with little cigars and cigarillos. To address this knowledge gap, we characterized the bacterial community composition of the tobacco and wrapper components of the following four products: Swisher Sweets Original; Swisher Sweets, Sweet Cherry; Cheyenne Cigars Full Flavor 100's; and Cheyenne Menthol Box. Each product was stored under three different conditions of temperature and relative humidity to mimic different user storage conditions: room (20°C 50% RH), refrigerator (5°C 18% RH) and pocket (25°C 30% RH). On days 0, 5, 9 and 14, subsamples were collected, the wrapper and tobacco were separated, and their total DNA was extracted separately and purified. Resulting DNA was then used in PCR assays targeting the V3 V4 region of the bacterial 16S rRNA gene, followed by sequencing using Illumina HiSeq 300bp PE. Resulting sequences were processed using the Quantitative Insights Into Microbial Ecology (QIIME) software package, followed by analyses in R using the Phyloseq and Vegan packages. A single bacterial phylum, Firmicutes, dominated in the wrapper subsamples whereas the tobacco subsamples were dominated by Proteobacteria. Cheyenne Menthol Box (CMB) samples were characterized by significant differential abundances for 23 bacterial operational taxonomic units (OTUs) in tobacco subsamples and 27 OTUs in the wrapper subsamples between day 0 and day 14 under all conditions. OTUs from the genera Acinetobacter and Bacillus significantly increased in the CMB tobacco subsamples, and OTUs from Bacillus, Streptococcus, Lactobacillus, and Enterococcus significantly increased in the CMB wrapper subsamples over time. These initial results suggest that the bacterial communities of little cigars and cigarillos are dynamic over time and varying storage conditions.}, }
@article {pmid31707464, year = {2019}, author = {Polonca, S}, title = {Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01455-y}, pmid = {31707464}, issn = {1432-184X}, support = {US/18-19-091//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-8228//Javna Agencija za Raziskovalno Dejavnost RS/ ; P4-0116//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-9302//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, abstract = {Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species.}, }
@article {pmid31705383, year = {2019}, author = {Queiroz, LL and Costa, MS and de Abreu Pereira, A and de Paula Avila, M and Costa, PS and Nascimento, AMA and Lacorte, GA}, title = {Dynamics of microbial contaminants is driven by selection during ethanol production.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, doi = {10.1007/s42770-019-00147-6}, pmid = {31705383}, issn = {1678-4405}, support = {156/2013//Instituto Federal de Minas Gerais/ ; }, abstract = {Brazil is the second largest ethanol producer in the world and largest using sugarcane feedstock. Bacteria contamination is one of the most important issues faced by ethanol producers that seek to increase production efficiency. Each step of production is a selection event due to the environmental and biological changes that occur. Therefore, we evaluated the influence of the selection arising from the ethanol production process on diversity and composition of bacteria. Our objectives were to test two hypotheses, (1) that species richness will decrease during the production process and (2) that lactic acid bacteria will become dominant with the advance of ethanol production. Bacterial community assemblage was accessed using 16S rRNA gene sequencing from 19 sequential samples. Temperature is of great importance in shaping microbial communities. Species richness increased between the decanter and must steps of the process. Low Simpson index values were recorded at the fermentation step, indicating a high dominance of Lactobacillus. Interactions between Lactobacillus and yeast may be impairing the efficiency of industrial ethanol production.}, }
@article {pmid31705158, year = {2019}, author = {Jeong, SY and Choi, JY and Kim, TG}, title = {Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01453-0}, pmid = {31705158}, issn = {1432-184X}, support = {2018R1D1A1B07048872//National research foundation of Korea/ ; }, abstract = {Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R2 ≥ 0.31), except between Fungi and Metazoa (R2 = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.}, }
@article {pmid31704994, year = {2019}, author = {Fu, S and Hao, J and Yang, Q and Lan, R and Wang, Y and Ye, S and Liu, Y and Li, R}, title = {Long-distance transmission of pathogenic Vibrio species by migratory waterbirds: a potential threat to the public health.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16303}, pmid = {31704994}, issn = {2045-2322}, abstract = {A potential mechanism for the global distribution of waterborne pathogens is through carriage by the migratory waterbirds. However, this mode of transmission has yet been confirmed epidemiologically. Here, we conducted whole genome sequencing of Vibrio spp. collected from waterbirds, sediments, and mollusks in the estuary of the Liaohe River in China to investigate this transmission mode. We found that a V. parahaemolyticus strain isolated from a waterbird was clonally related to the other V. parahaemolyticus strains obtained from the sediments and mollusks, and three V. mimicus strains isolated from bird feces were genomically related to those found in the mollusks and upstream groundwater, suggesting that the bird-carried Vibrio strains were acquired through the direct predation of the local mollusks. Surprisingly, two bird-carried V. parahaemolyticus strains belonging to the same clone were identified in Panjin and Shanghai, which are over 1,150 km apart, and another two were found at two locations 50 km apart, further supporting that waterbirds are capable of carrying and disseminating these pathogens over long distances. Our results provide the first evidence of direct transmission from mollusks to waterbirds and confirm that waterbirds act as disseminating vehicles of waterborne pathogens. Effective surveillance of migratory waterbirds along their routes will be valuable for predicting future epidemics of infectious diseases.}, }
@article {pmid31704678, year = {2020}, author = {Schloss, PD}, title = {Reintroducing mothur: 10 Years Later.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {2}, pages = {}, pmid = {31704678}, issn = {1098-5336}, abstract = {More than 10 years ago, we published the paper describing the mothur software package in Applied and Environmental Microbiology Our goal was to create a comprehensive package that allowed users to analyze amplicon sequence data using the most robust methods available. mothur has helped lead the community through the ongoing sequencing revolution and continues to provide this service to the microbial ecology community. Beyond its success and impact on the field, mothur's development exposed a series of observations that are generally translatable across science. Perhaps the observation that stands out the most is that all science is done in the context of prevailing ideas and available technologies. Although it is easy to criticize choices that were made 10 years ago through a modern lens, if we were to wait for all of the possible limitations to be solved before proceeding, science would stall. Even preceding the development of mothur, it was necessary to address the most important problems and work backwards to other problems that limited access to robust sequence analysis tools. At the same time, we strive to expand mothur's capabilities in a data-driven manner to incorporate new ideas and accommodate changes in data and desires of the research community. It has been edifying to see the benefit that a simple set of tools can bring to so many other researchers.}, }
@article {pmid31704461, year = {2020}, author = {Coggins, LX and Larma, I and Hinchliffe, A and Props, R and Ghadouani, A}, title = {Flow cytometry for rapid characterisation of microbial community dynamics in waste stabilisation ponds.}, journal = {Water research}, volume = {169}, number = {}, pages = {115243}, doi = {10.1016/j.watres.2019.115243}, pmid = {31704461}, issn = {1879-2448}, mesh = {Flow Cytometry ; *Microbiota ; *Ponds ; Waste Disposal, Fluid ; Waste Water ; }, abstract = {Algal and bacterial communities play a major role in the treatment performance and efficiency of waste stabilisation ponds (WSPs); however, the study of these WSP microbial communities has been challenging. Flow cytometry (FCM) has been used widely as a rapid, culture-independent method of characterising algae and/or bacteria in a range of freshwater and marine environments, and in conventional wastewater treatment processes, but its application to WSP wastewater has been underexplored. In this study, a method for the characterisation of both algal and bacterial microbial populations in WSP wastewater is presented and standardised, using cultures and field samples. We show that SYTO 16 dye is more effective than SYBR Green I for the concurrent detection of both algae and bacteria in samples. Through gating and phenotypic diversity analysis, the FCM results show both spatial and temporal shifts in pond microbial communities. The ability to rapidly determine the spatiotemporal shifts in pond populations is not only important for the improvement of pond operation and monitoring strategies, but also for the planning and management. Flow cytometry has the potential to become a diagnostic tool for ponds to assess treatment performance and determine the most optimal operating conditions.}, }
@article {pmid31703886, year = {2020}, author = {Aldrete-Tapia, JA and Escalante-Minakata, P and Martínez-Peniche, RA and Tamplin, ML and Hernández-Iturriaga, M}, title = {Yeast and bacterial diversity, dynamics and fermentative kinetics during small-scale tequila spontaneous fermentation.}, journal = {Food microbiology}, volume = {86}, number = {}, pages = {103339}, doi = {10.1016/j.fm.2019.103339}, pmid = {31703886}, issn = {1095-9998}, abstract = {The study of microbial communities associated with spontaneous fermentation of agave juice for tequila production is required to develop starter cultures that improve both yield and quality of the final product. Quantification by HPLC of primary metabolites produced during the fermentations was determined. A polyphasic approach using plate count, isolation and identification of microorganisms, denaturing gradient gel electrophoresis and next generation sequencing was carried out to describe the diversity and dynamics of yeasts and bacteria during small-scale spontaneous fermentations of agave juice from two-year samplings. High heterogeneity in microbial populations and fermentation parameters were observed, with bacteria showing higher diversity than yeast. The core microorganisms identified were Saccharomyces cerevisiae and Lactobacillus fermentum. Practices in tequila production changed during the two-year period, which affected microbial community structure and the time to end fermentation. Bacterial growth and concomitant lactic acid production were associated with low ethanol production, thus bacteria could be defined as contaminants in tequila fermentation and efforts to control them should be implemented.}, }
@article {pmid31702484, year = {2019}, author = {Basilua, JM and Sawoo, O and Mangin, I and Dossou-Yovo, F and Boussard, A and Chevillard, L and Lutete, GT and Eto, B and Peytavin, G and Pochart, P}, title = {Higher Atazanavir Plasma Exposure in Rats is Associated with Gut Microbiota Changes Induced by Cotrimoxazole.}, journal = {Current drug metabolism}, volume = {20}, number = {11}, pages = {898-906}, doi = {10.2174/1389200220666191023105609}, pmid = {31702484}, issn = {1875-5453}, abstract = {BACKGROUND: Cotrimoxazole (TMP-SMX) is concomitantly used as a primary prophylaxis of opportunistic infections with antiretroviral agents, such as Atazanavir (ATV). Results from an ex vivo study showed changes in intestinal absorption of ATV when rats were pretreated with TMP-SMX. The objective of this in vivo study is to determine the effect of TMP-SMX on the pharmacokinetics of ATV in rats. We also studied changes in gut microbiota induced by TMP-SMX.<br><br>METHODS: We used the non-compartment analysis to compare the pharmacokinetics of ATV in a parallel group of rats treated with a low or therapeutic dose of TMP-SMX for nine days to untreated control rats. Gut microbiota was characterized using qPCR and High Throughput Sequencing of 16S rDNA.<br><br>RESULTS: Rats treated with TMP-SMX showed a much broader exposure to ATV compared to the control group (AUC0-8h (ng.mL-1.h), 25975.9±4048.7 versus 2587.6±546.9, p=0.001). The main observation regarding the gut microbiota was a lower proportion of enterobacteria related to the administration of TMP-SMX. Moreover, the Total Gastrointestinal Transit Time (TGTT) was longer in the TMP-SMX treated group.<br><br>CONCLUSION: Concomitant administration of TMP-SMX and ATV significantly increased ATV exposure in rats. This increase could be the result of a prolonged TGTT leading to an increase in the intestinal residence time of ATV favoring its absorption. Gut microbiota changes induced by TMP-SMX could be at the origin of this prolonged TGTT. If demonstrated in humans, this potential interaction could be accompanied by an increase in the adverse effects of ATV.}, }
@article {pmid31701171, year = {2019}, author = {Ni, J and Hatori, S and Wang, Y and Li, YY and Kubota, K}, title = {Uncovering Viable Microbiome in Anaerobic Sludge Digesters by Propidium Monoazide (PMA)-PCR.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01449-w}, pmid = {31701171}, issn = {1432-184X}, support = {NA//Strategic International Collaborative Research Program/ ; NA//Ministry of Land, Infrastructure, Transport and Tourism/ ; KAKENHI Grant Number JP18H01564//Japan Society for the Promotion of Science/ ; }, abstract = {Use of anaerobic sludge digester is a common practice around the world for solids digestion and methane generation from municipal sewage sludge. Understanding microbial community structure is vital to get better insight into the anaerobic digestion process and to gain better process control. However, selective analysis of viable microorganisms is limited by DNA-based assays. In this study, propidium monoazide (PMA)-PCR with 16S rRNA gene sequencing analysis was used to distinguish live and dead microorganisms based on cell membrane integrity. Microbial community structures of PMA-treated and PMA-untreated anaerobic digester sludge samples were compared. Quantitative PCR revealed that 5-30% of the rRNA genes were derived from inactive or dead cells in anaerobic sludge digesters. This caused a significant decrease in the numbers of operational taxonomic units and Chao1 and Shannon indices compared with that of the PMA-untreated sludge. Microbial community analysis showed that majority of the viable microbiome consisted of Euryarchaeota, Bacteroidetes, Deltaproteobacteria, Chloroflexi, Firmicutes, WWE1, Spirochaetes, Synergistetes, and Caldiserica. On the other hand, after the PMA treatment, numbers of Alphaproteobacteria and Betaproteobacteria declined. These were considered residual microbial members. The network analysis also revealed a relationship among the OTUs belonging to WWE1 and Bacteroidales. PMA-PCR-based 16S rRNA gene sequencing analysis is an effective tool for uncovering viable microbiome in complex environmental samples.}, }
@article {pmid31701033, year = {2019}, author = {Testa, S and Berger, S and Piccardi, P and Oechslin, F and Resch, G and Mitri, S}, title = {Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {405}, pmid = {31701033}, issn = {2399-3642}, abstract = {Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a sensitive Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.}, }
@article {pmid31700900, year = {2019}, author = {Han, MM and Zhu, XY and Peng, YF and Lin, H and Liu, DC and Li, L}, title = {The alterations of gut microbiota in mice with chronic pancreatitis.}, journal = {Annals of translational medicine}, volume = {7}, number = {18}, pages = {464}, pmid = {31700900}, issn = {2305-5839}, abstract = {Background: The changes of intestinal microbiome are associated with inflammatory, metabolic, and malignant disorders, and there are no studies assessing the intestinal microbiota of mice with chronic pancreatitis (CP). Thus, we aim to investigate the variations in diversity, composition and function of intestinal microbiota in CP mice.<br><br>Methods: Sixteen male C57BL/6 mice were randomly selected, and divided into two groups, treated intraperitoneally with saline (normal control group, CT group) or ethanol + cerulein (experimental group, CP group) for 6 weeks. Body weight as measured in entire processes. Histopathological examination of CP index was conducted to verify the CP induction. Extracted DNA from colon samples was used for Illumina HiSeq sequencing of the bacterial V4 region of 16S rRNA gene and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Functional profiling of microbial communities was predicted with BugBase.<br><br>Results: Significant alterations of the gut microbiota were found in the CP mice compared to CT groups, as revealed by significant decrease in bacterial richness and diversity, declined the relative abundance of Lachnospiraceae_NK4A136, Ruminiclostridium and Roseburia, and increased the relative abundances of Bacteroides and Alloprevotella genera. Analysis of microbial community-level phenotypes revealed significant differences in nine phenotypes (aerobic, anaerobic, containing mobile elements, facultatively anaerobic, biofilm forming, gram-negative, gram-positive, potentially pathogenic, and stress tolerant) between CP group and CT group.<br><br>Conclusions: This study indicated that mice with CP had a distinct microbiota profile.}, }
@article {pmid31700196, year = {2019}, author = {Zheng, Q and Hu, Y and Zhang, S and Noll, L and Böckle, T and Dietrich, M and Herbold, CW and Eichorst, SA and Woebken, D and Richter, A and Wanek, W}, title = {Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity.}, journal = {Soil biology &amp; biochemistry}, volume = {136}, number = {}, pages = {107521}, pmid = {31700196}, issn = {0038-0717}, abstract = {Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.}, }
@article {pmid31700119, year = {2020}, author = {Avalos, M and Garbeva, P and Raaijmakers, JM and van Wezel, GP}, title = {Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {569-583}, doi = {10.1038/s41396-019-0537-2}, pmid = {31700119}, issn = {1751-7370}, support = {864.11.015//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, abstract = {Soil-inhabiting streptomycetes are nature's medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatiles, molecules that disperse through the soil matrix and may impact other (micro)organisms from a distance. Here, we show that soil- and surface-grown streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile ammonia, dispersing over long distances to inhibit the growth of Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system nullified ammonia biosynthesis and concomitantly air-borne antibiosis. Reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ is used as a resistance strategy by E. coli cells to survive ammonia-mediated antibiosis. Finally, ammonia was shown to enhance the activity of canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis from a distance.}, }
@article {pmid31699144, year = {2019}, author = {Park, R and Dzialo, MC and Spaepen, S and Nsabimana, D and Gielens, K and Devriese, H and Crauwels, S and Tito, RY and Raes, J and Lievens, B and Verstrepen, KJ}, title = {Microbial communities of the house fly Musca domestica vary with geographical location and habitat.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {147}, pmid = {31699144}, issn = {2049-2618}, abstract = {House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically relevant pathogens. Previous studies have demonstrated that house flies carry a complex and variable prokaryotic microbiota, but the main drivers underlying this variability and the influence of habitat on the microbiota remain understudied. Moreover, the differences between the external and internal microbiota and the eukaryotic components have not been examined. To obtain a comprehensive view of the fly microbiota and its environmental drivers, we sampled over 400 flies from two geographically distinct countries (Belgium and Rwanda) and three different environments-farms, homes, and hospitals. Both the internal as well as external microbiota of the house flies were studied, using amplicon sequencing targeting both bacteria and fungi. Results show that the house fly's internal bacterial community is very diverse yet relatively consistent across geographic location and habitat, dominated by genera Staphylococcus and Weissella. The external bacterial community, however, varies with geographic location and habitat. The fly fungal microbiota carries a distinct signature correlating with the country of sampling, with order Capnodiales and genus Wallemia dominating Belgian flies and genus Cladosporium dominating Rwandan fly samples. Together, our results reveal an intricate country-specific pattern for fungal communities, a relatively stable internal bacterial microbiota and a variable external bacterial microbiota that depends on geographical location and habitat. These findings suggest that vectoring of a wide spectrum of environmental microbes occurs principally through the external fly body surface, while the internal microbiome is likely more limited by fly physiology.}, }
@article {pmid31699041, year = {2019}, author = {Yuen, B and Polzin, J and Petersen, JM}, title = {Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {820}, pmid = {31699041}, issn = {1471-2164}, support = {VRG14-021//Vienna Science and Technology Fund/ ; }, abstract = {BACKGROUND: The lucinid clam Loripes orbiculatus lives in a nutritional symbiosis with sulphur-oxidizing bacteria housed in its gills. Although our understanding of the lucinid endosymbiont physiology and metabolism has made significant progress, relatively little is known about how the host regulates the symbiosis at the genetic and molecular levels. We generated transcriptomes from four L. orbiculatus organs (gills, foot, visceral mass, and mantle) for differential expression analyses, to better understand this clam's physiological adaptations to a chemosymbiotic lifestyle, and how it regulates nutritional and immune interactions with its symbionts.<br><br>RESULTS: The transcriptome profile of the symbiont-housing gill suggests the regulation of apoptosis and innate immunity are important processes in this organ. We also identified many transcripts encoding ion transporters from the solute carrier family that possibly allow metabolite exchange between host and symbiont. Despite the clam holobiont's clear reliance on chemosynthesis, the clam's visceral mass, which contains the digestive tract, is characterised by enzymes involved in digestion, carbohydrate recognition and metabolism, suggesting that L. orbiculatus has a mixotrophic diet. The foot transcriptome is dominated by the biosynthesis of glycoproteins for the construction of mucus tubes, and receptors that mediate the detection of chemical cues in the environment.<br><br>CONCLUSIONS: The transcriptome profiles of gills, mantle, foot and visceral mass provide insights into the molecular basis underlying the functional specialisation of bivalve organs adapted to a chemosymbiotic lifestyle.}, }
@article {pmid31698527, year = {2019}, author = {Roesch, LFW and Dobbler, PT and Pylro, VS and Kolaczkowski, B and Drew, JC and Triplett, EW}, title = {pime: A package for discovery of novel differences among microbial communities.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13116}, pmid = {31698527}, issn = {1755-0998}, support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 5R21AI120195-02/GF/NIH HHS/United States ; 1-INO-2018-637-A-N//JDRF/United States ; }, abstract = {The data used for profiling microbial communities is usually sparse with some microbes having high abundance in a few samples and being nearly absent in others. However, current bioinformatics tools able to deal with this sparsity are lacking. pime (Prevalence Interval for Microbiome Evaluation) was designed to remove those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of pime were compared against existing methods and tested using 16S rRNA independent data sets. pime filters microbial taxa not shared in a per treatment prevalence interval started at 5% prevalence with increasing increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees were calculated to predict the likelihood of detecting differences in treatments. The best prevalence-filtered data set was user-selected by choosing the prevalence interval that kept a large portion of the 16S rRNA sequences in the data set while also showing the lowest error rate. To obtain the likelihood of introducing type I error while building prevalence-filtered data sets, an error detection step based was also included. A pime reanalysis of published data sets uncovered other expected microbial associations than previously reported, which may be masked when only relative abundance was considered.}, }
@article {pmid31693956, year = {2020}, author = {Burges, A and Fievet, V and Oustriere, N and Epelde, L and Garbisu, C and Becerril, JM and Mench, M}, title = {Long-term phytomanagement with compost and a sunflower - Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil.}, journal = {The Science of the total environment}, volume = {700}, number = {}, pages = {134529}, doi = {10.1016/j.scitotenv.2019.134529}, pmid = {31693956}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; Composting ; Copper/analysis/*metabolism ; Helianthus/*physiology ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; Tobacco/*physiology ; }, abstract = {At a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery.}, }
@article {pmid31692676, year = {2019}, author = {Vera-Gutiérrez, T and García-Muñoz, MC and Otálvaro-Alvarez, AM and Mendieta-Menjura, O}, title = {Effect of processing technology and sugarcane varieties on the quality properties of unrefined non-centrifugal sugar.}, journal = {Heliyon}, volume = {5}, number = {10}, pages = {e02667}, pmid = {31692676}, issn = {2405-8440}, abstract = {In this research, the unrefined non-centrifugal sugar (UNCS) quality obtained from two sugarcane varieties (RD 7511 and CC 8475) and using two types of technologies (traditional and Ward-Cimpa production facilities) were evaluated. The parameters monitored through the process were impurities, total soluble solids, acidity, pH, and temperature profile. Microbiological analyses were carried out on beating, molding, packing, and storage operations; and finally, an organoleptic analysis was carried out on the final UNCS product. Results showed that the UNCS obtained from variety CC 8475 had higher consumer acceptance; meanwhile, the technologies assessed did not show significant differences in final product quality. However, these technologies showed significant differences in the highest temperature, syrup, and juice properties. Microbiological analyses highlighted beating and molding as the critical points in UNCS production safety. Finally, it was evident that the implementation of new technologies or the improvement of the furnace, as in the Ward-Cimpa production facility, is not enough to achieve food safety requirements, as many other conditions affect the microbiological quality of the product. Although the temperatures reached on the Ward-Cimpa furnace are higher than those reached with the traditional furnace and thus, enough to kill all the harmful microorganisms, contamination in downstream operations still occurs.}, }
@article {pmid31690886, year = {2020}, author = {Pernice, M and Raina, JB and Rädecker, N and Cárdenas, A and Pogoreutz, C and Voolstra, CR}, title = {Down to the bone: the role of overlooked endolithic microbiomes in reef coral health.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {325-334}, doi = {10.1038/s41396-019-0548-z}, pmid = {31690886}, issn = {1751-7370}, support = {Competitive Research Grant//King Abdullah University of Science and Technology (KAUST)/ ; Competitive Research Grant//King Abdullah University of Science and Technology (KAUST)/ ; DE160100636//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2-3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the &quot;overlooked&quot; coral skeleton.}, }
@article {pmid31690591, year = {2019}, author = {Maslov, S and Sneppen, K}, title = {Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31690591}, issn = {2379-5077}, abstract = {The competition between bacteria often involves both nutrients and phage predators and may give rise to abrupt regime shifts between the alternative stable states characterized by different species compositions. While such transitions have been previously studied in the context of competition for nutrients, the case of phage-induced bistability between competing bacterial species has not been considered yet. Here we demonstrate a possibility of regime shifts in well-mixed phage-bacterium ecosystems. In one of the bistable states, the fast-growing bacteria competitively exclude the slow-growing ones by depleting their common nutrient. Conversely, in the second state, the slow-growing bacteria with a large burst size generate such a large phage population that the other species cannot survive. This type of bistability can be realized as the competition between a strain of bacteria protected from phage by abortive infection and another strain with partial resistance to phage. It is often desirable to reliably control the state of microbial ecosystems, yet bistability significantly complicates this task. We discuss successes and limitations of one control strategy in which one adds short pulses to populations of individual species. Our study proposes a new type of phage therapy, where introduction of the phage is supplemented by the addition of a partially resistant host bacteria.IMPORTANCE Phage-microbe communities play an important role in human health as well as natural and industrial environments. Here we show that these communities can assume several alternative species compositions separated by abrupt regime shifts. Our model predicts these regime shifts in the competition between bacterial strains protected by two different phage defense mechanisms: abortive infection/CRISPR and partial resistance. The history dependence caused by regime shifts greatly complicates the task of manipulation and control of a community. We propose and study a successful control strategy via short population pulses aimed at inducing the desired regime shifts. In particular, we predict that a fast-growing pathogen could be eliminated by a combination of its phage and a slower-growing susceptible host.}, }
@article {pmid31689403, year = {2019}, author = {Wood, K}, title = {Microbial Ecology: Complex Bacterial Communities Reduce Selection for Antibiotic Resistance.}, journal = {Current biology : CB}, volume = {29}, number = {21}, pages = {R1143-R1145}, doi = {10.1016/j.cub.2019.09.017}, pmid = {31689403}, issn = {1879-0445}, abstract = {Competition between antibiotic-resistant and -susceptible bacteria is well studied in single-species communities, but less is known about selection for resistance in more complex ecologies. A new experiment shows natural microbial communities can hinder selection by increasing the fitness costs of resistance or by offering protection to drug-sensitive strains.}, }
@article {pmid31688899, year = {2019}, author = {Wong, YY and Lee, CW and Bong, CW and Lim, JH and Narayanan, K and Sim, EUH}, title = {Environmental control of Vibrio spp. abundance and community structure in tropical waters.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {11}, pages = {}, doi = {10.1093/femsec/fiz176}, pmid = {31688899}, issn = {1574-6941}, abstract = {We measured Vibrio spp. distribution and community profile in the tropical estuary of Port Klang and coastal water of Port Dickson, Malaysia. Vibrio spp. abundance ranged from 15 to 2395 colony forming units mL-1, and was driven by salinity and chlorophyll a (Chl a) concentration. However, the effect of salinity was pronounced only when salinity was <20 ppt. A total of 27 Vibrio spp. were identified, and theVibrio spp. community at Port Dickson was more diverse (H' = 1.94 ± 0.21). However species composition between Port Dickson and Port Klang were similar. Two frequently occurring Vibrio spp. were V. owensii and V. rotiferianus, which exhibited relatively higher growth rates (ANCOVA: F > 4.338, P < 0.05). Co-culture experiments between fast- and slow-growing Vibrio spp. revealed that fast-growing Vibrio spp. (r-strategists) were overwhelmed by slower-growing Vibrio spp. (K-strategists) when nutrient conditions were set towards oligotrophy. In response to resource availability, the intrinsic growth strategy of each Vibrio spp. determined its occurrence and the development of Vibrio spp. community composition.}, }
@article {pmid31686026, year = {2020}, author = {McCall, LI and Callewaert, C and Zhu, Q and Song, SJ and Bouslimani, A and Minich, JJ and Ernst, M and Ruiz-Calderon, JF and Cavallin, H and Pereira, HS and Novoselac, A and Hernandez, J and Rios, R and Branch, OH and Blaser, MJ and Paulino, LC and Dorrestein, PC and Knight, R and Dominguez-Bello, MG}, title = {Home chemical and microbial transitions across urbanization.}, journal = {Nature microbiology}, volume = {5}, number = {1}, pages = {108-115}, doi = {10.1038/s41564-019-0593-4}, pmid = {31686026}, issn = {2058-5276}, abstract = {Urbanization represents a profound shift in human behaviour, and has considerable cultural and health-associated consequences1,2. Here, we investigate chemical and microbial characteristics of houses and their human occupants across an urbanization gradient in the Amazon rainforest, from a remote Peruvian Amerindian village to the Brazilian city of Manaus. Urbanization was found to be associated with reduced microbial outdoor exposure, increased contact with housing materials, antimicrobials and cleaning products, and increased exposure to chemical diversity. The degree of urbanization correlated with changes in the composition of house bacterial and microeukaryotic communities, increased house and skin fungal diversity, and an increase in the relative abundance of human skin-associated fungi and bacteria in houses. Overall, our results indicate that urbanization has large-scale effects on chemical and microbial exposures and on the human microbiota.}, }
@article {pmid31684148, year = {2019}, author = {Gomes, A and Oudot, C and Macià, A and Foito, A and Carregosa, D and Stewart, D and Van de Wiele, T and Berry, D and Motilva, MJ and Brenner, C and Dos Santos, CN}, title = {Berry-Enriched Diet in Salt-Sensitive Hypertensive Rats: Metabolic Fate of (Poly)Phenols and the Role of Gut Microbiota.}, journal = {Nutrients}, volume = {11}, number = {11}, pages = {}, pmid = {31684148}, issn = {2072-6643}, support = {ANR-13-ISV1-0001-01//Agence Nationale de la Recherche/ ; ANR-11-IDEX-0003-01//Agence Nationale de la Recherche/ ; FCTANR/BEX-BCM/0001/2013//Fundação para a Ciência e Tecnologia/ ; SFRH/BD/103155/2014//Fundação para a Ciência e Tecnologia/ ; IF/01097/2013//Fundação para a Ciência e Tecnologia/ ; FWF P26127-B20//Austrian Science Fund/ ; FunKeyGut 741623/ERC_/European Research Council/International ; Rural &amp; Environment Science &amp; Analytical Services//Scottish Government/ ; LISBOA-01-0145-FEDER-007344//iNOVA4Health Research Unit/ ; }, abstract = {Diets rich in (poly)phenols are associated with a reduced reduction in the incidence of cardiovascular disorders. While the absorption and metabolism of (poly)phenols has been described, it is not clear how their metabolic fate is affected under pathological conditions. This study evaluated the metabolic fate of berry (poly)phenols in an in vivo model of hypertension as well as the associated microbiota response. Dahl salt-sensitive rats were fed either a low-salt diet (0.26% NaCl) or a high-salt diet (8% NaCl), with or without a berry mixture (blueberries, blackberries, raspberries, Portuguese crowberry and strawberry tree fruit) for 9 weeks. The salt-enriched diet promoted an increase in the urinary excretion of berry (poly)phenol metabolites, while the abundance of these metabolites decreased in faeces, as revealed by UPLC-MS/MS. Moreover, salt and berries modulated gut microbiota composition as demonstrated by 16S rRNA analysis. Some changes in the microbiota composition were associated with the high-salt diet and revealed an expansion of the families Proteobacteria and Erysipelotrichaceae. However, this effect was mitigated by the dietary supplementation with berries. Alterations in the metabolic fate of (poly)phenols occur in parallel with the modulation of gut microbiota in hypertensive rats. Thus, beneficial effects of (poly)phenols could be related with these interlinked modifications, between metabolites and microbiota environments.}, }
@article {pmid31682986, year = {2019}, author = {Brackmann, M and Leib, SL and Tonolla, M and Schürch, N and Wittwer, M}, title = {Antimicrobial resistance classification using MALDI-TOF-MS is not that easy: lessons from vancomycin-resistant Enterococcus faecium.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2019.10.027}, pmid = {31682986}, issn = {1469-0691}, }
@article {pmid31681511, year = {2019}, author = {Kobayashi, K and Aoyagi, H}, title = {Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the candidate division FBP.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7876}, pmid = {31681511}, issn = {2167-8359}, abstract = {Background: The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark.<br><br>Methods: In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed.<br><br>Results: At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and candidate division FBP, which contain many uncultured microbial species, existed in the A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, some genera belonging to the phyla mentioned were detected. A total of 70 isolates could be isolated and cultured using the low-nutrient agar media DR2A and PE03. Strains belonging to the phylum Actinobacteria were isolated most frequently. In addition, the newly identified bacterial strain IAP-33, presumed to belong to Acidobacteria, was isolated on PE03 medium. Of the isolated bacteria, 44 strains demonstrated less than 97% 16S rDNA sequence-similarity with type strains. Molecular phylogenetic analysis of IAD-21 showed the lowest similarity (79%), and analyses suggested it belongs to candidate division FBP. Culture of the strain IAD-21 was deposited in Japan Collection of Microorganisms (JCM) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as JCM 32665 and DSM 108248, respectively.<br><br>Discussion: Our results suggest that a variety of uncultured microorganisms exist in A. palmatum bark. Microorganisms acquirable from the bark may prove valuable for academic pursuits, such as studying microbial ecology, and the bark might be a promising source of uncultured bacterial isolates.}, }
@article {pmid31681249, year = {2019}, author = {He, H and Fu, L and Liu, Q and Fu, L and Bi, N and Yang, Z and Zhen, Y}, title = {Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2404}, pmid = {31681249}, issn = {1664-302X}, abstract = {The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.}, }
@article {pmid31680681, year = {2019}, author = {Temkin, MI and Carlson, CM and Stubbendieck, AL and Currie, CR and Stubbendieck, RM}, title = {High Throughput Co-culture Assays for the Investigation of Microbial Interactions.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {152}, pages = {}, doi = {10.3791/60275}, pmid = {31680681}, issn = {1940-087X}, abstract = {The study of interactions between microorganisms has led to numerous discoveries, from novel antimicrobials to insights in microbial ecology. Many approaches used for the study of microbial interactions require specialized equipment and are expensive and time intensive. This paper presents a protocol for co-culture interaction assays that are inexpensive, scalable to large sample numbers, and easily adaptable to numerous experimental designs. Microorganisms are cultured together, with each well representing one pairwise combination of microorganisms. A test organism is cultured on one side of each well and first incubated in monoculture. Subsequently, target organisms are simultaneously inoculated onto the opposite side of each well using a 3D-printed inoculation stamp. After co-culture, the completed assays are scored for visual phenotypes, such as growth or inhibition. These assays can be used to confirm phenotypes or identify patterns among isolates of interest. Using this simple and effective method, users can analyze combinations of microorganisms rapidly and efficiently. This co-culture approach is applicable to antibiotic discovery as well as culture-based microbiome research and has already been successfully applied to both applications.}, }
@article {pmid31679006, year = {2019}, author = {Hourcade, MG and Braga, MR and Campo, EMD and Ascaso, C and Patiño, C and Casano, LM}, title = {Ultrastructural and biochemical analyses reveal cell wall remodelling in lichen-forming microalga submitted to cyclic desiccation-rehydration.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcz181}, pmid = {31679006}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: One of the most distinctive features of desiccation-tolerant plants is their high cell wall (CW) flexibility. Most lichen microalgae can tolerate drastic dehydration-rehydration (D/R) conditions, however their mechanisms of D/R tolerance are scarcely understood. We tested the hypothesis that D/R-tolerant microalgae would have flexible CWs due to species-specific CW ultrastructure and biochemical composition, which could be remodelled by exposure to cyclic D/R.<br><br>METHODS: Two lichen microalgae, Trebouxia sp. TR9 (TR9, adapted to rapid D/R cycles) and Coccomyxa simplex (Csol, adapted to seasonal dry periods) were exposed to 0 or 4 cycles of desiccation [25-30% RH (TR9) or 55-60% RH (Csol)] and 16 h rehydration (100% RH). LTSEM, ESEM and freeze-substitution TEM were employed to visualize structural alterations induced by D/R. Besides, CWs were extracted, sequentially fractionated with hot water and KOH, and the gel permeation profile of polysaccharides was analysed in each fraction. The glycosyl composition and linkage of the main polysaccharides of each CW fraction were analysed by GC-MS.<br><br>KEY RESULTS: All ultrastructural analyses consistently showed that desiccation caused progressive cell shrinkage and deformation in both microalgae, which could be rapidly reversed when water availability increased. Notably, TR9 and Csol plasma membrane remained in close contact with the deformed CW. Exposure to D/R strongly altered the size distribution of TR9 hot water-soluble polysaccharides composed mainly of a β-3-linked rhamnogalactofuranan and Csol KOH-soluble β-glucans.<br><br>CONCLUSIONS: Cyclic D/R induces biochemical remodelling of the CW that could increase CW flexibility, allowing regulated shrinkage and expansion of D/R-tolerant microalgae.}, }
@article {pmid31678751, year = {2020}, author = {Contreras-Dávila, CA and Carrión, VJ and Vonk, VR and Buisman, CNJ and Strik, DPBTB}, title = {Consecutive lactate formation and chain elongation to reduce exogenous chemicals input in repeated-batch food waste fermentation.}, journal = {Water research}, volume = {169}, number = {}, pages = {115215}, doi = {10.1016/j.watres.2019.115215}, pmid = {31678751}, issn = {1879-2448}, mesh = {Bioreactors ; Butyrates ; Fatty Acids ; Fermentation ; *Food ; *Refuse Disposal ; }, abstract = {The production of biochemicals from renewables through biorefinery processes is important to reduce the anthropogenic impact on the environment. Chain elongation processes based on microbiomes have been successfully developed to produce medium-chain fatty acids (MCFA) from organic waste streams. Yet, the sustainability of chain elongation can still be improved by reducing the use of electron donors and additional chemicals. This work aimed to couple lactate production and subsequent chain elongation to decrease chemicals input such as electron donors and hydroxide for pH control in repeated-batch food waste fermentation. Food waste with adjusted pH was used as substrate and fermentation proceeded without pH control. During fermentation, lactate was first formed through the homolactic pathway and then converted to fatty acids (FA), mainly n-butyrate and n-caproate. The highest n-caproate carbon selectivities (mmol C/mmol CFA) and production rates were 38% and 4.2 g COD/L-d, respectively. Hydroxide input was reduced over time to a minimum of 0.47 mol OH-/mol MCFA or 0.79 mol OH-/kg CODFA. Lactate was a key electron donor for chain elongation and its conversion was observed at pH as low as 4.3. The microbiome enriched in this work was dominated by Lactobacillus spp. and Caproiciproducens spp. The high abundance of Caproiciproducens spp. and their co-occurrence with Lactobacillus spp. suggest Caproiciproducens spp. used lactate as electron donor for chain elongation. This work shows the production of n-caproate from food waste with decreased use of hydroxide and no use of exogenous electron donors.}, }
@article {pmid31677344, year = {2019}, author = {Dumack, K and Fiore-Donno, AM and Bass, D and Bonkowski, M}, title = {Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria).}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13112}, pmid = {31677344}, issn = {1755-0998}, support = {BO 1907/13-2//Deutsche Forschungsgemeinschaft/ ; BO 1907/18-1//Deutsche Forschungsgemeinschaft/ ; Priority Program 1374//Deutsche Forschungsgemeinschaft/ ; NE/H000887/1//NERC Science of the Environment/ ; NE/H009426/1//NERC Science of the Environment/ ; }, abstract = {We have compiled a database of functional traits for two widespread and ecologically important groups of protists, Cercozoa and Endomyxa (Rhizaria). The functional traits of microorganisms are crucially important for interpreting results from environmental sequencing surveys. Linking morphological and ecological traits to environmental factors is common practice in studies involving micro- and macroorganisms, but is rarely applied to protists. Our database provides functional and ecologically significant traits linked to morphology, nutrition, locomotion and habitats. We discuss how the use of functional traits may help to unveil underlying ecosystem processes. This database is intended as a common reference for the molecular ecology community and will boost the understanding of ecosystem functions, especially those driven by biological interactions.}, }
@article {pmid31676992, year = {2019}, author = {Kublanovskaya, A and Solovchenko, A and Fedorenko, T and Chekanov, K and Lobakova, E}, title = {Natural Communities of Carotenogenic Chlorophyte Haematococcus lacustris and Bacteria from the White Sea Coastal Rock Ponds.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01437-0}, pmid = {31676992}, issn = {1432-184X}, support = {18-29-25050//Российский Фонд Фундаментальных Исследований (РФФИ)/ ; }, abstract = {Haematococcus lacustris is a biotechnologically important green unicellular alga producing widely used keta-karotenoid astaxanthin. In natural habitats, it exists in the form of algal-bacterial community, and under laboratory conditions, it is also accompanied by bacteria. The issue of the bacterial composition of industrial algal cultures is widely recognized as important. However, there is a dearth of information about bacterial composition of H. lacustris communities. In current work, we analyze the composition of natural H. lacustris communities from the White Sea coastal temporal rock ponds. For the first time, a 16S rRNA gene-based metagenome of natural H. lacustris bacterial communities has been generated. Main results of its analysis are as follow. Bacterial families Comamonadaceae, Cytophagaceae, Xanthomonadaceae, Acetobacteraceae, Rhodobacteraceae, and Rhodocyclaceae were observed in all studied H. lacustris natural communities. They also contained genera Hydrogenophaga and Cytophaga. Bacteria from the Hydrogenophaga genus were present in H. lacustris cultures after their isolation under the conditions of laboratory cultivation. Similar to other planktonic microalgae, H. lacustris forms a phycosphere around the cells. In this zone, bacteria attached to the algal surface. The contact between H. lacustris and bacteria is maintained even after sample drying. The study provides information about possible members of H. lacustris core microbiome, which can be presented in the industrial and laboratory cultures of the microalga.}, }
@article {pmid31676479, year = {2020}, author = {Dyer, SW and Needoba, JA}, title = {Use of High-Resolution Pressure Nephelometry To Measure Gas Vesicle Collapse as a Means of Determining Growth and Turgor Changes in Planktonic Cyanobacteria.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {2}, pages = {}, pmid = {31676479}, issn = {1098-5336}, abstract = {Previous work has demonstrated that the physical properties of intracellular bacterial gas vesicles (GVs) can be analyzed in vivo using pressure nephelometry. In analyzing the buoyant state of GV-containing cyanobacteria, hydrostatic pressure within a sample cell is increased in a stepwise manner, where the concomitant collapse of GVs due to pressure and the resultant decrease in suspended cells are detected by changes in nephelometric scattering. As the relative pressure at which GVs collapse is a function of turgor pressure and cellular osmotic gradients, pressure nephelometry is a powerful tool for assaying changes in metabolism that affect turgor, such as photosynthetic and osmoregulatory processes. We have developed an updated and automated pressure nephelometer that utilizes visible-infrared (Vis-IR) spectra to accurately quantify GV critical collapse pressure, critical collapse pressure distribution, and cell turgor pressure. Here, using the updated pressure nephelometer and axenic cultures of Microcystis aeruginosa PCC7806, we demonstrate that GV critical collapse pressure is stable during mid-exponential growth phase, introduce pressure-sensitive turbidity as a robust metric for the abundance of gas-vacuolate cyanobacteria, and demonstrate that pressure-sensitive turbidity is a more accurate proxy for abundance and growth than photopigment fluorescence. As cyanobacterium-dominated harmful algal bloom (cyanoHAB) formation is dependent on the constituent cells possessing gas vesicles, characterization of environmental cyanobacteria populations via pressure nephelometry is identified as an underutilized monitoring method. Applications of this instrument focus on physiological and ecological studies of cyanobacteria, for example, cyanoHAB dynamics and the drivers associated with cyanotoxin production in aquatic ecosystems.IMPORTANCE The increased prevalence of bloom-forming cyanobacteria and associated risk of exposure to cyanobacterial toxins through drinking water utilities and recreational waterways are growing public health concerns. Cost-effective, early-detection methodologies specific to cyanobacteria are crucial for mitigating these risks, with a gas vesicle-specific signal offering a number of benefits over photopigment fluorescence, including improved detection limits and discrimination against non-gas-vacuolate phototrophs. Here, we present a multiplexed instrument capable of quantifying the relative abundance of cyanobacteria based on the signal generated from the presence of intracellular gas vesicles specific to bloom-forming cyanobacteria. Additionally, as cell turgor can be measured in vivo via pressure nephelometry, the measurement furnishes information about the internal osmotic pressure of gas-vacuolate cyanobacteria, which relates to the metabolic state of the cell. Together these advances may improve routine waterway monitoring and the mitigation of human health threats due to cyanobacterial blooms.}, }
@article {pmid31676478, year = {2019}, author = {Oh, JH and Lin, XB and Zhang, S and Tollenaar, SL and Özçam, M and Dunphy, C and Walter, J and van Pijkeren, JP}, title = {Prophages in Lactobacillus reuteri Are Associated with Fitness Trade-Offs but Can Increase Competitiveness in the Gut Ecosystem.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {1}, pages = {}, pmid = {31676478}, issn = {1098-5336}, abstract = {The gut microbiota harbors a diverse phage population that is largely derived from lysogens, which are bacteria that contain dormant phages in their genome. While the diversity of phages in gut ecosystems is getting increasingly well characterized, knowledge is limited on how phages contribute to the evolution and ecology of their host bacteria. Here, we show that biologically active prophages are widely distributed in phylogenetically diverse strains of the gut symbiont Lactobacillus reuteri Nearly all human- and rodent-derived strains, but less than half of the tested strains of porcine origin, contain active prophages, suggesting different roles of phages in the evolution of host-specific lineages. To gain insight into the ecological role of L. reuteri phages, we developed L. reuteri strain 6475 as a model to study its phages. After administration to mice, L. reuteri 6475 produces active phages throughout the intestinal tract, with the highest number detected in the distal colon. Inactivation of recA abolished in vivo phage production, which suggests that activation of the SOS response drives phage production in the gut. In conventional mice, phage production reduces bacterial fitness as fewer wild-type bacteria survive gut transit compared to the mutant lacking prophages. However, in gnotobiotic mice, phage production provides L. reuteri with a competitive advantage over a sensitive host. Collectively, we uncovered that the presence of prophages, although associated with a fitness trade-off, can be advantageous for a gut symbiont by killing a competitor strain in its intestinal niche.IMPORTANCE Bacteriophages derived from lysogens are abundant in gut microbiomes. Currently, mechanistic knowledge is lacking on the ecological ramifications of prophage carriage yet is essential to explain the abundance of lysogens in the gut. An extensive screen of the bacterial gut symbiont Lactobacillus reuteri revealed that biologically active prophages are widely distributed in this species. L. reuteri 6475 produces phages throughout the mouse intestinal tract, but phage production is associated with reduced fitness of the lysogen. However, phage production provides a competitive advantage in direct competition with a nonlysogenic strain of L. reuteri that is sensitive to these phages. This combination of increased competition with a fitness trade-off provides a potential explanation for the domination of lysogens in gut ecosystem and how lysogens can coexist with sensitive hosts.}, }
@article {pmid31672892, year = {2019}, author = {Carrión, VJ and Perez-Jaramillo, J and Cordovez, V and Tracanna, V and de Hollander, M and Ruiz-Buck, D and Mendes, LW and van Ijcken, WFJ and Gomez-Exposito, R and Elsayed, SS and Mohanraju, P and Arifah, A and van der Oost, J and Paulson, JN and Mendes, R and van Wezel, GP and Medema, MH and Raaijmakers, JM}, title = {Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6465}, pages = {606-612}, doi = {10.1126/science.aaw9285}, pmid = {31672892}, issn = {1095-9203}, abstract = {Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.}, }
@article {pmid31670141, year = {2019}, author = {Ouoba, LII and Vouidibio Mbozo, AB and Anyogu, A and Obioha, PI and Lingani-Sawadogo, H and Sutherland, JP and Jespersen, L and Ghoddusi, HB}, title = {Environmental heterogeneity of Staphylococcus species from alkaline fermented foods and associated toxins and antimicrobial resistance genetic elements.}, journal = {International journal of food microbiology}, volume = {311}, number = {}, pages = {108356}, doi = {10.1016/j.ijfoodmicro.2019.108356}, pmid = {31670141}, issn = {1879-3460}, mesh = {Anti-Bacterial Agents/pharmacology ; Burkina Faso ; Coagulase/genetics ; Congo ; DNA-Directed RNA Polymerases/genetics ; Drug Resistance, Bacterial/genetics ; Enterotoxins/*genetics ; Erythromycin/pharmacology ; Fermented Foods and Beverages/*microbiology ; Genotype ; Microbial Sensitivity Tests ; Phenotype ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Staphylococcus/classification/drug effects/genetics/isolation &amp; purification ; Tetracycline/pharmacology ; }, abstract = {Different samples of three products including Bikalga and Soumbala from Burkina Faso (West Africa) and Ntoba Mbodi from Congo-Brazzaville (Central Africa) were evaluated. The bacteria (400) were phenotyped and genotypically characterized by Rep-PCR, PFGE, 16S rRNA and rpoB gene sequencing and spa typing. Their PFGE profiles were compared with those of 12,000 isolates in the Center for Disease Control (CDC, USA) database. They were screened for the production of enterotoxins, susceptibility to 19 antimicrobials, presence of 12 staphylococcal toxin and 38 AMR genes and the ability to transfer erythromycin and tetracycline resistance genes to Enterococcus faecalis JH2-2. Fifteen coagulase negative (CoNS) and positive (CoPS) species characterized by 25 Rep-PCR/PFGE clusters were identified: Staphylococcus arlettae, S. aureus, S. cohnii, S. epidermidis, S. gallinarum, S. haemolyticus, S. hominis, S. pasteuri, S. condimenti, S. piscifermentans, S. saprophyticus, S. sciuri, S. simulans, S. warneri and Macrococcus caseolyticus. Five species were specific to Soumbala, four to Bikalga and four to Ntoba Mbodi. Two clusters of S. gallinarum and three of S. sciuri were particular to Burkina Faso. The S. aureus isolates exhibited a spa type t355 and their PFGE profiles did not match any in the CDC database. Bacteria from the same cluster displayed similar AMR and toxin phenotypes and genotypes, whereas clusters peculiar to a product or a location generated distinct profiles. The toxin genes screened were not detected and the bacteria did not produce the staphylococcal enterotoxins A, B, C and D. AMR genes including blazA, cat501, dfr(A), dfr(G), mecA, mecA1, msr(A) and tet(K) were identified in CoNS and CoPS. Conjugation experiments produced JH2-2 isolates that acquired resistance to erythromycin and tetracycline, but no gene transfer was revealed by PCR. The investigation of the heterogeneity of Staphylococcus species from alkaline fermented foods, their relationship with clinical and environmental isolates and their safety in relation to antimicrobial resistance (AMR) and toxin production is anticipated to contribute to determining the importance of staphylococci in alkaline fermented foods, especially in relation to the safety of the consumers.}, }
@article {pmid31666490, year = {2019}, author = {Sharma, NC and Kumar, D and Sarkar, A and Chowdhury, G and Mukhopadhyay, AK and Ramamurthy, T}, title = {Prevalence of MDR salmonellae with increasing frequency of S. Kentucky and S. Virchow serovars among hospitalized diarrheal cases in and around Delhi, India.}, journal = {Japanese journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.7883/yoken.JJID.2019.063}, pmid = {31666490}, issn = {1884-2836}, abstract = {Non-typhoidal salmonellae (NTS) are a major cause of acute diarrhea with characteristic multidrug resistance. In a hospital based study, 81 NTS were isolated and tested for serotypes and antimicrobial resistance (AMR). Salmonella enterica isolates were classified into 7 different typable serovars and 19 (23%) isolates remained untypable. The most common serovars were S. Kentucky (48%), and S. Virchow (22%). Most of the NTS isolates displayed resistance to nalidixic acid (73%), ciprofloxacin (48%), ampicillin and norfloxacin (36% each) and gentamicin (31%). The AMR profiles for gentamicin and nalidixic acid (CN-NA) and ampicillin, ciprofloxacin, nalidixic acid and norfloxacin (AM-CIP-NA-NOR) were found to be high in S. Virchow (83%) and S. Kentucky (43%), respectively. Analysis of pulsed-field gel electrophoresis patterns of S. Kentucky revealed three clusters. The appearance of closely related clones of S. Kentucky in Delhi has been prominent in recent years. The AMR appears to be constant with a change in MDR patterns during 2014-2017. Prevalence of S. Kentucky, S. Virchow in large number of diarrheal cases was recorded for the first time. The NTS are mostly resistant to fluoroquinolones, which is the current drug of choice for treating diarrheal cases. MDR is very common among clonally related S. Kentucky.}, }
@article {pmid31665274, year = {2020}, author = {Wuyts, K and Smets, W and Lebeer, S and Samson, R}, title = {Green infrastructure and atmospheric pollution shape diversity and composition of phyllosphere bacterial communities in an urban landscape.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {1}, pages = {}, doi = {10.1093/femsec/fiz173}, pmid = {31665274}, issn = {1574-6941}, abstract = {The microbial habitat on leaf surfaces, also called the phyllosphere, is a selective environment for bacteria, harbouring specific phyllosphere bacterial communities (PBCs). These communities influence plant health, plant-community diversity, ecosystem functioning and ecosystem services. Host plants in an urban environment accommodate different PBCs than those in non-urban environments, but previous studies did not address individual urban factors. In this study, the PBC composition and diversity of 55 London plane (Platanus x acerifolia) trees throughout an urban landscape (Antwerp, Belgium) were determined using 16S rRNA amplicon sequencing. An increasing proportion of green infrastructure in the surrounding of the trees, and subsequently decreasing proportion of anthropogenic land use, was linked with taxa loss, expressed in lower phyllosphere alpha diversity and higher abundances of typical phyllosphere bacteria such as Hymenobacter, Pseudomonas and Beijerinckia. Although air pollution exposure, as assessed by leaf magnetic analysis, did not link with alpha diversity, it correlated with shifts in PBC composition in form of turnover, an equilibrium of taxa gain and taxa loss. We found that both urban landscape composition and air pollution exposure - each in their own unique way - influence bacterial communities in the urban tree phyllosphere.}, }
@article {pmid31665056, year = {2019}, author = {Kieran, TJ and Arnold, KMH and Thomas, JC and Varian, CP and Saldaña, A and Calzada, JE and Glenn, TC and Gottdenker, NL}, title = {Regional biogeography of microbiota composition in the Chagas disease vector Rhodnius pallescens.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {504}, pmid = {31665056}, issn = {1756-3305}, support = {DGE-1545433//National Science Foundation/ ; COL11-043//Secretaría Nacional de Ciencia, Tecnología e Innovación/ ; }, abstract = {BACKGROUND: Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama.<br><br>METHODS: We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software.<br><br>RESULTS: We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48-72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status.<br><br>CONCLUSIONS: We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.}, }
@article {pmid31664477, year = {2019}, author = {Kolátková, V and Čepička, I and Gargiulo, GM and Vohník, M}, title = {Enigmatic Phytomyxid Parasite of the Alien Seagrass Halophila stipulacea: New Insights into Its Ecology, Phylogeny, and Distribution in the Mediterranean Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01450-3}, pmid = {31664477}, issn = {1432-184X}, support = {1308218//Grantová Agentura, Univerzita Karlova (CZ)/ ; }, abstract = {Marine phytomyxids represent often overlooked obligate biotrophic parasites colonizing diatoms, brown algae, and seagrasses. An illustrative example of their enigmatic nature is the phytomyxid infecting the seagrass Halophila stipulacea (a well-known Lessepsian migrant from the Indo-Pacific to the Mediterranean Sea). In the Mediterranean, the occurrence of this phytomyxid was first described in 1995 in the Strait of Messina (southern Italy) and the second time in 2017 in the Aegean coast of Turkey. Here we investigated, using scuba diving, stereomicroscopy, light and scanning electron microscopy, and molecular methods, whether the symbiosis is still present in southern Italy, its distribution in this region and its relation to the previous reports. From the total of 16 localities investigated, the symbiosis has only been found at one site. A seasonal pattern was observed with exceptionally high abundance (> 40% of the leaf petioles colonized) in September 2017, absence of the symbiosis in May/June 2018, and then again high infection rates (~ 30%) in September 2018. In terms of anatomy and morphology as well as resting spore dimensions and arrangement, the symbiosis seems to be identical to the preceding observations in the Mediterranean. According to the phylogenetic analyses of the 18S rRNA gene, the phytomyxid represents the first characterized member of the environmental clade &quot;TAGIRI-5&quot;. Our results provide new clues about its on-site ecology (incl. possible dispersal mechanisms), hint that it is rare but established in the Mediterranean, and encourage further research into its distribution, ecophysiology, and taxonomy.}, }
@article {pmid31662456, year = {2019}, author = {Chase, AB and Arevalo, P and Brodie, EL and Polz, MF and Karaoz, U and Martiny, JBH}, title = {Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31662456}, issn = {2150-7511}, abstract = {For free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several obstacles to the study of the processes contributing to microbial diversification. These obstacles are particularly high in soil, where high bacterial diversity inhibits the study of closely related genotypes and therefore the factors structuring microbial populations. Here, we isolated strains within a single Curtobacterium ecotype from surface soil (leaf litter) across a regional climate gradient and investigated the phylogenetic structure, recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. Our results indicate that microbial populations are delineated by gene flow discontinuities, with distinct populations cooccurring at multiple sites. Bacterial population structure was further delineated by genomic features allowing for the identification of candidate genes possibly contributing to local adaptation. These results suggest that the genetic structure within this bacterium is maintained both by ecological specialization in localized microenvironments (isolation by environment) and by dispersal limitation between geographic locations (isolation by distance).IMPORTANCE Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit equivalent to a eukaryotic species, defined as highly clustered genotypic and phenotypic strains with the same ecological niche. Using a combination of genomic and computational analyses, we assessed the phylogenetic structure, extent of recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. To our knowledge, this study is the first to do so for a dominant soil bacterium. Our results indicate that bacterial soil populations, similarly to those in other environments, are structured by gene flow discontinuities and exhibit distributional patterns consistent with both isolation by distance and isolation by environment. Thus, both dispersal limitation and local environments contribute to the divergence among closely related soil bacteria as observed in macroorganisms.}, }
@article {pmid31662077, year = {2019}, author = {Madison, JD and Ouellette, SP and Schmidt, EL and Kerby, JL}, title = {Serratia marcescens shapes cutaneous bacterial communities and influences survival of an amphibian host.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1914}, pages = {20191833}, pmid = {31662077}, issn = {1471-2954}, abstract = {Ongoing investigations into the interactions between microbial communities and their associated hosts are changing how emerging diseases are perceived and ameliorated. Of the numerous host-microbiome-disease systems of study, the emergence of chytridiomycosis (caused by Batrachochytrium dendrobatidis, hereafter Bd) has been implicated in ongoing declines and extinction events of amphibians worldwide. Interestingly, there has been differential survival among amphibians in resisting Bd infection and subsequent disease. One factor thought to contribute to this resistance is the host-associated cutaneous microbiota. This has raised the possibility of using genetically modified probiotics to restructure the host-associated microbiota for desired anti-fungal outcomes. Here, we use a previously described strain of Serratia marcescens (Sm) for the manipulation of amphibian cutaneous microbiota. Sm was genetically altered to have a dysfunctional pathway for the production of the extracellular metabolite prodigiosin. This genetically altered strain (Δpig) and the functional prodigiosin producing strain (wild-type, WT) were compared for their microbial community and anti-Bd effects both in vitro and in vivo. In vitro, Bd growth was significantly repressed in the presence of prodigiosin. In vivo, the inoculation of both Sm strains was shown to significantly influence amphibian microbiota diversity with the Δpig-Sm treatment showing increasing alpha diversity, and the WT-Sm having no temporal effect on diversity. Differences were also seen in host mortality with Δpig-Sm treatments exhibiting significantly decreased survival probability when compared with WT-Sm in the presence of Bd. These results are an important proof-of-concept for linking the use of genetically modified probiotic bacteria to host microbial community structure and disease outcomes, which in the future may provide a way to ameliorate disease and address critical frontiers in disease and microbial ecology.}, }
@article {pmid31660948, year = {2019}, author = {Waters, JL and Ley, RE}, title = {The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {83}, pmid = {31660948}, issn = {1741-7007}, abstract = {The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.}, }
@article {pmid31659049, year = {2019}, author = {Gusareva, ES and Acerbi, E and Lau, KJX and Luhung, I and Premkrishnan, BNV and Kolundžija, S and Purbojati, RW and Wong, A and Houghton, JNI and Miller, D and Gaultier, NE and Heinle, CE and Clare, ME and Vettath, VK and Kee, C and Lim, SBY and Chénard, C and Phung, WJ and Kushwaha, KK and Nee, AP and Putra, A and Panicker, D and Yanqing, K and Hwee, YZ and Lohar, SR and Kuwata, M and Kim, HL and Yang, L and Uchida, A and Drautz-Moses, DI and Junqueira, ACM and Schuster, SC}, title = {Microbial communities in the tropical air ecosystem follow a precise diel cycle.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {46}, pages = {23299-23308}, pmid = {31659049}, issn = {1091-6490}, abstract = {The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% of the generated sequence data currently being assignable to taxa, the air harbored a microbial diversity that rivals the complexity of other planetary ecosystems. The airborne microbial organisms followed a clear diel cycle, possibly driven by environmental factors. Interday taxonomic diversity exceeded day-to-day and month-to-month variation. Environmental time series revealed the existence of a large core of microbial taxa that remained invariable over 13 mo, thereby underlining the long-term robustness of the airborne community structure. Unlike terrestrial or aquatic environments, where prokaryotes are prevalent, the tropical airborne biomass was dominated by DNA from eukaryotic phyla. Specific fungal and bacterial species were strongly correlated with temperature, humidity, and CO2 concentration, making them suitable biomarkers for studying the bioaerosol dynamics of the atmosphere.}, }
@article {pmid31657947, year = {2019}, author = {Ilgrande, C and Defoirdt, T and Vlaeminck, SE and Boon, N and Clauwaert, P}, title = {Media Optimization, Strain Compatibility, and Low-Shear Modeled Microgravity Exposure of Synthetic Microbial Communities for Urine Nitrification in Regenerative Life-Support Systems.}, journal = {Astrobiology}, volume = {19}, number = {11}, pages = {1353-1362}, doi = {10.1089/ast.2018.1981}, pmid = {31657947}, issn = {1557-8070}, abstract = {Urine is a major waste product of human metabolism and contains essential macro- and micronutrients to produce edible microorganisms and crops. Its biological conversion into a stable form can be obtained through urea hydrolysis, subsequent nitrification, and organics removal, to recover a nitrate-enriched stream, free of oxygen demand. In this study, the utilization of a microbial community for urine nitrification was optimized with the focus for space application. To assess the role of selected parameters that can impact ureolysis in urine, the activity of six ureolytic heterotrophs (Acidovorax delafieldii, Comamonas testosteroni, Cupriavidus necator, Delftia acidovorans, Pseudomonas fluorescens, and Vibrio campbellii) was tested at different salinities, urea, and amino acid concentrations. The interaction of the ureolytic heterotrophs with a nitrifying consortium (Nitrosomonas europaea ATCC 19718 and Nitrobacter winogradskyi ATCC 25931) was also tested. Lastly, microgravity was simulated in a clinostat utilizing hardware for in-flight experiments with active microbial cultures. The results indicate salt inhibition of the ureolysis at 30 mS cm-1, while amino acid nitrogen inhibits ureolysis in a strain-dependent manner. The combination of the nitrifiers with C. necator and V. campbellii resulted in a complete halt of the urea hydrolysis process, while in the case of A. delafieldii incomplete nitrification was observed, and nitrite was not oxidized further to nitrate. Nitrate production was confirmed in all the other communities; however, the other heterotrophic strains most likely induced oxygen competition in the test setup, and nitrite accumulation was observed. Samples exposed to low-shear modeled microgravity through clinorotation behaved similarly to the static controls. Overall, nitrate production from urea was successfully demonstrated with synthetic microbial communities under terrestrial and simulated space gravity conditions, corroborating the application of this process in space.}, }
@article {pmid31656973, year = {2019}, author = {Otto-Hanson, LK and Kinkel, LL}, title = {Densities and inhibitory phenotypes among indigenous Streptomyces spp. vary across native and agricultural habitats.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01443-2}, pmid = {31656973}, issn = {1432-184X}, support = {9977907//National Science Foundation/ ; 2006-35319-17445//U.S. Department of Agriculture/ ; }, abstract = {Streptomyces spp. perform vital roles in natural and agricultural soil ecosystems including in decomposition and nutrient cycling, promotion of plant growth and fitness, and plant disease suppression. Streptomyces densities can vary across the landscape, and inhibitory phenotypes are often a result of selection mediated by microbial competitive interactions in soil communities. Diverse environmental factors, including those specific to habitat, are likely to determine microbial densities in the soil and the outcomes of microbial species interactions. Here, we characterized indigenous Streptomyces densities and inhibitory phenotypes from soil samples (n = 82) collected in 6 distinct habitats across the Cedar Creek Ecosystem Science Reserve (CCESR; agricultural, prairie, savanna, wetland, wet-woodland, and forest). Significant variation in Streptomyces density and the frequency of antagonistic Streptomyces were observed among habitats. There was also significant variation in soil chemical properties among habitats, including percent carbon, percent nitrogen, available phosphorus, extractable potassium, and pH. Density and frequency of antagonists were significantly correlated with one or more environmental parameters across all habitats, though relationships with some parameters differed among habitats. In addition, we found that habitat rather than spatial proximity was a better predictor of variation in Streptomyces density and inhibitory phenotypes. Moreover, habitats least conducive for Streptomyces growth and proliferation, as determined by population density, had increased frequencies of inhibitory phenotypes. Identifying environmental parameters that structure variation in density and frequency of antagonistic Streptomyces can provide insight for determining factors that mediate selection for inhibitory phenotypes across the landscape.}, }
@article {pmid31656023, year = {2019}, author = {Farias, GC and Nunes, KG and Soares, MA and de Siqueira, KA and Lima, WC and Neves, ALR and de Lacerda, CF and Filho, EG}, title = {Dark septate endophytic fungi mitigate the effects of salt stress on cowpea plants.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, doi = {10.1007/s42770-019-00173-4}, pmid = {31656023}, issn = {1678-4405}, abstract = {The association of plant with microorganisms, such as dark septate endophytic fungi, has mitigated the harmful effects of chemical, physical, and biological agents on the host. The objective of this work was to evaluate the interaction of the dark septate endophytic fungi with cowpea plants under salt stress. Endophytic fungi were isolated from Vochysia divergens root system, and molecular identification of fungi was performed by sequencing the ITS region. We selected and identified Sordariomycetes sp1-B'2 and Melanconiella elegans-21W2 for their ability to infect V. divergens root in vitro with development of typical dark septate fungi structures. Cowpea plants-inoculated or not inoculated with Sordariomycetes sp1-B'2 and M. elegans 21W2-were cultivated in 5-L pots under greenhouse conditions and submitted to four different electrical conductivities of irrigation water (1.2, 2.2, 3.6, and 5.0 dS m-1). The salinity caused decrease in leaf concentration of K and increased leaf concentration of calcium, sodium, and chlorine; and no influence of dark septate endophytic fungi was observed in these responses. On the other hand, root colonization with Sordariomycetes sp1-B'2 and M. elegans 21W2 resulted in improved nutrition with N and P in cowpea under salt stress, favoring the growth and rate of liquid photosynthesis. However, such positive responses were evident only at moderate levels of salinity.}, }
@article {pmid31655872, year = {2019}, author = {Biedunkiewicz, A and Sucharzewska, E and Kulesza, K and Nowacka, K and Kubiak, D}, title = {Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi-Potential Human Pathogens.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01447-y}, pmid = {31655872}, issn = {1432-184X}, support = {12.610.009-300//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; }, abstract = {This study analysed whether the littoral zone in the immediate vicinity of bathing sites retains potentially pathogenic yeasts on the phyllosphere surface and to what extent the species composition of microfungi in the phyllosphere and in surface waters is similar. The research was carried out in selected lakes located within the administrative boundaries of the city of Olsztyn, the largest city in the Masurian Lake District (NE Poland). The experiment was conducted in three summer seasons near bathing sites in three lakes, which are the most popular as recreational sites (Lake Kortowskie, Lake Tyrsko, and Lake Skanda). Microfungi isolated from the phyllosphere of 13 plant species of the littoral zone from dropped leaves of coast plants with no disease symptoms were used as the study material. The isolated fungi were identified in accordance with the accepted diagnostic procedures applied in mycological laboratories. A total of 36 yeast species of 16 genera were identified. Fungi found earlier at the bathing sites of the lakes were identified in 60% of the cases. Nine species were categorised as class BSL-2 fungi. This study provides a valuable complement of data concerning the natural composition of the littoral microbiota.}, }
@article {pmid31654911, year = {2019}, author = {Masteling, R and Lombard, L and de Boer, W and Raaijmakers, JM and Dini-Andreote, F}, title = {Harnessing the microbiome to control plant parasitic weeds.}, journal = {Current opinion in microbiology}, volume = {49}, number = {}, pages = {26-33}, pmid = {31654911}, issn = {1879-0364}, abstract = {Microbiomes can significantly expand the genomic potential of plants, contributing to nutrient acquisition, plant growth promotion and tolerance to (a)biotic stresses. Among biotic stressors, root parasitic weeds (RPWs), mainly of the genera Orobanche, Phelipanche and Striga, are major yield-limiting factors of a wide range of staple crops, particularly in developing countries. Here, we provide a conceptual synthesis of putative mechanisms by which soil and plant microbiomes could be harnessed to control RPWs. These mechanisms are partitioned in direct and indirect modes of action and discussed in the context of past and present studies on microbe-mediated suppression of RPWs. Specific emphasis is given to the large but yet unexplored potential of root-associated microorganisms to interfere with the chemical signalling cascade between the host plant and the RPWs. We further provide concepts and ideas for future research directions and prospective designs of novel control strategies.}, }
@article {pmid31654107, year = {2019}, author = {Reyns, W and Rineau, F and Spaak, JW and Franken, O and Berg, MP and Van Der Plas, F and Bardgett, RD and Beenaerts, N and De Laender, F}, title = {Food Web Uncertainties Influence Predictions of Climate Change Effects on Soil Carbon Sequestration in Heathlands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01444-1}, pmid = {31654107}, issn = {1432-184X}, support = {BOF15DOCNA02//Bijzonder Onderzoeksfonds/ ; }, abstract = {Carbon cycling models consider soil carbon sequestration a key process for climate change mitigation. However, these models mostly focus on abiotic soil processes and, despite its recognized critical mechanistic role, do not explicitly include interacting soil organisms. Here, we use a literature study to show that even a relatively simple soil community (heathland soils) contains large uncertainties in temporal and spatial food web structure. Next, we used a Lotka-Volterra-based food web model to demonstrate that, due to these uncertainties, climate change can either increase or decrease soil carbon sequestration to varying extents. Both the strength and direction of changes strongly depend on (1) the main consumer's (enchytraeid worms) feeding preferences and (2) whether decomposers (fungi) or enchytraeid worms are more sensitive to stress. Hence, even for a soil community with a few dominant functional groups and a simulation model with a few parameters, filling these knowledge gaps is a critical first step towards the explicit integration of soil food web dynamics into carbon cycling models in order to better assess the role soils play in climate change mitigation.}, }
@article {pmid31654106, year = {2019}, author = {Schappe, T and Albornoz, FE and Turner, BL and Jones, FA}, title = {Co-occurring Fungal Functional Groups Respond Differently to Tree Neighborhoods and Soil Properties Across Three Tropical Rainforests in Panama.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01446-z}, pmid = {31654106}, issn = {1432-184X}, support = {DEB 1542681//National Science Foundation/ ; NA//Smithsonian Tropical Research Institute/ ; }, abstract = {Abiotic and biotic drivers of co-occurring fungal functional guilds across regional-scale environmental gradients remain poorly understood. We characterized fungal communities using Illumina sequencing from soil cores collected across three Neotropical rainforests in Panama that vary in soil properties and plant community composition. We classified each fungal OTU into different functional guilds, namely plant pathogens, saprotrophs, arbuscular mycorrhizal (AM), or ectomycorrhizal (ECM). We measured soil properties and nutrients within each core and determined the tree community composition and richness around each sampling core. Canonical correspondence analyses showed that soil pH and moisture were shared potential drivers of fungal communities for all guilds. However, partial the Mantel tests showed different strength of responses of fungal guilds to composition of trees and soils. Plant pathogens and saprotrophs were more strongly correlated with soil properties than with tree composition; ECM fungi showed a stronger correlation with tree composition than with soil properties; and AM fungi were correlated with soil properties, but not with trees. In conclusion, we show that co-occurring fungal guilds respond differently to abiotic and biotic environmental factors, depending on their ecological function. This highlights the joint role that abiotic and biotic factors play in determining composition of fungal communities, including those associated with plant hosts.}, }
@article {pmid31653831, year = {2019}, author = {Sonner, JK and Keil, M and Falk-Paulsen, M and Mishra, N and Rehman, A and Kramer, M and Deumelandt, K and Röwe, J and Sanghvi, K and Wolf, L and von Landenberg, A and Wolff, H and Bharti, R and Oezen, I and Lanz, TV and Wanke, F and Tang, Y and Brandao, I and Mohapatra, SR and Epping, L and Grill, A and Röth, R and Niesler, B and Meuth, SG and Opitz, CA and Okun, JG and Reinhardt, C and Kurschus, FC and Wick, W and Bode, HB and Rosenstiel, P and Platten, M}, title = {Dietary tryptophan links encephalogenicity of autoreactive T cells with gut microbial ecology.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4877}, pmid = {31653831}, issn = {2041-1723}, abstract = {The interaction between the mammalian host and its resident gut microbiota is known to license adaptive immune responses. Nutritional constituents strongly influence composition and functional properties of the intestinal microbial communities. Here, we report that omission of a single essential amino acid - tryptophan - from the diet abrogates CNS autoimmunity in a mouse model of multiple sclerosis. Dietary tryptophan restriction results in impaired encephalitogenic T cell responses and is accompanied by a mild intestinal inflammatory response and a profound phenotypic shift of gut microbiota. Protective effects of dietary tryptophan restriction are abrogated in germ-free mice, but are independent of canonical host sensors of intracellular tryptophan metabolites. We conclude that dietary tryptophan restriction alters metabolic properties of gut microbiota, which in turn have an impact on encephalitogenic T cell responses. This link between gut microbiota, dietary tryptophan and adaptive immunity may help to develop therapeutic strategies for protection from autoimmune neuroinflammation.}, }
@article {pmid31653789, year = {2019}, author = {Kleyer, H and Tecon, R and Or, D}, title = {Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {1}, pages = {}, pmid = {31653789}, issn = {1098-5336}, abstract = {The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments.IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.}, }
@article {pmid31650676, year = {2020}, author = {Bennett, JA and Koch, AM and Forsythe, J and Johnson, NC and Tilman, D and Klironomos, J}, title = {Resistance of soil biota and plant growth to disturbance increases with plant diversity.}, journal = {Ecology letters}, volume = {23}, number = {1}, pages = {119-128}, doi = {10.1111/ele.13408}, pmid = {31650676}, issn = {1461-0248}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Biota ; *Ecosystem ; Plants ; *Soil ; Soil Microbiology ; }, abstract = {Plant diversity is critical to the functioning of ecosystems, potentially mediated in part by interactions with soil biota. Here, we characterised multiple groups of soil biota across a plant diversity gradient in a long-term experiment. We then subjected soil samples taken along this gradient to drought, freezing and a mechanical disturbance to test how plant diversity affects the responses of soil biota and growth of a focal plant to these disturbances. High plant diversity resulted in soils that were dominated by fungi and associated soil biota, including increased arbuscular mycorrhizal fungi and reduced plant-feeding nematodes. Disturbance effects on the soil biota were reduced when plant diversity was high, resulting in higher growth of the focal plant in all but the frozen soils. These results highlight the importance of plant diversity for soil communities and their resistance to disturbance, with potential feedback effects on plant productivity.}, }
@article {pmid31649246, year = {2019}, author = {Wagg, C and Schlaeppi, K and Banerjee, S and Kuramae, EE and van der Heijden, MGA}, title = {Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4841}, pmid = {31649246}, issn = {2041-1723}, abstract = {The soil microbiome is highly diverse and comprises up to one quarter of Earth's diversity. Yet, how such a diverse and functionally complex microbiome influences ecosystem functioning remains unclear. Here we manipulated the soil microbiome in experimental grassland ecosystems and observed that microbiome diversity and microbial network complexity positively influenced multiple ecosystem functions related to nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed microbial networks and reduced microbial richness had the lowest multifunctionality due to fewer taxa present that support the same function (redundancy) and lower diversity of taxa that support different functions (reduced functional uniqueness). Moreover, different microbial taxa explained different ecosystem functions pointing to the significance of functional diversity in microbial communities. These findings indicate the importance of microbial interactions within and among fungal and bacterial communities for enhancing ecosystem performance and demonstrate that the extinction of complex ecological associations belowground can impair ecosystem functioning.}, }
@article {pmid31648128, year = {2020}, author = {Tortosa, G and Torralbo, F and Maza-Márquez, P and Aranda, E and Calvo, C and González-Murua, C and Bedmar, EJ}, title = {Assessment of the diversity and abundance of the total and active fungal population and its correlation with humification during two-phase olive mill waste (''alperujo&quot;) composting.}, journal = {Bioresource technology}, volume = {295}, number = {}, pages = {122267}, doi = {10.1016/j.biortech.2019.122267}, pmid = {31648128}, issn = {1873-2976}, mesh = {*Ascomycota ; *Basidiomycota ; *Composting ; *Olea ; Soil ; }, abstract = {Metagenomic and transcriptomic techniques applied to composting could increase our understanding of the overall microbial ecology and could help us to optimise operational conditions which are directly related with economic interest. In this study, the fungal diversity and abundance of two-phase olive mill waste (&quot;alperujo&quot;) composting was studied using Illumina MiSeq sequencing and quantitative PCR, respectively. The results showed an increase of the fungal diversity during the process, with Ascomycota being the predominant phylum. Penicillium was the main genera identified at the mesophilic and maturation phases, with Debaryomyces and Sarocladium at the thermophilic phase, respectively. The fungal abundance was increased during composting, which confirms their important role during thermophilic and maturation phases. Some Basidiomycota showed an increased during the process, which showed a positive correlation with the humification parameters. According to that, the genus Cystofilobasidium could be used as a potential fungal biomarker to assess alperujo compost maturation.}, }
@article {pmid31642982, year = {2019}, author = {Landberg, R and Manach, C and Kerckhof, FM and Minihane, AM and Saleh, RNM and De Roos, B and Tomas-Barberan, F and Morand, C and Van de Wiele, T}, title = {Future prospects for dissecting inter-individual variability in the absorption, distribution and elimination of plant bioactives of relevance for cardiometabolic endpoints.}, journal = {European journal of nutrition}, volume = {58}, number = {Suppl 2}, pages = {21-36}, pmid = {31642982}, issn = {1436-6215}, support = {FA1403//EU - COST Action FA-1403 (2014-2018)/ ; }, abstract = {PURPOSE: The health-promoting potential of food-derived plant bioactive compounds is evident but not always consistent across studies. Large inter-individual variability may originate from differences in digestion, absorption, distribution, metabolism and excretion (ADME). ADME can be modulated by age, sex, dietary habits, microbiome composition, genetic variation, drug exposure and many other factors. Within the recent COST Action POSITIVe, large-scale literature surveys were undertaken to identify the reasons and extent of inter-individual variability in ADME of selected plant bioactive compounds of importance to cardiometabolic health. The aim of the present review is to summarize the findings and suggest a framework for future studies designed to investigate the etiology of inter-individual variability in plant bioactive ADME and bioefficacy.<br><br>RESULTS: Few studies have reported individual data on the ADME of bioactive compounds and on determinants such as age, diet, lifestyle, health status and medication, thereby limiting a mechanistic understanding of the main drivers of variation in ADME processes observed across individuals. Metabolomics represent crucial techniques to decipher inter-individual variability and to stratify individuals according to metabotypes reflecting the intrinsic capacity to absorb and metabolize bioactive compounds.<br><br>CONCLUSION: A methodological framework was developed to decipher how the contribution from genetic variants or microbiome variants to ADME of bioactive compounds can be predicted. Future study design should include (1) a larger number of study participants, (2) individual and full profiling of all possible determinants of internal exposure, (3) the presentation of individual ADME data and (4) incorporation of omics platforms, such as genomics, microbiomics and metabolomics in ADME and efficacy studies.}, }
@article {pmid31642672, year = {2019}, author = {Yuan, Y and Zheng, Y and Zhou, J and Geng, Y and Zou, P and Li, Y and Zhang, C}, title = {Polyphenol-Rich Extracts from Brown Macroalgae Lessonia trabeculate Attenuate Hyperglycemia and Modulate Gut Microbiota in High-Fat Diet and Streptozotocin-Induced Diabetic Rats.}, journal = {Journal of agricultural and food chemistry}, volume = {67}, number = {45}, pages = {12472-12480}, doi = {10.1021/acs.jafc.9b05118}, pmid = {31642672}, issn = {1520-5118}, mesh = {Animals ; Blood Glucose/metabolism ; Diabetes Mellitus, Experimental/*drug therapy/metabolism/microbiology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hyperglycemia/*drug therapy/metabolism/microbiology ; Hypoglycemic Agents/*administration &amp; dosage ; Male ; Mice, Inbred C57BL ; Phaeophyta/*chemistry ; Plant Extracts/*administration &amp; dosage ; Polyphenols/*administration &amp; dosage ; Rats ; Seaweed/*chemistry ; Streptozocin/adverse effects ; }, abstract = {Brown macroalgae are an important source of polyphenols with multiple health functions. In this work, polyphenol extracts from Lessonia trabeculate were purified and investigated for the antidiabetic activity in vitro and in vivo. The purified polyphenol extracts exhibited good antioxidant activities, α-glucosidase and lipase inhibition activities (IC50 < 0.25 mg/mL). The HPLC-DAD-ESI-MS/MS analysis indicated that the compounds in polyphenol extracts were mainly phlorotannin derivatives, phenolic acid derivatives, and gallocatechin derivatives. In vivo, C57BL/6J rats treated with polyphenol extracts for 4 weeks had lower fasting blood glucose levels, insulin levels, as well as better serum lipid profiles and antioxidant stress parameters, compared with the diabetic control (DC) group. Histopathology revealed that polyphenol extracts preserved the architecture and function of the liver. Short-chain fatty acid contents in rats' fecal samples with polyphenols administration were significantly recovered as compared with the DC group. Furthermore, the gut microflora of rats was investigated with high-throughput 16S rRNA gene sequencing and results indicated that polyphenol extracts had a positive effect on regulating the dysbiosis of the microbial ecology in diabetic rats. All of the results from the study provided a scientific reference of the potentially beneficial effects of L. trabeculate polyphenols on diabetes management.}, }
@article {pmid31642093, year = {2019}, author = {Deepika, S and Mittal, A and Kothamasi, D}, title = {HCN-producing Pseudomonas protegens CHA0 affects intraradical viability of Rhizophagus irregularis in Sorghum vulgare roots.}, journal = {Journal of basic microbiology}, volume = {59}, number = {12}, pages = {1229-1237}, doi = {10.1002/jobm.201900364}, pmid = {31642093}, issn = {1521-4028}, mesh = {Biomass ; Glomeromycota/*physiology ; Hydrogen Cyanide/*metabolism ; *Microbial Interactions ; Mycorrhizae/*physiology ; Nutrients/metabolism ; Plant Growth Regulators/genetics/*metabolism ; Plant Roots/metabolism/microbiology ; Pseudomonas/genetics/*metabolism ; Rhizosphere ; Soil Microbiology ; Sorghum/metabolism/*microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria inhabit the plant rhizosphere. Both functional groups can influence plant community structures, and interactions between them can vary from being synergistic to antagonistic. HCN-producing Pseudomonas protegens CHA0 is a plant growth-promoting rhizobacterium. P. protegens CHA0 has been shown to weakly attach to AMF hyphae. Here, we analyze the effect of P. protegens CHA0 on the viability of intraradical AMF hyphae. Using pot experiments, we have grown mycorrhizal and nonmycorrhizal Sorghum vulgare var. M35 with P. protegens CHA0 or HCN- mutant P. protegens CHA77, which did not produce HCN. Mycorrhizal and nonmycorrhizal Sorghum grown without CHA0 or CHA77 served as the control. While metabolically active AMF was not detected in mycorrhizal plants grown with HCN+ CHA0, the percentage of root colonization of metabolically active AMF in plants grown with HCN- CHA77 was lower than in the control. Root phosphorus was highest in mycorrhizal plants grown with HCN+ CHA0, but root Fe was higher in plants grown with the bacterial strains. Our results indicate that HCN-producing P. protegens can affect the viability of intraradical AMF.}, }
@article {pmid31640813, year = {2019}, author = {Chen, S and Waghmode, TR and Sun, R and Kuramae, EE and Hu, C and Liu, B}, title = {Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {136}, pmid = {31640813}, issn = {2049-2618}, support = {2017YFD0200100//National Key R&amp;D Program of China/ ; 2017YFD0800604//National Key R&amp;D Program of China/ ; no. 41530859//the Key Program of the National Natural Science Foundation of China/ ; 41601511//the National Natural Science Foundation of China/ ; CAS//the Hundred Talents Program of the Chinese Academy of China/ ; 729.004.016//Netherlands Organization for Scientific Research/ ; }, abstract = {BACKGROUND: Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates.<br><br>METHODS: The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat (Triticum aestivum L.) under four levels of long-term inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified.<br><br>RESULTS: ROC levels varied dramatically across wheat growth stages and correlated more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter, Bacillus and Devosia, correlated significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels.<br><br>CONCLUSIONS: Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage demostrated a stronger influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to N fertilization, and their abundance correlated significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.}, }
@article {pmid31640783, year = {2019}, author = {Chen, W and Ren, K and Isabwe, A and Chen, H and Liu, M and Yang, J}, title = {Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {138}, pmid = {31640783}, issn = {2049-2618}, support = {91851104//National Natural Science Foundation of China/ ; 31672312//National Natural Science Foundation of China/ ; 2019J02016//Natural Science Foundation of Fujian Province of China/ ; }, abstract = {BACKGROUND: The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared the spatiotemporal and biogeographical patterns of microeukaryotic community using high-throughput sequencing of 18S rRNA gene and multivariate statistical analyses from a subtropical river during wet and dry seasons.<br><br>RESULTS: Our results provide the first description of biogeographical patterns of microeukaryotic communities in the Tingjiang River, the largest river in the west of Fujian province, southeastern China. The results showed that microeukaryotes from both wet and dry seasons exhibited contrasting community compositions, which might be owing to planktonic microeukaryotes having seasonal succession patterns. Further, all components of the microeukaryotic communities (including total, dominant, always rare, and conditionally rare taxa) exhibited a significant distance-decay pattern in both seasons, and these communities had a stronger distance-decay relationship during the dry season, especially for the conditionally rare taxa. Although several variables had a significant influence on the microeukaryotic communities, the environmental and spatial factors showed minor roles in shaping the communities. Importantly, these microeukaryotic communities were strongly driven by stochastic processes, with 89.9%, 88.5%, and 89.6% of the community variation explained by neutral community model during wet, dry, and both seasons, respectively. The neutral community model also explained a large fraction of the community variation across different taxonomic groups and levels. Additionally, the microeukaryotic taxa, which were above and below the neutral prediction, were ecologically and taxonomically distinct groups, which might be interactively structured by deterministic and stochastic processes.<br><br>CONCLUSIONS: This study demonstrated that stochastic processes are sufficient in shaping substantial variation in river microeukaryotic metacommunity across different hydrographic regimes, thereby providing a better understanding of spatiotemporal patterns, processes, and mechanisms of microeukaryotic community in waters.}, }
@article {pmid31640497, year = {2019}, author = {Brunner, JD and Chia, N}, title = {Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species-species modelling.}, journal = {Journal of the Royal Society, Interface}, volume = {16}, number = {159}, pages = {20190423}, pmid = {31640497}, issn = {1742-5662}, abstract = {Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behaviour of microbial communities. We seek a modelling strategy that can capture emergent behaviour when built from sets of universal individual interactions. Our investigation reveals that species-metabolite interaction (SMI) modelling is better able to capture emergent behaviour in community composition dynamics than direct species-species modelling. Using publicly available data, we examine the ability of species-species models and species-metabolite models to predict trio growth experiments from the outcomes of pair growth experiments. We compare quadratic species-species interaction models and quadratic SMI models and conclude that only species-metabolite models have the necessary complexity to explain a wide variety of interdependent growth outcomes. We also show that general species-species interaction models cannot match the patterns observed in community growth dynamics, whereas species-metabolite models can. We conclude that species-metabolite modelling will be important in the development of accurate, clinically useful models of microbial communities.}, }
@article {pmid31640295, year = {2019}, author = {Giuliani, C and Marzorati, M and Daghio, M and Franzetti, A and Innocenti, M and Van de Wiele, T and Mulinacci, N}, title = {Effects of Olive and Pomegranate By-Products on Human Microbiota: A Study Using the SHIME® in Vitro Simulator.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {20}, pages = {}, pmid = {31640295}, issn = {1420-3049}, support = {DD6107/2013//Tuscany Region/ ; CRF 2016.959//Foundation CR of Florence/ ; }, abstract = {Two by-products containing phenols and polysaccharides, a &quot;pâté&quot; (OP) from the extra virgin olive oil milling process and a decoction of pomegranate mesocarp (PM), were investigated for their effects on human microbiota using the SHIME® system. The ability of these products to modulate the microbial community was studied simulating a daily intake for nine days. Microbial functionality, investigated in terms of short chain fatty acids (SCFA) and NH4+, was stable during the treatment. A significant increase in Lactobacillaceae and Bifidobacteriaceae at nine days was induced by OP mainly in the proximal tract. Polyphenol metabolism indicated the formation of tyrosol from OP mainly in the distal tract, while urolithins C and A were produced from PM, identifying the human donor as a metabotype A. The results confirm the SHIME® system as a suitable in vitro tool to preliminarily investigate interactions between complex botanicals and human microbiota before undertaking more challenging human studies.}, }
@article {pmid31637799, year = {2020}, author = {Dedysh, SN and Henke, P and Ivanova, AA and Kulichevskaya, IS and Philippov, DA and Meier-Kolthoff, JP and Göker, M and Huang, S and Overmann, J}, title = {100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii.}, journal = {Environmental microbiology}, volume = {22}, number = {1}, pages = {198-211}, doi = {10.1111/1462-2920.14838}, pmid = {31637799}, issn = {1462-2920}, support = {16-04-00290//Russian Foundation for Basic Research/ ; }, abstract = {The first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous freshwater bacterium is a rare example of as-yet-uncultivated prokaryotes with validly published names and unknown identity. We report the results of molecular identification of this elusive bacterium, which was detected in a eutrophic boreal lake in Northern Russia. By using high-performance cell sorting, P. bekefii-like cell rosettes were selectively enriched from lake water. The retrieved 16S rRNA gene sequence was nearly identical to those in dozens of metagenomes assembled from freshwater lakes during cyanobacterial blooms and was phylogenetically placed within a large group of environmental sequences originating from various freshwater habitats worldwide. In contrast, 16S rRNA gene sequence similarity to all currently described members of the order Planctomycetales was only 83%-92%. The metagenome assembled for P. bekefii reached 43% genome coverage and showed the potential for degradation of peptides, pectins, and sulfated polysaccharides. Tracing the seasonal dynamics of P. bekefii by Illumina paired-end sequencing of 16S rRNA gene fragments and by fluorescence in situ hybridization revealed that these bacteria only transiently surpass the detection limit, with a characteristic population peak of up to 104 cells ml-1 following cyanobacterial blooms.}, }
@article {pmid31637492, year = {2019}, author = {Zhu, X and Wang, J and De Belie, N and Boon, N}, title = {Complementing urea hydrolysis and nitrate reduction for improved microbially induced calcium carbonate precipitation.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {21-22}, pages = {8825-8838}, doi = {10.1007/s00253-019-10128-2}, pmid = {31637492}, issn = {1432-0614}, support = {File No. 201706140108//Distinguished International Students Scholarship/ ; reference code: 01SC4918//Universiteit Gent/ ; }, abstract = {Microbial-induced CaCO3 precipitation has been widely applied in bacterial-based self-healing concrete. However, the limited biogenetic CaCO3 production by bacteria after they were introduced into the incompatible concrete matrix is a major challenge of this technology. In the present study, the potential of combining two metabolic pathways, urea hydrolysis and nitrate reduction, simultaneously in one bacteria strain for improving the bacterial CaCO3 yield has been investigated. One bacterial strain, Ralstonia eutropha H16, which has the highest Ca2+ tolerance and is capable of performing both urea hydrolysis and nitrate reduction in combined media was selected among three bacterial candidates based on the enzymatic examinations. Results showed that H16 does not need oxygen for urea hydrolysis and urease activity was determined primarily by cell concentration. However, the additional urea in the combined medium slowed down the nitrate reduction rate to 7 days until full NO3- decomposition. Moreover, the nitrate reduction of H16 was significantly restricted by an increased Ca2+ ion concentration in the media. Nevertheless, the overall CaCO3 precipitation yield can be improved by 20 to 30% after optimization through the combination of two metabolic pathways. The highest total CaCO3 precipitation yield achieved in an orthogonal experiment was 14 g/L. It can be concluded that Ralstonia eutropha H16 is a suitable bacterium for simultaneous activation of urea hydrolysis and nitrate reduction for improving the CaCO3 precipitation and it can be studied later, on activation of multiple metabolic pathways in bacteria-based self-healing concrete.}, }
@article {pmid31637468, year = {2019}, author = {de Roos, B and Aura, AM and Bronze, M and Cassidy, A and Conesa, MG and Gibney, ER and Greyling, A and Kaput, J and Kerem, Z and Knežević, N and Kroon, P and Landberg, R and Manach, C and Milenkovic, D and Rodriguez-Mateos, A and Tomás-Barberán, FA and van de Wiele, T and Morand, C}, title = {Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications.}, journal = {European journal of nutrition}, volume = {58}, number = {Suppl 2}, pages = {65-73}, pmid = {31637468}, issn = {1436-6215}, support = {FA 1403//European Cooperation in Science and Technology/ ; }, abstract = {BACKGROUND: A healthy diet and optimal lifestyle choices are amongst the most important actions for the prevention of cardiometabolic diseases. Despite this, it appears difficult to convince consumers to select more nutritious foods. Furthermore, the development and production of healthier foods do not always lead to economic profits for the agro-food sector. Most dietary recommendations for the general population represent a &quot;one-size-fits-all approach&quot; which does not necessarily ensure that everyone has adequate exposure to health-promoting constituents of foods. Indeed, we now know that individuals show a high variability in responses when exposed to specific nutrients, foods, or diets.<br><br>PURPOSE: This review aims to highlight our current understanding of inter-individual variability in response to dietary bioactives, based on the integration of findings of the COST Action POSITIVe. We also evaluate opportunities for translation of scientific knowledge on inter-individual variability in response to dietary bioactives, once it becomes available, into practical applications for stakeholders, such as the agro-food industry. The potential impact from such applications will form an important impetus for the food industry to develop and market new high quality and healthy foods for specific groups of consumers in the future. This may contribute to a decrease in the burden of diet-related chronic diseases.}, }
@article {pmid31635887, year = {2019}, author = {Čanković, M and Žučko, J and Radić, ID and Janeković, I and Petrić, I and Ciglenečki, I and Collins, G}, title = {Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {6}, pages = {126016}, doi = {10.1016/j.syapm.2019.126016}, pmid = {31635887}, issn = {1618-0984}, mesh = {Archaea/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Biodiversity ; Climate Change ; Databases, Chemical ; Ireland ; Lakes/chemistry/*microbiology ; *Microbiota/genetics ; Oxygen/analysis/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seasons ; Water Microbiology ; }, abstract = {Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.}, }
@article {pmid31633390, year = {2019}, author = {Baker, JL and He, X and Shi, W}, title = {Precision Reengineering of the Oral Microbiome for Caries Management.}, journal = {Advances in dental research}, volume = {30}, number = {2}, pages = {34-39}, pmid = {31633390}, issn = {1544-0737}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms ; *Dental Caries ; *Dental Plaque ; Humans ; *Microbiota ; Streptococcus mutans ; }, abstract = {Technological advancements have revolutionized our understanding of the complexity and importance of the human microbiome. This progress has also emphasized the need for precision therapeutics, as it has underscored the dilemmas, such as dysbiosis and increasing antibiotic resistance, associated with current, broad-spectrum treatment modalities. Dental caries remains the most common chronic disease worldwide, accompanied by a tremendous financial and social burden, despite widespread and efficacious fluoride and hygienic regimens. Over the past several decades, various precision approaches to combat dental caries, including vaccines, probiotics, and antimicrobial compounds, have been pursued. Despite the distinct overall conceptual strengths of each approach, for various reasons, there are currently no approved precision antibiotic therapeutics to prevent dental caries. Specifically targeted antimicrobial peptides (STAMPs) are synthetic molecules that combine the antibiotic moiety of a traditional antimicrobial peptide with a targeting domain to provide specificity against a particular organism. Conjoining the killing domain from the antimicrobial, novispirin G10, and a targeting domain derived from the Streptococcus mutans pheromone, CSP, the STAMP C16G2 was designed to provide targeted killing of S. mutans, widely considered the keystone species in dental caries pathogenesis. C16G2 was able to selectively eliminate S. mutans from complex ecosystems while leaving closely related, yet health-associated, oral species unharmed. This remodeling of the dental plaque community is expected to have significant advantages compared to conventional broad-spectrum mouthwashes, as the intact, surviving community is apt to prevent reinfection by pathogens. Following successful phase I clinical trials that evaluated the safety and basic microbiology of C16G2 treatments, the phase II trials of several C16G2 formulations are currently in progress. C16G2 represents an exciting advance in precision therapeutics, and the STAMP platform provides vast opportunities for both the development of additional therapeutics and the overall study of microbial ecology.}, }
@article {pmid31633060, year = {2019}, author = {Krych, Ł and Castro-Mejía, JL and Forero-Junco, LM and Moesby, DN and Mikkelsen, MB and Rasmussen, MA and Sykulski, M and Nielsen, DS}, title = {DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {369}, pmid = {31633060}, issn = {2399-3642}, abstract = {Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.}, }
@article {pmid31632370, year = {2019}, author = {Mendes, LW and de Chaves, MG and Fonseca, MC and Mendes, R and Raaijmakers, JM and Tsai, SM}, title = {Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2252}, pmid = {31632370}, issn = {1664-302X}, abstract = {The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community toward a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.}, }
@article {pmid31630686, year = {2019}, author = {Kavagutti, VS and Andrei, AŞ and Mehrshad, M and Salcher, MM and Ghai, R}, title = {Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {135}, pmid = {31630686}, issn = {2049-2618}, support = {17-04828S//Grantová Agentura České Republiky/ ; 17-04828S//Grantová Agentura České Republiky/ ; 17-04828S//Grantová Agentura České Republiky/ ; GAJU 158/2016/P//The Grant Agency of the Faculty of Science, University of South Bohemia/ ; MSM200961801//Akademie Věd České Republiky/ ; L200961651//Akademie Věd České Republiky/ ; CZ.02.1.01/0.0/0.0/16_025/0007417//ERDF/ESF/ ; }, abstract = {The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small &quot;miniphages&quot; and large &quot;megaphages&quot; infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.}, }
@article {pmid31624348, year = {2020}, author = {Gwak, JH and Jung, MY and Hong, H and Kim, JG and Quan, ZX and Reinfelder, JR and Spasov, E and Neufeld, JD and Wagner, M and Rhee, SK}, title = {Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {335-346}, doi = {10.1038/s41396-019-0538-1}, pmid = {31624348}, issn = {1751-7370}, support = {NRF-2015R1A4A1041869//National Research Foundation of Korea (NRF)/ ; NRF-2015M3D3A1A01064881//National Research Foundation of Korea (NRF)/ ; }, abstract = {Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.}, }
@article {pmid31624166, year = {2019}, author = {Schultz, J and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica.}, journal = {Microbiology resource announcements}, volume = {8}, number = {42}, pages = {}, pmid = {31624166}, issn = {2576-098X}, abstract = {The thermophilic Geobacillus sp. strain LEMMJ02 was isolated from Fumarole Bay sediment on Deception Island, an active Antarctic volcano. Here, we report the draft genome of LEMMJ02, which consists of 3,160,938 bp with 52.8% GC content and 3,523 protein-coding genes.}, }
@article {pmid31623889, year = {2019}, author = {Christiaens, MER and De Paepe, J and Ilgrande, C and De Vrieze, J and Barys, J and Teirlinck, P and Meerbergen, K and Lievens, B and Boon, N and Clauwaert, P and Vlaeminck, SE}, title = {Urine nitrification with a synthetic microbial community.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {6}, pages = {126021}, doi = {10.1016/j.syapm.2019.126021}, pmid = {31623889}, issn = {1618-0984}, mesh = {Ammonia/metabolism ; Bioreactors/*microbiology ; Comamonadaceae/metabolism ; Delftia acidovorans/metabolism ; *Microbiota ; *Nitrification ; Nitrites/metabolism ; Nitrobacter/metabolism ; Nitrosomonas europaea/metabolism ; Pseudomonas fluorescens/metabolism ; Urea/metabolism ; Urine/*chemistry ; Waste Disposal, Fluid/*methods ; }, abstract = {During long-term extra-terrestrial missions, food is limited and waste is generated. By recycling valuable nutrients from this waste via regenerative life support systems, food can be produced in space. Astronauts' urine can, for instance, be nitrified by micro-organisms into a liquid nitrate fertilizer for plant growth in space. Due to stringent conditions in space, microbial communities need to be be defined (gnotobiotic); therefore, synthetic rather than mixed microbial communities are preferred. For urine nitrification, synthetic communities face challenges, such as from salinity, ureolysis, and organics. In this study, a synthetic microbial community containing an AOB (Nitrosomonas europaea), NOB (Nitrobacter winogradskyi), and three ureolytic heterotrophs (Pseudomonas fluorescens, Acidovorax delafieldii, and Delftia acidovorans) was compiled and evaluated for these challenges. In reactor 1, salt adaptation of the ammonium-fed AOB and NOB co-culture was possible up to 45mScm-1, which resembled undiluted nitrified urine, while maintaining a 44±10mgNH4+-NL-1d-1 removal rate. In reactor 2, the nitrifiers and ureolytic heterotrophs were fed with urine and achieved a 15±6mg NO3--NL-1d-1 production rate for 1% and 10% synthetic and fresh real urine, respectively. Batch activity tests with this community using fresh real urine even reached 29±3mgNL-1d-1. Organics removal in the reactor (69±15%) should be optimized to generate a nitrate fertilizer for future space applications.}, }
@article {pmid31623169, year = {2019}, author = {García-Mantrana, I and Calatayud, M and Romo-Vaquero, M and Espín, JC and Selma, MV and Collado, MC}, title = {Urolithin Metabotypes Can Determine the Modulation of Gut Microbiota in Healthy Individuals by Tracking Walnuts Consumption over Three Days.}, journal = {Nutrients}, volume = {11}, number = {10}, pages = {}, pmid = {31623169}, issn = {2072-6643}, support = {RTI2018-097982-B-I00//Spanish Ministry of Science, Innovation and Universities (MICINN)/ ; ERC starting grant, n° 639226/ERC_/European Research Council/International ; }, abstract = {Walnuts are rich in polyphenols ellagitannins, modulate gut microbiota (GM), and exert health benefits after long-term consumption. The metabolism of ellagitannins to urolithins via GM depends on urolithin metabotypes (UM-A, -B, or -0), which have been reported to predict host responsiveness to a polyphenol-rich intervention. This study aims to assess whether UMs were associated with differential GM modulation after short-term walnut consumption. In this study, 27 healthy individuals consumed 33 g of peeled raw walnuts over three days. GM profiling was determined using 16S rRNA illumina sequencing and specific real-time quantitative polymerase chain reactions (qPCRs), as well as microbial activity using short-chain fatty acids analysis in stool samples. UMs stratification of volunteers was assessed using ultra performance liquid chromatography-electro spray ionization-quadrupole time of flight-mass spectrometry (UPLC-ESI-QTOF-MS) analysis of urolithins in urine samples. The gut microbiota associated with UM-B was more sensitive to the walnut intervention. Blautia, Bifidobacterium, and members of the Coriobacteriaceae family, including Gordonibacter, increased exclusively in UM-B subjects, while some members of the Lachnospiraceae family decreased in UM-A individuals. Coprococcus and Collinsella increased in both UMs and higher acetate and propionate production resulted after walnuts intake. Our results show that walnuts consumption after only three days modulates GM in a urolithin metabotype-depending manner and increases the production of short-chain fatty acids (SCFA).}, }
@article {pmid31622236, year = {2019}, author = {Cho, GY and Whang, KS}, title = {Aliifodinibius saliphilus sp. nov., a moderately halophilic bacterium isolated from sediment of a crystallizing pond of a saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003765}, pmid = {31622236}, issn = {1466-5034}, abstract = {Two Gram-stain-negative, moderately halophilic bacteria, designated strains ECH52T and KHM46, were isolated from the sediment of a grey saltern located in Sinui island at Shinan, Korea. The isolates were aerobic, non-motile, short rods and grew at 15-45 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 8.0) and with 3-25 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains ECH52T and KHM46 belonged to the genus Aliifodinibius in the family Balneolaceae with sequence similarities of 94.3-98.6 % and showed the highest sequence similarity to Aliifodinibius halophilus 2W32T (98.6 %), A. sediminis YIM J21T (94.7%), A. salicampi KHM44T (94.6 %) and A. roseus YIM D15T (94.3 %). The DNA G+C content of the genomic DNA of strain ECH52T was 40.8 mol%. The predominant isoprenoid quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were iso-C17 : 1ω9c, iso-C15 : 0, and C16 : 1ω7c and/or iso-C15 : 0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and four unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic data, strains ECH52T and KHM46 are considered to represent a novel species of the genus Aliifodinibius, for which the name Aliifodinibiussaliphilus sp. nov. is proposed. The type strain is ECH52T (=KACC 19126T=NBRC 112664T).}, }
@article {pmid31615877, year = {2019}, author = {Deng, J and Auchtung, JM and Konstantinidis, KT and Brettar, I and Höfle, MG and Tiedje, JM}, title = {Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31615877}, issn = {2379-5077}, abstract = {Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT).IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.}, }
@article {pmid31613739, year = {2019}, author = {Dumolin, C and Peeters, C and Ehsani, E and Tahon, G and De Canck, E and Cnockaert, M and Boon, N and Vandamme, P}, title = {Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003786}, pmid = {31613739}, issn = {1466-5034}, abstract = {Strain LMG 30378T was isolated from a hydrogen-oxidizing bacteria enrichment reactor inoculated with forest soil. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Achromobacter. Multilocus sequence analysis combined with sequence analysis of a 765 bp nrdA gene fragment both showed Achromobacter agilis LMG 3411T and Achromobacter denitrificans LMG 1231T to be the closest-related neighbours to strain LMG 30378T. Genome sequence analysis revealed a draft genome of 6.81 Mb with a G+C content of 67.2 mol%. In silico DNA-DNA hybridization with A. denitrificans LMG 1231T and A. agilis LMG 3411T showed 42.7 and 42.5% similarity, respectively, confirming that strain LMG 30378T represented a novel Achromobacter species. Phenotypic and metabolic characterization revealed acid phosphatase activity and the absence of phosphoamidase activity as distinctive features. The draft genome composes all necessary metabolic components to fix carbon dioxide and to oxidize molecular hydrogen, suggesting that strain LMG 30378T is a key organism in the enrichment reactor. Together, these data demonstrate that strain LMG 30378T represents a novel species of the genus Achromobacter, for which the name Achromobacter veterisilvae sp. nov. is proposed. The type strain is LMG 30378T (=CCUG 71558T).}, }
@article {pmid31612608, year = {2019}, author = {Seto, M and Iwasa, Y}, title = {The fitness of chemotrophs increases when their catabolic by-products are consumed by other species.}, journal = {Ecology letters}, volume = {22}, number = {12}, pages = {1994-2005}, pmid = {31612608}, issn = {1461-0248}, support = {19K06853//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research (C)/ ; }, mesh = {Biomass ; *Ecology ; *Ecosystem ; Symbiosis ; }, abstract = {Chemotrophic microorganisms synthesise biomass by utilising energy obtained from a set of chemical reactions that convert resources to by-products, forming catabolic interactions. The amount of energy obtained per catabolic reaction decreases with the abundance of the by-product named as the 'abundant resource premium'. Consider two species, Species 1 and 2, Species 1 obtains energy from a reaction that converts resource A to by-product B. Species 2 then utilises B as its resource, extracting energy from a reaction that converts B to C. Thus, the presence of Species 2 reduces the abundance of B, which improves the fitness of Species 1 by increasing the energy acquisition per reaction of A to B. We discuss the population dynamic implication of this effect and its importance in expanding a realised niche, boosting material flow through the ecosystem and providing mutualistic interactions among species linked by the material flow. Introducing thermodynamics into population ecology could offer us fundamental ecological insights into understanding the ecology of chemotrophic microorganisms dominating the subsurface realm.}, }
@article {pmid31612601, year = {2019}, author = {Simonsen, AK and Barrett, LG and Thrall, PH and Prober, SM}, title = {Novel model-based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient.}, journal = {Ecology letters}, volume = {22}, number = {12}, pages = {2077-2086}, doi = {10.1111/ele.13389}, pmid = {31612601}, issn = {1461-0248}, support = {//OCE Postdoctoral Fellowship, Australian Research Council/ ; }, mesh = {*Climate ; Ecotype ; *Genome, Bacterial ; Phylogeny ; Soil Microbiology ; }, abstract = {A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome-based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate-associated ecotypes in populations of nitrogen-fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate-associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.}, }
@article {pmid31612432, year = {2019}, author = {Rattes de Almeida Couto, C and Catharine de Assis Leite, D and Jurelevicius, D and van Elsas, JD and Seldin, L}, title = {Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, doi = {10.1007/s42770-019-00153-8}, pmid = {31612432}, issn = {1678-4405}, support = {01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; -//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {The use of dispersants in marine environments is a common practice worldwide for oil spill remediation. While the effects of chemical dispersants have been extensively studied, those of biosurfactants, mainly surfactin that is considered one of the most effective surfactants produced by bacteria, have been less considered. We constructed microcosms containing marine water collected from Grumari beach (W_GB, Brazil) and from Schiermonnikoog beach (W_SI, The Netherlands) with the addition of oil (WO), Ultrasperse II plus oil (WOS), surfactin plus oil (WOB), and both dispersants (WS or WB) individually. In these treatments, the composition of bacterial communities and their predictive biodegradation potential were determined over time. High-throughput sequencing of the rrs gene encoding bacterial 16S rRNA revealed that Bacteroidetes (Flavobacteria class) and Proteobacteria (mainly Gammaproteobacteria and Alphaproteobacteria classes) were the most abundant phyla found among the W_GB and W_SI microbiomes, and the relative abundance of the bacterial types in the different microcosms varied based on the treatment applied. Non-metrical multidimensional scaling (NMDS) revealed a clear clustering based on the addition of oil and on the dispersant type added to the GB or SI microcosms, i.e., WB and WOB were separated from WS and WOS in both marine ecosystems studied. The potential presence of diverse enzymes involved in oil degradation was indicated by predictive bacterial metagenome reconstruction. The abundance of predicted genes for degradation of petroleum hydrocarbons increased more in surfactin-treated microcosms than those treated with Ultrasperse II, mainly in the marine water samples from Grumari beach.}, }
@article {pmid31612324, year = {2019}, author = {Norte, AC and Lopes de Carvalho, I and Núncio, MS and Araújo, PM and Matthysen, E and Albino Ramos, J and Sprong, H and Heylen, D}, title = {Getting under the birds' skin: tissue tropism of Borrelia burgdorferi s.l. in naturally and experimentally infected avian hosts.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01442-3}, pmid = {31612324}, issn = {1432-184X}, support = {MARE - UID/MAR/04292/2013//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/108197/2015//Fundação para a Ciência e Tecnologia/ ; na//Portuguese National Institute of Health Doutor Ricardo Jorge/ ; Marie 544 Sklodowska-Curie Actions, Individual Global Fellowship, project n° 545 799609//European Union - Horizon2020/ ; G0.049.10//Fund for Scientific Research - Flanders/ ; na//Bill and Melinda Gates Foundation/ ; }, abstract = {Wild birds are frequently exposed to the zoonotic tick-borne bacteria Borrelia burgdorferi sensu lato (s.l.), and some bird species act as reservoirs for some Borrelia genospecies. Studying the tropism of Borrelia in the host, how it is sequestered in different organs, and whether it is maintained in circulation and/or in the host's skin is important to understand pathogenicity, infectivity to vector ticks and reservoir competency.We evaluated tissue dissemination of Borrelia in blackbirds (Turdus merula) and great tits (Parus major), naturally and experimentally infected with Borrelia genospecies from enzootic foci. We collected both minimally invasive biological samples (feathers, skin biopsies and blood) and skin, joint, brain and visceral tissues from necropsied birds. Infectiousness of the host was evaluated through xenodiagnoses and infection rates in fed and moulted ticks. Skin biopsies were the most reliable method for assessing avian hosts' Borrelia infectiousness, which was supported by the agreement of infection status results obtained from the analysis of chin and lore skin samples from necropsied birds and of their xenodiagnostic ticks, including a significant correlation between the estimated concentration of Borrelia genome copies in the skin and the Borrelia infection rate in the xenodiagnostic ticks. This confirms a dermatropism of Borrelia garinii, B. valaisiana and B. turdi in its avian hosts. However, time elapsed from exposure to Borrelia and interaction between host species and Borrelia genospecies may affect the reliability of skin biopsies. The blood was not useful to assess infectiousness of birds, even during the period of expected maximum spirochetaemia. From the tissues sampled (foot joint, liver, spleen, heart, kidney, gut and brain), Borrelia was detected only in the gut, which could be related with infection mode, genospecies competition, genospecies-specific seasonality and/or excretion processes.}, }
@article {pmid31611655, year = {2020}, author = {Jiao, S and Yang, Y and Xu, Y and Zhang, J and Lu, Y}, title = {Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China.}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {202-216}, pmid = {31611655}, issn = {1751-7370}, abstract = {Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.}, }
@article {pmid31611646, year = {2019}, author = {Ansorge, R and Romano, S and Sayavedra, L and Porras, MÁG and Kupczok, A and Tegetmeyer, HE and Dubilier, N and Petersen, J}, title = {Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2487-2497}, doi = {10.1038/s41564-019-0572-9}, pmid = {31611646}, issn = {2058-5276}, abstract = {Genetic diversity of closely related free-living microorganisms is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Accordingly, strain diversity is assumed to be highly restricted in intracellular bacteria associated with animals. Here, we sequenced metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key functions, such as the use of energy and nutrient sources, electron acceptors and viral defence mechanisms. Most strain-specific genes were expressed, highlighting their potential to affect fitness. We show that fine-scale diversity is pervasive in Bathymodiolus sulfur-oxidizing symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, rather than the host, feeds the symbionts.}, }
@article {pmid31608034, year = {2019}, author = {Cai, Y and Cao, Y and Tang, C}, title = {Evidence for the Primary Role of Phytoplankton on Nitrogen Cycle in a Subtropical Reservoir: Reflected by the Stable Isotope Ratios of Particulate Nitrogen and Total Dissolved Nitrogen.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2202}, pmid = {31608034}, issn = {1664-302X}, abstract = {Knowledge about the primary factor controlling stable isotope ratios of particulate nitrogen (δ15NPN) and total dissolved nitrogen (δ15NTDN) in a subtropical reservoir can improve the understanding of regional and global nitrogen cycles. Taking Lianhe Reservoir as a representative subtropical reservoir, we studied the spatial and temporal distributions of δ15NPN andδ15NTDN and their relationships with the surrounding physicochemical factors and phytoplankton. The results showed that variations in δ15NPN and δ15NTDN followed seasonal thermal cycles. The values of δ15NTDN were inversely proportional to those of δ15NPN. PCA showed that phytoplankton cell density and pH were the primary drivers of the variation of δ15NPN (45.2%). The primary factors influencing δ15NTDN were Chl a and phytoplankton cell density, which both indicated phytoplankton biomass. We also determined that the dominant species was Microcystis densa during the thermal stratification period and Staurodesmus aristiferus during the mixing period. Laboratory experiments showed that δ15NPN values in both M. densa (from 19.5 to 14.6‰) and S. aristiferus (from 19.4 to 16.0 ‰) media decreased significantly as the algal cells grew. Furthermore, the δ15NTDN values increased from 4.9 to 7.9‰ and from 4.7 to 6.9‰ in M. densa and S. aristiferus media, respectively, when the δ15NPN values decreased. These experimental results were consistent with field investigation results and indicated that variations in δ15NPN and δ15NTDN were mainly controlled by phytoplankton cell density, especially the cell density of the dominant species, in both the thermal stratification and mixing periods. The results also suggested that cell density, not phytoplankton species, was the key factor regulating the distribution of nitrogen stable isotopes. These results together indicated that phytoplankton cell density is the primary factor in the regulation of nitrogen stable isotope composition and that its influence is greater than that of other physical and chemical factors. This study provided detailed information supporting the primary role of phytoplankton in the nitrogen geochemical cycle and improved the understanding of biochemical processes in natural subtropical reservoirs.}, }
@article {pmid31605197, year = {2019}, author = {Hess, AL and Benítez-Páez, A and Blædel, T and Larsen, LH and Iglesias, JR and Madera, C and Sanz, Y and Larsen, TM and , }, title = {The effect of inulin and resistant maltodextrin on weight loss during energy restriction: a randomised, placebo-controlled, double-blinded intervention.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-019-02099-x}, pmid = {31605197}, issn = {1436-6215}, support = {613979//Seventh Framework Programme/ ; }, abstract = {PURPOSE: The objective of this study was to investigate the additive effects of combining energy restriction with dietary fibres on change in body weight and gut microbiota composition.<br><br>METHODS: The study was a 12-week randomised, placebo-controlled, double-blinded, parallel intervention trial. A total of 116 overweight or obese participants were assigned randomly either to 10 g inulin plus 10 g resistant maltodextrin or to 20 g of placebo supplementation through 400 mL of milk a day, while on a - 500 kcal/day energy restricted diet.<br><br>RESULTS: Altogether, 86 participants completed the intervention. There were no significant differences in weight loss or body composition between the groups. The fibre supplement reduced systolic (5.35 ± 2.4 mmHg, p = 0.043) and diastolic (2.82 ± 1.3 mmHg, p = 0.047) blood pressure to a larger extent than placebo. Furthermore, a larger decrease in serum insulin was observed in the placebo group compared to the fibre group (- 26.0 ± 9.2 pmol/L, p = 0.006). The intake of fibre induced changes in the composition of gut microbiota resulting in higher abundances of Parabacteroides and Bifidobacteria, compared to placebo. The effects on blood pressure and glucose metabolism were mainly observed in women, and could be attributed to a higher gut microbiota diversity after intervention. Finally, the fibre group experienced a higher degree of gastrointestinal symptoms, which attenuated over time.<br><br>CONCLUSIONS: Supplementation of inulin and resistant maltodextrin did not provide an additional weight loss during an energy-restricted diet, but reduced both systolic and diastolic blood pressure. Furthermore, the fibre supplement did stimulate the growth of potentially beneficial bacteria genera.<br><br>CLINICAL TRIAL REGISTRY: The study was registered at http://www.clinicaltrials.gov , NCT03135041.}, }
@article {pmid31600966, year = {2019}, author = {Lin, X and Gao, D and Lu, K and Li, X}, title = {Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {20}, pages = {}, pmid = {31600966}, issn = {1660-4601}, abstract = {Effects of nitrogen pollution on bacterial community shifts in river sediments remain barely understood. Here, we investigated the bacterial communities in sediments of urban and suburban rivers in a highly urbanized city, Shanghai. Sediment nitrate (NO3-) and ammonia (NH4+) were highly accumulated in urban river. Operation Taxonomic Units (OTUs), Abundance-based Coverage Estimators (ACEs) and Chao 1 estimator in urban rivers were slightly lower than those in suburban rivers, while Shannon and Simpson indices were higher in urban rivers than those in suburban rivers. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum communities, accounting for 68.5-84.9% of all communities. In particular, the relative abundances of Firmicutes and Nitrospirae were significantly higher in suburban rivers than in urban rivers, while relative abundances of Bacteroidetes, Verrucomicrobia, and Spirochaetes were significantly lower in suburban rivers than in urban rivers. NH4+ was significantly and negatively correlated with abundances of Firmicutes, Nitrospirae, and Actinobacteria. Importantly, the significant and negative effects of sediment NH4+ on bacterial richness and diversity suggested that nitrogen pollution likely contribute to the decrease in the bacterial richness and diversity. The results highlight that nitrogen enrichment could drive the shifts of bacterial abundance and diversity in the urban river sediments where are strongly influenced by human activities under the rapid urbanization stress.}, }
@article {pmid31599931, year = {2019}, author = {Cavaco, MA and St Louis, VL and Engel, K and St Pierre, KA and Schiff, SL and Stibal, M and Neufeld, JD}, title = {Freshwater microbial community diversity in a rapidly changing High Arctic watershed.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {11}, pages = {}, doi = {10.1093/femsec/fiz161}, pmid = {31599931}, issn = {1574-6941}, abstract = {Current models predict increases in High Arctic temperatures and precipitation that will have profound impacts on the Arctic hydrological cycle, including enhanced glacial melt and thawing of active layer soils. However, it remains uncertain how these changes will impact the structure of downstream resident freshwater microbial communities and ensuing microbially driven freshwater ecosystem services. Using the Lake Hazen watershed (Nunavut, Canada; 82°N, 71°W) as a sentinel system, we related microbial community composition (16S rRNA gene sequencing) to physicochemical parameters (e.g. dissolved oxygen and nutrients) over an annual hydrological cycle in three freshwater compartments within the watershed: (i) glacial rivers; (ii) active layer thaw-fed streams and waterbodies and (iii) Lake Hazen, into which (i) and (ii) drain. Microbial communities throughout these freshwater compartments were strongly interconnected, hydrologically, and often correlated with the presence of melt-sourced chemicals (e.g. dissolved inorganic carbon) as the melt season progressed. Within Lake Hazen itself, water column microbial communities were generally stable over spring and summer, despite fluctuating lake physicochemistry, indicating that these communities and the potential ecosystem services they provide therein may be resilient to environmental change. This work helps to establish a baseline understanding of how microbial communities and the ecosystem services they provide in Arctic watersheds might respond to future climate change.}, }
@article {pmid31598761, year = {2019}, author = {Brunel, C and Beifen, Y and Pouteau, R and Li, J and van Kleunen, M}, title = {Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01438-z}, pmid = {31598761}, issn = {1432-184X}, support = {2016YFC1201100//Chinese National Key Research and Development Program/ ; 15-2//International Science and Technology Cooperation Programme/ ; 30800133//National Natural Science Foundation of China/ ; }, abstract = {Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.}, }
@article {pmid31598755, year = {2019}, author = {Sodhi, KK and Kumar, M and Balan, B and Dhaulaniya, AS and Singh, DK}, title = {Isolation and characterization of amoxicillin-resistant bacteria and amoxicillin-induced alteration in its protein profiling and RNA yield.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-019-01737-6}, pmid = {31598755}, issn = {1432-072X}, support = {(NASF/CA-6030/2017-18)//Indian Council of Agricultural Research/ ; }, abstract = {Amoxicillin-resistant bacteria were isolated using selective enrichment procedure. The morphological, biochemical and molecular characterization based on 16S rRNA gene sequencing and phylogenetic analysis of the bacterial strain WA5 confirmed that the strain belongs to the genus Stenotrophomonas. The bacteria were named as Stenotrophomonas sp. strain WA5 (MK110499). Substantial growth was seen in M9 minimal media supplemented with 5 mg L-1 of amoxicillin as a sole source of carbon and energy. RNA yield was also observed to be decreased in the presence of amoxicillin. Amoxicillin (5 mg L-1)-induced alteration is seen on bacterial protein profile and unique polypeptide bands were seen to be induced in the presence of amoxicillin, the bands were subjected to trypsin digestion, and LC-MS/MS analysis showed that the bands belong to the family of DNA-dependent RNA polymerase subunit β (rpoC). Plasmid DNA isolation indicated the presence of antibiotic-resistant genes being harboured by the plasmid.}, }
@article {pmid31598633, year = {2019}, author = {Baruzzo, G and Patuzzi, I and Di Camillo, B}, title = {SPARSim Single Cell: a count data simulator for scRNA-seq data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz752}, pmid = {31598633}, issn = {1367-4811}, abstract = {MOTIVATION: Single cell RNA-seq (scRNA-seq) count data shows many differences compared to bulk RNA-seq count data, making the application of many RNA-seq preprocessing/analysis methods not straightforward or even inappropriate.For this reason, the development of new methods for handling scRNA-seq count data is currently one of the most active research field in bioinformatics. To help the development of such new methods, the availability of simulated data could play a pivotal role. However, only few scRNA-seq count data simulators are available, often showing poor or not demonstrated similarity with real data.<br><br>RESULTS: In this article we present SPARSim, a scRNA-seq count data simulator based on a Gamma-Multivariate Hypergeometric model. We demonstrate that SPARSim allows to generate count data that resemble real data in terms of count intensity, variability and sparsity, performing comparably or better than one of the most used scRNA-seq simulator, Splat. In particular, SPARSim simulated count matrices well resemble the distribution of zeros across different expression intensities observed in real count data.<br><br>AVAILABILITY: SPARSim R package is freely available at http://sysbiobig.dei.unipd.it/?q=SPARSim and at https://gitlab.com/sysbiobig/sparsim.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid31595680, year = {2019}, author = {Wepking, C and Badgley, B and Barrett, JE and Knowlton, KF and Lucas, JM and Minick, KJ and Ray, PP and Shawver, SE and Strickland, MS}, title = {Prolonged exposure to manure from livestock-administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling.}, journal = {Ecology letters}, volume = {22}, number = {12}, pages = {2067-2076}, doi = {10.1111/ele.13390}, pmid = {31595680}, issn = {1461-0248}, support = {1832888//NSF/ ; 2013-67019-21363//USDA-NIFA/ ; }, mesh = {Animals ; Anti-Bacterial Agents ; Carbon ; Cattle ; *Ecosystem ; Livestock ; *Manure ; Nitrogen ; Soil ; Soil Microbiology ; }, abstract = {Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse-chase. Exposure to manure from antibiotic-treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two-fold increase in ecosystem respiration of recently fixed-carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic-treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.}, }
@article {pmid31595328, year = {2019}, author = {Li, F and Li, P and Hua, H and Hou, M and Wang, F}, title = {Diversity, Tissue Localization, and Infection Pattern of Bacterial Symbionts of the White-Backed Planthopper, Sogatella furcifera (Hemiptera: Delphacidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01433-4}, pmid = {31595328}, issn = {1432-184X}, support = {2018YFD0200300//National Key R&amp;D Project of China/ ; 31371951//National Natural Science Foundation of China/ ; }, abstract = {The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is a destructive pest of rice. Bacterial symbionts play an important role in insect hosts, especially hemipteran hosts. This study was designed to examine the bacterial symbionts of the WBPH using 16S rDNA high-throughput sequencing. A total of 63 and 177 operational taxonomic units (OTUs) were identified in females and males of three WBPH populations, respectively. These OTUs included bacteria of 75 genera from 11 phyla, where Wolbachia, Cardinium, and Asaia were the dominant genera, accounting for over 97.99% of all the symbiotic bacteria. Fluorescence in situ hybridization detected Wolbachia, Cardinium, and Asaia in the salivary glands, guts, testes, and eggs of the WBPH, indicating the potential for both horizontal and vertical transmission. Moreover, the infection pattern of the three dominant bacterial symbionts was detected in six WBPH populations. The frequencies of Wolbachia infection of females and Cardinium infection of both sexes were over 96.7%. Wolbachia infection of males ranged between 46.7 and 63.3%, which was significantly lower than that observed for females. Asaia infection of both sexes varied substantially among the populations. These results indicate that the complex host-symbiotic bacteria interaction is influenced by host sex and geographical origin and potentially by the transmission modes of the symbionts.}, }
@article {pmid31595008, year = {2019}, author = {Soffe, R and Bernach, M and Remus-Emsermann, MNP and Nock, V}, title = {Replicating Arabidopsis Model Leaf Surfaces for Phyllosphere Microbiology.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14420}, pmid = {31595008}, issn = {2045-2322}, abstract = {Artificial surfaces are commonly used in place of leaves in phyllosphere microbiology to study microbial behaviour on plant leaf surfaces. These surfaces enable a reductionist approach to be undertaken, to enable individual environmental factors influencing microorganisms to be studied. Commonly used artificial surfaces include nutrient agar, isolated leaf cuticles, and reconstituted leaf waxes. Recently, replica surfaces mimicking the complex topography of leaf surfaces for phyllosphere microbiology studies are appearing in literature. Replica leaf surfaces have been produced in agar, epoxy, polystyrene, and polydimethylsiloxane (PDMS). However, none of these protocols are suitable for replicating fragile leaves such as of the model plant Arabidopsis thaliana. This is of importance, as A. thaliana is a model system for molecular plant genetics, molecular plant biology, and microbial ecology. To overcome this limitation, we introduce a versatile replication protocol for replicating fragile leaf surfaces into PDMS. Here we demonstrate the capacity of our replication process using optical microscopy, atomic force microscopy (AFM), and contact angle measurements to compare living and PDMS replica A. thaliana leaf surfaces. To highlight the use of our replica leaf surfaces for phyllosphere microbiology, we visualise bacteria on the replica leaf surfaces in comparison to living leaf surfaces.}, }
@article {pmid31593911, year = {2019}, author = {Prévoteau, A and Carvajal-Arroyo, JM and Ganigué, R and Rabaey, K}, title = {Microbial electrosynthesis from CO2: forever a promise?.}, journal = {Current opinion in biotechnology}, volume = {62}, number = {}, pages = {48-57}, doi = {10.1016/j.copbio.2019.08.014}, pmid = {31593911}, issn = {1879-0429}, abstract = {Microbial electrosynthesis (MES) is an electrochemical process used to drive microbial metabolism for bio-production, such as the reduction of CO2 into industrially relevant organic products as an alternative to current fossil-fuel-derived commodities. After a decade of research on MES from CO2, figures of merit have increased significantly but are plateauing yet far from those expected to allow competitiveness for synthesis of commodity chemicals. Here we discuss the substantial technological shortcomings still associated with MES and evoke possible ways to mitigate them. It appears particularly challenging to obtain both relevant production rates (driven by high current densities) and energy conversion efficiency (i.e. low cell voltage) in microbial-compatible electrolytes. More competitive processes could arise by decoupling effective abiotic electroreductions (e.g. CO2 to CO or ethanol; H2 evolution) with subsequent fermentation processes.}, }
@article {pmid31593527, year = {2020}, author = {Tabima, JF and Søndreli, KL and Keriö, S and Feau, N and Sakalidis, ML and Hamelin, RC and LeBoldus, JM}, title = {Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {33}, number = {2}, pages = {189-199}, doi = {10.1094/MPMI-05-19-0131-R}, pmid = {31593527}, issn = {0894-0282}, abstract = {Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.}, }
@article {pmid31591493, year = {2020}, author = {Ben Maamar, S and Hu, J and Hartmann, EM}, title = {Implications of indoor microbial ecology and evolution on antibiotic resistance.}, journal = {Journal of exposure science &amp; environmental epidemiology}, volume = {30}, number = {1}, pages = {1-15}, doi = {10.1038/s41370-019-0171-0}, pmid = {31591493}, issn = {1559-064X}, abstract = {The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide &quot;healthy&quot; building design.}, }
@article {pmid31590609, year = {2020}, author = {Diaz, PI and Valm, AM}, title = {Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties.}, journal = {Journal of dental research}, volume = {99}, number = {1}, pages = {18-25}, pmid = {31590609}, issn = {1544-0591}, support = {R03 DE028042/DE/NIDCR NIH HHS/United States ; }, abstract = {Oral microbial communities are extraordinarily complex in taxonomic composition and comprise interdependent biological systems. The bacteria, archaea, fungi, and viruses that thrive within these communities engage in extensive cell-cell interactions, which are both beneficial and antagonistic. Direct physical interactions among individual cells mediate large-scale architectural biofilm arrangements and provide spatial proximity for chemical communication and metabolic cooperation. In this review, we summarize recent work in identifying specific molecular components that mediate cell-cell interactions and describe metabolic interactions, such as cross-feeding and exchange of electron acceptors and small molecules, that modify the growth and virulence of individual species. We argue, however, that although pairwise interaction models have provided useful information, complex community-like systems are needed to study the properties of oral communities. The networks of multiple synergistic and antagonistic interactions within oral biofilms give rise to the emergent properties of persistence, stability, and long-range spatial structure, with these properties mediating the dysbiotic transitions from health to oral diseases. A better understanding of the fundamental properties of interspecies networks will lead to the development of effective strategies to manipulate oral communities.}, }
@article {pmid31589437, year = {2019}, author = {Syrpas, M and Bukauskaitė, J and Ramanauskienė, K and Karosienė, JR and Majienė, D and Bašinskienė, L and Venskutonis, PR}, title = {Ultrasound-Assisted Extraction and Assessment of Biological Activity of Phycobiliprotein-Rich Aqueous Extracts from Wild Cyanobacteria (Aphanizomenon flos-aquae).}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.9b05483}, pmid = {31589437}, issn = {1520-5118}, abstract = {Cyanobacteria are photosynthetic microorganisms that are considered as an important source of bioactive metabolites, among which phycobiliproteins (PBPs) are a class of water-soluble macromolecules of cyanobacteria with a wide range of applications. Massive proliferation of cyanobacteria can lead to excessive surface water blooms, of which removal, as a management measure, should be prioritized. In this study, the utilization of wild cyanobacteria biomass (Aphanizomenon flos-aquae) for extraction of phycobiliproteins is reported. Extraction of phycobiliproteins by conventional methods, such as homogenization, freeze-thaw cycles, and solid-liquid extraction, were optimized prior to ultrasound-assisted extraction. Standardization of ultrasonication for different parameters, such as ultrasonication amplitude (38, 114, and 190 μm) and ultrasonication time (1, 5.5, and 10 min), was carried out using a central composite design and response surface methodology for each of the primary techniques. A substantial increase on the individual and total phycobiliprotein yields was observed after ultrasonic treatment. The highest total PBP yield (115.37 mg/g of dry weight) was observed with samples treated with a homogenizer (30 min, 30 °C, and 1 cycle) combined with ultrasound treatment (8.7 min at 179 μm). Moreover, in vitro antioxidant capacity was observed for the obtained extracts in the Folin-Ciocalteu and ABTS* + assays. In addition, a cytotoxic effect against C6 glioma cells was observed for A. flos-aquae PBPs. Conclusively, wild cyanobacteria could be considered as an alternative feedstock for recovery of PBPs.}, }
@article {pmid31588957, year = {2019}, author = {Le, D and Nguyen, P and Nguyen, D and Dierckens, K and Boon, N and Lacoere, T and Kerckhof, FM and De Vrieze, J and Vadstein, O and Bossier, P}, title = {Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01436-1}, pmid = {31588957}, issn = {1432-184X}, support = {ZIUS2015AP026//VLIR-IUC/ ; }, abstract = {We investigated the gut microbiota of rabbit fish larvae at three locations in Vietnam (ThuanAn-northern, QuangNam-intermediate, BinhDinh-southern sampling site) over a three-year period. In the wild, the first food for rabbit fish larvae remains unknown, while the juveniles and adults are herbivores, forming schools near the coasts, lagoons, and river mouths, and feeding mainly on filamentous algae. This is the first study on the gut microbiota of the wild fish larvae and with a large number of individuals analyzed spatially and temporally. The Clostridiales order was the most predominant in the gut, and location-by-location alpha diversity showed significant differences in Chao-1, Hill number 1, and evenness. Analysis of beta diversity indicated that the location, not year, had an effect on the composition of the microbiota. In 2014, the gut microbiota of fish from QuangNam was different from that in BinhDinh; in 2015, the gut microbiota was different for all locations; and, in 2016, the gut microbiota in ThuanAn was different from that in the other locations. There was a time-dependent trend in the north-south axis for the gut microbiota, which is considered to be tentative awaiting larger datasets. We found limited variation in the gut microbiota geographically and in time and strong indications for a core microbiome. Five and fifteen OTUs were found in 100 and 99% of the individuals, respectively. This suggests that at this life stage the gut microbiota is under strong selection due to a combination of fish-microbe and microbe-microbe interactions.}, }
@article {pmid31587650, year = {2019}, author = {Sebastián, M and Gasol, JM}, title = {Visualization is crucial for understanding microbial processes in the ocean.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1786}, pages = {20190083}, pmid = {31587650}, issn = {1471-2970}, abstract = {Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and their in situ level of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems. This article is part of a discussion meeting issue 'Single cell ecology'.}, }
@article {pmid31585384, year = {2019}, author = {Wang, D and Tooker, NB and Srinivasan, V and Li, G and Fernandez, LA and Schauer, P and Menniti, A and Maher, C and Bott, CB and Dombrowski, P and Barnard, JL and Onnis-Hayden, A and Gu, AZ}, title = {Side-stream enhanced biological phosphorus removal (S2EBPR) process improves system performance - A full-scale comparative study.}, journal = {Water research}, volume = {167}, number = {}, pages = {115109}, doi = {10.1016/j.watres.2019.115109}, pmid = {31585384}, issn = {1879-2448}, mesh = {Bioreactors ; *Phosphorus ; Polyphosphates ; *Rivers ; Sewage ; Waste Water ; }, abstract = {To address the common challenges in enhanced biological phosphorus removal (EBPR) related to stability and unfavorable influent carbon to phosphorus ratio, a side-stream EBPR (S2EBPR) process that involves a side-stream anaerobic biological sludge hydrolysis and fermentation reactor was proposed as an emerging alternative. In this study, a full-scale pilot testing was performed with side-by-side operation of a conventional anaerobic-anoxic-aerobic (A2O) process versus a S2EBPR process. A comparison of the performance, activity and microbial community between the two configurations was performed. The results demonstrated that, with the same influent wastewater characteristics, S2EBPR configuration showed improved P removal performance and stability than the conventional A2O configuration, especially when the mixers in the side-stream anaerobic reactor were operated intermittently. Mass balance analysis illustrated that both denitrification and EBPR were enhanced in S2EBPR configuration, where return activated sludge was diverted into the anaerobic zone to promote fermentation and enrichment of polyphosphate accumulating organisms (PAOs), and the influent was bypassed to the anoxic zone for enhancing denitrification. A relatively higher PAO activity and total PAO abundance were observed in S2EBPR than in A2O configuration, accompanied by a higher degree of dependence on glycolysis pathway than tricarboxylic acid cycle. No significant difference in the relative abundances of putative PAOs, including Ca. Accumulibacter and Tetrasphaera, were observed between the two configurations. However, higher microbial community diversity indices were observed in S2EBPR configuration than in conventional one. In addition, consistently lower relative abundance of known glycogen accumulating organisms (GAOs) was observed in S2EBPR system. Extended anaerobic retention time and conditions that generate continuous and more complex volatile fatty acids in the side-stream anaerobic reactor of S2EBPR process likely give more competitive advantage for PAOs over GAOs. PAOs exhibited sustained EBPR activity and delayed decay under extended anaerobic condition, likely due to their versatile metabolic pathways depending on the availability and utilization of multiple intracellular polymers. This study provided new insights into the effects of implementing side-stream EBPR configuration on microbial populations, EBPR activity profiles and resulted system performance.}, }
@article {pmid31584168, year = {2020}, author = {Browne, PD and Kot, W and Jørgensen, TS and Hansen, LH}, title = {The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {253-264}, doi = {10.1007/978-1-4939-9877-7_18}, pmid = {31584168}, issn = {1940-6029}, abstract = {Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.}, }
@article {pmid31582458, year = {2019}, author = {Schultz, J and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Draft Genome Sequence of Brevibacillus sp. Strain LEMMJ03, Isolated from an Antarctic Volcano.}, journal = {Microbiology resource announcements}, volume = {8}, number = {40}, pages = {}, pmid = {31582458}, issn = {2576-098X}, abstract = {Here, we announce the draft genome sequence of Brevibacillus sp. strain LEMMJ03, isolated from Whalers Bay sediment (Deception Island, Antarctica). In total, 4,500 coding sequences (CDS), among those 102 coding for tRNAs and 5 for noncoding RNAs (ncRNAs), were predicted from the 4.64-Mb genome. Predicted functions were for bacteriocin and degradation of aromatic compounds.}, }
@article {pmid31580006, year = {2019}, author = {Li, X and Garbeva, P and Liu, X and Klein Gunnewiek, PJA and Clocchiatti, A and Hundscheid, MPJ and Wang, X and de Boer, W}, title = {Volatile-mediated antagonism of soil bacterial communities against fungi.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14808}, pmid = {31580006}, issn = {1462-2920}, support = {BK20190040//Excellent Youth Foundation of Jiangsu Province/ ; 41671306//National Natural Science Foundation of China/ ; 2017YFD0200604//National Key Research and Development Program of China/ ; }, abstract = {Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil-borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non-sterile soil inoculums during exposure to volatiles emitted by soil-derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile-mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.}, }
@article {pmid31579614, year = {2019}, author = {Benucci, GMN and Longley, R and Zhang, P and Zhao, Q and Bonito, G and Yu, F}, title = {Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7744}, pmid = {31579614}, issn = {2167-8359}, abstract = {Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.}, }
@article {pmid31578554, year = {2019}, author = {An, SQ and Potnis, N and Dow, M and Vorhölter, FJ and He, YQ and Becker, A and Teper, D and Li, Y and Wang, N and Bleris, L and Tang, JL}, title = {Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuz024}, pmid = {31578554}, issn = {1574-6976}, abstract = {Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.}, }
@article {pmid31575762, year = {2019}, author = {Brewer, TE and Aronson, EL and Arogyaswamy, K and Billings, SA and Botthoff, JK and Campbell, AN and Dove, NC and Fairbanks, D and Gallery, RE and Hart, SC and Kaye, J and King, G and Logan, G and Lohse, KA and Maltz, MR and Mayorga, E and O'Neill, C and Owens, SM and Packman, A and Pett-Ridge, J and Plante, AF and Richter, DD and Silver, WL and Yang, WH and Fierer, N}, title = {Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31575762}, issn = {2150-7511}, abstract = {While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.}, }
@article {pmid31574348, year = {2019}, author = {Carney, RL and Labbate, M and Siboni, N and Tagg, KA and Mitrovic, SM and Seymour, JR}, title = {Urban beaches are environmental hotspots for antibiotic resistance following rainfall.}, journal = {Water research}, volume = {167}, number = {}, pages = {115081}, doi = {10.1016/j.watres.2019.115081}, pmid = {31574348}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; *Bacteria ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; RNA, Ribosomal, 16S ; Tetracycline ; *Waste Water ; }, abstract = {To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.}, }
@article {pmid31572496, year = {2019}, author = {Mondo, SJ and Jiménez, DJ and Hector, RE and Lipzen, A and Yan, M and LaButti, K and Barry, K and van Elsas, JD and Grigoriev, IV and Nichols, NN}, title = {Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery.}, journal = {Biotechnology for biofuels}, volume = {12}, number = {}, pages = {229}, pmid = {31572496}, issn = {1754-6834}, abstract = {Background: Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1).<br><br>Results: The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source.<br><br>Conclusions: We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and &quot;eco-enzymology&quot; of lignocellulolytic Coniochaeta species.}, }
@article {pmid31572347, year = {2019}, author = {Dagher, DJ and de la Providencia, IE and Pitre, FE and St-Arnaud, M and Hijri, M}, title = {Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2144}, pmid = {31572347}, issn = {1664-302X}, abstract = {Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.}, }
@article {pmid31572346, year = {2019}, author = {Schweitzer-Natan, O and Ofek-Lalzar, M and Sher, D and Sukenik, A}, title = {Particle-Associated Microbial Community in a Subtropical Lake During Thermal Mixing and Phytoplankton Succession.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2142}, pmid = {31572346}, issn = {1664-302X}, abstract = {Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 μm) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.}, }
@article {pmid31572315, year = {2019}, author = {Shin, GY and Schachterle, JK and Shyntum, DY and Moleleki, LN and Coutinho, TA and Sundin, GW}, title = {Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2075}, pmid = {31572315}, issn = {1664-302X}, abstract = {To successfully infect plant hosts, the collective regulation of virulence factors in a bacterial pathogen is crucial. Hfq is an RNA chaperone protein that facilitates the small RNA (sRNA) regulation of global gene expression at the post-transcriptional level. In this study, the functional role of Hfq in a broad host range phytopathogen Pantoea ananatis was determined. Inactivation of the hfq gene in P. ananatis LMG 2665T resulted in the loss of pathogenicity and motility. In addition, there was a significant reduction of quorum sensing signal molecule acyl-homoserine lactone (AHL) production and biofilm formation. Differential sRNA expression analysis between the hfq mutant and wild-type strains of P. ananatis revealed 276 sRNAs affected in their abundance by the loss of hfq at low (OD600 = 0.2) and high cell (OD600 = 0.6) densities. Further analysis identified 25 Hfq-dependent sRNAs, all showing a predicted Rho-independent terminator of transcription and mapping within intergenic regions of the P. ananatis genome. These included known sRNAs such as ArcZ, FnrS, GlmZ, RprA, RyeB, RyhB, RyhB2, Spot42, and SsrA, and 16 novel P. ananatis sRNAs. The current study demonstrated that Hfq is an important component of the collective regulation of virulence factors and sets a foundation for understanding Hfq-sRNA mediated regulation in the phytopathogen P. ananatis.}, }
@article {pmid31566612, year = {2019}, author = {Šimek, K and Sirova, D}, title = {Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {151}, pages = {}, doi = {10.3791/59903}, pmid = {31566612}, issn = {1940-087X}, abstract = {Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tracer, which allows for reliable quantitation of the grazing rates in aquatic predatory eukaryotes and estimation of nutrient transfer to higher trophic levels.}, }
@article {pmid31565058, year = {2019}, author = {Ahmed, EH and Hassan, HM and El-Sherbiny, NM and Soliman, AMA}, title = {Bacteriological Monitoring of Inanimate Surfaces and Equipment in Some Referral Hospitals in Assiut City, Egypt.}, journal = {International journal of microbiology}, volume = {2019}, number = {}, pages = {5907507}, pmid = {31565058}, issn = {1687-918X}, abstract = {Hospital-acquired infections represent a serious public health problem in all countries. It is clear that monitoring of the hospital environment is an essential element in the control and a part of the policy for preventing nosocomial infections. It allows a better understanding of the microbial ecology for the purpose of conducting preventive and corrective actions. The aims of this work were to determine the percentage of bacterial contamination of environmental samples and to identify potential nosocomial pathogens isolated from environments of seven referral hospitals from 2009 to 2015. By using the swab technique, 12863 samples were collected. Qualitative and quantitative cultures were performed. The organisms were primarily identified by colony morphology, microscopy of Gram stain, and standard biochemical tests. 25.6% of total samples showed contamination (93% was monomicrobial and 7.0% was polymicrobial). The predominant species was coagulase-negative staphylococcus (CNS) (32%), followed by methicillin-resistant S. aureus (MRSA) (26%) and then K. pneumonia (10.6%). The percentage of contamination varied among the covered hospitals and according to the year of monitoring with highly statistically significant difference (p value < 0.001). Direct contact with environmental surfaces or equipment transmits the majority of nosocomial infection. Major nosocomial pathogens have been identified. Hospital managers and healthcare bodies must be aware of the reality of the concept of environmental bacterial tanks and the need for respect of biocleaning procedures and choice of biocleaning tools.}, }
@article {pmid31563048, year = {2019}, author = {Villegas-Plazas, M and Sanabria, J and Junca, H}, title = {A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems.}, journal = {Journal of environmental management}, volume = {251}, number = {}, pages = {109581}, doi = {10.1016/j.jenvman.2019.109581}, pmid = {31563048}, issn = {1095-8630}, mesh = {Acids ; Biodegradation, Environmental ; Bioreactors ; *Microbiota ; *Mining ; }, abstract = {Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.}, }
@article {pmid31562384, year = {2020}, author = {Assié, A and Leisch, N and Meier, DV and Gruber-Vodicka, H and Tegetmeyer, HE and Meyerdierks, A and Kleiner, M and Hinzke, T and Joye, S and Saxton, M and Dubilier, N and Petersen, JM}, title = {Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {104-122}, pmid = {31562384}, issn = {1751-7370}, abstract = {Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (&quot;Candidatus Thiobarba&quot;) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that &quot;Ca. Thiobarba&quot; switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated &quot;Ca. Thiobarba&quot;. Direct stable isotope fingerprinting showed that &quot;Ca. Thiobarba&quot; has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.}, }
@article {pmid31562166, year = {2019}, author = {Joyce, RE and Lavender, H and Farrar, J and Werth, JT and Weber, CF and D'Andrilli, J and Vaitilingom, M and Christner, BC}, title = {Biological Ice-Nucleating Particles Deposited Year-Round in Subtropical Precipitation.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {23}, pages = {}, pmid = {31562166}, issn = {1098-5336}, abstract = {Airborne bacteria that nucleate ice at relatively warm temperatures (>-10°C) can interact with cloud water droplets, affecting the formation of ice in clouds and the residency time of the cells in the atmosphere. We sampled 65 precipitation events in southeastern Louisiana over 2 years to examine the effect of season, meteorological conditions, storm type, and ecoregion source on the concentration and type of ice-nucleating particles (INPs) deposited. INPs sensitive to heat treatment were inferred to be biological in origin, and the highest concentrations of biological INPs (∼16,000 INPs liter-1 active at ≥-10°C) were observed in snow and sleet samples from wintertime nimbostratus clouds with cloud top temperatures as warm as -7°C. Statistical analysis revealed three temperature classes of biological INPs (INPs active from -5 to -10°C, -11 to -12°C, and -13 to -14°C) and one temperature class of INPs that were sensitive to lysozyme (i.e., bacterial INPs, active from -5 to -10°C). Significant correlations between the INP data and abundances of taxa in the Bacteroidetes, Firmicutes, and unclassified bacterial divisions implied that certain members of these phyla may possess the ice nucleation phenotype. The interrelation between the INP classes and fluorescent dissolved organic matter, major ion concentrations (Na+, Cl-, SO42-, and NO3-), and backward air mass trajectories indicated that the highest concentrations of INPs were sourced from high-latitude North American and Asian continental environments, whereas the lowest values were observed when air was sourced from marine ecoregions. The intra- and extracontinental regions identified as sources of biological INPs in precipitation deposited in the southeastern United States suggests that these bioaerosols can disperse and affect meteorological conditions thousands of kilometers from their terrestrial points of origin.IMPORTANCE The particles most effective at inducing the freezing of water in the atmosphere are microbiological in origin; however, information on the species harboring this phenotype, their environmental distribution, and ecological sources are very limited. Analysis of precipitation collected over 2 years in Louisiana showed that INPs active at the warmest temperatures were sourced from terrestrial ecosystems and displayed behaviors that implicated specific bacterial taxa as the source of the ice nucleation activity. The abundance of biological INPs was highest in precipitation from winter storms and implied that their in-cloud concentrations were sufficient to affect the formation of ice and precipitation in nimbostratus clouds.}, }
@article {pmid31559142, year = {2019}, author = {Zheng, P and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Pan, J and Duan, J and Liang, W and Yin, B and Deng, F and Perry, SW and Wong, ML and Licinio, J and Wei, H and Yu, G and Xie, P}, title = {Perturbed Microbial Ecology in Myasthenia Gravis: Evidence from the Gut Microbiome and Fecal Metabolome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {6}, number = {18}, pages = {1901441}, doi = {10.1002/advs.201901441}, pmid = {31559142}, issn = {2198-3844}, abstract = {Myasthenia gravis (MG) is a devastating acquired autoimmune disease. Emerging evidence indicates that the gut microbiome plays a key role in maintaining immune system homeostasis. This work reports that MG is characterized by decreased α-phylogenetic diversity, and significantly disturbed gut microbiome and fecal metabolome. The altered gut microbial composition is associated with fecal metabolome changes, with 38.75% of altered bacterial operational taxonomic units showing significant correlations with a range of metabolite biomarkers. Some microbes are particularly linked with MG severity. Moreover, a combination of microbial makers and their correlated metabolites enable discriminating MG from healthy controls (HCs) with 100% accuracy. To investigate whether disturbed gut mcirobiome might contribute to the onset of MG, germ-free (GF) mice are initially colonized with MG microbiota (MMb) or healthy microbiota (HMb), and then immunized in a classic mouse model of MG. The MMb mice demonstrate substantially impaired locomotion ability compared with the HMb mice. This effect could be reversed by cocolonizing GF mice with both MMb and HMb. The MMb mice also exhibit similar disturbances of fecal metabolic pathways as found in MG. Together these data demonstrate disturbances in microbiome composition and activity that are likely to be relevant to the pathogenesis of MG.}, }
@article {pmid31557953, year = {2019}, author = {Zhang, Z and Mocanu, V and Cai, C and Dang, J and Slater, L and Deehan, EC and Walter, J and Madsen, KL}, title = {Impact of Fecal Microbiota Transplantation on Obesity and Metabolic Syndrome-A Systematic Review.}, journal = {Nutrients}, volume = {11}, number = {10}, pages = {}, pmid = {31557953}, issn = {2072-6643}, support = {./CAPMC/CIHR/Canada ; }, abstract = {Fecal microbiota transplantation (FMT) is a gut microbial-modulation strategy that has been investigated for the treatment of a variety of human diseases, including obesity-associated metabolic disorders. This study appraises current literature and provides an overview of the effectiveness and limitations of FMT as a potential therapeutic strategy for obesity and metabolic syndrome (MS). Five electronic databases and two gray literature sources were searched up to 10 December 2018. All interventional and observational studies that contained information on the relevant population (adult patients with obesity and MS), intervention (receiving allogeneic FMT) and outcomes (metabolic parameters) were eligible. From 1096 unique citations, three randomized placebo-controlled studies (76 patients with obesity and MS, body mass index = 34.8 ± 4.1 kg/m2, fasting plasma glucose = 5.8 ± 0.7 mmol/L) were included for review. Studies reported mixed results with regards to improvement in metabolic parameters. Two studies reported improved peripheral insulin sensitivity (rate of glucose disappearance, RD) at 6 weeks in patients receiving donor FMT versus patients receiving the placebo control. In addition, one study observed lower HbA1c levels in FMT patients at 6 weeks. No differences in fasting plasma glucose, hepatic insulin sensitivity, body mass index (BMI), or cholesterol markers were observed between two groups across all included studies. While promising, the influence of FMT on long-term clinical endpoints needs to be further explored. Future studies are also required to better understand the mechanisms through which changes in gut microbial ecology and engraftment of microbiota affect metabolic outcomes for patients with obesity and MS. In addition, further research is needed to better define the optimal fecal microbial preparation, dosing, and method of delivery.}, }
@article {pmid31557655, year = {2019}, author = {Wang, Y and Lin, Z and He, L and Huang, W and Zhou, J and He, Q}, title = {Simultaneous partial nitrification, anammox and denitrification (SNAD) process for nitrogen and refractory organic compounds removal from mature landfill leachate: Performance and metagenome-based microbial ecology.}, journal = {Bioresource technology}, volume = {294}, number = {}, pages = {122166}, doi = {10.1016/j.biortech.2019.122166}, pmid = {31557655}, issn = {1873-2976}, mesh = {Bioreactors ; Denitrification ; Metagenome ; *Nitrification ; Nitrogen ; Oxidation-Reduction ; *Water Pollutants, Chemical ; }, abstract = {In this study, a simultaneous partial nitrification, Anammox and denitrification (SNAD) bioreactor was constructed for mature landfill leachate treatment, which exhibited favorable NH4+-N (98.9-99.9%), TN (90.7-94.9%) and bio-refractory organic compounds (46.2-67.7%) removal efficiencies. Stoichiometric analysis demonstrated that the synergy of ammonium-oxidizing bacteria and Anammox bacteria dominated TN removal (96.1-97.2%). NO3--N produced in Anammox could be further reduced through (partial) denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The results highlighted that humic-like and their intermediates might serve as the electron donor for these (partial) denitrifiers and DNRA bacteria to remove NO3--N, and could be effectively removed from mature landfill leachate in SNAD bioreactor. Metagenomic characterization further demonstrated that phyla Chloroflexi, Chlorobi and genera Nitrosomonas, Ignavibacterium and Aminiphilus might be responsible for such humic-like degradation. Overall, this work offers new insights into the metagenome-based bioinformatic roles for the previously understudied microorganisms in SNAD bioreactor for mature landfill leachate treatment.}, }
@article {pmid31557445, year = {2020}, author = {Þorsteinsdóttir, GV and Blischke, A and Sigurbjörnsdóttir, MA and Òskarsson, F and Arnarson, ÞS and Magnússon, KP and Vilhelmsson, O}, title = {Gas seepage pockmark microbiomes suggest the presence of sedimentary coal seams in the Öxarfjörður graben of northeastern Iceland.}, journal = {Canadian journal of microbiology}, volume = {66}, number = {1}, pages = {25-38}, doi = {10.1139/cjm-2019-0081}, pmid = {31557445}, issn = {1480-3275}, abstract = {Natural gas seepage pockmarks are found off- and onshore in the Öxarfjörður graben, Iceland. The bacterial communities of two onshore seepage sites were analysed by 16S rRNA gene amplicon sequencing; the geochemical characteristics, hydrocarbon content, and the carbon isotope composition of the sites were also determined. While one site was found to be characterised by biogenic origin of methane gas, with a carbon isotope ratio (δ13C (‰)) of -63.2, high contents of organic matter and complex hydrocarbons, the other site showed a mixed origin of the methane gas (δ13C (‰) = -26.6) with geothermal characteristics and lower organic matter content. While both sites harboured Proteobacteria as the most abundant bacterial phyla, the Deltaproteobacteria were more abundant at the geothermal site and the Alphaproteobacteria at the biogenic site. The Dehalococcoidia class of phylum Chloroflexi was abundant at the geothermal site while the Anaerolineae class was more abundant at the biogenic site. Bacterial strains from the seepage pockmarks were isolated on a variety of selective media targeting bacteria with bioremediation potential. A total of 106 strains were isolated and characterised, including representatives from the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. This article describes the first microbial study on gas seepage pockmarks in Iceland.}, }
@article {pmid31556187, year = {2020}, author = {Tang, HC and Sieo, CC and Abdullah, N and Chong, CW and Gan, HM and Mohd Asrore, MS and Yong, CY and Omar, AR and Ho, YW}, title = {Effects of supplementing freeze-dried Mitsuokella jalaludinii phytase on the growth performance and gut microbial diversity of broiler chickens.}, journal = {Journal of animal physiology and animal nutrition}, volume = {104}, number = {1}, pages = {116-125}, doi = {10.1111/jpn.13208}, pmid = {31556187}, issn = {1439-0396}, support = {06-01-04-SF1376//eScience Fund/ ; }, abstract = {Inclusion of phytase in animal feedstuff is a common practice to enhance nutrients availability. However, little is known about the effects of phytase supplementation on the microbial ecology of the gastrointestinal tract. In this study, freeze-dried Mitsuokella jalaludinii phytase (MJ) was evaluated in a feeding trial with broilers fed a low available phosphorus (aP) diet. A total of 180 male broiler chicks (day-old Cobb) were assigned into three dietary treatments: Control fed with 0.4% (w/w) of available phosphorus (aP); Group T1 fed low aP [0.2% (w/w)] supplemented with MJ; and T2 fed low aP and deactivated MJ. The source of readily available P, dicalcium phosphate (DCP), was removed from low aP diet, whereby additional limestone was provided to replace the amount of Ca normally found in DCP. For each treatment, 4 replicate pens were used, where each pen consisted of 15 animals. The animals' energy intake and caecal bacterial community were monitored weekly for up to 3 weeks. The apparent metabolizable energy (AME) and apparent digestibility of dry matter (ADDM) of broilers fed with different diets were determined. In addition, the caecal microbial diversities of broilers were assessed using high-throughput next-generation sequencing targeting the V3-V4 region of bacterial 16S rRNA. The results showed that broilers fed with T1 diet have better feed conversion ratio (FCR) when compared to the Control (p < .05) and T2 diets (p < .05), demonstrating the efficiency of MJ as a supplement to low aP diet. Nevertheless, MJ did not significantly affect the microbial population and diversity in broilers' caeca, which mainly consists of members from Bacteroidetes, Firmicutes, and Proteobacteria. Regardless, significant variations in the caecal bacterial composition were observed over time, probably due to succession as the broilers aged. This is the first reported study on the effect of MJ on the microbial diversity of broiler's caeca.}, }
@article {pmid31555253, year = {2019}, author = {Sarkar, A and Morita, D and Ghosh, A and Chowdhury, G and Mukhopadhyay, AK and Okamoto, K and Ramamurthy, T}, title = {Altered Integrative and Conjugative Elements (ICEs) in Recent Vibrio cholerae O1 Isolated From Cholera Cases, Kolkata, India.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2072}, doi = {10.3389/fmicb.2019.02072}, pmid = {31555253}, issn = {1664-302X}, abstract = {The self-transferring integrative and conjugative elements (ICEs) are large genomic segments carrying several bacterial adaptive functions including antimicrobial resistance (AMR). SXT/R391 family is one of the ICEs extensively studied in cholera-causing pathogen Vibrio cholerae. The genetic characteristics of ICE-SXT/R391 in V. cholerae are dynamic and region-specific. These ICEs in V. cholerae are strongly correlated with resistance to several antibiotics such as tetracycline, streptomycin and trimethoprim-sulfamethoxazole. We screened V. cholerae O1 strains isolated from cholera patients in Kolkata, India from 2008 to 2015 for antibiotic susceptibility and the presence of ICEs, and subsequently sequenced their conserved genes. Resistance to tetracycline, streptomycin and trimethoprim-sulfamethoxazole was detected in strains isolated during 2008-2010 and 2014-2015. The genes encoding resistance to tetracycline (tetA), trimethoprim-sulfamethoxazole (dfrA1 and sul2), streptomycin (strAB), and chloramphenicol (floR) were detected in the ICEs of these strains. There was a decrease in overall drug resistance in V. cholerae associated with the ICEs in 2011. DNA sequence analysis also showed that AMR in these strains was conferred mainly by two types of ICEs, i.e., ICETET (comprising tetA, strAB, sul2, and dfrA1) and ICEGEN (floR, strAB, sul2, and dfrA1). Based on the genetic structure, Kolkata strains of V. cholerae O1 had distinct genetic traits different from the ICEs reported in other cholera endemic regions. Transfer of AMR was confirmed by conjugation with sodium azide resistant Escherichia coli J53. In addition to the acquired resistance to streptomycin and trimethoprim-sulfamethoxazole, the conjugally transferred (CT) E. coli J53 with ICE showed higher resistance to chloramphenicol and tetracycline than the donor V. cholerae. Pulsed-field gel electrophoresis (PFGE) based clonal analysis revealed that the V. cholerae strains could be grouped based on their ICEs and AMR patterns. Our findings demonstrate the epidemiological importance of ICEs and their role in the emergence of multidrug resistance (MDR) in El Tor vibrios.}, }
@article {pmid31555238, year = {2019}, author = {Pires, ES and Hardoim, CCP and Miranda, KR and Secco, DA and Lobo, LA and de Carvalho, DP and Han, J and Borchers, CH and Ferreira, RBR and Salles, JF and Domingues, RMCP and Antunes, LCM}, title = {The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2003}, doi = {10.3389/fmicb.2019.02003}, pmid = {31555238}, issn = {1664-302X}, abstract = {During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.}, }
@article {pmid31554820, year = {2019}, author = {Riva, A and Kuzyk, O and Forsberg, E and Siuzdak, G and Pfann, C and Herbold, C and Daims, H and Loy, A and Warth, B and Berry, D}, title = {A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4366}, doi = {10.1038/s41467-019-12413-0}, pmid = {31554820}, issn = {2041-1723}, mesh = {Animals ; Colon/*microbiology ; *Diet ; Dietary Fiber/*deficiency ; Gastrointestinal Microbiome/genetics/*physiology ; Intestinal Mucosa/microbiology ; Metagenomics/methods ; Mice, Inbred C57BL ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.}, }
@article {pmid31554088, year = {2019}, author = {Vissenaekens, H and Grootaert, C and Rajkovic, A and De Schutter, K and Raes, K and Smagghe, G and Van de Wiele, T and Van Camp, J}, title = {Cell line-dependent increase in cellular quercetin accumulation upon stress induced by valinomycin and lipopolysaccharide, but not by TNF-α.}, journal = {Food research international (Ottawa, Ont.)}, volume = {125}, number = {}, pages = {108596}, doi = {10.1016/j.foodres.2019.108596}, pmid = {31554088}, issn = {1873-7145}, abstract = {As the interface between the luminal and internal environment, the intestinal epithelium is strongly exposed to food-related, host-related and microbial stress. Furthermore, the endothelial stress response plays an important role in vascular disease development, which may be improved upon consumption of dietary bioactives such as polyphenols. The impact of the latter, however, is largely individual-dependent and effects are, in most cases, only observed under mild diseased conditions. Here, it is hypothesized that the individual's stressor levels may contribute to this variable response. To this end, the impact of the stressors (i) valinomycin (as model for cereulide, food-related microbial metabolite), (ii) TNF-α (host-related) and (iii) lipopolysaccharide (gram-negative bacterial cell related) on flavonoid accumulation was investigated in several intestinal and endothelial cell lines. Flow cytometry, confocal microscopy and an in-house developed, robust and high-throughput spectrofluorometric method, showed that quercetin accumulated in all tested cell lines in a dose-dependent manner. Upon stress induced by valinomycin and to a lesser extent by lipopolysaccharide, but not by TNF-α, an increased quercetin accumulation was observed in proliferating intestinal and endothelial cells and not in differentiated intestinal or quiescent endothelial cells. Therefore, flavonoid accumulation may be a potential cellular stress response mechanism which strongly depends on the applied stressor, flavonoid, cell line and even growth conditions. This opens perspectives for further understanding the mechanisms by which cellular stress may shape the individual's response to bioactive compounds.}, }
@article {pmid31553939, year = {2019}, author = {Zhang, Y and Shen, Z and Zhang, F and Yu, Y and Li, J and Lin, X}, title = {Taxonomy and phylogeny of Pseudovorticella littoralis sp. n. and P. alani sp. n. (Ciliophora: Peritrichia) from coastal waters of southern China.}, journal = {European journal of protistology}, volume = {71}, number = {}, pages = {125635}, doi = {10.1016/j.ejop.2019.125635}, pmid = {31553939}, issn = {1618-0429}, mesh = {China ; Oligohymenophorea/*classification/cytology/genetics ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Seawater/*parasitology ; Species Specificity ; }, abstract = {The morphology, infraciliature, and silverline system of two peritrich ciliates, Pseudovorticella littoralis sp. n. and P. alani sp. n., isolated from coastal waters of southern China, were investigated based on both living and silver-stained specimens. Pseudovorticella littoralis sp. n. is characterized by the following combination of characters: cell inverted cone-shaped; contractile vacuole ventral; J-shaped macronucleus; infundibular polykinety 3 with two kinetosome rows of equal length; 19-26 silverlines from peristome to trochal band and 5-14 from trochal band to scopula. Pseudovorticella alani sp. n. is characterized by: cell inverted bell-shaped; contractile vacuole ventral; J-shaped macronucleus recurved almost forming a loop; infundibular polykinety 3 with three kinetosome rows, outer two rows longer than inner one; 48-61 silverlines between peristome and aboral trochal band, and 12-20 between aboral trochal band and scopula. The SSU rDNA sequences of both new species are reported and their genetic distances with congeners and phylogenetic relationships are investigated. Pseudovorticella and Epicarchesium cluster into two subclades with low support values. One subclade contains nearly all the available sequences of Pseudovorticella and Epicarchesium. Another one contains P. monilata and E. pectinatum. This calls on the need of a generic re-classification of Pseudovorticella and Epicarchesium based on more morphological and molecular data.}, }
@article {pmid31553931, year = {2019}, author = {Subirats, J and Di Cesare, A and Varela Della Giustina, S and Fiorentino, A and Eckert, EM and Rodriguez-Mozaz, S and Borrego, CM and Corno, G}, title = {High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance.}, journal = {Water research}, volume = {167}, number = {}, pages = {114895}, doi = {10.1016/j.watres.2019.114895}, pmid = {31553931}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; Integrases ; Integrons ; *Microbiota ; *Waste Water ; }, abstract = {We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L-1 of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (blaTEM, blaCTX-M, blaOXA, and blaKPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (blaCTX-M, blaOXA, and blaKPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.}, }
@article {pmid31553930, year = {2019}, author = {Regnery, J and Parrhysius, P and Schulz, RS and Möhlenkamp, C and Buchmeier, G and Reifferscheid, G and Brinke, M}, title = {Wastewater-borne exposure of limnic fish to anticoagulant rodenticides.}, journal = {Water research}, volume = {167}, number = {}, pages = {115090}, doi = {10.1016/j.watres.2019.115090}, pmid = {31553930}, issn = {1879-2448}, mesh = {Animals ; Anticoagulants ; Environmental Monitoring ; Germany ; Retrospective Studies ; *Rodenticides ; Waste Water ; *Water Pollutants, Chemical ; }, abstract = {The recent emergence of second-generation anticoagulant rodenticides (AR) in the aquatic environment emphasizes the relevance and impact of aquatic exposure pathways during rodent control. Pest control in municipal sewer systems of urban and suburban areas is thought to be an important emission pathway for AR to reach wastewater and municipal wastewater treatment plants (WWTP), respectively. To circumstantiate that AR will enter streams via effluent discharges and bioaccumulate in aquatic organisms despite very low predicted environmental emissions, we conducted a retrospective biological monitoring of fish tissue samples from different WWTP fish monitoring ponds exclusively fed by municipal effluents in Bavaria, Germany. At the same time, information about rodent control in associated sewer systems was collected by telephone survey to assess relationships between sewer baiting and rodenticide residues in fish. In addition, mussel and fish tissue samples from several Bavarian surface waters with different effluent impact were analyzed to evaluate the prevalence of anticoagulants in indigenous aquatic organisms. Hepatic AR residues were detected at 12 out of 25 WWTP sampling sites in the low μg/kg range, thereof six sites with one or more second-generation AR (i.e., brodifacoum, difenacoum, bromadiolone). 14 of 18 surveyed sites confirmed sewer baiting with AR and detected hepatic residues matched the reported active ingredients used for sewer baiting at six sites. Furthermore, second-generation AR were detected in more than 80% of fish liver samples from investigated Bavarian streams. Highest total hepatic AR concentrations in these fish were 9.1 and 8.5 μg/kg wet weight, respectively and were observed at two riverine sampling sites characterized by close proximity to upstream WWTP outfalls. No anticoagulant residues were found in fish liver samples from two lakes without known influences of effluent discharges. The findings of our study clearly show incomplete removal of anticoagulants during conventional wastewater treatment and confirm exposure of aquatic organisms via municipal effluents. Based on the demonstrated temporal and spatial coherence between sewer baiting and hepatic AR residues in effluent-exposed fish, sewer baiting in combined sewer systems contributes to the release of active ingredients into the aquatic environment.}, }
@article {pmid31552450, year = {2019}, author = {Wagner, AO and Praeg, N and Illmer, P}, title = {Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment.}, journal = {Current microbiology}, volume = {76}, number = {12}, pages = {1425-1434}, pmid = {31552450}, issn = {1432-0991}, support = {P 22815/FWF_/Austrian Science Fund FWF/Austria ; P 22815//Austrian Science Fund/ ; }, mesh = {Affinity Labels/*chemistry ; Azides/*chemistry ; Bacteriological Techniques/*methods ; Colony Count, Microbial ; DNA, Bacterial/*chemistry/genetics/isolation &amp; purification ; Listeria monocytogenes/genetics/isolation &amp; purification/*physiology ; *Microbial Viability ; Polymerase Chain Reaction ; Soil Microbiology ; }, abstract = {In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.}, }
@article {pmid31551063, year = {2019}, author = {Keiser, CN and Hammer, TJ and Pruitt, JN}, title = {Social spider webs harbour largely consistent bacterial communities across broad spatial scales.}, journal = {Biology letters}, volume = {15}, number = {9}, pages = {20190436}, pmid = {31551063}, issn = {1744-957X}, mesh = {Animals ; Bacteria ; Predatory Behavior ; *Silk ; *Spiders ; }, abstract = {Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbour microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbours compositionally distinct microbes from the more ephemeral capture webs in the desert social spider, Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harboured similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey and web samples. These data suggest that social spider webs can harbour characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.}, }
@article {pmid31550548, year = {2020}, author = {De Vrieze, J and Verbeeck, K and Pikaar, I and Boere, J and Van Wijk, A and Rabaey, K and Verstraete, W}, title = {The hydrogen gas bio-based economy and the production of renewable building block chemicals, food and energy.}, journal = {New biotechnology}, volume = {55}, number = {}, pages = {12-18}, doi = {10.1016/j.nbt.2019.09.004}, pmid = {31550548}, issn = {1876-4347}, abstract = {The carrying capacity of the planet is being exceeded, and there is an urgent need to bring forward revolutionary approaches, particularly in terms of energy supply, carbon emissions and nitrogen inputs into the biosphere. Hydrogen gas, generated by means of renewable energy through water electrolysis, can be a platform molecule to drive the future bioeconomy and electrification in the 21st century. The potential to use hydrogen gas in microbial metabolic processes is highly versatile, and this opens a broad range of opportunities for novel biotechnological developments and applications. A first approach concerns the central role of hydrogen gas in the production of bio-based building block chemicals using the methane route, thus, bypassing the inherent low economic value of methane towards higher-value products. Second, hydrogen gas can serve as a key carbon-neutral source to produce third-generation proteins, i.e. microbial protein for food applications, whilst simultaneously enabling carbon capture and nutrient recovery, directly at their point of emission. Combining both approaches to deal with the intermittent nature of renewable energy sources maximises the ability for efficient use of renewable resources.}, }
@article {pmid31550268, year = {2019}, author = {Mahjoubi, M and Aliyu, H and Cappello, S and Naifer, M and Souissi, Y and Cowan, DA and Cherif, A}, title = {The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0221574}, pmid = {31550268}, issn = {1932-6203}, abstract = {Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.}, }
@article {pmid31548611, year = {2019}, author = {Soares-Castro, P and Araújo-Rodrigues, H and Godoy-Vitorino, F and Ferreira, M and Covelo, P and López, A and Vingada, J and Eira, C and Santos, PM}, title = {Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13679}, pmid = {31548611}, issn = {2045-2322}, support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; }, abstract = {The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.}, }
@article {pmid31548387, year = {2019}, author = {Petersen, J and Vollmers, J and Ringel, V and Brinkmann, H and Ellebrandt-Sperling, C and Spröer, C and Howat, AM and Murrell, JC and Kaster, AK}, title = {A marine plasmid hitchhiking vast phylogenetic and geographic distances.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {41}, pages = {20568-20573}, pmid = {31548387}, issn = {1091-6490}, abstract = {Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.}, }
@article {pmid31547186, year = {2019}, author = {Messal, M and Slippers, B and Naidoo, S and Bezuidt, O and Kemler, M}, title = {Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, pmid = {31547186}, issn = {2076-2607}, abstract = {Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal-host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal-plant and fungal-microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant-microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant-microbe interactions.}, }
@article {pmid31547035, year = {2019}, author = {Wang, J and Sun, Y and Tao, D and Wang, S and Li, C and Zheng, F and Wu, Z}, title = {Reduction of Escherichia coli O157:H7, Listeria monocytogenes, and Naturally Present Microbe Counts on Lettuce using an Acid Mixture of Acetic and Lactic Acid.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, pmid = {31547035}, issn = {2076-2607}, abstract = {Lactic acid (LA) and acetic acid (AA) are independently used to disinfect fresh leaf vegetables. LA has a higher efficacy but costs more than AA. Herein, we compared the disinfection efficacy of LA, AA, and their mixture on lettuce to determine whether the cheaper acid mixture shows similar or more efficacy than LA. Quality analysis indicated that the acid mixture and individual acids did not cause additional loss of instrument color and polyphenolic content compared with that of the control; however, visible defects were observed at AA concentrations exceeding 0.8%. Analysis of Escherichia coli O157:H7, Listeria monocytogenes, and naturally present microbes (aerobic mesophilic and psychrotrophic bacteria, coliforms, molds, and yeasts) showed that the acid mixture led to the highest reduction in microbial count during storage. 16S rRNA sequencing was further employed to understand the effects of the acid mixture and individual acids on lettuce microbial ecology. During storage, the acid mixture and individual acids significantly decreased the abundance of Massilia spp. and Alkanindiges spp. but there was a marked increase in Escherichia-Shigella abundance (LA: 0.003-58.82%; AA: 0.01-55.34%; acid mixture: undetected to 50.71%; control: 0.007-33.09%), indicating that acid disinfection altered the microbial ecology to stimulate Escherichia-Shigella growth. These results enhance our understanding of the relationship between lettuce disinfection and ecological changes.}, }
@article {pmid31546184, year = {2020}, author = {Pietro-Souza, W and de Campos Pereira, F and Mello, IS and Stachack, FFF and Terezo, AJ and Cunha, CND and White, JF and Li, H and Soares, MA}, title = {Mercury resistance and bioremediation mediated by endophytic fungi.}, journal = {Chemosphere}, volume = {240}, number = {}, pages = {124874}, doi = {10.1016/j.chemosphere.2019.124874}, pmid = {31546184}, issn = {1879-1298}, mesh = {*Biodegradation, Environmental ; Fungi/*chemistry ; Mercury/*chemistry ; }, abstract = {The present study proposes the use of endophytic fungi for mercury bioremediation in in vitro and host-associated systems. We examined mercury resistance in 32 strains of endophytic fungi grown in culture medium supplemented with toxic metal concentrations. The residual mercury concentrations were quantified after mycelial growth. Aspergillus sp. A31, Curvularia geniculata P1, Lindgomycetaceae P87, and Westerdykella sp. P71 were selected and further tested for mercury bioremediation and bioaccumulation in vitro, as well as for growth promotion of Aeschynomene fluminensis and Zea mays in the presence or absence of the metal. Aspergillus sp. A31, C. geniculata P1, Lindgomycetaceae P87 and Westerdykella sp. P71 removed up to 100% of mercury from the culture medium in a species-dependent manner and they promoted A. fluminensis and Z. mays growth in substrates containing mercury or not (Dunnett's test, p < 0.05). Lindgomycetaceae P87 and C. geniculata P1 are dark septate endophytic fungi that endophytically colonize root cells of their host plants. The increase of host biomass correlated with the reduction of soil mercury concentration due to the metal bioaccumulation in host tissues and its possible volatilization. The soil mercury concentration was decreased by 7.69% and 57.14% in A. fluminensis plants inoculated with Lindgomycetaceae P87 + Aspergillus sp. A31 and Lindgomycetaceae P87, respectively (Dunnet's test, p < 0.05). The resistance mechanisms of mercury volatilization and bioaccumulation in plant tissues mediated by these endophytic fungi can contribute to bioremediation programs. The biochemical and genetic mechanisms involved in bioaccumulation and volatilization need to be elucidated in the future.}, }
@article {pmid31546029, year = {2019}, author = {Pikaar, I and Flugen, M and Lin, HW and Salehin, S and Li, J and Donose, BC and Dennis, PG and Bethke, L and Johnson, I and Rabaey, K and Yuan, Z}, title = {Full-scale investigation of in-situ iron and alkalinity generation for efficient sulfide control.}, journal = {Water research}, volume = {167}, number = {}, pages = {115032}, doi = {10.1016/j.watres.2019.115032}, pmid = {31546029}, issn = {1879-2448}, mesh = {*Hydrogen Sulfide ; *Iron ; Sewage ; Sulfides ; Waste Water ; }, abstract = {Hydrogen sulfide induced corrosion of concrete sewer pipes is a major issue for wastewater utilities globally. One of the most commonly used methods to combat hydrogen sulfide is the addition of ferric chloride. While a reliable and effective method, ferric chloride is acidic causing OH&amp;S concerns as well as alkalinity consumption in sewage. This study investigates, under full-scale field conditions, an alternative method for sulfide control by in-situ electrochemical generation of iron ions using sacrificial iron electrodes. This method concomitantly produces alkalinity through cathodic OH- generation, rather than consumption. The gaseous hydrogen sulfide concentrations at the discharge wet well of a real-life rising main (length: ∼1 km in, diameter: 150 mm) decreased from 173 ppm to 43 ppm (90 percentile of peak values), when a current of 0.86 A/m3 of sewage was applied. The 90 percentile peak H2S value was further reduced to 6.6 ppm when the applied current was increased to 1.14 A/m3 sewage. Moreover, methane generation was almost completely inhibited from 25.3 ± 1.46 mg COD/L to 0.06 ± 0.04 mg COD/L. The overall cell voltage remained constant throughout the experimental period clearly showing the stability of the process. Detailed characterization of the down-stream sewer pipe biofilm revealed the complexity of the iron chemistry as the in-situ produced iron ions undergo transformation into a variety of iron species. Overall, this study demonstrates that in-situ generation of iron and alkalinity is an effective alternative method for hydrogen sulfide control in sewers.}, }
@article {pmid31545283, year = {2019}, author = {Huang, X and Chen, W and Yan, C and Yang, R and Chen, Q and Xu, H and Huang, Y}, title = {Gypenosides improve the intestinal microbiota of non-alcoholic fatty liver in mice and alleviate its progression.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {118}, number = {}, pages = {109258}, doi = {10.1016/j.biopha.2019.109258}, pmid = {31545283}, issn = {1950-6007}, abstract = {Gypenosides (GP) are a type of traditional Chinese medicine (TCM) extracted from plants and commonly applied for treatment of metabolic diseases. This study aims to explore the effects of GP extracts on alleviating non-alcoholic fatty liver disease (NAFLD). In this experiment, C57BL/6 J mice were randomly assigned into normal diet control (ND), HFHC (high-fat and high-cholesterol) and HFHC + GP (GP) groups. Mice in HFHC group were fed HFHC diet combined with fructose drinking water for 12 weeks to induce the animal model of NAFLD, followed by ordinary drinking water until the end of the experiment. In the HFHC + GP group, mice were fed HFHC diet combined with fructose drinking water for 12 weeks, followed by GP-containing drinking water till the end. Mouse body weight was measured weekly. After animal procedures, mouse liver and serum samples were collected. It is shown that GP administration reduced body weight, enhanced the sensitivity to insulin resistance (IR) and decreased serum levels of ALT, AST and TG in NAFLD mice. In addition, GP treatment alleviated steatohepatitis, and downregulated ACC1, PPARγ, CD36, APOC3 and MTTP levels in mice fed with HFHC diet. Furthermore, GP treatment markedly improved intestinal microbiota, and reduced relative abundance ratio of Firmicutes / Bacteroidetes in the feces of NAFLD mice. Our results suggested that GP alleviated NAFLD in mice through improving intestinal microbiota.}, }
@article {pmid31543873, year = {2019}, author = {Alviz-Gazitua, P and Fuentes-Alburquenque, S and Rojas, LA and Turner, RJ and Guiliani, N and Seeger, M}, title = {Corrigendum: The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2014}, doi = {10.3389/fmicb.2019.02014}, pmid = {31543873}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.01499.].}, }
@article {pmid31541814, year = {2019}, author = {Petrin, S and Patuzzi, I and Di Cesare, A and Tiengo, A and Sette, G and Biancotto, G and Corno, G and Drigo, M and Losasso, C and Cibin, V}, title = {Evaluation and quantification of antimicrobial residues and antimicrobial resistance genes in two Italian swine farms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {255}, number = {Pt 1}, pages = {113183}, doi = {10.1016/j.envpol.2019.113183}, pmid = {31541814}, issn = {1873-6424}, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Feces/chemistry ; Female ; *Genes, Bacterial ; Italy ; Male ; Manure/microbiology ; Plasmids ; Swine/*microbiology ; }, abstract = {Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances in bacteria. The occurrence of ARGs in Italian swine farming - which has specific characteristics - was investigated in order to explore resistance spread dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.}, }
@article {pmid31539855, year = {2019}, author = {Santos-Clotas, E and Cabrera-Codony, A and Boada, E and Gich, F and Muñoz, R and Martín, MJ}, title = {Efficient removal of siloxanes and volatile organic compounds from sewage biogas by an anoxic biotrickling filter supplemented with activated carbon.}, journal = {Bioresource technology}, volume = {294}, number = {}, pages = {122136}, doi = {10.1016/j.biortech.2019.122136}, pmid = {31539855}, issn = {1873-2976}, mesh = {*Biofuels ; Bioreactors ; Charcoal ; Filtration ; Sewage ; Siloxanes ; *Volatile Organic Compounds ; }, abstract = {The removal of siloxanes (D4 and D5) and volatile organic contaminants (hexane, toluene and limonene) typically found in sewage biogas was investigated in a lab-scale biotrickling filter (BTF) packed with lava rock under anoxic conditions. Complete removal efficiencies for toluene and limonene were recorded at all empty bed residence time (EBRT) tested. The influence of EBRT was remarkable on the abatement of D5, whose removal decreased from 37% at 14.5 min to 16% at 4 min, while the removal of D4 and hexane remained below 16%. The packing material was supplemented with 20% of activated carbon aiming at increasing the mass transfer of the most hydrophobic pollutants. This strategy supported high removal efficiencies of 43 and 45% for hexane and D5 at the lowest EBRT. CO2 and silica were identified as mineralization products along with the presence of metabolites in the trickling solution such as dimethylsilanediol, 2-carene and α-terpinene.}, }
@article {pmid31538807, year = {2019}, author = {Tomar, SL}, title = {Oral Health Effects of Tobacco Products: Science and Regulatory Policy.}, journal = {Advances in dental research}, volume = {30}, number = {1}, pages = {2-3}, doi = {10.1177/0022034519872481}, pmid = {31538807}, issn = {1544-0737}, mesh = {*Health Policy ; Humans ; *Oral Health ; Science ; *Tobacco Products/legislation &amp; jurisprudence ; Tobacco Use Disorder ; }, }
@article {pmid31536878, year = {2019}, author = {Lambrecht, E and Van Coillie, E and Van Meervenne, E and Boon, N and Heyndrickx, M and Van de Wiele, T}, title = {Commensal E. coli rapidly transfer antibiotic resistance genes to human intestinal microbiota in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME).}, journal = {International journal of food microbiology}, volume = {311}, number = {}, pages = {108357}, doi = {10.1016/j.ijfoodmicro.2019.108357}, pmid = {31536878}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cefotaxime/pharmacology ; Chickens/microbiology ; *Computer Simulation ; Conjugation, Genetic/*genetics ; Drug Resistance, Bacterial/*genetics ; Ecosystem ; Escherichia coli/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Intestinal Mucosa/*microbiology ; Intestines/microbiology ; Plasmids/genetics ; }, abstract = {Food-producing animals are indicated as a reservoir of antibiotic resistance genes and a potential vector for transmission of plasmid-encoded antibiotic resistance genes by conjugation to the human intestinal microbiota. In this study, transfer of an antibiotic resistance plasmid from a commensal E. coli originating from a broiler chicken towards the human intestinal microbiota was assessed by using a Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). This in vitro model mimics the human intestinal ecosystem and received a single dose of 109E. coli MB6212, which harbors a plasmid known to confer resistance towards several antibiotics including tetracycline, sulfamethoxazole and cefotaxime. Since the degree of stress imposed by stomach pH and bile acids vary with the consumed meal size, the effect of meal size on E. coli donor survival and on plasmid transfer towards lumen and mucosal coliforms and anaerobes was determined. The administered commensal E. coli strain survived stomach acid and bile salt stress and was able to grow in the colon environment during the timeframe of the experiment (72 h). Transfer of antibiotic resistance was observed rapidly since cultivable transconjugant coliforms and anaerobes were already detected in the lumen and mucosa after 2 h in the simulated proximal colon. The presence of the resistance plasmid in the transconjugants was confirmed by PCR. Differences in meal size and adapted digestion had neither a detectable impact on antibiotic resistance transfer, nor on the survival of the E. coli donor strain, nor on short chain fatty acid profiles. The median number of resistant indigenous coliforms in the lumen of the inoculated colon vessels was 5.00 × 105 cfu/ml [min - max: 3.47 × 104-3.70 × 108 cfu/ml], and on the mucosa 1.44 × 107 cfu/g [min-max: 4.00 × 103-4.00 × 108 cfu/g]. Exact quantification of the anaerobic transconjugants was difficult, as (intrinsic) resistant anaerobic background microbiota were present. QPCR data supported the observation of plasmid transfer in the simulated colon. Moreover, inoculation of E. coli MB6212 had no significant impact on the microbial diversity in the lumen as determined by 16 S ribosomal gene based next generation sequencing on lumen samples. This study demonstrates that a commensal, antibiotic resistant E. coli strain present in food can transfer its antibiotic resistance plasmid relatively quickly to intestinal microbiota in the M-SHIME. The spread and persistence of antibiotic resistance genes and resistant bacteria in our intestinal system is an alarming scenario which might present clinical challenges, since it implies a potential reservoir for dissemination to pathogenic bacteria.}, }
@article {pmid31535335, year = {2020}, author = {Contador, CA and Veas-Castillo, L and Tapia, E and Antipán, M and Miranda, N and Ruiz-Tagle, B and García-Araya, J and Andrews, BA and Marin, M and Dorador, C and Asenjo, JA}, title = {Atacama Database: a platform of the microbiome of the Atacama Desert.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {2}, pages = {185-195}, doi = {10.1007/s10482-019-01328-x}, pmid = {31535335}, issn = {1572-9699}, support = {FB0001//Comisión Nacional de Investigación Científica y Tecnológica/ ; }, abstract = {The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.}, }
@article {pmid31534146, year = {2019}, author = {Harkes, P and Suleiman, AKA and van den Elsen, SJJ and de Haan, JJ and Holterman, M and Kuramae, EE and Helder, J}, title = {Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13521}, doi = {10.1038/s41598-019-49854-y}, pmid = {31534146}, issn = {2045-2322}, support = {870.15.021//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 870.15.021//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, abstract = {Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.}, }
@article {pmid31533344, year = {2019}, author = {Zwart, MP and Ali, G and Strien, EAV and Schijlen, EGWM and Wang, M and Werf, WV and Vlak, JM}, title = {Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing.}, journal = {Viruses}, volume = {11}, number = {9}, pages = {}, pmid = {31533344}, issn = {1999-4915}, support = {CF7554/2011//Netherlands Organization for International Cooperation in Higher Education/ ; }, abstract = {Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.}, }
@article {pmid31528722, year = {2019}, author = {Tiwari, UP and Singh, AK and Jha, R}, title = {Fermentation characteristics of resistant starch, arabinoxylan, and β-glucan and their effects on the gut microbial ecology of pigs: A review.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {5}, number = {3}, pages = {217-226}, doi = {10.1016/j.aninu.2019.04.003}, pmid = {31528722}, issn = {2405-6383}, abstract = {Dietary fibers (DF) contain an abundant amount of energy, although the mammalian genome does not encode most of the enzymes required to degrade them. However, a mutual dependence is developed between the host and symbiotic microbes, which has the potential to extract the energy present in these DF. Dietary fibers escape digestion in the foregut and are fermented in the hindgut, producing short-chain fatty acids (SCFA) that alter the microbial ecology in the gastrointestinal tract (GIT) of pigs. Most of the carbohydrates are fermented in the proximal part, allowing protein fermentation in the distal part, resulting in colonic diseases. The structures of resistant starch (RS), arabinoxylan (AX), and β-glucan (βG) are complex; hence, makes their way into the hindgut where these are fermented and provide energy substrates for the colonic epithelial cells. Different microbes have different preferences of binding to different substrates. The RS, AX and βG act as a unique substrate for the microbes and modify the relative composition of the gut microbial community. The granule dimension and surface area of each substrate are different, which influences the penetration capacity of microbes. Arabinose and xylan are 2 different hemicelluloses, but arabinose is substituted on the xylan backbone and occurs in the form of AX. Fermentation of xylan produces butyrate primarily in the small intestine, whereas arabinose produces butyrate in the large intestine. Types of RS and forms of βG also exert beneficial effects by producing different metabolites and modulating the intestinal microbiota. Therefore, it is important to have information of different types of RS, AX and βG and their roles in microbial modulation to get the optimum benefits of fiber fermentation in the gut. This review provides relevant information on the similarities and differences that exist in the way RS, AX, and βG are fermented, and their positive and negative effects on SCFA production and gut microbial ecology of pigs. These insights will help nutritionists to develop dietary strategies that can modulate specific SCFA production and promote beneficial microbiota in the GIT of swine.}, }
@article {pmid31527408, year = {2019}, author = {Connor, R and Brister, R and Buchmann, JP and Deboutte, W and Edwards, R and Martí-Carreras, J and Tisza, M and Zalunin, V and Andrade-Martínez, J and Cantu, A and D'Amour, M and Efremov, A and Fleischmann, L and Forero-Junco, L and Garmaeva, S and Giluso, M and Glickman, C and Henderson, M and Kellman, B and Kristensen, D and Leubsdorf, C and Levi, K and Levi, S and Pakala, S and Peddu, V and Ponsero, A and Ribeiro, E and Roy, F and Rutter, L and Saha, S and Shakya, M and Shean, R and Miller, M and Tully, B and Turkington, C and Youens-Clark, K and Vanmechelen, B and Busby, B}, title = {NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.}, journal = {Genes}, volume = {10}, number = {9}, pages = {}, pmid = {31527408}, issn = {2073-4425}, support = {R35 CA220523/CA/NCI NIH HHS/United States ; }, abstract = {A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work of this complexity and scale could be done in a hackathon setting. Ten teams comprised of over 40 participants from six countries, assembled to create a crowd-sourced set of analysis and processing pipelines for a complex biological data set in a three-day event on the San Diego State University campus starting 9 January 2019. Prior to the hackathon, 141,676 metagenomic data sets from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) were pre-assembled into contiguous assemblies (contigs) by NCBI staff. During the hackathon, a subset consisting of 2953 SRA data sets (approximately 55 million contigs) was selected, which were further filtered for a minimal length of 1 kb. This resulted in 4.2 million (Mio) contigs, which were aligned using BLAST against all known virus genomes, phylogenetically clustered and assigned metadata. Out of the 4.2 Mio contigs, 360,000 contigs were labeled with domains and an additional subset containing 4400 contigs was screened for virus or virus-like genes. The work yielded valuable insights into both SRA data and the cloud infrastructure required to support such efforts, revealing analysis bottlenecks and possible workarounds thereof. Mainly: (i) Conservative assemblies of SRA data improves initial analysis steps; (ii) existing bioinformatic software with weak multithreading/multicore support can be elevated by wrapper scripts to use all cores within a computing node; (iii) redesigning existing bioinformatic algorithms for a cloud infrastructure to facilitate its use for a wider audience; and (iv) a cloud infrastructure allows a diverse group of researchers to collaborate effectively. The scientific findings will be extended during a follow-up event. Here, we present the applied workflows, initial results, and lessons learned from the hackathon.}, }
@article {pmid31526457, year = {2019}, author = {de Los Santos Villalobos, S and Robles, RI and Parra Cota, FI and Larsen, J and Lozano, P and Tiedje, JM}, title = {Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {12}, pages = {3939-3945}, doi = {10.1099/ijsem.0.003711}, pmid = {31526457}, issn = {1466-5034}, mesh = {Bacillus/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Endophytes/classification/isolation &amp; purification ; Fatty Acids/chemistry ; Mexico ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Triticum/*microbiology ; }, abstract = {Strain TE3T, an endophytic plant growth promoting bacterium, was isolated from wheat (Triticumturgidum subsp. durum) sampled in the Yaqui Valley, Mexico. Biochemical, phenotypic and genotypic approaches were used to clarify the taxonomic affiliation of this strain. Based on analysis of its full-length 16S rRNA gene, strain TE3T was assigned to the genus Bacillus (similarity ≥98.7 %). This finding was supported by morphological and metabolic characteristics, such as rod shape, strictly aerobic metabolism, spore formation, Gram-positive staining, catalase-positive activity, reduction of nitrate to nitrite, starch and casein hydrolysis, growth in presence of lysozyme and 2 % NaCl, citrate utilization, growth pH from 6.0 to 8.0, and acid and indole production from glucose and tryptophan, respectively. The whole-genome phylogenetic relationship showed that TE3T formed an individual clade with Bacillus tequilensis KCTC 13622T, distant from that generated by all Bacillus subtilis subspecies. The maximum values for average nucleotide identity and in silico DNA-DNA hybridization were 93.85 and 54.30 %, respectively, related to Bacillus subtilissubsp. inaquosorum KCTC 13429T. Analysis of its fatty acid content showed the ability of strain TE3T to bio-synthetize fatty acids that are not present in closely related Bacillus species, such as C12 : 0, C12 : 0 2OH, C12 : 0 3OH, C17 : 0, iso-C17 : 0 3OH and C18 : 1ω9c. These results provide evidence that strain TE3T is a novel species of the genus Bacillus, for which the name Bacilluscabrialesii sp. nov. is proposed. The type strain of Bacilluscabrialesii is TE3T (CM-CNRG TB54T=CCStamb A1T).}, }
@article {pmid31523442, year = {2019}, author = {Koga, Y and Ohtsu, T and Kimura, K and Asami, Y}, title = {Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota.}, journal = {BMJ open gastroenterology}, volume = {6}, number = {1}, pages = {e000314}, doi = {10.1136/bmjgast-2019-000314}, pmid = {31523442}, issn = {2054-4774}, abstract = {Objective: To describe probiotics including a Lactobacillus gasseri strain LG21 used for the upper gastrointestinal tract, which are considered to act through improvement of indigenous microbiota inhabiting there.<br><br>Background and design: Because the early definition of probiotics emphasized their effects on improving the intestinal microbial ecology, their effects on the intestinal tract and its immunity have been considered common general benefits associated with probiotics. This conclusion was also based on a body of successful clinical trials whose endpoints were the prevention or treatment of intestinal diseases. In contrast to intestinal microbiota, our understanding of the role of gastric microbiota in human health and physiology remains poor, as the bacterial load in the stomach is considered too small to exert a significant effect due to the highly acidic environment of the human stomach. Therefore, the intervention using probiotics in the stomach is still limited at present.Results:In this article using representative 38 quoted articles, we first describe the gastric microbiota, as the indigenous microbiota in the stomach is thought to be significantly involved in the pathophysiology of this organ, since probiotics exert their beneficial effects through improving the resident microbiota. We then review the present status and future prospects of probiotics for the treatment of upper gastrointestinal diseases by quoting representative published articles, including our basic and clinical data.<br><br>Conclusions: Probiotics have been demonstrated to suppress Helicobacter pylori in the stomach, and are also expected to improve functional dyspepsia through the correction of dysbiotic gastric microbiota.}, }
@article {pmid31520875, year = {2019}, author = {Wichmann, S and Ardern, Z}, title = {Optimality in the standard genetic code is robust with respect to comparison code sets.}, journal = {Bio Systems}, volume = {185}, number = {}, pages = {104023}, doi = {10.1016/j.biosystems.2019.104023}, pmid = {31520875}, issn = {1872-8324}, abstract = {The genetic code and its evolution have been studied by many different approaches. One approach is to compare the properties of the standard genetic code (SGC) to theoretical alternative codes in order to determine how optimal it is and from this infer whether or not it is likely that it has undergone a selective evolutionary process. Many different properties have been studied in this way in the literature. Less focus has been put on the alternative code sets which are used as a comparison to the standard code. Each implicitly represents an evolutionary hypothesis and the sets used differ greatly across the literature. Here we determine the influence of the comparison set on the results of the optimality calculation by using codes based upon different sub-structures of the SGC. With these results we can generalize the results to different evolutionary hypotheses. We find that the SGC's optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses. Our results provide important information for any future studies on the evolution of the standard genetic code. We also studied properties of the SGC concerning overlapping genes, which have recently been found to be more widespread than often believed. Although our results are not conclusive yet we find additional intriguing structures in the SGC that need explanation.}, }
@article {pmid31518408, year = {2019}, author = {Bugge Harder, C and Nyrop Albers, C and Rosendahl, S and Aamand, J and Ellegaard-Jensen, L and Ekelund, F}, title = {Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {11}, pages = {}, doi = {10.1093/femsec/fiz148}, pmid = {31518408}, issn = {1574-6941}, abstract = {As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro- and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.}, }
@article {pmid31517286, year = {2019}, author = {Duysburgh, C and Van den Abbeele, P and Krishnan, K and Bayne, TF and Marzorati, M}, title = {A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro.}, journal = {International journal of pharmaceutics: X}, volume = {1}, number = {}, pages = {100021}, doi = {10.1016/j.ijpx.2019.100021}, pmid = {31517286}, issn = {2590-1567}, abstract = {A standardized in vitro simulation of the human gastrointestinal tract (M-SHIME®) was used to assess the effect of repeated daily administration of a synbiotic formulation, containing five spore-forming Bacillus strains and a prebiotic fiber blend, on the microbial activity and composition of three simulated human subjects. Firstly, while confirming recent findings, deeper phylogenetic insight was obtained in the resident M-SHIME® microbiota, demonstrating that the model maintains a diverse and representative, colon region-specific luminal and mucosal microbial community. Supplementation of the synbiotic concept increased microbial diversity in the distal colon areas, whereas specific enhancement of Bacillaceae levels was observed in the ascending colon suggesting a successful engraftment of the Bacillus spores, which probably resulted in a stimulatory effect on, among others, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Tannerellaceae and Faecalibacterium prausnitzii contributing directly or indirectly to stimulation of acetate, propionate and butyrate production. When compared with a previous study investigating the Bacillus strains, the generated data suggest a synergistic effect on the intestinal microbiota for the synbiotic formulation. Given the fact that the probiotic strains have been shown to impact post-prandial metabolic endotoxemia in human individuals, it might be interesting to further investigate the efficacy of the synbiotic concept in protecting against obesity-related disorders.}, }
@article {pmid31515652, year = {2020}, author = {Lee, HJ and Shin, SY and Whang, KS}, title = {Paenibacillus pinistramenti sp. nov., isolated from pine litter.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {2}, pages = {155-163}, doi = {10.1007/s10482-019-01325-0}, pmid = {31515652}, issn = {1572-9699}, abstract = {A Gram-stain-positive bacterium, designated strain ASL46T, was isolated from litter layer of a pine forest located in Anmyondo, Korea. Strain ASL46T was found to be an aerobic, motile, endospore-forming rod which can grow at 20-45 °C (optimum, 37 °C), at pH 6.0-11.0 (optimum, pH 7.0) and at salinities of 0-2% (w/v) NaCl (optimum, 1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ASL46T belongs to the genus Paenibacillus, showing highest sequence similarity to P. yonginensis DCY84T (98.3%), P. physcomitrella XBT (97.4%) and P. faecis CIP 101062T (96.6%). The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain ASL46T and P. physcomitrella XBT and P. yonginensis DCY84T yielded ANI values of 84.6 and 84.5% and DNA-DNA relatedness of 11.7 ± 0.7 and 10.9 ± 0.2%, respectively. The DNA G+C content of the genomic DNA of strain ASL46T was 52.1 mol%. The predominant isoprenoid quinone was identified as menaquinone-7 and the major cellular fatty acids were determined to be anteiso-C15:0, C16:0 and iso-C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, an unidentified phospholipid and an unidentified glycolipid. The whole-cell sugar was found to be ribose and cell wall peptidoglycan contained meso-diaminopimelic acid. On the basis of phylogenetic analyses, and phenotypic and chemotaxonomic characteristics, strain ASL46T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus pinistramenti sp. nov. is proposed. The type strain is ASL46T (= KACC 18701T = NBRC 111876T).}, }
@article {pmid31512011, year = {2019}, author = {Sekhohola-Dlamini, L and Tekere, M}, title = {Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing.}, journal = {Biodegradation}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10532-019-09890-x}, pmid = {31512011}, issn = {1572-9729}, abstract = {Municipal solid waste landfills are widely used as a waste management tool and landfill microbiology is at the core of waste degradation in these ecosystems. This review investigates the microbiology of municipal solid waste landfills, focusing on the current state of knowledge pertaining to microbial diversity and functions facilitating in situ waste bioprocessing, as well as ecological factors influencing microbial dynamics in landfills. Bioprocessing of waste in municipal landfills emanates from substrate metabolism and co-metabolism by several syntrophic microorganisms, resulting in partial transformation of complex substrates into simpler polymeric compounds and complete mineralisation into inorganic salts, water and gases including the biofuel gas methane. The substrate decomposition is characterised by evolution and interactions of different bacterial, archaeal and fungal groups due to prevailing biotic and abiotic conditions in the landfills, allowing for hydrolytic, fermentative, acetogenic and methanogenic processes to occur. Application of metagenomics studies based on high throughput Next Generation Sequencing technique has advanced research on profiling of the microbial communities in municipal solid waste landfills. However, functional diversity and bioprocess dynamics, as well as key factors influencing the in situ bioprocesses involved in landfill waste degradation; the very elements that are key in determining the efficiency of municipal landfills as tools of waste management, remain ambiguous. Such gaps also hinder progressive understanding of fundamentals that underlie technology development based on waste biodegradation, and exploration of municipal waste as a bioresource.}, }
@article {pmid31511911, year = {2019}, author = {Wang, L and Han, M and Li, X and Ginawi, A and Ning, K and Yan, Y}, title = {Niche and Neutrality Work Differently in Microbial Communities in Fluidic and Non-fluidic Ecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01439-y}, pmid = {31511911}, issn = {1432-184X}, abstract = {This data-intensive study investigated the delicate balance of niche and neutrality underlying microbial communities in freshwater ecosystems through comprehensive application of high-throughput sequencing, species abundance distribution (SAD), and the neutral community model (NCM), combined with species diversity and phylogenetic measures, which unite the traditional and microbial ecology. On the genus level, 45.10% and 41.18% of the water samples could be explained by the log-normal and Volkov model respectively, among which 31.37% could fit both models. Meanwhile, 55.56% of the sediment samples could be depicted by the log-normal model, and Volkov-fitted samples comprised only 13.33%. Besides, operational taxonomic units (OTUs) from water samples fit Sloan's neutral model significantly better than those in sediment. Therefore, it was concluded that deterministic processes played a great role in both water and sediment ecosystems, whereas neutrality was much more involved in water assemblages than in non-fluidic sediment ecosystems. Secondly, log-normal fitted samples had lower phylogenetic species variability (PSV) than Volkov-fitted ones, indicating that niche-based communities were more phylogenetically clustered than neutrally assembled counterparts. Additionally, further testing showed that the relative richness of rare species was vital to SAD modeling, either niche-based or neutral, and communities containing fewer rare species were more easily captured by theoretical SAD models.}, }
@article {pmid31511558, year = {2019}, author = {Makarchuk, S and Braz, VC and Araújo, NAM and Ciric, L and Volpe, G}, title = {Enhanced propagation of motile bacteria on surfaces due to forward scattering.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4110}, doi = {10.1038/s41467-019-12010-1}, pmid = {31511558}, issn = {2041-1723}, mesh = {Computer Simulation ; Escherichia coli/*cytology ; Movement ; Probability ; Surface Properties ; }, abstract = {How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence a cell's propulsion mechanism, thus leading many flagellated bacteria to describe long circular trajectories stably entrapped by the surface. Experimental studies on near-surface bacterial motility have, however, neglected the fact that real environments have typical microstructures varying on the scale of the cells' motion. Here, we show that micro-obstacles influence the propagation of peritrichously flagellated bacteria on a flat surface in a non-monotonic way. Instead of hindering it, an optimal, relatively low obstacle density can significantly enhance cells' propagation on surfaces due to individual forward-scattering events. This finding provides insight on the emerging dynamics of chiral active matter in complex environments and inspires possible routes to control microbial ecology in natural habitats.}, }
@article {pmid31507553, year = {2019}, author = {Durán-Viseras, A and Andrei, AS and Ghai, R and Sánchez-Porro, C and Ventosa, A}, title = {New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1928}, doi = {10.3389/fmicb.2019.01928}, pmid = {31507553}, issn = {1664-302X}, abstract = {Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15BT and F9-27T) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525T, Halonotius aquaticus F13-13T and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15BT = CECT 9688T = CCM 8954T) and Halonotius roseus sp. nov. (type strain F9-27T = CECT 9745T = CCM 8956T) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B12) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide &quot;expensive&quot; commodities (i.e., vitamin B12) to the halophilic microbial communities at large.}, }
@article {pmid31507541, year = {2019}, author = {Bates, KA and Shelton, JMG and Mercier, VL and Hopkins, KP and Harrison, XA and Petrovan, SO and Fisher, MC}, title = {Captivity and Infection by the Fungal Pathogen Batrachochytrium salamandrivorans Perturb the Amphibian Skin Microbiome.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1834}, doi = {10.3389/fmicb.2019.01834}, pmid = {31507541}, issn = {1664-302X}, abstract = {The emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal) is responsible for the catastrophic decline of European salamanders and poses a threat to amphibians globally. The amphibian skin microbiome can influence disease outcome for several host-pathogen systems, yet little is known of its role in Bsal infection. In addition, many experimental in-vivo amphibian disease studies to date have relied on specimens that have been kept in captivity for long periods without considering the influence of environment on the microbiome and how this may impact the host response to pathogen exposure. We characterized the impact of captivity and exposure to Bsal on the skin bacterial and fungal communities of two co-occurring European newt species, the smooth newt, Lissotriton vulgaris and the great-crested newt, Triturus cristatus. We show that captivity led to significant losses in bacterial and fungal diversity of amphibian skin, which may be indicative of a decline in microbe-mediated protection. We further demonstrate that in both L. vulgaris and T. cristatus, Bsal infection was associated with changes in the composition of skin bacterial communities with possible negative consequences to host health. Our findings advance current understanding of the role of host-associated microbiota in Bsal infection and highlight important considerations for ex-situ amphibian conservation programmes.}, }
@article {pmid31506821, year = {2019}, author = {Callejas, C and Fernández, A and Passeggi, M and Wenzel, J and Bovio, P and Borzacconi, L and Etchebehere, C}, title = {Microbiota adaptation after an alkaline pH perturbation in a full-scale UASB anaerobic reactor treating dairy wastewater.}, journal = {Bioprocess and biosystems engineering}, volume = {42}, number = {12}, pages = {2035-2046}, doi = {10.1007/s00449-019-02198-3}, pmid = {31506821}, issn = {1615-7605}, abstract = {The aim of this study was to understand how the microbial community adapted to changes, including a pH perturbation, occurring during the start-up and operation processes in a full-scale methanogenic UASB reactor designed to treat dairy wastewater. The reactor performance, prokaryotic community, and lipid degradation capacity were monitored over a 9-month period. The methanogenic community was studied by mcrA/mrtA gene copy-number quantification and methanogenic activity tests. A diverse prokaryotic community characterized the seeding sludge as assessed by sequencing the V4 region of the 16S rRNA gene. As the feeding began, the bacterial community was dominated by Firmicutes, Synergistetes, and Proteobacteria phyla. After an accidental pH increase that affected the microbial community structure, a sharp increase in the relative abundance of Clostridia and a decrease in the mcrA/mrtA gene copy number and methanogenic activity were observed. After a recovery period, the microbial population regained diversity and methanogenic activity. Alkaline shocks are likely to happen in dairy wastewater treatment because of the caustic soda usage. In this work, the plasticity of the prokaryotic community was key to surviving changes to the external environment and supporting biogas production in the reactor.}, }
@article {pmid31506760, year = {2019}, author = {Lamei, S and Stephan, JG and Nilson, B and Sieuwerts, S and Riesbeck, K and de Miranda, JR and Forsgren, E}, title = {Feeding Honeybee Colonies with Honeybee-Specific Lactic Acid Bacteria (Hbs-LAB) Does Not Affect Colony-Level Hbs-LAB Composition or Paenibacillus larvae Spore Levels, Although American Foulbrood Affected Colonies Harbor a More Diverse Hbs-LAB Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01434-3}, pmid = {31506760}, issn = {1432-184X}, support = {222-2013-423//Svenska Forskningsrådet Formas/ ; }, abstract = {The main current methods for controlling American Foulbrood (AFB) in honeybees, caused by the bacterial pathogen Paenibacillus larvae, are enforced incineration or prophylactic antibiotic treatment, neither of which is fully satisfactory. This has led to an increased interest in the natural relationships between the pathogenic and mutualistic microorganisms of the honeybee microbiome, in particular, the antagonistic effects of Honeybee-Specific Lactic Acid Bacteria (hbs-LAB) against P. larvae. We investigated whether supplemental administration of these bacteria affected P. larvae infection at colony level over an entire flowering season. Over the season, the supplements affected neither colony-level hbs-LAB composition nor naturally subclinical or clinical P. larvae spore levels. The composition of hbs-LAB in colonies was, however, more diverse in apiaries with a history of clinical AFB, although this was also unrelated to P. larvae spore levels. During the experiments, we also showed that qPCR could detect a wider range of hbs-LAB, with higher specificity and sensitivity than mass spectrometry. Honeybee colonies are complex super-organisms where social immune defenses, natural homeostatic mechanisms, and microbiome diversity and function play a major role in disease resistance. This means that observations made at the individual bee level cannot be simply extrapolated to infer similar effects at colony level. Although individual laboratory larval assays have clearly demonstrated the antagonistic effects of hbs-LAB on P. larvae infection, the results from the experiments presented here indicate that direct conversion of such practice to colony-level administration of live hbs-LAB is not effective.}, }
@article {pmid31506516, year = {2019}, author = {Bridier, A and Le Grandois, P and Moreau, MH and Prénom, C and Le Roux, A and Feurer, C and Soumet, C}, title = {Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12947}, doi = {10.1038/s41598-019-49464-8}, pmid = {31506516}, issn = {2045-2322}, abstract = {To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as Salmonella in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of Salmonella and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. Salmonella were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that Salmonella surface associated communities were highly dominated by the Moraxellaceae family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of Salmonella susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as Rothia and Psychrobacter. Such data participate to the construction of a comprehensive view of Salmonella ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.}, }
@article {pmid31506265, year = {2019}, author = {Zhang, CJ and Pan, J and Duan, CH and Wang, YM and Liu, Y and Sun, J and Zhou, HC and Song, X and Li, M}, title = {Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, doi = {10.1128/mSystems.00442-19}, pmid = {31506265}, issn = {2379-5077}, abstract = {Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.}, }
@article {pmid31506264, year = {2019}, author = {Dumolin, C and Aerts, M and Verheyde, B and Schellaert, S and Vandamme, T and Van der Jeugt, F and De Canck, E and Cnockaert, M and Wieme, AD and Cleenwerck, I and Peiren, J and Dawyndt, P and Vandamme, P and Carlier, A}, title = {Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, doi = {10.1128/mSystems.00437-19}, pmid = {31506264}, issn = {2379-5077}, support = {//Wellcome Trust/United Kingdom ; }, abstract = {The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDEIMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.}, }
@article {pmid31506260, year = {2019}, author = {Rubbens, P and Schmidt, ML and Props, R and Biddanda, BA and Boon, N and Waegeman, W and Denef, VJ}, title = {Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, doi = {10.1128/mSystems.00093-19}, pmid = {31506260}, issn = {2379-5077}, abstract = {High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically associated with these groups, and by extension, productivity has remained elusive. Here, we addressed this knowledge gap by using a machine learning-based variable selection approach that integrated FCM and 16S rRNA gene sequencing data collected from 14 freshwater lakes spanning a broad range in physicochemical conditions. There was a strong association between bacterial heterotrophic production and HNA absolute cell abundances (R2 = 0.65), but not with the more abundant LNA cells. This solidifies findings, mainly from marine systems, that HNA and LNA bacteria could be considered separate functional groups, the former contributing a disproportionately large share of carbon cycling. Taxa selected by the models could predict HNA and LNA absolute cell abundances at all taxonomic levels. Selected operational taxonomic units (OTUs) ranged from low to high relative abundance and were mostly lake system specific (89.5% to 99.2%). A subset of selected OTUs was associated with both LNA and HNA groups (12.5% to 33.3%), suggesting either phenotypic plasticity or within-OTU genetic and physiological heterogeneity. These findings may lead to the identification of system-specific putative ecological indicators for heterotrophic productivity. Generally, our approach allows for the association of OTUs with specific functional groups in diverse ecosystems in order to improve our understanding of (microbial) biodiversity-ecosystem functioning relationships.IMPORTANCE A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system specific, regularly rare members of the community, and that some could possibly switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production.}, }
@article {pmid31504446, year = {2019}, author = {Blackwell, N and Perkins, W and Palumbo-Roe, B and Bearcock, J and Lloyd, JR and Edwards, A}, title = {Seasonal blooms of neutrophilic Betaproteobacterial Fe(II) oxidizers and Chlorobi in iron-rich coal mine drainage sediments.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {10}, pages = {}, doi = {10.1093/femsec/fiz140}, pmid = {31504446}, issn = {1574-6941}, abstract = {Waters draining from flooded and abandoned coal mines in the South Wales Coalfield (SWC) are substantial sources of pollution to the environment characterized by circumneutral pH and elevated dissolved iron concentrations (>1 mg L-1). The discharged Fe precipitates to form Fe(III) (oxyhydr)oxides which sustain microbial communities. However, while several studies have investigated the geochemistry of mine drainage in the SWC, less is known about the microbial ecology of the sites presenting a gap in our understanding of biogeochemical cycling and pollutant turnover. This study investigated the biogeochemistry of the Ynysarwed mine adit in the SWC. Samples were collected from nine locations within sediment at the mine entrance from the upper and lower layers three times over one year for geochemical and bacterial 16S rRNA gene sequence analysis. During winter, members of the Betaproteobacteria bloomed in relative abundance (>40%) including the microaerophilic Fe(II)-oxidizing genus Gallionella. A concomitant decrease in Chlorobi-associated bacteria occurred, although by summer the community composition resembled that observed in the previous autumn. Here, we provide the first insights into the microbial ecology and seasonal dynamics of bacterial communities of Fe(III)-rich deposits in the SWC and demonstrate that neutrophilic Fe(II)-oxidizing bacteria are important and dynamic members of these communities.}, }
@article {pmid31499451, year = {2019}, author = {Chen, S and Smith, AL}, title = {Performance and microbial ecology of methane-driven microbial fuel cells at temperatures ranging from 25 to 5 °C.}, journal = {Water research}, volume = {166}, number = {}, pages = {115036}, doi = {10.1016/j.watres.2019.115036}, pmid = {31499451}, issn = {1879-2448}, mesh = {*Bioelectric Energy Sources ; Electrodes ; *Geobacter ; Methane ; RNA, Ribosomal, 16S ; Temperature ; }, abstract = {The effluent of mainstream anaerobic processes is saturated with dissolved methane, representing a lost energy source and potent greenhouse gas emission if left unmanaged. This study investigated the impact of operational temperature on methane-driven microbial fuel cells (MFCs) designed for continuous operation to mitigate dissolved methane emissions in anaerobic effluents. Two bench-scale, single-chamber MFCs were operated sequentially at 25, 20, 15, 10 and 5 °C. Voltage production from both MFCs ranged from approximately 0.463 to 0.512 V over 1 kΩ resistance at temperatures ≥15 °C, but abruptly dropped as temperature decreased to 10 and 5 °C, averaging just 0.156 and 0.190 V for the replicate systems. Dissolved methane removal efficiency remained relatively stable across all operational temperatures, ranging from 53.0% to 63.6%. High-throughput sequencing of 16S rRNA genes and reverse transcription quantitative polymerase chain reaction indicated distinct distribution of methanotrophs (e.g., Methylomonas) and exoelectrogens (e.g., Geobacter) on the cathode and anode, respectively. Spearman's rank correlation suggested that an indirect interaction between methanotrophs and exoelectrogens via fermentative bacteria (e.g., Acetobacterium) may play a role in system function. Notably, diversity of the anode microbial community was positively correlated with both voltage production and Coulombic efficiency, suggesting overall diversity, as opposed to abundance or activity of exoelectrogens, was the primary factor governing performance at varying temperatures.}, }
@article {pmid31497590, year = {2019}, author = {Ramamurthy, T and Mutreja, A and Weill, FX and Das, B and Ghosh, A and Nair, GB}, title = {Corrigendum: Revisiting the Global Epidemiology of Cholera in Conjunction With the Genomics of Vibrio cholerae.}, journal = {Frontiers in public health}, volume = {7}, number = {}, pages = {237}, doi = {10.3389/fpubh.2019.00237}, pmid = {31497590}, issn = {2296-2565}, abstract = {[This corrects the article DOI: 10.3389/fpubh.2019.00203.].}, }
@article {pmid31494089, year = {2019}, author = {Hsu, RH and Clark, RL and Tan, JW and Ahn, JC and Gupta, S and Romero, PA and Venturelli, OS}, title = {Microbial Interaction Network Inference in Microfluidic Droplets.}, journal = {Cell systems}, volume = {9}, number = {3}, pages = {229-242.e4}, doi = {10.1016/j.cels.2019.06.008}, pmid = {31494089}, issn = {2405-4720}, support = {T32 GM130550/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, abstract = {Microbial interactions are major drivers of microbial community dynamics and functions but remain challenging to identify because of limitations in parallel culturing and absolute abundance quantification of community members across environments and replicates. To this end, we developed Microbial Interaction Network Inference in microdroplets (MINI-Drop). Fluorescence microscopy coupled to computer vision techniques were used to rapidly determine the absolute abundance of each strain in hundreds to thousands of droplets per condition. We showed that MINI-Drop could accurately infer pairwise and higher-order interactions in synthetic consortia. We developed a stochastic model of community assembly to provide insight into the heterogeneity in community states across droplets. Finally, we elucidated the complex web of interactions linking antibiotics and different species in a synthetic consortium. In sum, we demonstrated a robust and generalizable method to infer microbial interaction networks by random encapsulation of sub-communities into microfluidic droplets.}, }
@article {pmid31493988, year = {2019}, author = {Calatayud, M and Koren, O and Collado, MC}, title = {Maternal Microbiome and Metabolic Health Program Microbiome Development and Health of the Offspring.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {30}, number = {10}, pages = {735-744}, doi = {10.1016/j.tem.2019.07.021}, pmid = {31493988}, issn = {1879-3061}, abstract = {Maternal nutritional, metabolic, and physiological states, as well as exposure to various environmental factors during conception, gestation, and lactation, have a fundamental role in the health programming of the offspring. Therefore, alterations affecting the maternal microbiota might indirectly influence fetal development. In addition, such alterations could be transmitted to the progeny at different stages of infant development (e.g., preconception, prenatal, or postnatal), thereby favoring the development of an altered microbiota in the neonate. Microbial changes of this kind have been linked to an increased risk of non-communicable diseases (NCDs), including obesity and metabolic syndrome, allergy-related problems, and diabetes. In this review, we summarize the relevance of the maternal microbiota to fetal-neonatal health programming, with a focus on maternal nutritional and metabolic states.}, }
@article {pmid31492977, year = {2019}, author = {Expósito, JR and Coello, AJ and Barreno, E and Casano, LM and Catalá, M}, title = {Endogenous NO Is Involved in Dissimilar Responses to Rehydration and Pb(NO3)2 in Ramalina farinacea Thalli and Its Isolated Phycobionts.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01427-2}, pmid = {31492977}, issn = {1432-184X}, support = {PROMETEOIII /2017/039 GVA//Generalitat Valenciana/ ; CGL2016-79158-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; CGL2016-40058-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; }, abstract = {Lichens undergo desiccation/rehydration cycles and are permeable to heavy metals, which induce free radicals. Nitrogen monoxide (NO) regulates important cellular functions, but the research on lichen NO is still very scarce. In Ramalina farinacea thalli, NO seems to be involved in the peroxidative damage caused by air pollution, antioxidant defence and regulation of lipid peroxidation and photosynthesis. Our hypothesis is that NO also has a critical role during the rehydration and in the responses to lead of its isolated phycobionts (Trebouxia sp. TR9 and Trebouxia jamesii). Therefore, we studied the intracellular reactive oxygen species (ROS) production, lipid peroxidation and chlorophyll autofluorescence during rehydration of thalli and isolated microalgae in the presence of a NO scavenger and Pb(NO3)2. During rehydration, NO scavenging modulates free radical release and chlorophyll autofluorescence but not lipid peroxidation in both thalli and phycobionts. Pb(NO3)2 reduced free radical release (hormetic effect) both in the whole thallus and in microalgae. However, only in TR9, the ROS production, chlorophyll autofluorescence and lipid peroxidation were dependent on NO. In conclusion, Pb hormetic effect seems to depend on NO solely in TR9, while is doubtful for T. jamesii and the whole thalli.}, }
@article {pmid31489900, year = {2019}, author = {Jaswal, R and Pathak, A and Chauhan, A}, title = {Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, pmid = {31489900}, issn = {2076-2607}, support = {DE-AC09-08SR22470//Savannah River National Laboratory/ ; }, abstract = {Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the &quot;core&quot; microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired &quot;core&quot; microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired &quot;core&quot; bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.}, }
@article {pmid31488068, year = {2019}, author = {Pereira-Flores, E and Glöckner, FO and Fernandez-Guerra, A}, title = {Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {453}, doi = {10.1186/s12859-019-3031-y}, pmid = {31488068}, issn = {1471-2105}, support = {57129354//Deutscher Akademischer Austauschdienst/ ; POS_EXT_2012_1_10105//Agencia Nacional de Investigación e Innovación/ ; 634486//Horizon 2020 Framework Programme/ ; }, mesh = {Benchmarking ; DNA Copy Number Variations ; Databases, Genetic ; *Gene Dosage ; *Genome Size ; Metagenome/*genetics ; Metagenomics/*methods ; Oceans and Seas ; RNA, Ribosomal, 16S/*genetics ; Time Factors ; }, abstract = {BACKGROUND: Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis workflows has the potential to improve the exploitation of metagenomic data. Metagenomic traits are organisms' characteristics linked to their performance. They are measured at the genomic level taking a random sample of individuals in a community. As such, these traits provide valuable information to uncover microorganisms' ecological patterns. The Average Genome Size (AGS) and the 16S rRNA gene Average Copy Number (ACN) are two highly informative metagenomic traits that reflect microorganisms' ecological strategies as well as the environmental conditions they inhabit.<br><br>RESULTS: Here, we present the ags.sh and acn.sh tools, which analytically derive the AGS and ACN metagenomic traits. These tools represent an advance on previous approaches to compute the AGS and ACN traits. Benchmarking shows that ags.sh is up to 11 times faster than state-of-the-art tools dedicated to the estimation AGS. Both ags.sh and acn.sh show comparable or higher accuracy than existing tools used to estimate these traits. To exemplify the applicability of both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological strategies associated with different water layers.<br><br>CONCLUSION: We took advantage of recent advances in gene annotation to develop the ags.sh and acn.sh tools to combine easy tool usage with fast and accurate performance. Our tools compute the AGS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metagenomic data analysis to gain deeper insights into microorganisms' ecology. The ags.sh and acn.sh tools are publicly available using Docker container technology at https://github.com/pereiramemo/AGS-and-ACN-tools .}, }
@article {pmid31487597, year = {2019}, author = {Griffero, L and Alcántara-Durán, J and Alonso, C and Rodríguez-Gallego, L and Moreno-González, D and García-Reyes, JF and Molina-Díaz, A and Pérez-Parada, A}, title = {Basin-scale monitoring and risk assessment of emerging contaminants in South American Atlantic coastal lagoons.}, journal = {The Science of the total environment}, volume = {697}, number = {}, pages = {134058}, doi = {10.1016/j.scitotenv.2019.134058}, pmid = {31487597}, issn = {1879-1026}, abstract = {Emerging contaminants (ECs) such as pharmaceuticals, personal care products, drugs of abuse and polar pesticides are under particular attention due to their high consumption, frequent detection in the environment and reported ecotoxicological risk. This study investigates the occurrence and distribution of multiclass of ECs in surface waters at basin scale of two Atlantic coastal lagoons of Uruguay, South America. For this purpose, a target screening approach covering up to 362 compounds was employed using nanoflow liquid chromatography - high resolution mass spectrometry (nanoLC/HRMS). 56 compounds were identified including five banned pesticides in the European Union: atrazine, carbendazim, chlorpyrifos ethyl, diazinon, and ethion. Pharmaceuticals, hormones and drugs of abuse showed maximum detection frequencies and concentrations downstream cities. The highest occurrence of pesticides was found in lagoons and streams with neighboring agricultural activity. ECs were also found in coastal sea. Environmental risk assessment revealed that the hormones 17α-ethinylestradiol and 17-β-estradiol showed the highest risk to aquatic organisms in these basins. This study represents the first basin- scale monitoring of ECs in superficial waters encompassing streams, lagoons, and coastal seas in Uruguay, South America.}, }
@article {pmid31487593, year = {2019}, author = {Field, HR and Whitaker, AH and Henson, JA and Duckworth, OW}, title = {Sorption of copper and phosphate to diverse biogenic iron (oxyhydr)oxide deposits.}, journal = {The Science of the total environment}, volume = {697}, number = {}, pages = {134111}, doi = {10.1016/j.scitotenv.2019.134111}, pmid = {31487593}, issn = {1879-1026}, mesh = {Adsorption ; Copper/*chemistry ; Iron/*chemistry ; Models, Chemical ; Organic Chemicals ; Oxidation-Reduction ; Oxides ; Phosphates/*chemistry ; }, abstract = {Iron (Fe) transformations partially control the biogeochemical cycling of biologically and environmentally important elements, such as carbon (C), nitrogen (N), phosphorus (P), and trace metals. In marine and freshwater environments, iron oxidizing bacteria commonly promote the oxidation of ferrous iron (Fe(II)) at circumneutral oxic-anoxic interfaces, resulting in the formation of mineral-organic composites known as biogenic Fe(III) (oxyhydr)oxides (BIOS). Previous studies have examined the microbial ecology, composition, morphology, and sorption reactivity of BIOS. However, a broad survey of BIOS properties and sorption reactivity is lacking. To further explore these relationships, this study utilized X-ray absorption spectroscopy (XAS) to characterize the Fe mineral species, acid digestions and elemental analysis to determine composition, Brunauer-Emmett-Teller (BET) analysis to measure specific surface area, and copper (Cu) and phosphorus (P) adsorption experiments at concentrations designed to measure maximum sorption to evaluate reactivity of BIOS samples collected in lakes and streams of the North Carolina Piedmont. Sample composition varied widely, with Fe and C content ranging from 6.3 to 34% and 3.4-13%, respectively. XAS spectra were best fit with 42-100% poorly crystalline Fe (oxyhydr)oxides, with the remainder composed of crystalline Fe minerals and organic complexes. On a sorbent mass basis, Cu and P sorption varied by a factor of two and 15, respectively. Regression analyses reveal interrelationships between physicochemical properties, and suggest that differences in P binding are driven by sorption to Fe(III) (oxyhydr)oxide surfaces. In total, results suggest that the physical and chemical characteristics of organic and Fe(III) (oxyhydr)oxide phases in BIOS interplay to control the sorption of solutes, and thus influence nutrient and contaminant cycling in soil and natural waters.}, }
@article {pmid31486865, year = {2019}, author = {Hernández-Del Amo, E and Ramió-Pujol, S and Gich, F and Trias, R and Bañeras, L}, title = {Changes in the Potential Activity of Nitrite Reducers and the Microbial Community Structure After Sediment Dredging and Plant Removal in the Empuriabrava FWS-CW.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01425-4}, pmid = {31486865}, issn = {1432-184X}, support = {IF-UDG2013//Universitat de Girona/ ; (MPCUdG2016/121//Universitat de Girona/ ; CGL2009-08338/BOS//Ministerio de Educación, Cultura y Deporte/ ; 2017SGR-548//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; }, abstract = {In constructed wetlands (CW), denitrification usually accounts for > 60% of nitrogen removal and is supposedly affected by wetland management practices, such as dredging (and plant removal). These practices cause an impact in sediment properties and microbial communities living therein. We have quantified the effects of a sediment dredging event on dissimilatory nitrite reduction by analysing the structure and activities of the microbial community before and after the event. Potential rates for nitrate reduction to ammonia and denitrification were in accordance with changes in the physicochemical conditions. Denitrification was the predominant pathway for nitrite removal (> 60%) and eventually led to the complete removal of nitrate. On the contrary, dissimilatory nitrite reduction to ammonia (DNRA) increased from 5 to 18% after the dredging event. Both actual activities and abundances of 16S rRNA, nirK and nirS significantly decreased after sediment dredging. However, genetic potential for denitrification (qnirS + qnirK/q16S rRNA) remained unchanged. Analyses of the 16S rRNA gene sequences revealed the importance of vegetation in shaping microbial community structures, selecting specific phylotypes potentially contributing to the nitrogen cycle. Overall, we confirmed that sediment dredging and vegetation removal exerted a measurable effect on the microbial community, but not on potential nitrite + nitrate removal rates. According to redundancy analysis, nitrate concentration and pH were the main variables affecting sediment microbial communities in the Empuriabrava CWs. Our results highlight a high recovery of the functionality of an ecosystem service after a severe intervention and point to metabolic redundancy of denitrifiers. We are confident these results will be taken into account in future management strategies in CWs.}, }
@article {pmid31483625, year = {2019}, author = {Cruz, H and Law, YY and Guest, JS and Rabaey, K and Batstone, D and Laycock, B and Verstraete, W and Pikaar, I}, title = {Mainstream Ammonium Recovery to Advance Sustainable Urban Wastewater Management.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {19}, pages = {11066-11079}, doi = {10.1021/acs.est.9b00603}, pmid = {31483625}, issn = {1520-5851}, mesh = {*Ammonium Compounds ; Ecosystem ; Sewage ; Waste Disposal, Fluid ; *Waste Water ; }, abstract = {Throughout the 20th century, the prevailing approach toward nitrogen management in municipal wastewater treatment was to remove ammonium by transforming it into dinitrogen (N2) using biological processes such as conventional activated sludge. While this has been a very successful strategy for safeguarding human health and protecting aquatic ecosystems, the conversion of ammonium into its elemental form is incompatible with the developing circular economy of the 21st century. Equally important, the activated sludge process and other emerging ammonium removal pathways have several environmental and technological limitations. Here, we assess that the theoretical energy embedded in ammonium in domestic wastewater represents roughly 38-48% of the embedded chemical energy available in the whole of the discharged bodily waste. The current routes for ammonium removal not only neglect the energy embedded in ammonium, but they can also produce N2O, a very strong greenhouse gas, with such emissions comprising the equivalent of 14-26% of the overall carbon footprint of wastewater treatment plants. N2O emissions often exceed the carbon emissions related to the electricity consumption for the process requirements of WWTPs. Considering these limitations, there is a need to develop alternative ammonium management approaches that center around recovery of ammonium from domestic wastewater rather than deal with its &quot;destruction&quot; into elemental dinitrogen. Current ammonium recovery techniques are applicable only at orders of magnitude above domestic wastewater strength, and so new techniques based on physicochemical adsorption are of particular interest. A new pathway is proposed that allows for mainstream ammonium recovery from wastewater based on physicochemical adsorption through development of polymer-based adsorbents. Provided adequate adsorbents corresponding to characteristics outlined in this paper are designed and brought to industrial production, this adsorption-based approach opens perspectives for mainstream continuous adsorption coupled with side-stream recovery of ammonium with minimal chemical requirements. This proposed pathway can bring forward an effective resource-oriented approach to upgrade the fate of ammonium in urban water management without generating hidden externalized environmental costs.}, }
@article {pmid31482748, year = {2019}, author = {Arias-Borrego, A and Callejón-Leblic, B and Calatayud, M and Gómez-Ariza, JL and Collado, MC and García-Barrera, T}, title = {Insights into cancer and neurodegenerative diseases through selenoproteins and the connection with gut microbiota - current analytical methodologies.}, journal = {Expert review of proteomics}, volume = {16}, number = {10}, pages = {805-814}, doi = {10.1080/14789450.2019.1664292}, pmid = {31482748}, issn = {1744-8387}, abstract = {Introduction: Selenium plays many key roles in health especially in connection with cancer and neurodegenerative diseases. However, it needs to be appreciated that the essentiality/toxicity of selenium depends on both, a narrow range of concentration and the chemical specie involved. In this context, selenoproteins are essential biomolecules against these disorders, mainly due to its antioxidant action. To this end, analytical methodologies may allow identifying and quantifying individual selenospecies in human biofluids and tissues. Areas covered: This review focus on the role of selenoproteins in medicine, with special emphasis in cancer and neurodegenerative diseases, considering the possible link with gut microbiota. In particular, this article reviews the analytical techniques and procedures recently developed for the absolute quantification of selenoproteins and selenometabolites in human biofluids and tissues. Expert commentary: The beneficial role of selenium in human health has been extensively studied and reviewed. However, several challenges remain unsolved as discussed in this article: (i) speciation of selenium (especially selenoproteins) in cancer and neurodegenerative disease patients; (ii) supplementation of selenium in humans using functional foods and nutraceuticals; (iii) the link between selenium and selenoproteins expression and the gut microbiota and (iv) analytical methods and pitfalls for the absolute quantification of selenoproteins and selenometabolites.}, }
@article {pmid31482287, year = {2019}, author = {Veach, AM and Zeglin, LH}, title = {Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01432-5}, pmid = {31482287}, issn = {1432-184X}, support = {EPS-0903806//Kansas NSF-EPSCoR First Award/ ; }, abstract = {A history of drought exposure promoted by variable precipitation regimes can select for drought-tolerant soil microbial taxa, but the mechanisms of survival and death of microbial populations through the selective stresses of soil drying and re-wet are not well understood. We subjected soils collected from a 15-year field drought experiment (&quot;Altered&quot; precipitation history with extended dry periods, versus the &quot;Ambient&quot; field control) to a laboratory drying/re-wetting experiment, to learn whether selective population survival, death, or maintenance of protein synthesis potential and microbial respiration through variable soil water conditions was affected by field drought legacy. Microbial community composition, as measured by Illumina MiSeq sequencing of the 16S rRNA and 16S rRNA gene, shifted with laboratory drying/re-wet and field drought treatments. In Ambient soils, there was a higher proportion of reduced OTU abundance (indicative of mortality) during re-wet, whereas Altered soils had a greater proportion of stable OTU populations that did not change in abundance (indicative of survival) through drying/re-wet. Altered soils also had a lower proportion of rRNA:rRNA genes (lower protein synthesis potential) during dry-down, a greater weighted mean rRNA operon number (potential growth rate and r-selection) which was associated with higher abundance of Firmicutes (order Bacillales), and lower average microbial respiration rates. These data demonstrate that soils with a weaker historical drought legacy exhibit a higher prevalence of microbial water-stress mortality and differential survival and death at OTU levels following short-term dryingand re-wetting, concurrent with higher carbon loss potential. This work provides novel insight into the mechanisms and consequences of soil microbial changes resulting from extended drought conditions.}, }
@article {pmid31482282, year = {2019}, author = {Ehsani, E and Dumolin, C and Arends, JBA and Kerckhof, FM and Hu, X and Vandamme, P and Boon, N}, title = {Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {19}, pages = {8241-8253}, doi = {10.1007/s00253-019-10082-z}, pmid = {31482282}, issn = {1432-0614}, support = {Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006)//Universiteit Gent/ ; Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006)//Universiteit Gent/ ; }, mesh = {Ammonium Compounds/metabolism ; Bacteria/*classification/genetics/*metabolism ; Bacteriological Techniques ; Carbon Dioxide/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Hydrogen/*metabolism ; Metagenomics ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.}, }
@article {pmid31482007, year = {2019}, author = {Keshvardoust, P and Huron, VAA and Clemson, M and Constancias, F and Barraud, N and Rice, SA}, title = {Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {}, pages = {22}, doi = {10.1038/s41522-019-0095-4}, pmid = {31482007}, issn = {2055-5008}, abstract = {Despite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.}, }
@article {pmid31475212, year = {2019}, author = {Godoy-Vitorino, F}, title = {Human microbial ecology and the rising new medicine.}, journal = {Annals of translational medicine}, volume = {7}, number = {14}, pages = {342}, doi = {10.21037/atm.2019.06.56}, pmid = {31475212}, issn = {2305-5839}, abstract = {The first life forms on earth were Prokaryotic, and the evolution of all Eukaryotic life occurred with the help of bacteria. Animal-associated microbiota also includes members of the archaea, fungi, protists, and viruses. The genomes of this host-associated microbial life are called the microbiome. Across the mammalian tree, microbiomes guarantee the development of immunity, physiology, and resistance to pathogens. In humans, all surfaces and cavities are colonized by a microbiome, maintained by a careful balance between the host response and its colonizers-thus humans are considered now supraorganisms. These microbiomes supply essential ecosystem services that benefit health through homeostasis, and the loss of the indigenous microbiota leads to dysbiosis, which can have significant consequences to disease. This educational review aims to describe the importance of human microbial ecology, explain the ecological terms applied to the study of the human microbiome, developments within the cutting-edge microbiome field, and implications to diagnostic and treatment.}, }
@article {pmid31469487, year = {2019}, author = {Overholt, WA and Schwing, P and Raz, KM and Hastings, D and Hollander, DJ and Kostka, JE}, title = {The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4316-4329}, doi = {10.1111/1462-2920.14794}, pmid = {31469487}, issn = {1462-2920}, support = {C-IMAGE II//Gulf of Mexico Research Initiative/ ; C-IMAGE III//Gulf of Mexico Research Initiative/ ; 2013172310//National Science Foundation/ ; }, abstract = {The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.}, }
@article {pmid31466158, year = {2019}, author = {Zhang, L and Shen, Z and Fang, W and Gao, G}, title = {Composition of bacterial communities in municipal wastewater treatment plant.}, journal = {The Science of the total environment}, volume = {689}, number = {}, pages = {1181-1191}, doi = {10.1016/j.scitotenv.2019.06.432}, pmid = {31466158}, issn = {1879-1026}, mesh = {Bacteria/classification ; Bacteroidetes/genetics ; China ; Firmicutes ; *Microbiota ; Phylogeny ; Proteobacteria/genetics ; Sewage/microbiology ; *Waste Disposal, Fluid ; Waste Water/*microbiology ; }, abstract = {Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.}, }
@article {pmid31466157, year = {2019}, author = {Xu, M and Stedtfeld, RD and Wang, F and Hashsham, SA and Song, Y and Chuang, Y and Fan, J and Li, H and Jiang, X and Tiedje, JM}, title = {Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history.}, journal = {The Science of the total environment}, volume = {689}, number = {}, pages = {1172-1180}, doi = {10.1016/j.scitotenv.2019.06.376}, pmid = {31466157}, issn = {1879-1026}, mesh = {*Composting ; Drug Resistance, Microbial/*genetics ; Farms ; Fertilizers ; *Genes, Bacterial ; Manure/*microbiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.}, }
@article {pmid31463982, year = {2019}, author = {Elghandour, MMY and Khusro, A and Adegbeye, MJ and Tan, Z and Abu Hafsa, SH and Greiner, R and Ugbogu, EA and Anele, UY and Salem, AZM}, title = {Dynamic role of single-celled fungi in ruminal microbial ecology and activities.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14427}, pmid = {31463982}, issn = {1365-2672}, abstract = {In ruminants, high fermentation capacity is necessary to develop more efficient ruminant production systems. Greater level of production depends on the ability of the microbial ecosystem to convert organic matter into precursors of milk and meat. This has led to increased interest by animal nutritionists, biochemists and microbiologists in evaluating different strategies to manipulate the rumen biota to improve animal performance, production efficiency and animal health. One of such strategies is the use of natural feed additives such as single-celled fungi yeast. The main objectives of using yeasts as natural additives in ruminant diets include; (i) to prevent rumen microflora disorders, (ii) to improve and sustain higher production of milk and meat, (iii) to reduce rumen acidosis and bloat which adversely affect animal health and performance, (iv) to decrease the risk of ruminant-associated human pathogens and (v) to reduce the excretion of nitrogenous-based compounds, carbon dioxide and methane. Yeast, a natural feed additive, has the potential to enhance feed degradation by increasing the concentration of volatile fatty acids during fermentation processes. In addition, microbial growth in the rumen is enhanced in the presence of yeast leading to the delivery of a greater amount of microbial protein to the duodenum and high nitrogen retention. Single-celled fungi yeast has demonstrated its ability to increase fibre digestibility and lower faecal output of organic matter due to improved digestion of organic matter, which subsequently improves animal productivity. Yeast also has the ability to alter the fermentation process in the rumen in a way that reduces methane formation. Furthermore, yeast inclusion in ruminant diets has been reported to decrease toxins absorption such as mycotoxins and promote epithelial cell integrity. This review article provides information on the impact of single-celled fungi yeast as a feed supplement on ruminal microbiota and its function to improve the health and productive longevity of ruminants.}, }
@article {pmid31463664, year = {2019}, author = {Erni-Cassola, G and Wright, RJ and Gibson, MI and Christie-Oleza, JA}, title = {Early Colonization of Weathered Polyethylene by Distinct Bacteria in Marine Coastal Seawater.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01424-5}, pmid = {31463664}, issn = {1432-184X}, support = {NE/K009044/1//Natural Environment Research Council/ ; NE/S005501/1//Natural Environment Research Council/ ; CENTA//Natural Environment Research Council/ ; BB/M01116X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Plastic debris in aquatic environments is rapidly colonized by a diverse community of microorganisms, often referred to as the &quot;Plastisphere.&quot; Given that common plastics are derived from fossil fuels, one would expect that Plastispheres should be enriched with obligate hydrocarbon-degrading bacteria (OHCB). So far, though, different polymer types do not seem to exert a strong effect on determining the composition of the Plastisphere, and putative biodegrading bacteria are only found as rare taxa within these biofilms. Here, we show through 16S rRNA gene sequencing that the enrichment of a prominent OHCB member on weathered and non-weathered polyethylene only occurred at early stages of colonization (i.e., after 2 days of incubation in coastal marine water; 5.8% and 3.7% of relative abundance, respectively, vs. 0.6% on glass controls). As biofilms matured, these bacteria decreased in relative abundance on all materials (< 0.3% after 9 days). Apart from OHCB, weathered polyethylene strongly enriched for other distinct organisms during early stages of colonization, such as a specific member of the Roseobacter group and a member of the genus Aestuariibacter (median 26.9% and 1.8% of the community, respectively), possibly as a consequence of the availability of short-oxidized chains generated from weathering. Our results demonstrate that Plastispheres can vary in accordance with the weathering state of the material and that very early colonizing communities are enriched with taxa that can potentially degrade hydrocarbons. Given the lack of persistent enrichment and overall community convergence between materials over time, common non-hydrolysable polymers might not serve as an important source of carbon for mature Plastispheres once the labile substrates generated from weathering have been depleted.}, }
@article {pmid31463663, year = {2019}, author = {Baselga-Cervera, B and García-Balboa, C and Díaz-Alejo, HM and Costas, E and López-Rodas, V}, title = {Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01431-6}, pmid = {31463663}, issn = {1432-184X}, support = {CTM-2013-44366-R.//Spanish Secretaría de Estado, Investigación, Desarrollo e Innovación/ ; BES-2014-067580.//Secretaría de Estado, Investigación, Desarrollo e Innovación/ ; }, abstract = {Anthropogenic extreme environments are emphasized as interesting sites for the study of evolutionary pathways, biodiversity, and extremophile bioprospection. Organisms that grow under these conditions are usually regarded as extremophiles; however, the extreme novelty of these environments may have favor adaptive radiations of facultative extremophiles. At the Iberian Peninsula, uranium mining operations have rendered highly polluted extreme environments in multiple locations. In this study, we examined the phytoplankton diversity, community structure, and possible determining factors in separate uranium mining-impacted waters. Some of these human-induced extreme environments may be able to sustain indigenous facultative extremophile phytoplankton species, as well as alleged obligate extremophiles. Therefore, we investigated the adaptation capacity of three laboratory strains, two Chlamydomonas reinhardtii and a Dictyosphaerium chlorelloides, to uranium-polluted waters. The biodiversity among the sampled waters was very low, and despite presenting unique taxonomic records, ecological patterns can be identified. The microalgae adaptation experiments indicated a gradient of ecological novelty and different phenomena of adaptation, from acclimation in some waters to non-adaptation in the harshest anthropogenic environment. Certainly, phytoplankton extremophiles might have been often overlooked, and the ability to flourish in extreme environments might be a functional feature in some neutrophilic species. Evolutionary biology and microbial biodiversity can benefit the study of recently evolved systems such as uranium-polluted waters. Moreover, anthropogenic extremophiles can be harnessed for industrial applications.}, }
@article {pmid31462415, year = {2019}, author = {McGonigle, JM and Bernau, JA and Bowen, BB and Brazelton, WJ}, title = {Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSphere.00378-19}, pmid = {31462415}, issn = {2379-5042}, abstract = {We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.}, }
@article {pmid31456784, year = {2019}, author = {Gogulancea, V and González-Cabaleiro, R and Li, B and Taniguchi, D and Jayathilake, PG and Chen, J and Wilkinson, D and Swailes, D and McGough, AS and Zuliani, P and Ofiteru, ID and Curtis, TP}, title = {Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1871}, doi = {10.3389/fmicb.2019.01871}, pmid = {31456784}, issn = {1664-302X}, abstract = {Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·105 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances.}, }
@article {pmid31455798, year = {2019}, author = {Park, CH and Lee, JG and Lee, AR and Eun, CS and Han, DS}, title = {Network construction of gastric microbiome and organization of microbial modules associated with gastric carcinogenesis.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12444}, doi = {10.1038/s41598-019-48925-4}, pmid = {31455798}, issn = {2045-2322}, support = {NRF-2017R1C1B5015928//National Research Foundation of Korea (NRF)/ ; }, abstract = {In addition to Helicobacter pylori infection, nitrosating/nitrate-reducing bacteria and type IV secretion system (T4SS) protein gene-contributing bacteria have been proposed as potential causes of gastric cancer development. However, bacterial modules related with gastric carcinogenesis have not been clarified. In this study, we analyzed gastric microbiome using the gastric mucosal samples obtained from the Hanyang University Gastric Microbiome Cohort by 16S rRNA gene sequencing. Weighted correlation network analysis was performed to construct a microbiome network and to identify microbial modules associated with gastric carcinogenesis. At the family level, 420 bacterial taxa were identified in the gastric microbiome of 83 participants. Through network analysis, 18 microbial modules were organized. Among them, two modules-pink and brown-were positively correlated with a higher-risk of gastric cancer development such as intestinal metaplasia with no current H. pylori infection (correlation coefficient [γ]: pink module, 0.31 [P = 0.004], brown module, 0.26 [P = 0.02]). At the family level, twenty-two and thirty-two bacterial taxa belonged to the pink and brown modules, respectively. They included nitrosating/nitrate-reducing bacteria, T4SS protein gene-contributing bacteria, and various other bacteria, including Gordoniaceae, Tsukamurellaceae, Prevotellaceae, Cellulomonadaceae, Methylococcaceae, and Procabacteriaceae. The blue module, which included H. pylori, was correlated negatively with intestinal metaplasia (γ = -0.49 [P < 0.001]). In conclusion, intragastric bacterial taxa associated with gastric carcinogenesis can be classified by network analysis. Microbial modules may provide an integrative view of the microbial ecology relevant to precancerous lesions in the stomach.}, }
@article {pmid31454177, year = {2019}, author = {Goulart, MC and Cueva-Yesquén, LG and Hidalgo Martinez, KJ and Attili-Angelis, D and Fantinatti-Garboggini, F}, title = {Comparison of specific endophytic bacterial communities in different developmental stages of Passiflora incarnata using culture-dependent and culture-independent analysis.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e896}, pmid = {31454177}, issn = {2045-8827}, support = {141298/2017-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 15/02395-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Plants and endophytic microorganisms have coevolved unique relationships over many generations. Plants show a specific physiological status in each developmental stage, which may determine the occurrence an