@article {pmid31835131,
year = {2019},
author = {Keller, LJ and Babin, BM and Lakemeyer, M and Bogyo, M},
title = {Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities.},
journal = {Current opinion in chemical biology},
volume = {54},
number = {},
pages = {45-53},
doi = {10.1016/j.cbpa.2019.10.007},
pmid = {31835131},
issn = {1879-0402},
abstract = {Activity-based protein profiling (ABPP) is a robust chemoproteomic technique that uses activity-based probes to globally measure endogenous enzymatic activity in complex proteomes. It has been utilized extensively to characterize human disease states and identify druggable targets in diverse disease conditions. ABPP has also recently found applications in microbiology. This includes using activity-based probes (ABPs) for functional studies of pathogenic bacteria as well as complex communities within a microbiome. This review will focus on recent advances in the use of ABPs to profile enzyme activity in disease models, screen for selective inhibitors of key enzymes, and develop imaging tools to better understand the host-bacterial interface.},
}

@article {pmid31835114,
year = {2019},
author = {Ma, Y and Guo, Y and Ye, H and Zhang, J and Ke, Y},
title = {Perinatal Triclosan exposure in the rat induces long-term disturbances in metabolism and gut microbiota in adulthood and old age.},
journal = {Environmental research},
volume = {182},
number = {},
pages = {109004},
doi = {10.1016/j.envres.2019.109004},
pmid = {31835114},
issn = {1096-0953},
abstract = {Triclosan (TCS), as a widely used antimicrobial compound, is commonly detected in pregnant women and newborns indicating exposure risk during early development. However, whether perinatal TCS exposure has long-term effects on the host microbiome which further contributes to metabolic disorder is still unclear. The long-term effects of perinatal TCS exposure on gut microbiota and liver metabolism in adulthood and old age were investigated. Rats were given 0, 10 or 50 mg TCS/kg body weight per day, administered daily by gavage from gestation day 0 until lactation day 21. RNA-sequencing and 16 S rDNA amplicon sequencing analysis were performed to explore the potential mechanisms. Increased blood glucose and serum HDL-C were observed at 10 mg/kg/day in old rats and at 50 mg/kg/day in both adult and old rats. Serum leptin were increased at two doses in old rats. Serum TG and LDL-C were increased at two doses in both adult and old rats. Hepatic glycogen were decreased at 50 mg/kg/day in adult rats and at two doses in old rats. Increased hepatic TG were observed at two doses in old rats. Hepatic RNA-sequencing revealed that more differentially expressed genes were found at 50 mg/kg/day in both adult and old rats. More up-regulated genes in pathways of carbohydrate and lipid metabolism were observed in old rats at 50 mg/kg/day. Diversity reduction and compositional alteration were found in gut microbiota at 50 mg/kg/day in adult rats and at two doses in old rats. These effects lasted for a long time even without TCS exposure and accumulated over time inducing metabolic disorder in old rat offspring. TCS exposure during early life causes disturbances in metabolism and gut microbiota which last a lifetime and accumulated over time at 50 mg/kg/day. Further research is needed to investigate the effects of early life TCS exposure on metabolism and gut microbiota in humans.},
}

@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},
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 {pmid31834952,
year = {2019},
author = {Han, SH and Lee, JS and Song, KH and Choe, YB and Ahn, KJ and Lee, YW},
title = {Differences in Foot Skin Microbiomes Between Patients with Type 2 Diabetes and Healthy Individuals.},
journal = {Mycoses},
volume = {},
number = {},
pages = {},
doi = {10.1111/myc.13046},
pmid = {31834952},
issn = {1439-0507},
abstract = {BACKGROUND: Impaired immunity and changes in the microenvironment in patients with diabetes might influence the composition of the cutaneous microbiome. However, data on the cutaneous microbiome of these patients are scarce.

OBJECTIVES: This study compared the fungal and bacterial components of the skin microbiome between patients with type 2 diabetes mellitus (DM) and healthy individuals.

METHODS: We obtained skin swab samples from the plantar forefoot of 17 patients with DM and 18 healthy individuals to conduct a cross-sectional study. The samples were profiled with culture-independent sequencing of the V3 to V4 regions of the bacterial 16S rRNA gene and the fungal ITS2 region, followed by direct DNA extraction and molecular polymerase chain reaction (PCR).

RESULTS: We observed a differential cutaneous microbiome, especially for fungi, in patients with type 2 diabetes compared to that in healthy controls. Trichophyton rubrum was more abundant in DM samples. The Shannon diversity index for fungi was lower in the DM patients. Principal coordinate analysis plots and permutational multivariate analysis of variance (PERMANOVA) tests based on Bray-Curtis distances between samples supported the association of the fungal microbiome with DM at the species level.

CONCLUSIONS: The results suggest that clinicians should pay attention to both fungi and bacteria and provide appropriate prevention and therapeutic strategies for diabetic cutaneous complications including diabetic foot ulcers. These data also contribute to future research associated with diabetes and cutaneous microbiomes.},
}

@article {pmid31834908,
year = {2019},
author = {Loo, WT and Dudaniec, RY and Kleindorfer, S and Cavanaugh, CM},
title = {An inter-island comparison of Darwin's finches reveals the impact of habitat, host phylogeny, and island on the gut microbiome.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0226432},
doi = {10.1371/journal.pone.0226432},
pmid = {31834908},
issn = {1932-6203},
abstract = {Darwin's finch species in the Galapagos Archipelago are an iconic adaptive radiation that offer a natural experiment to test for the various factors that influence gut microbiome composition. The island of Floreana has the longest history of human settlement within the archipelago and offers an opportunity to compare island and habitat effects on Darwin's finch microbiomes. In this study, we compare gut microbiomes in Darwin's finch species on Floreana Island to test for effects of host phylogeny, habitat (lowlands, highlands), and island (Floreana, Santa Cruz). We used 16S rRNA Illumina sequencing of fecal samples to assess the gut microbiome composition of Darwin's finches, complemented by analyses of stable isotope values and foraging data to provide ecological context to the patterns observed. Overall bacterial composition of the gut microbiome demonstrated co-phylogeny with Floreana hosts, recapitulated the effect of habitat and diet, and showed differences across islands. The finch phylogeny uniquely explained more variation in the microbiome than did foraging data. Finally, there were interaction effects for island × habitat, whereby the same Darwin's finch species sampled on two islands differed in microbiome for highland samples (highland finches also had different diets across islands) but not lowland samples (lowland finches across islands had comparable diet). Together, these results corroborate the influence of phylogeny, age, diet, and sampling location on microbiome composition and emphasize the necessity for comprehensive sampling given the multiple factors that influence the gut microbiome in Darwin's finches, and by extension, in animals broadly.},
}

@article {pmid31834574,
year = {2019},
author = {Clanner-Engelshofen, BM and French, LE and Reinholz, M},
title = {Methods for extraction and ex-vivo experimentation with the most complex human commensal, Demodex spp.},
journal = {Experimental & applied acarology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10493-019-00450-9},
pmid = {31834574},
issn = {1572-9702},
abstract = {Demodex spp. mites are the most complex organisms of the human skin microbiome and were discovered more than 175 years ago, yet only little basic research is published about them. As they can be pathophysiologically relevant ectoparasites associated with rosacea, pityriasis folliculorum, and other inflammatory skin diseases, more research should be encouraged. Being a large microorganism or a tiny animal, there are no established basic methods to handle these mites. Here, we describe techniques enabling the extraction of Demodex mites from human skin, their analysis in different ex-vivo settings, the lysis of their exoskeleton, their preservation by freezing, and observation microscopically using specific fluorescent dyes or their inherent autofluorescence. These procedures should facilitate future Demodex research and fuel further the generation of knowledge. Furthermore it is intended to ultimatively enable the mite's cultivation in vitro and reveal its pathophysiological mechanisms.},
}

@article {pmid31833956,
year = {2019},
author = {Mourah, S and Louveau, B and Dumaz, N},
title = {Mechanisms of resistance and predictive biomarkers of response to targeted therapies and immunotherapies in metastatic melanoma.},
journal = {Current opinion in oncology},
volume = {},
number = {},
pages = {},
doi = {10.1097/CCO.0000000000000603},
pmid = {31833956},
issn = {1531-703X},
abstract = {PURPOSE OF REVIEW: Thanks to mitogen-activated protein kinase inhibitors (MAPKi) and immune checkpoint inhibitors (ICI), major progress has been made in the field of melanoma treatment. However, long-term success is still scarce because of the development of resistance. Understanding these mechanisms of resistance and identifying predictive genomic biomarkers are now key points in the therapeutic management of melanoma patients.

RECENT FINDINGS: Multiple and complex mechanisms of resistance to MAPKi or ICI have been uncovered in the past few years. The lack of response can be driven by mutations and nonmutational events in tumor cells, as well as by changes in the tumor microenvironment. Melanoma cells are also capable of rapidly switching their molecular and cellular phenotype, leading to an initial drug-tolerant favorizing melanoma resistance. Tumor molecular profiling and circulating tumor cell analyses are of high interest as predictive biomarkers as well as studying immunogenic changes and microbiome in ICI-treated patients.

SUMMARY: Resistance to MAPKi and ICI is a key point in therapeutic management of metastatic melanoma patients. Validated biomarkers predicting response to therapy are urgently needed to move toward personalized medicine. Combinatory treatments guided by the understanding of resistance mechanisms will be of major importance in the future of melanoma therapy.},
}

@article {pmid31833799,
year = {2019},
author = {Ravilla, R and Coleman, HN and Chow, CE and Chan, L and Fuhrman, BJ and Greenfield, WW and Robeson, MS and Iverson, K and Spencer, H and Nakagawa, M},
title = {Cervical Microbiome and Response to a Human Papillomavirus Therapeutic Vaccine for Treating High-Grade Cervical Squamous Intraepithelial Lesion.},
journal = {Integrative cancer therapies},
volume = {18},
number = {},
pages = {1534735419893063},
doi = {10.1177/1534735419893063},
pmid = {31833799},
issn = {1552-695X},
support = {R01 CA143130/CA/NCI NIH HHS/United States ; },
abstract = {Human papillomavirus (HPV) infection is associated with the vast majority of cervical cancer cases as well as with other anogenital cancers. PepCan is an investigational HPV therapeutic vaccine for treating cervical high-grade squamous intraepithelial lesions. The present study was performed to test whether the cervical microbiome influences vaccine responses and to explore host factors as determinants of the cervical microbiome composition in women with biopsy-proven high-grade squamous intraepithelial lesions. In a recently completed Phase I clinical trial of PepCan, histological response rate of 45% (14 of 31 patients), a significant increase in circulating T-helper type 1 cells, and a significant decrease in HPV 16 viral load were reported. DNA, extracted from liquid cytology specimens collected before and after vaccinations, were amplified and then hybridized to a G4 PhyloChip assay to characterize the microbiome. We describe trends that certain bacterial taxa in the cervix may be enriched in non-responders in comparison to responders (Padj = .052 for phylum Caldithrix and Padj = .059 for phylum Nitrospirae). There was no difference in bacterial diversity between the 2 groups. A permutational analysis of variance performed for various demographic and immune parameters showed significant clustering with microbiome beta diversity for race, HPV 16 status, peripheral T-helper type 1 cells, and HLA-B40 (P = .001, .014, .037, and .024, respectively). Further analyses showed significant differences at the empirical Operational Taxonomic Unit level for race and HPV 16 status. As these results are from a small Phase I study, further studies are needed to examine the role of cervical microbiome in response to HPV therapeutic vaccines.},
}

@article {pmid31833543,
year = {2019},
author = {Turner, D and Bishai, J and Reshef, L and Abitbol, G and Focht, G and Marcus, D and Ledder, O and Lev-Tzion, R and Orlanski-Meyer, E and Yerushalmi, B and Aloi, M and Griffiths, AM and Albenberg, L and Kolho, KL and Assa, A and Cohen, S and Gophna, U and Vlamakis, H and Lurz, E and Levine, A},
title = {Antibiotic Cocktail for Pediatric Acute Severe Colitis and the Microbiome: The PRASCO Randomized Controlled Trial.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izz298},
pmid = {31833543},
issn = {1536-4844},
abstract = {BACKGROUND: Alterations in the microbiome have been postulated to drive inflammation in IBD. In this pilot randomized controlled trial, we evaluated the effectiveness of quadruple antibiotic cocktail in addition to intravenous-corticosteroids (IVCSs) in acute severe colitis (ASC).

METHODS: Hospitalized children with ASC (pediatric ulcerative colitis activity index [PUCAI] ≥65) were randomized into 2 arms: the first received antibiotics in addition to IVCS (amoxicillin, vancomycin, metronidazole, doxycycline/ciprofloxacin [IVCS+AB]), whereas the other received only IVCS for 14 days. The primary outcome was disease activity (PUCAI) at day 5. Microbiome was analyzed using 16S rRNA gene and metagenome.

RESULTS: Twenty-eight children were included: 16 in the AB + IVCS arm and 12 in the IVCS arm (mean age 13.9 ± 4.1 years and 23 [82%] with extensive colitis). The mean day-5 PUCAI was 25 ± 16.7 vs 40.4 ± 20.4, respectively (P = 0.037). Only 3 and 2 children, respectively, required colectomy during 1-year follow-up (P = 0.89). Microbiome data at time of admission were analyzed for 25 children, of whom 17 (68%) had a predominant bacterial species (>33% abundance); response was not associated with the specific species, whereas decreased microbiome diversity at admission was associated with day-5 response in the IVCS arm.

CONCLUSION: Patients with ASC have alterations in the microbiome characterized by loss of diversity and presence of predominant bacterial species. Quadruple therapy in addition to IVCS improved disease activity on day 5, but larger studies are needed to determine whether this is associated with improved long-term outcomes (clinicaltrials.gov NCT02033408).},
}

@article {pmid31833440,
year = {2019},
author = {Wang, L and Li, X},
title = {Steering soil microbiome to enhance soil system resilience.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/1040841X.2019.1700906},
pmid = {31833440},
issn = {1549-7828},
abstract = {Pathogens in soil play a tremendous role in soil health and subsequent food production. Soil-borne pathogens can cause serious losses to global harvest and are considered as a difficult problem to manage worldwide. The emergence of soil disease is largely dependent on the pathogen-host-environment complex, which can be employed to generate pathogen control strategies. Usually, the resources of resistant plant varieties are limited, and chemical control is insufficiently effective with possible secondary soil pollution. Therefore, there is now a compulsory need to enhance the ability of soil per se to defend against invading pathogens (i.e. soil immunity). Soil immunity is normally attributed to the activities of the functional microbiome. In the meanwhile, pathogen-microbiome interactions in soil are sensitive to soil contaminants which would filter out unique groups of microbial communities. Steering functional soil microbiome will not only limit disease development, but also reduce the level of soil pollution. It is thus of great importance to develop microbiome-based techniques to improve soil immunity and resilience. This review provided an up-to-date understanding of the mechanisms for microbiome-based disease suppression and potential management strategies for better sustainable agricultural system.},
}

@article {pmid31833210,
year = {2020},
author = {Witkin, SS and Forney, LJ},
title = {The microbiome and women's health: perspectives and controversies.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {127},
number = {2},
pages = {127},
doi = {10.1111/1471-0528.16010},
pmid = {31833210},
issn = {1471-0528},
}

@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 {pmid31832691,
year = {2019},
author = {Panda, M and Rai, AK and Rahman, T and Das, A and Das, R and Sarma, A and Kataki, AC and Chattopadhyay, I},
title = {Alterations of salivary microbial community associated with oropharyngeal and hypopharyngeal squamous cell carcinoma patients.},
journal = {Archives of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00203-019-01790-1},
pmid = {31832691},
issn = {1432-072X},
support = {BT/PR16886/NER/95/336/2015//Department of Biotechnology/ ; },
abstract = {The highest number (35.1% of global incident cases) of new oropharyngeal (OP) and hypopharyngeal (HP) cancer cases was reported in South-Central Asia. The highest incidence of HP cancer in India was reported in East Khasi Hills District of Meghalaya, Aizawl District of Mizoram, and Kamrup Urban District of Assam. HP and OP cancer showed the highest mortality rate, worst prognoses and the highest rate of nodal metastases and distant metastases. Thus, research is required to detect specific biomarkers for early prevention and diagnosis for these cancers. Oral microbiome signatures in saliva are considered as a potential diagnostic biomarker for OP and HP cancer. Bacterial profile alterations in OP and HP cancer have not been reported in India population, to establish the association of oral bacteria in the progression of OP and HP cancer; we studied bacterial communities in saliva of eight OP and seven HP cancer patients as compared to healthy controls using 16S rRNA V3-V4 region sequencing. The higher abundance of Haemophilus parainfluenzae, Haemophilus influenzae and Prevotella copri and lower abundance of Rothia mucilaginosa, Aggregatibacter segnis, Veillonella dispar, Prevotella nanceiensis, Rothia aeria, Capnocytophaga ochracea, Neisseria bacilliformis, Prevotella nigrescens and Selenomonas noxia in saliva of OP and HP cancer patients may be considered as a non-invasive diagnostic biomarker for OP and HP cancer patients. Streptococcus anginosus may be considered as a non-invasive diagnostic biomarker for OP cancer patients only. Therefore, evaluation of salivary microbial biomarkers may be informative to understand the pathobiology and carcinogenesis of OP and HP cancer.},
}

@article {pmid31832638,
year = {2019},
author = {D'Souza, AW and Moodley-Govender, E and Berla, B and Kelkar, T and Wang, B and Sun, X and Daniels, B and Coutsoudis, A and Trehan, I and Dantas, G},
title = {Cotrimoxazole prophylaxis increases resistance gene prevalence and α-diversity but decreases β-diversity in the gut microbiome of HIV-exposed, uninfected infants.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciz1186},
pmid = {31832638},
issn = {1537-6591},
abstract = {BACKGROUND: Prophylactic cotrimoxazole treatment is recommended in HIV exposed, uninfected (HEU) infants, but the effects of this treatment on developing HEU infant gut microbiotas and resistomes are largely undefined.

METHODS: We analyzed whole-metagenome sequencing data from 163 longitudinally collected stool samples from 63 HEU infants randomized to receive (n=34) or to not receive (n=29) prophylactic cotrimoxazole treatment. We generated taxonomic, functional pathway, and resistance gene profiles for each sample and compared microbiome signatures between cotrimoxazole treated HEU infants (CTX-T infants) and HEU infants not treated with cotrimoxazole (CTX-N infants).

RESULTS: Metagenomic analysis did not reveal significant differences in taxonomic or functional pathway α-diversity between CTX-T infants and CTX-N infants. In contrast, resistance gene prevalence (p=0.00719) and α-diversity (p=0.0045) increased in CTX-T. These differences increased over time for both resistance gene prevalence measured by log normalized abundance (4 months mean 0.71, 95% CI [0.2, 1.2] and 6 months mean 0.85; 95% CI [0.1, 1.7]) and α-diversity (p=0.0045). Unlike α-diversity, interindividual gut microbiome taxonomic (mean -0.11; 95% CI [-0.15, -0.077]), functional taxonomic (mean -0.050; 95% CI [-0.084, -0.017]), and resistance gene (mean -0.13; 95% CI [-0.17, -0.099]) β-diversity decreased in CTX-T infants compared to CTX-N infants. These results are consistent with persistent antibiotic selection pressure.

CONCLUSIONS: Cotrimoxazole prophylaxis in HEU infants decreased gut microbiome β-diversity and increased antibiotic resistance gene α-diversity and prevalence. Antibiotic resistance is a growing threat, especially in low- and middle-income countries where the higher perinatal HIV-exposure rates result in cotrimoxazole prophylaxis. Understanding effects from current HEU infant antibiotic prophylaxis guidelines will inform guideline revisions and efforts to reduce increasing antibiotic resistance.},
}

@article {pmid31832590,
year = {2019},
author = {Golder, AM and Steele, CW and Conn, D and MacKay, GJ and McMillan, DC and Horgan, PG and Roxburgh, CS and McSorley, ST},
title = {Effect of preoperative oral antibiotics in combination with mechanical bowel preparation on inflammatory response and short-term outcomes following left-sided colonic and rectal resections.},
journal = {BJS open},
volume = {3},
number = {6},
pages = {830-839},
doi = {10.1002/bjs5.50224},
pmid = {31832590},
issn = {2474-9842},
abstract = {Background: Preoperative oral antibiotics in addition to intravenous antibiotics and mechanical bowel preparation (MBP) may influence the gut microbiome and reduce both the postoperative systemic inflammatory response to surgery and postoperative infective complications following colorectal resection. This propensity score-matched study compared outcomes of patients undergoing left-sided colonic or rectal resection with or without a combination of oral antibiotics and MBP.

Methods: The addition of oral antibiotics and MBP to prophylactic intravenous antibiotics in left-sided colonic and rectal resections was introduced in 2015-2016 at a single institution. Propensity score matching was undertaken to compare the effects of oral antibiotics plus MBP versus neither oral antibiotics nor MBP on the postoperative systemic inflammatory response and short-term outcomes in patients undergoing left-sided colonic or rectal resection between 2013 and 2018.

Results: Of 396 patients who had propensity score matching for host, anaesthetic and operative factors, 204 matched patients were identified. The addition of oral antibiotics and MBP was associated with a significantly reduced postoperative inflammatory response (reduced postoperative Glasgow Prognostic Score) on day 3 (odds ratio (OR) 0·66, 95 per cent c.i. 0·44 to 0·99; P = 0·013) and day 4 (OR 0·46, 0·30 to 0·71; P = 0·001). Significantly reduced overall complications (OR 0·31, 0·17 to 0·56; P < 0·001), infective complications (OR 0·41, 0·22 to 0·77; P = 0·011), surgical-site infection (OR 0·37, 0·17 to 0·83; P = 0·024) and postoperative length of hospital stay (median 7 days versus 8 days in patients who had intravenous antibiotics alone; P = 0·050) were also observed.

Conclusion: Preoperative oral antibiotics and MBP in addition to prophylactic intravenous antibiotics were associated with a reduction in the postoperative systemic inflammatory response and postoperative complications in patients undergoing resectional left-sided colonic or rectal surgery.},
}

@article {pmid31832548,
year = {2019},
author = {Koo, SH and Chu, CW and Khoo, JJC and Cheong, M and Soon, GH and Ho, EXP and Law, NM and De Sessions, PF and Fock, KM and Ang, TL and Lee, EJD and Hsiang, JC},
title = {A pilot study to examine the association between human gut microbiota and the host's central obesity.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {3},
number = {6},
pages = {480-487},
doi = {10.1002/jgh3.12184},
pmid = {31832548},
issn = {2397-9070},
abstract = {Background and Aim: Perturbance in the composition of human gut microbiota has been associated with metabolic disorders such as obesity, diabetes mellitus, and insulin resistance. The objectives of this study are to examine the effects of ethnicity, central obesity, and recorded dietary components on potentially influencing the human gut microbiome. We hypothesize that these factors have an influence on the composition of the gut microbiome.

Methods: Subjects of Chinese (n = 14), Malay (n = 10), and Indian (n = 11) ancestry, with a median age of 39 years (range: 22-70 years old), provided stool samples for gut microbiome profiling using 16S rRNA sequencing and completed a dietary questionnaire. The serum samples were assayed for a panel of biomarkers (interleukin-6, tumor necrosis factor alpha, adiponectin, cleaved cytokeratin 18, lipopolysaccharide-binding protein, and limulus amebocyte lysate). Central obesity was defined by waist circumference cut-off values for Asians.

Results: There were no significant differences in Shannon alpha diversity for ethnicity and central obesity and no associations between levels of inflammatory cytokines and obesity. The relative abundances of Anaerofilum (P = 0.02), Gemellaceae (P = 0.02), Streptococcaceae (P = 0.03), and Rikenellaceae (P = 0.04) were significantly lower in the obese group. From principle coordinate analysis, the effects of the intake of fiber and fat/saturated fat were in contrast with each other, with clustering of obese individuals leaning toward fiber.

Conclusion: The study demonstrated that there were differences in the gut microbiome in obese individuals. Certain bacterial taxa were present in lower abundance in the group with central obesity. Fiber and fat/saturated fat diets were not the key determinants of central obesity.},
}

@article {pmid31832327,
year = {2019},
author = {Ma, ZS and Li, W},
title = {How and Why Men and Women Differ in Their Microbiomes: Medical Ecology and Network Analyses of the Microgenderome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {6},
number = {23},
pages = {1902054},
doi = {10.1002/advs.201902054},
pmid = {31832327},
issn = {2198-3844},
abstract = {Microgenderome or sexual dimorphism in microbiome refers to the bidirectional interactions between microbiotas, sex hormones, and immune systems, and it is highly relevant to disease susceptibility. A critical step in exploring microgenderome is to dissect the sex differences in key community ecology properties, which has not been systematically analyzed. This study aims at filling the gap by reanalyzing the Human Microbiome Project datasets with two objectives: (i) dissecting the sex differences in community diversity and their intersubject scaling, species composition, core/periphery species, and high-salience skeletons (species interactions); (ii) offering mechanistic interpretations for (i). Conceptually, the Vellend-Hanson synthesis of community ecology that stipulates selection, drift, speciation, and dispersal as the four processes driving community dynamics is followed. Methodologically, seven approaches reflecting the state-of-the-art research in medical ecology of human microbiomes are harnessed to achieve the objectives. It is postulated that the revealed microgenderome characteristics (categorized as seven aspects of differences/similarities) exert far reaching influences on disease susceptibility, and are primarily due to the sex difference in selection effects (deterministic fitness differences in microbial species and/or species interactions with each other or with their hosts), which are, in turn, shaped/modulated by host physiology (immunity, hormones, gut-brain communications, etc.).},
}

@article {pmid31832156,
year = {2019},
author = {Lumibao, CY and Borer, ET and Condon, B and Kinkel, L and May, G and Seabloom, EW},
title = {Site-specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales.},
journal = {Ecology and evolution},
volume = {9},
number = {21},
pages = {12231-12244},
doi = {10.1002/ece3.5711},
pmid = {31832156},
issn = {2045-7758},
abstract = {The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within-host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.},
}

@article {pmid31832110,
year = {2019},
author = {Abdelhamid, AG and El-Masry, SS and El-Dougdoug, NK},
title = {Probiotic Lactobacillus and Bifidobacterium strains possess safety characteristics, antiviral activities and host adherence factors revealed by genome mining.},
journal = {The EPMA journal},
volume = {10},
number = {4},
pages = {337-350},
doi = {10.1007/s13167-019-00184-z},
pmid = {31832110},
issn = {1878-5077},
abstract = {Background: Probiotics belonging to Lactobacillus and Bifidobacterium spp. have been exploited for their health benefits in treatment and prevention of many pathological conditions and promoting human health. Recent advances in understanding probiotics-human interaction through microbiome research in the context of various medical conditions suggest their provisional role in preventive, personalized, and predictive medicine. To streamline their application in disease prevention, development of personalized-based treatments, or their use as biomarkers for predictive diagnosis, in vitro screening for strains with potential probiotic properties should be performed. In this work, we aimed to emphasize the probiotic features of four Lactobacillus and two Bifidobacterium probiotic strains which showed antagonistic properties against microbial pathogens.

Methods: Firstly, cytotoxicity assessment of cell-free preparations from these strains was performed using a baby hamster kidney (BHK) cells and cell viability was measured by means of sulfo-rhodamine B stain. Secondly, Newcastle disease (ND) and infectious bursal disease (IBD) viruses which pose a great threat in infected poultry were used for assessing antiviral activity of probiotics. Thirdly, the genomes of six probiotic strains were used to identify genes encoding host adherence factors that mediate interaction with human tissues.

Results: Probiotic preparations exhibited insignificant toxicity as indicated by the high survival rate of BHK cells (surviving fraction varied from 0.82 to 0.99) as compared to the untreated control. Cell-free preparations of probiotics mixed with equal volume of ND and IBD viruses (106 and 104 Tissue Culture Infectious Dose 50, respectively) reduced the titer of ND and IBD viruses on chicken embryo fibroblast cells. Genome mining analysis revealed that the draft genomes of these strains were predicted to encode LPXTG-containing proteins, surface layer proteins, tight adherence pili, sortase-dependent pili, fibronectin, or collagen binding proteins and other factors that adhere to human tissues such as mucus. Such adherence factors enable probiotic bacteria to interact and colonize the host.

Conclusion: Taken together, safety privileges, antiviral activities, and genomically encoded host interaction factors confirmed probiotic features of the six probiotic strains and their potential in promoting human health.},
}

@article {pmid31832109,
year = {2019},
author = {Bubnov, R and Babenko, L and Lazarenko, L and Kryvtsova, M and Shcherbakov, O and Zholobak, N and Golubnitschaja, O and Spivak, M},
title = {Can tailored nanoceria act as a prebiotic? Report on improved lipid profile and gut microbiota in obese mice.},
journal = {The EPMA journal},
volume = {10},
number = {4},
pages = {317-335},
doi = {10.1007/s13167-019-00190-1},
pmid = {31832109},
issn = {1878-5077},
abstract = {Background: Microbiome modulation is a pillar intervention to treat metabolic syndrome, prestages, and cascade of related pathologies such as atherosclerosis, among others. Lactobacillus and Bifidobacterium probiotic strains demonstrate efficacy to reduce obesity, dyslipidemia, and improve metabolic health. Novel prebiotic substances composed with known probiotics may strongly synergize health benefits to the host. The aim of this study was to evaluate beneficial effects of Lactobacillus and Bifidobacterium strains (probiotics) if composed with nanoceria (potential prebiotic) to reduce cholesterol levels and restore gut microbiota in obese mice.

Materials and Methods: Two lines of mice were used in the study: BALB/c mice (6-8 weeks, 18-24 g) and CBA mice (11-12 months, 20-26 g); experimental animals were fed by fat-enriched diet 3 weeks before the evaluation. Animals were divided into groups to test probiotic strains and nanoceria. All groups received probiotic strains orally and cerium dioxide orally or intravenously in various composition. A group of untreated animals was used as a control. Cholesterol level and gut microbiota of mice were studied.

Results: Cerium dioxide nanoparticles, probiotic strain L. casei ІМV В-7280, and composition B. animalis VKB/B. animalis VKL applied separately and in different combinations all reduced at different levels free and bound cholesterol in blood serum of mice fed by fat-enriched diet. The combination of 0.01 M nanoceria and probiotic strain L. casei ІМV В-7280 resulted in the fastest cholesterol level decrease in both young and mature animals. Oral administration of CeO2 applied alone reduced the number of microscopic fungi in the gut of mice and Gram-positive cocci (staphylococci and/or streptococci). Application of L. casei IMV B-7280 as a probiotic strain increased most significantly the number of lactobacilli and bifidobacteria in the gut of mice. The most significant normalization of gut microbiota was observed after oral administration of alternatively either L. casei IMV B-7280 + 0.1 M CeO2 or L. casei IMV B-7280 + 0.01 M CeO2.

Conclusion: Dietary application of nanoceria combined with probiotic strains L. casei IMV B-7280, B. animalis VKB, and B. animals VKL has significantly reduced both free and bound cholesterol levels in serum. Simultaneous administration of probiotics and cerium nanoparticles as a prebiotic, in various combinations, significantly enhanced positive individual effects of them on the gut microbiota spectrum. The presented results provide novel insights into mechanisms behind nutritional supplements and open new perspectives for application of probiotics combined with substances demonstrating prebiotic qualities benefiting, therefore, the host health. Follow-up translational measures are discussed to bring new knowledge from lab to the patient. If validated in a large-scale clinical study, this approach might be instrumental for primary and secondary prevention in obese individual and patients diagnosed with diabetes. To this end, individualized prediction and treatments tailored to the person are strongly recommended to benefit the health condition of affected individuals.},
}

@article {pmid31832105,
year = {2019},
author = {Liang, D and Leung, RK and Guan, W and Au, WW},
title = {Correction to: Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities.},
journal = {Gut pathogens},
volume = {11},
number = {},
pages = {57},
doi = {10.1186/s13099-019-0339-0},
pmid = {31832105},
issn = {1757-4749},
abstract = {[This corrects the article DOI: 10.1186/s13099-018-0230-4.].},
}

@article {pmid31832051,
year = {2019},
author = {Kim, MJ and Do, H and Cho, G and Jeong, RD and Kwak, YS},
title = {Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit.},
journal = {The plant pathology journal},
volume = {35},
number = {6},
pages = {705-711},
doi = {10.5423/PPJ.NT.08.2019.0216},
pmid = {31832051},
issn = {1598-2254},
abstract = {Understanding the microbial community and function are crucial knowledge for crop management. In this study, bacterial and fungal community structures both rhizosphere and endosphere in kiwifruit were analyzed to gain our knowledge in kiwifruit microbiome. Microbial community in rhizosphere was less variation than endosphere community. Functional prediction results demonstrated that abundance of saprotrophic fungi was similar in both rhizosphere and endosphere, but potential pathogenic fungi was more abundance in endosphere than in rhizosphere. This finding suggested that maintain healthy soil is the first priority to protect the host plant against biotic stresses.},
}

@article {pmid31832000,
year = {2019},
author = {Czaja, AJ},
title = {Examining pathogenic concepts of autoimmune hepatitis for cues to future investigations and interventions.},
journal = {World journal of gastroenterology},
volume = {25},
number = {45},
pages = {6579-6606},
doi = {10.3748/wjg.v25.i45.6579},
pmid = {31832000},
issn = {2219-2840},
abstract = {Multiple pathogenic mechanisms have been implicated in autoimmune hepatitis, but they have not fully explained susceptibility, triggering events, and maintenance or escalation of the disease. Furthermore, they have not identified a critical defect that can be targeted. The goals of this review are to examine the diverse pathogenic mechanisms that have been considered in autoimmune hepatitis, indicate investigational opportunities to validate their contribution, and suggest interventions that might evolve to modify their impact. English abstracts were identified in PubMed by multiple search terms. Full length articles were selected for review, and secondary and tertiary bibliographies were developed. Genetic and epigenetic factors can affect susceptibility by influencing the expression of immune regulatory genes. Thymic dysfunction, possibly related to deficient production of programmed cell death protein-1, can allow autoreactive T cells to escape deletion, and alterations in the intestinal microbiome may help overcome immune tolerance and affect gender bias. Environmental factors may trigger the disease or induce epigenetic changes in gene function. Molecular mimicry, epitope spread, bystander activation, neo-antigen production, lymphocytic polyspecificity, and disturbances in immune inhibitory mechanisms may maintain or escalate the disease. Interventions that modify epigenetic effects on gene expression, alter intestinal dysbiosis, eliminate deleterious environmental factors, and target critical pathogenic mechanisms are therapeutic possibilities that might reduce risk, individualize management, and improve outcome. In conclusion, diverse pathogenic mechanisms have been implicated in autoimmune hepatitis, and they may identify a critical factor or sequence that can be validated and used to direct future management and preventive strategies.},
}

@article {pmid31831775,
year = {2019},
author = {Rosado, D and Xavier, R and Severino, R and Tavares, F and Cable, J and Pérez-Losada, M},
title = {Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax).},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18946},
doi = {10.1038/s41598-019-55314-4},
pmid = {31831775},
issn = {2045-2322},
abstract = {The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens. Infectious diseases are one of the main constraints to aquaculture growth leading to huge economic losses. Despite their negative impacts on microbial diversity and overall fish health, antibiotics are still the method of choice to treat many such diseases. Here, we use 16 rRNA V4 metataxonomics to study over a 6 week period the dynamics of the gill and skin microbiomes of farmed seabass before, during and after a natural disease outbreak and subsequent antibiotic treatment with oxytetracycline. Photobacterium damselae was identified as the most probable causative agent of disease. Both infection and antibiotic treatment caused significant, although asymmetrical, changes in the microbiome composition of the gills and skin. The most dramatic changes in microbial taxonomic abundance occurred between healthy and diseased fish. Disease led to a decrease in the bacterial core diversity in the skin, whereas in the gills there was both an increase and a shift in core diversity. Oxytetracycline caused a decrease in core diversity in the gill and an increase in the skin. Severe loss of core diversity in fish mucosae demonstrates the disruptive impact of disease and antibiotic treatment on the microbial communities of healthy fish.},
}

@article {pmid31831639,
year = {2019},
author = {Guo, CJ and Allen, BM and Hiam, KJ and Dodd, D and Van Treuren, W and Higginbottom, S and Nagashima, K and Fischer, CR and Sonnenburg, JL and Spitzer, MH and Fischbach, MA},
title = {Depletion of microbiome-derived molecules in the host using Clostridium genetics.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6471},
pages = {},
doi = {10.1126/science.aav1282},
pmid = {31831639},
issn = {1095-9203},
abstract = {The gut microbiota produce hundreds of molecules that are present at high concentrations in the host circulation. Unraveling the contribution of each molecule to host biology remains difficult. We developed a system for constructing clean deletions in Clostridium spp., the source of many molecules from the gut microbiome. By applying this method to the model commensal organism Clostridium sporogenes, we knocked out genes for 10 C. sporogenes-derived molecules that accumulate in host tissues. In mice colonized by a C. sporogenes for which the production of branched short-chain fatty acids was knocked out, we discovered that these microbial products have immunoglobulin A-modulatory activity.},
}

@article {pmid31831617,
year = {2019},
author = {Williams, AN and MacLea, KS},
title = {Draft Genome Sequence of Dermacoccus nishinomiyaensis TSA37, Isolated from Wood Ash.},
journal = {Microbiology resource announcements},
volume = {8},
number = {50},
pages = {},
doi = {10.1128/MRA.01370-19},
pmid = {31831617},
issn = {2576-098X},
abstract = {Dermacoccus nishinomiyaensis is a common bacterial resident of the human skin microbiome, among other environments. D. nishinomiyaensis strain TSA37 was isolated from the ash pan of a residential wood pellet stove. A genome assembly of 3,130,592 bp was generated, with an N50 value of 197,547 bp and a calculated G+C content of 69.01%.},
}

@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},
doi = {10.1186/s40168-019-0762-y},
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 {pmid31830335,
year = {2019},
author = {Hong, AS and Yu, WY and Hong, JM and Cross, CL and Azab, M and Ohning, G and Jayaraj, M},
title = {PROTON PUMP INHIBITOR IN UPPER GASTROINTESTINAL FECAL MICROBIOTA TRANSPLANT: A SYSTEMATIC REVIEW AND ANALYSIS.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.14958},
pmid = {31830335},
issn = {1440-1746},
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is used in recurrent Clostridioides difficile infections. However, protocols are facility dependent, and one variable is whether pre-procedural proton pump inhibitors (PPIs) are given. In theory, PPIs reduce acidity and protect the transplanted microbiome for the most potent dose. We conducted a systematic review to study the effect of PPIs on FMT delivered by upper gastrointestinal (GI) routes.

METHODS: We searched Pubmed/Medline, Cochrane Library, Embase, Scopus, and Web of Science through December 16th, 2018 using variations of keywords "fecal microbiota transplant" and "Clostridium difficile infection". Two authors independently reviewed 4210 results and found 11 qualifying studies with data on upper GI FMT, use of PPIs, and the rate of treatment failure at follow-up.

RESULTS: Of 233 included patients, treatment failure occurred in 20.6% of those with use of PPIs versus 22.6% in the group without (RR 0.91; CI 0.56-1.50). Limitations include the lack of studies directly comparing outcomes based on use of PPIs, and inability to control for possible confounders such as chronic PPI use, amount of stool transplanted, and pre-FMT antibiotics.

CONCLUSIONS: We did not find evidence supporting a clinically significant benefit from routine use of PPIs in FMT protocol. It is possible that the theoretical benefit from improved survival of transplanted microbiota is offset by negative effects on the microbiome. We suggest that routine use of PPIs in upper GI FMT be reconsidered. Further investigation is needed to optimize protocols for safety and efficacy.},
}

@article {pmid31830254,
year = {2019},
author = {Pretorius, IS},
title = {Tasting the terroir of wine yeast innovation.},
journal = {FEMS yeast research},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsyr/foz084},
pmid = {31830254},
issn = {1567-1364},
abstract = {Wine is an archetypal traditional fermented beverage with strong territorial and socio-cultural connotations. Its 7,000-year history is patterned by a tradition of innovation. Every value-adding innovation - whether in the vineyard, winery, supply chain or marketplace - that led to the invention of a new tradition spurred progress and created a brighter future from past developments. In a way, wine traditions can be defined as remembered innovations from the distant past - inherited knowledge and wisdom that withstood the test of time. Therefore, it should not be assumed a priori that tradition and innovation are polar opposites. The relations between the forces driven by the anchors of tradition and the wings of innovation do not necessarily involve displacement, conflict or exclusiveness. Innovation can strengthen wine tradition, and the reinvention of a tradition-bound practice, approach or concept can foster innovation. In cases where a paradigm-shifting innovation disrupts a tradition, the process of such an innovation transitioning into a radically-new tradition can become protracted while proponents of divergent opinions duke it out. Sometimes these conflicting opinions are based on fact, and sometimes not. The imperfections of such a debate between the 'ancients' and the 'moderns' can, from time to time, obscure the line between myth and reality. Therefore, finding the right balance between traditions worth keeping and innovations worth implementing can be complex. The intent here is to harness the creative tension between science fiction and science fact when innovation's first-principles challenge the status quo by re-examining the foundational principles about a core traditional concept, such as terroir. Poignant questions are raised about the importance of the terroir (biogeography) of yeasts and the value of the microbiome of grapes to wine quality. This article imagines a metaphorical terroir free from cognitive biases where diverse perspectives can converge to uncork the effervescent power of territorial yeast populations as well as 'nomadic' yeast starter cultures. At the same time, this paper also engages in mental time-travel. A future scenario is imagined, explored, tested and debated where terroir-less yeast avatars are equipped with designer genomes to safely and consistently produce, individually or in combination with region-specific wild yeasts and or other starter cultures, high-quality wine according to the preferences of consumers in a range of markets. The purpose of this review is to look beyond the horizon and to synthesise a link between what we know now and what could be. This article informs readers where to look without suggesting what they must see as a way forward. In the context of one of the world's oldest fermentation industries - steeped in a rich history of tradition and innovation - the mantra here is: respect the past, lead the present, and secure the future of wine.},
}

@article {pmid31830087,
year = {2019},
author = {Abdo, Z and LeCureux, J and LaVoy, A and Eklund, B and Ryan, EP and Dean, GA},
title = {Impact of oral probiotic Lactobacillus acidophilus vaccine strains on the immune response and gut microbiome of mice.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225842},
doi = {10.1371/journal.pone.0225842},
pmid = {31830087},
issn = {1932-6203},
abstract = {The potential role of probiotic bacteria as adjuvants in vaccine trials led to their use as nonparenteral live mucosal vaccine vectors. Yet, interactions between these vectors, the host and the microbiome are poorly understood. This study evaluates impact of three probiotic, Lactobacillus acidophilus, vector strains, and their interactions with the host's immune response, on the gut microbiome. One strain expressed the membrane proximal external region from HIV-1 (MPER). The other two expressed MPER and either secreted interleukin-1ß (IL-1ß) or expressed the surface flagellin subunit C (FliC) as adjuvants. We also used MPER with rice bran as prebiotic supplement. We observed a strain dependent, differential effect suggesting that MPER and IL-1β induced a shift of the microbiome while FliC had minimal impact. Joint probiotic and prebiotic use resulted in a compound effect, highlighting a potential synbiotic approach to impact efficacy of vaccination. Careful consideration of constitutive adjuvants and use of prebiotics is needed depending on whether or not to target microbiome modulation to improve vaccine efficacy. No clear associations were observed between total or MPER-specific IgA and the microbiome suggesting a role for other immune mechanisms or a need to focus on IgA-bound, resident microbiota, most affected by an immune response.},
}

@article {pmid31830061,
year = {2019},
author = {Masha, SC and Owuor, C and Ngoi, JM and Cools, P and Sanders, EJ and Vaneechoutte, M and Crucitti, T and de Villiers, EP},
title = {Comparative analysis of the vaginal microbiome of pregnant women with either Trichomonas vaginalis or Chlamydia trachomatis.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225545},
doi = {10.1371/journal.pone.0225545},
pmid = {31830061},
issn = {1932-6203},
abstract = {BACKGROUND: Although the significance of the human vaginal microbiome for health and disease is increasingly acknowledged, there is paucity of data on the differences in the composition of the vaginal microbiome upon infection with different sexually transmitted pathogens.

METHOD: The composition of the vaginal bacterial community of women with Trichomonas vaginalis (TV, N = 18) was compared to that of women with Chlamydia trachomatis (CT, N = 14), and to that of controls (N = 21) (women negative for TV, CT and bacterial vaginosis). The vaginal bacterial composition was determined using high throughput sequencing with the Ion 16S metagenomics kit of the variable regions 2, 4 and 8 of the bacterial 16S ribosomal RNA gene from the vaginal swab DNA extract of the women. QIIME and R package "Phyloseq" were used to assess the α- and β-diversity and absolute abundance of the 16S rRNA gene per sample in the three groups. Differences in taxa at various levels were determined using the independent T-test.

RESULTS: A total of 545 operational taxonomic units (OTUs) were identified in all the three groups of which 488 occurred in all three groups (core OTUs). Bacterial α-diversity, by both Simpson's and Shannon's indices, was significantly higher, (p = 0.056) and (p = 0.001) respectively, among women with either TV or CT than among controls (mean α-diversity TV-infected > CT-infected > Controls). At the genus level, women infected with TV had a significantly (p < 0.01) higher abundance of Parvimonas and Prevotella species compared to both controls and CT-infected women, whereas women infected with CT had a significantly (p < 0.05) higher abundance of Anaerococcus, Collinsella, Corynebacterium and Dialister.

CONCLUSION: The vaginal microbiomes of TV and CT-infected women were markedly different from each other and from women without TV and CT. Future studies should determine whether the altered microbiomes are merely markers of disease, or whether they actively contribute to the pathology of the two genital infections.},
}

@article {pmid31830054,
year = {2019},
author = {Jiang, X and Hall, AB and Xavier, RJ and Alm, EJ},
title = {Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0223680},
doi = {10.1371/journal.pone.0223680},
pmid = {31830054},
issn = {1932-6203},
abstract = {Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method that enables the identification of the mobilizable unit of MGEs. We curated a database of 5,219 putative MGEs encompassing seven MGE classes called ImmeDB. We observed that many MGEs carry genes that could confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Horizontal transfer of MGEs is extensive within phyla but rare across phyla, supporting phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future studies on the gut microbiome and MGE communities.},
}

@article {pmid31829366,
year = {2019},
author = {Chen, Y and Guo, KM and Nagy, T and Guo, TL},
title = {Chronic oral exposure to glycated whey proteins increases survival of aged male NOD mice with autoimmune prostatitis by regulating the gut microbiome and anti-inflammatory responses.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9fo01740b},
pmid = {31829366},
issn = {2042-650X},
abstract = {Glycated whey proteins have been shown to be protective against type 1 diabetes in our previous studies, suggesting their potential application as medical food. To determine if the protection could be extended to other autoimmune diseases, aged male non-obese diabetic (NOD) mice that develop a wide spectrum of autoimmune pathologies, including spontaneous autoimmune prostatitis, were used. After a 6-month oral exposure to whey protein-derived early glycation products (EGPs), EGP-treated NOD mice had an increased survival rate, decreased macrophage infiltration in the anterior lobe and decreased inflammation in the prostate when compared to the mice that received non-reacted controls. The systemic immunity was regulated towards anti-inflammation, evidenced by an increase in serum IL-10 level and decreases in total splenocytes, splenic M1 macrophages, CD4+ T cells, CD8+ T cells and B cells. Consistent with an overall anti-inflammatory status, the gut microbiome was altered in abundance but not diversity, with increased Allobaculum, Anaerostipes, Bacteroides, Parabacteroides and Prevotella and decreased Adlercreutzia and Roseburia at the genus level. Moreover, increased Bacteroides acidifaciens correlated with most of the immune parameters measured. Collectively, chronic oral exposure to EGPs produced an anti-inflammatory effect in aged male NOD mice, which might contribute to the protective effects against spontaneous autoimmune prostatitis and/or other organ specific autoimmune diseases.},
}

@article {pmid31829172,
year = {2019},
author = {Pierce, D and Merone, L and Lewis, C and Rahman, T and Croese, J and Loukas, A and McDonald, M and Giacomin, P and McDermott, R},
title = {Safety and tolerability of experimental hookworm infection in humans with metabolic disease: study protocol for a phase 1b randomised controlled clinical trial.},
journal = {BMC endocrine disorders},
volume = {19},
number = {1},
pages = {136},
doi = {10.1186/s12902-019-0461-5},
pmid = {31829172},
issn = {1472-6823},
support = {NA//AITHM/ ; NA//Far North Queensland Hospital Foundation/ ; },
abstract = {BACKGROUND: Abdominal obesity and presence of the metabolic syndrome (MetS) significantly increase the risk of developing diseases such as Type 2 diabetes mellitus (T2DM) with escalating emergence of MetS and T2DM constituting a significant public health crisis worldwide. Lower prevalence of inflammatory and metabolic diseases such as T2DM in countries with higher incidences of helminth infections suggested a potential role for these parasites in the prevention and management of certain diseases. Recent studies confirmed the potential protective nature of helminth infection against MetS and T2DM via immunomodulation or, potentially, alteration of the intestinal microbiota. This Phase 1b safety and tolerability trial aims to assess the effect of inoculation with helminths on physical and metabolic parameters, immune responses, and the microbiome in otherwise healthy women and men.

METHODS: Participants eligible for inclusion are adults aged 18-50 with central obesity and a minimum of one additional feature of MetS recruited from the local community with a recruitment target of 54. In a randomised, double-blind, placebo-controlled design, three groups will receive either 20 or 40 stage three larvae of the human hookworm Necator americanus or a placebo. Eligible participants will provide blood and faecal samples at their baseline and 6-monthly assessment visits for a total of 24 months with an optional extension to 36 months. During each scheduled visit, participants will also undergo a full physical examination and complete diet (PREDIMED), physical activity, and patient health (PHQ-9) questionnaires. Outcome measurements include tolerability and safety of infection with Necator americanus, changes in metabolic and immunological parameters, and changes in the composition of the faecal microbiome.

DISCUSSION: Rising cost of healthcare associated with obesity-induced metabolic diseases urgently calls for new approaches in disease prevention. Findings from this trial will provide valuable information regarding the potential mechanisms by which hookworms, potentially via alterations in the microbiota, may positively influence metabolic health.

TRIAL REGISTRATION: The protocol was registered on ANZCTR.org.au on 05 June 2017 with identifier ACTRN12617000818336. Alternatively, a Google search using the above trial registration number will yield a direct link to the trial protocol within the ANZCTR website.},
}

@article {pmid31828683,
year = {2019},
author = {Ebrahimzadeh Leylabadlo, H and Ghotaslou, R and Samadi Kafil, H and Feizabadi, MM and Moaddab, SY and Farajnia, S and Sheykhsaran, E and Sanaie, S and Shanehbandi, D and Bannazadeh Baghi, H},
title = {Non-alcoholic fatty liver diseases: from role of gut microbiota to microbial-based therapies.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10096-019-03746-1},
pmid = {31828683},
issn = {1435-4373},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is the well-known disease of the liver in adults and children throughout the world. The main manifestations related to NAFLD are an unusual storage of lipid in hepatocytes (hepatic steatosis) and progression of inflammation for non-alcoholic steatohepatitis (NASH). NAFLD is described as a multifactorial complication due to the genetic predisposition, metabolic functions, inflammatory, gut microbiota (GM), and environmental factors. The GM dysregulation among these factors is correlated to NAFLD development. In recent decades, advanced microbial profiling methods are continuing to shed light on the nature of the changes in the GM caused by NASH and NAFLD. In the current review, we aim to perform a literature review in different library databases and electronic searches (Science Direct, PubMed, and Google Scholar) which were randomly obtained. This will be done in order to provide an overview of the relation between GM and NAFLD, and the role of prebiotics, probiotics, and fecal microbiota transplantation (FMT), as potential therapeutic challenges for NAFLD.},
}

@article {pmid31828607,
year = {2019},
author = {Berkes, E and Liao, YH and Neef, D and Grandalski, M and Monsul, N},
title = {Potentiated In Vitro Probiotic Activities of Lactobacillus fermentum LfQi6 Biofilm Biomass Versus Planktonic Culture.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12602-019-09624-8},
pmid = {31828607},
issn = {1867-1314},
support = {QI2019//Quorum Innovations LLC/ ; },
abstract = {In this study, we describe enhanced in vitro probiotic activities of preformed biofilms versus planktonic cultures of Lactobacillus fermentum LfQi6 (LfQi6), a lactic acid bacterium (LAB) isolated from the human microbiome. These evaluations are used to help predict host in vivo probiotic benefits and therefore indicate that LfQi6 may provide significant probiotic benefits in the human host when administered as preformed biofilms rather than as planktonic cultures. Specifically, LfQi6 biofilms demonstrated improved in vitro performance versus LfQi6 planktonic cultures for host gastrointestinal survival and engraftment, strain-specific antimicrobial and anti-biofilm activity against clinically significant pathogens, concurrent promotion of beneficial gastrointestinal commensal biofilms, beneficial commensal enzyme activities, and host cellular-protective glutathione antioxidant activity. Evaluation of LfQi6 according to the European Food Safety Authority (EFSA 2007, 2012, 2015) Guidelines and Joint FAO/WHO Expert Consultation on Evaluation of Health and Nutritional Properties of Probiotics in Food Evaluation of Probiotics in Food (FAO/WHO, 2002) demonstrates strain safety. In summary, in vitro evaluation of Lact. fermentum LfQi6 demonstrates significant evidence for strain-specific probiotic characteristics and safety. Moreover, strain-specific as well as biofilm-phenotype-specific benefits demonstrated in vitro furthermore suggest that in vivo use of LfQi6 biofilm biomass may be of greater benefit to the human host than the use of standard planktonic cultures. This concept - potentiating probiotic benefits through the use of preformed commensal biofilms - is novel and may serve to further broaden the application of microbial biofilms to human health.},
}

@article {pmid31828407,
year = {2019},
author = {Paddock, MB and Fernández-Bayo, JD and VanderGheynst, JS},
title = {The effect of the microalgae-bacteria microbiome on wastewater treatment and biomass production.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10246-x},
pmid = {31828407},
issn = {1432-0614},
support = {1438211//National Science Foundation/ ; ARV-15-008//California Energy Commission/ ; },
abstract = {The use of microalgae for wastewater treatment has been proposed as a cost-effective method to produce biofuels while remediating waste streams. This study examined the microalgae biomass production rate, wastewater treatment efficiency, and prokaryotic organism microbiome associated with microalgae Chlorella sorokiniana cultivated on anaerobic digestate effluent. Final microalgae biomass concentrations from nine photobioreactors were highly variable and had values that ranged between 0.14 g/L and 0.90 g/L. Nutrient removal efficiencies for TN (total nitrogen), N-NH4 (ammonium nitrogen), and COD (chemical oxygen demand) ranged from 34% to 67%, 65% to 97%, and-60% to 14%, respectively. Analysis of individual OTUs (operational taxonomic units) from the microbial community revealed that microalgae biomass concentrations were significantly correlated with the relative abundance of OTUs in the genus Pusillimonas. Predictive metagenomic analyses identified additional correlations associated with biomass production and nutrient removal. These results suggest that the microbial community present during microalgae cultivation on wastewater can impact the performance of the system for biomass production and wastewater treatment.},
}

@article {pmid31828074,
year = {2019},
author = {Joyce, SA and Kamil, A and Fleige, L and Gahan, CGM},
title = {The Cholesterol-Lowering Effect of Oats and Oat Beta Glucan: Modes of Action and Potential Role of Bile Acids and the Microbiome.},
journal = {Frontiers in nutrition},
volume = {6},
number = {},
pages = {171},
doi = {10.3389/fnut.2019.00171},
pmid = {31828074},
issn = {2296-861X},
abstract = {Consumption of sufficient quantities of oat products has been shown to reduce host cholesterol and thereby modulate cardiovascular disease risk. The effects are proposed to be mediated by the gel-forming properties of oat β-glucan which modulates host bile acid and cholesterol metabolism and potentially removes intestinal cholesterol for excretion. However, the gut microbiota has emerged as a major factor regulating cholesterol metabolism in the host. Oat β-glucan has been shown to modulate the gut microbiota, particularly those bacterial species that influence host bile acid metabolism and production of short chain fatty acids, factors which are regulators of host cholesterol homeostasis. Given a significant role for the gut microbiota in cholesterol metabolism it is likely that the effects of oat β-glucan on the host are multifaceted and involve regulation of microbe-host interactions at the gut interface. Here we consider the potential for oat β-glucan to influence microbial populations in the gut with potential consequences for bile acid metabolism, reverse cholesterol transport (RCT), short-chain fatty acid (SCFA) production, bacterial metabolism of cholesterol and microbe-host signaling.},
}

@article {pmid31828025,
year = {2019},
author = {Dandrieux, JRS and Mansfield, CS},
title = {Chronic Enteropathy In Canines: Prevalence, Impact And Management Strategies.},
journal = {Veterinary medicine (Auckland, N.Z.)},
volume = {10},
number = {},
pages = {203-214},
doi = {10.2147/VMRR.S162774},
pmid = {31828025},
issn = {2230-2034},
abstract = {In this article, the studies about the prevalence of chronic enteropathy are reviewed as well as the information regarding short- and long-term prognosis for dogs treated with the three most common therapies; these include dietary modification, antibiotics, and immunosuppressants. Although the data available are limited, most studies support a good to excellent long-term response in dogs that have a successful food trial, whereas the response is poor with antibiotics or on-going treatment is required to retain remission. There is a risk of antimicrobial resistance developing with inappropriate use of antimicrobials such as in these situations. The published information highlights the need for alternative strategies to antibiotic treatment to manipulate the GI microbiome, and in the final part of this article studies on the use of probiotic for the treatment of chronic enteropathy are reviewed.},
}

@article {pmid31827982,
year = {2019},
author = {Abid, MB and Shah, NN and Maatman, TC and Hari, PN},
title = {Gut microbiome and CAR-T therapy.},
journal = {Experimental hematology & oncology},
volume = {8},
number = {},
pages = {31},
doi = {10.1186/s40164-019-0155-8},
pmid = {31827982},
issn = {2162-3619},
abstract = {Considerable progress has been made in cancer therapeutics recently with targeted strategies that are efficacious and less toxic. Immunotherapy and chimeric antigen receptor (CAR) T-cells are increasingly being evaluated in a variety of tumors in the relapsed/refractory as well as frontline disease settings, predominantly in hematologic malignancies (HM). Despite impressive outcomes in select patients, there remains significant heterogeneity in clinical response to CAR T-cells. The gut microbiome has emerged as one of the key host factors that could potentially be modulated to enhance responses to immunotherapy. Several recent human studies receiving immunotherapy showed a significantly superior response and survival in patients with the more diverse gut microbiome. Currently, it is unknown if gut microbiota modulates anti-tumor responses to CAR T-cells. Based on molecular and immunological understanding, we hypothesize that strategically manipulating gut microbiota may enhance responses to CAR T-cells. In this review, we further discuss resistance mechanisms to CAR T-cells in HM, potential approaches to overcome resistance by harnessing gut microbiota and other related novel strategies.},
}

@article {pmid31827811,
year = {2019},
author = {Rapp, R},
title = {On mycohuman performances: fungi in current artistic research.},
journal = {Fungal biology and biotechnology},
volume = {6},
number = {},
pages = {22},
doi = {10.1186/s40694-019-0085-6},
pmid = {31827811},
issn = {2054-3085},
abstract = {This review reflects several artists and their artistic research in the field of hybrid art, bio art, or science art, working with Fungi as both subject matter and medium. The work of Saša Spačal, Tarsh Bates and Theresa Schubert is not representational in the manner of traditional fine art, but works rather through performative, multidisciplinary and research-based strategies to produce artwork through fungal material as such. My research results are based on the series "Nonhuman subjectivities" and "Nonhuman agents" that Christian de Lutz and I conceived and realized at Art Laboratory Berlin (2016-18) in various formats-exhibitions, workshops, lectures and a conference. The work of Saša Spačal and her colleagues involves creating interactive situations of symbiosis between the fungal and the human. An example of this is Myconnect, in which a biofeedback loop is related between the human participant and Oyster mushroom mycelia through a special encounter, which is mediated by non-linguistic forms of awareness and exchange-sonic, electronic and metabolic. Tarsh Bates' work with Candida albicans and Candida parapsilosis refers to a complex and intimate relation between the human and yeasts that form part of the human microbiome. Bates considers the relationship between humans and yeast as "CandidaHomo Ecologies" and sees both partners as equals. She explores this relationship through her work The Surface dynamics of adhesion, examines it from historical and metabolic levels through an installation that includes the live yeast growing on agar mixed with the artist's own blood. Theresa Schubert's installations and site-specific interventions treat living organisms, especially Fungi, as collaborators and co-creators. Her work Growing Geometries-Tattooing Mushrooms follows the morphological development of fungal fruiting bodies through the intervention of a tattoo. Her performative forest walks, especially the Forestal Psyche and also new actions for the "Mind the Fungi" project, engage the public in an intimate and multi sensory encounter with Fungi and their surrounding environment.},
}

@article {pmid31827639,
year = {2019},
author = {Lu, T and Chen, Y and Guo, Y and Sun, J and Shen, W and Yuan, M and Zhang, S and He, P and Jiao, X},
title = {Altered Gut Microbiota Diversity and Composition in Chronic Urticaria.},
journal = {Disease markers},
volume = {2019},
number = {},
pages = {6417471},
doi = {10.1155/2019/6417471},
pmid = {31827639},
issn = {1875-8630},
abstract = {Background: The pathogenesis of chronic urticaria (CU) is closely related to imbalances in immunity. The gastrointestinal microflora provides a vast and continuous stimulation for the immune system. However, the composition and diversity of gut microflora in CU patients are rarely reported.

Methods: 10 CU patients and 10 healthy individuals were selected in this study, and their intestinal microbiome was detected by 16S rRNA sequencing. The data were analyzed using R language software.

Results: 392 bacterial OTUs were common in the CU and healthy groups, but there were 159 OTUs particularly existing in the CU group, while 87 OTUs only were observed in healthy individuals. The bacterial diversity was reduced in CU patients compared with healthy individuals. The principal component analysis (PCA) and principal coordinate analysis (PCoA) revealed that the bacterial cluster in CU patients and the healthy controls were divided into different branches. Pathogenic strains including Escherichia coli were significantly higher in CU, while Faecalibacterium prausnitzii, Prevotella copri, and Bacteroides sp. were significantly lower in CU when compared with the healthy controls. CU patients with a high abundance of Escherichia coli had no ideal effect for probiotic therapy.

Conclusion: Our results demonstrated that the microbial composition was significantly different between CU patients and the healthy individual, which may be the reason leading to the various outcomes of probiotic treatment.},
}

@article {pmid31827247,
year = {2019},
author = {Cornuault, JK and Moncaut, E and Loux, V and Mathieu, A and Sokol, H and Petit, MA and De Paepe, M},
title = {The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0566-x},
pmid = {31827247},
issn = {1751-7370},
support = {FDT20170437017//Fondation pour la Recherche Médicale (Foundation for Medical Research in France)/ ; },
abstract = {Despite an overall temporal stability in time of the human gut microbiota at the phylum level, strong variations in species abundance have been observed. We are far from a clear understanding of what promotes or disrupts the stability of microbiome communities. Environmental factors, like food or antibiotic use, modify the gut microbiota composition, but their overall impacts remain relatively low. Phages, the viruses that infect bacteria, might constitute important factors explaining temporal variations in species abundance. Gut bacteria harbour numerous prophages, or dormant viruses, which can evolve to become ultravirulent phage mutants, potentially leading to important bacterial death. Whether such phenomenon occurs in the mammal's microbiota has been largely unexplored. Here we studied temperate phage-bacteria coevolution in gnotoxenic mice colonised with Roseburia intestinalis, a dominant symbiont of the human gut microbiota, and Escherichia coli, a sub-dominant member of the same microbiota. We show that R. intestinalis L1-82 harbours two active prophages, Jekyll and Shimadzu. We observed the systematic evolution in mice of ultravirulent Shimadzu phage mutants, which led to a collapse of R. intestinalis population. In a second step, phage infection drove the fast counter-evolution of host phage resistance mainly through phage-derived spacer acquisition in a clustered regularly interspaced short palindromic repeats array. Alternatively, phage resistance was conferred by a prophage originating from an ultravirulent phage with a restored ability to lysogenize. Our results demonstrate that prophages are a potential source of ultravirulent phages that can successfully infect most of the susceptible bacteria. This suggests that prophages can play important roles in the short-term temporal variations observed in the composition of the gut microbiota.},
}

@article {pmid31827191,
year = {2019},
author = {Kowalska-Duplaga, K and Gosiewski, T and Kapusta, P and Sroka-Oleksiak, A and Wędrychowicz, A and Pieczarkowski, S and Ludwig-Słomczyńska, AH and Wołkow, PP and Fyderek, K},
title = {Differences in the intestinal microbiome of healthy children and patients with newly diagnosed Crohn's disease.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18880},
doi = {10.1038/s41598-019-55290-9},
pmid = {31827191},
issn = {2045-2322},
support = {005790//Uniwersytet Jagielloński Collegium Medicum (Jagiellonian University Medical College)/ ; },
abstract = {The aetiology of inflammatory bowel diseases (IBD) seems to be strongly connected to changes in the enteral microbiome. The dysbiosis pattern seen in Crohn's disease (CD) differs among published studies depending on patients' age, disease phenotype and microbiome research methods. The aims was to investigate microbiome in treatment-naive paediatric patients to get an insight into its structure at the early stage of the disease in comparison to healthy. Stool samples were obtained from controls and newly diagnosed patients prior to any intervention. Microbiota was analysed by 16SrRNAnext-generation-sequencing (NGS). Differences in the within-sample phylotype richness and evenness (alpha diversity) were detected between controls and patients. Statistically significant dissimilarities between samples were present for all used metrics. We also found a significant increase in the abundance of OTUs of the Enterococcus genus and reduction in, among others, Bifidobacterium (B. adolescentis), Roseburia (R.faecis), Faecalibacterium (F. prausnitzii), Gemmiger (G. formicilis), Ruminococcus (R. bromii) and Veillonellaceae (Dialister). Moreover, differences in alpha and beta diversities in respect to calprotectin and PCDAI were observed: patients with calprotectin <100 µg/g and with PCDAI below 10 points vs those with calprotectin >100 µg/g and mild (10-27.7 points), moderate (27.5-40 points) or severe (>40 points) CD disease activity had higher richness and diversity of gut microbiota. The results of our study highlight reduced diversity and dysbiosis at the earliest stage of the disease. Microbial imbalance and low abundance of butyrate-producing bacteria, including Bifidobacterium adolescentis, may suggest benefits of microbial modification therapy.},
}

@article {pmid31827126,
year = {2019},
author = {Loo, WT and García-Loor, J and Dudaniec, RY and Kleindorfer, S and Cavanaugh, CM},
title = {Host phylogeny, diet, and habitat differentiate the gut microbiomes of Darwin's finches on Santa Cruz Island.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18781},
doi = {10.1038/s41598-019-54869-6},
pmid = {31827126},
issn = {2045-2322},
abstract = {Darwin's finches are an iconic example of an adaptive radiation with well-characterized evolutionary history, dietary preferences, and biogeography, offering an unparalleled opportunity to disentangle effects of evolutionary history on host microbiome from other factors like diet and habitat. Here, we characterize the gut microbiome in Darwin's finches, comparing nine species that occupy diverse ecological niches on Santa Cruz island. The finch phylogeny showed moderate congruence with the microbiome, which was comprised mostly of the bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria. Diet, as measured with stable isotope values and foraging observations, also correlated with microbiome differentiation. Additionally, each gut microbial community could easily be classified by the habitat of origin independent of host species. Altogether, these findings are consistent with a model of microbiome assembly in which environmental filtering via diet and habitat are primary determinants of the bacterial taxa present with lesser influence from the evolutionary history between finch species.},
}

@article {pmid31826975,
year = {2019},
author = {Elizaldi, SR and Verma, A and Walter, KA and Rolston, M and Dinasarapu, AR and Durbin-Johnson, BP and Settles, M and Kozlowski, PA and Raeman, R and Iyer, SS},
title = {Rectal Microbiome Composition Correlates with Humoral Immunity to HIV-1 in Vaccinated Rhesus Macaques.},
journal = {mSphere},
volume = {4},
number = {6},
pages = {},
doi = {10.1128/mSphere.00824-19},
pmid = {31826975},
issn = {2379-5042},
abstract = {The microbiome is an integral and dynamic component of the host and is emerging as a critical determinant of immune responses; however, its influence on vaccine immunogenicity is largely not well understood. Here, we examined the pivotal relationship between the mucosal microbiome and vaccine-induced immune responses by assessing longitudinal changes in vaginal and rectal microbiome profiles after intradermal immunization with a human immunodeficiency virus type 1 (HIV-1) DNA vaccine in adult rhesus macaques that received two prior DNA primes. We report that both vaginal and rectal microbiomes were dominated by Firmicutes but were composed of distinct genera, denoting microbiome specialization across mucosal tissues. Following immunization, the vaginal microbiome was resilient, except for a transient decrease in Streptococcus In contrast, the rectal microbiome was far more responsive to vaccination, exhibiting an increase in the ratio of Firmicutes to Bacteroidetes Within Bacteroidetes, multiple genera were significantly decreased, including Prevotella, Alloprevotella, Bacteroides, Acetobacteroides, Falsiporphyromonas, and Anaerocella. Decreased abundance of Prevotella correlated with induction of gut-homing α4β7+ effector CD4 T cells. Prevotella abundance also negatively correlated with rectal HIV-1 specific IgG levels. While rectal Lactobacillus was unaltered following DNA vaccination, baseline Lactobacillus abundance showed strong associations with higher rectal HIV-1 gp140 IgA induced following a protein boost. Similarly, the abundance of Clostridium in cluster IV was associated with higher rectal HIV-1 gp140 IgG responses. Collectively, these data reveal that the temporal stability of bacterial communities following DNA immunization is site dependent and highlight the importance of host-microbiome interactions in shaping HIV-1 vaccine responses. Our findings have significant implications for microbial manipulation as a strategy to enhance HIV vaccine-induced mucosal immunity.IMPORTANCE There is considerable effort directed toward evaluating HIV-1 vaccine platforms to select the most promising candidates for enhancing mucosal HIV-1 antibody. The most successful thus far, the RV144 trial provided partial protection due to waning HIV-1 antibody titers. In order to develop an effective HIV vaccine, it may therefore be important to understand how biological factors, such as the microbiome, modulate host immune responses. Furthermore, as intestinal microbiota antigens may generate antibodies cross-reactive to the HIV-1 envelope glycoprotein, understanding the relationship between gut microbiota composition and HIV-1 envelope antibody responses after vaccination is important. Here, we demonstrate for the first time in rhesus macaques that the rectal microbiome composition can influence HIV-1 vaccine immunogenicity, and we report temporal changes in the mucosal microbiome profile following HIV-1 vaccination. Our results could inform findings from the HIV Vaccine Trials Network (HVTN) vaccine studies and contribute to an understanding of how the microbiome influences HIV-1 antibody responses.},
}

@article {pmid31826255,
year = {2019},
author = {Jennings, A and Koch, M and Jensen, MK and Bang, C and Kassubek, J and Müller, HP and Nöthlings, U and Franke, A and Lieb, W and Cassidy, A},
title = {The role of the gut microbiome in the association between habitual anthocyanin intake and visceral abdominal fat in population-level analysis.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajcn/nqz299},
pmid = {31826255},
issn = {1938-3207},
abstract = {BACKGROUND: Flavonoid intake modifies the composition of the gut microbiome, which contributes to the metabolism of flavonoids. Few studies have examined the contribution of the gut microbiome to the health benefits associated with flavonoid intake.

OBJECTIVES: We aimed to examine associations between habitual intakes of flavonoid subclasses and MRI-determined visceral (VAT) and subcutaneous (SAT) adipose tissue. Uniquely, we also identified associations between the aforementioned measurements and gut microbiome composition sequenced from 16S ribosomal RNA genes.

METHODS: We undertook cross-sectional analyses of 618 men and women (n = 368 male), aged 25-83 y, from the PopGen cohort.

RESULTS: Higher intake of anthocyanins was associated with lower amounts of VAT [tertile (T)3-T1: -0.49 dm3; β: -8.9%; 95% CI: -16.2%, -1.1%; P = 0.03] and VAT:SAT ratio (T3-T1: -0.04; β: -7.1%; 95% CI: -13.5%, -0.3%; P = 0.03). Higher intakes of anthocyanin-rich foods were also inversely associated with VAT [quantile (Q)4-Q1: -0.39 dm3; β: -9.9%; 95% CI: -17.4%, -1.6%; P = 0.02] and VAT:SAT ratio (Q4-Q1: -0.04; β: -6.5%; 95% CI: -13.3%, -0.9%; P = 0.03). Participants with the highest intakes of anthocyanin-rich foods also had higher microbial diversity (Q4-Q1: β: 0.18; 95% CI: 0.06, 0.31; P < 0.01), higher abundances of Clostridiales (Q4-Q1: β: 449; 95% CI: 96.3, 801; P = 0.04) and Ruminococcaceae (Q4-Q1: β: 313; 95% CI: 33.6, 591; P = 0.04), and lower abundance of Clostridium XIVa (Q4-Q1: β: -41.1; 95% CI: -72.4, -9.8; P = 0.04). Participants with the highest microbial diversity, abundances of Clostridiales and Ruminococcaceae, and lower abundance of Clostridium XIVa had lower amounts of VAT. Up to 18.5% of the association between intake of anthocyanin-rich foods and VAT could be explained by the gut microbiome.

CONCLUSIONS: These novel data suggest that higher microbial diversity and abundance of specific taxa in the Clostridiales order may contribute to the association between higher intake of anthocyanins and lower abdominal adipose tissue.},
}

@article {pmid31825995,
year = {2019},
author = {Woloszynek, S and Mell, JC and Zhao, Z and Simpson, G and O'Connor, MP and Rosen, GL},
title = {Exploring thematic structure and predicted functionality of 16S rRNA amplicon data.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0219235},
doi = {10.1371/journal.pone.0219235},
pmid = {31825995},
issn = {1932-6203},
abstract = {Analysis of microbiome data involves identifying co-occurring groups of taxa associated with sample features of interest (e.g., disease state). Elucidating such relations is often difficult as microbiome data are compositional, sparse, and have high dimensionality. Also, the configuration of co-occurring taxa may represent overlapping subcommunities that contribute to sample characteristics such as host status. Preserving the configuration of co-occurring microbes rather than detecting specific indicator species is more likely to facilitate biologically meaningful interpretations. Additionally, analyses that use taxonomic relative abundances to predict the abundances of different gene functions aggregate predicted functional profiles across taxa. This precludes straightforward identification of predicted functional components associated with subsets of co-occurring taxa. We provide an approach to explore co-occurring taxa using "topics" generated via a topic model and link these topics to specific sample features (e.g., disease state). Rather than inferring predicted functional content based on overall taxonomic relative abundances, we instead focus on inference of functional content within topics, which we parse by estimating interactions between topics and pathways through a multilevel, fully Bayesian regression model. We apply our methods to three publicly available 16S amplicon sequencing datasets: an inflammatory bowel disease dataset, an oral cancer dataset, and a time-series dataset. Using our topic model approach to uncover latent structure in 16S rRNA amplicon surveys, investigators can (1) capture groups of co-occurring taxa termed topics; (2) uncover within-topic functional potential; (3) link taxa co-occurrence, gene function, and environmental/host features; and (4) explore the way in which sets of co-occurring taxa behave and evolve over time. These methods have been implemented in a freely available R package: https://cran.r-project.org/package=themetagenomics, https://github.com/EESI/themetagenomics.},
}

@article {pmid31825981,
year = {2019},
author = {Gallet, A and Koubbi, P and Léger, N and Scheifler, M and Ruiz-Rodriguez, M and Suzuki, MT and Desdevises, Y and Duperron, S},
title = {Low-diversity bacterial microbiota in Southern Ocean representatives of lanternfish genera Electrona, Protomyctophum and Gymnoscopelus (family Myctophidae).},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0226159},
doi = {10.1371/journal.pone.0226159},
pmid = {31825981},
issn = {1932-6203},
abstract = {Myctophids are among the most abundant mesopelagic teleost fishes worldwide. They are dominant in the Southern Ocean, an extreme environment where they are important both as consumers of zooplankton as well as food items for larger predators. Various studies have investigated myctophids diet, but no data is yet available regarding their associated microbiota, despite that the significance of bacterial communities to fish health and adaptation is increasingly acknowledged. In order to document microbiota in key fish groups from the Southern Ocean, the bacterial communities associated with the gut, fin, gills and light organs of members of six species within the three myctophid genera Electrona, Protomyctophum and Gymnoscopelus were characterized using a 16S rRNA-based metabarcoding approach. Gut communities display limited diversity of mostly fish-specific lineages likely involved in food processing. Fin and skin communities display diversity levels and compositions resembling more those found in surrounding seawater. Community compositions are similar between genera Electrona and Protomyctophum, that differ from those found in Gymnoscopelus and in water. Low abundances of potentially light-emitting bacteria in light organs support the hypothesis of host production of light. This first description of myctophid-associated microbiota, and among the first on fish from the Southern Ocean, emphasizes the need to extend microbiome research beyond economically-important species, and start addressing ecologically-relevant species.},
}

@article {pmid31825967,
year = {2019},
author = {Foditsch, C and Pereira, RVV and Siler, JD and Altier, C and Warnick, LD},
title = {Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and genetic function of dairy calves.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0219635},
doi = {10.1371/journal.pone.0219635},
pmid = {31825967},
issn = {1932-6203},
abstract = {The increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), a single treatment of enrofloxacin, or a single treatment of tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sequencing was conducted. The effect of antibiotic treatment on each taxon and genetic functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher relative abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other study groups. The SEED database was used for genetic functional analyses, which showed that calves in the enrofloxacin group started with a higher relative abundance of "Resistance to antibiotics and toxic compounds" function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. "Resistance to Fluoroquinolones" and "Erythromycin resistance", of relevance given the study groups, were not statistically different in relative abundance between study groups. "Resistance to fluoroquinolones" increased during the study period regardless of study group. Despite small differences over the first weeks between study groups, at Day 112 the microbiota composition and genetic functional profile was similar among all study groups. In our study, enrofloxacin or tulathromycin had minimal impacts on the microbial composition and genetic functional microbiota of calves over the study period.},
}

@article {pmid31825517,
year = {2019},
author = {Moreira, SM and Mendes, TAO and Santanta, MF and Huws, SA and Creevey, CJ and Mantovani, HC},
title = {Genomic and gene expression evidence of nonribosomal peptide and polyketide production among ruminal bacteria: a potential role in niche colonization?.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz198},
pmid = {31825517},
issn = {1574-6941},
abstract = {Genomic and transcriptomic analyses were performed to investigate non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) in 310 genomes of ruminal/fecal microorganisms. One hundred and nineteen biosynthetic genes potentially encoding distinct NRPs and PKs were predicted in the ruminal microbial genomes and functional annotation separated these genes into 19 functional categories. The phylogenetic reconstruction of the 16S rRNA sequences coupled to the distribution of the three 'backbone' genes involved in NRPS and PKS biosynthesis suggested that these genes were not acquired through horizontal gene transfer. Metatranscriptomic analyses revealed that the predominant genes involved in the synthesis of nonribosomal peptides and polyketides were more abundant in sheep rumen datasets. Reads mapping to the NRPS and PKS biosynthetic genes were represented in the active ruminal microbial community, with transcripts being highly expressed in the bacterial community attached to perennial ryegrass, and following the main changes occurring between primary and secondary colonization of the forage incubated with ruminal fluid. This study is the first comprehensive characterization demonstrating the rich genetic capacity for NRPS and PKS biosynthesis within rumen bacterial genomes, which highlights the potential functional roles of secondary metabolites in the rumen ecosystem.},
}

@article {pmid31825516,
year = {2019},
author = {Küngas, K and Bahram, M and Põldmaa, K},
title = {Host tree organ is the primary driver of endophytic fungal community structure in a hemiboreal forest.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz199},
pmid = {31825516},
issn = {1574-6941},
abstract = {Despite numerous studies on plant endophytes, little is known about fungal communities associated with different aboveground tissues of living trees. We used high-throughput sequencing (HTS) to compare the diversity and community structure of fungi inhabiting leaves, branches and trunks of Alnus incana and Corylus avellana growing at three hemiboreal forest sites. Our analysis revealed that tree organ is the main determinant of the structure of fungal communities, while the effects of host species and locality remained secondary and negligible, respectively. The structure of fungal communities in trunks was the most distinct compared to that in leaves and branches. Foliar fungal communities were more similar within than between individual trees, implying that certain fungi may grow through parts of the tree crown. The weak effect of locality compared to host organs and species identity suggests that the variation in fungal community structure in the aboveground parts of trees depends mainly on deterministic factors rather than dispersal limitation.},
}

@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},
doi = {10.7717/peerj.8133},
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.

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.

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.

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 {pmid31824755,
year = {2019},
author = {Solovyev, MM and Kashinskaya, EN and Bochkarev, NA and Andree, KB and Simonov, E},
title = {The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes (Coregonus lavaretus): one story more.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e8005},
doi = {10.7717/peerj.8005},
pmid = {31824755},
issn = {2167-8359},
abstract = {In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a "large" form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a "small" form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3-V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria (57.0-84.0%) for both whitefish. Throughout the intestine of C. l. pidschian the dominant phyla in mucosa were Proteobacteria (38.8%) and Firmicutes (15.6%), whereas for C. l. pravdinellus-Tenericutes (49.6%) and Proteobacteria (28.1%). For both forms, the phylum Spirochaetes was found in a significant amount (20.0-25.0%) in the mucosa of the posterior intestine. While for the content obtained from anterior, middle and posterior intestines, the dominant bacterial phyla were the same as those described for mucosa from the same parts of the intestine for both whitefish. The bacterial community of the prey and environment was significantly different from bacterial communities found for all parts of the gut mucosa for both whitefish, with the exception of the mucosa of the cardiac stomach. According to PICRUSt the highest level of differences between whitefish at the L3 level were found for the intestinal mucosa (75.3%), whereas the lowest one was registered for stomach content (38.8%).},
}

@article {pmid31824677,
year = {2019},
author = {Danielsson, R and Lucas, J and Dahlberg, J and Ramin, M and Agenäs, S and Bayat, AR and Tapio, I and Hammer, T and Roslin, T},
title = {Compound- and context-dependent effects of antibiotics on greenhouse gas emissions from livestock.},
journal = {Royal Society open science},
volume = {6},
number = {10},
pages = {182049},
doi = {10.1098/rsos.182049},
pmid = {31824677},
issn = {2054-5703},
abstract = {The use of antibiotics in livestock production may trigger ecosystem disservices, including increased emissions of greenhouse gases. To evaluate this, we conducted two separate animal experiments, administering two widely used antibiotic compounds (benzylpenicillin and tetracycline) to dairy cows over a 4- or 5-day period locally and/or systemically. We then recorded enteric methane production, total gas production from dung decomposing under aerobic versus anaerobic conditions, prokaryotic community composition in rumen and dung, and accompanying changes in nutrient intake, rumen fermentation, and digestibility resulting from antibiotic administration. The focal antibiotics had no detectable effect on gas emissions from enteric fermentation or dung in aerobic conditions, while they decreased total gas production from anaerobic dung. Microbiome-level effects of benzylpenicillin proved markedly different from those previously recorded for tetracycline in dung, and did not differ by the mode of administration (local or systemic). Antibiotic effects on gas production differed substantially between dung maintained under aerobic versus anaerobic conditions and between compounds. These findings demonstrate compound- and context-dependent impacts of antibiotics on methane emissions and underlying processes, and highlight the need for a global synthesis of data on agricultural antibiotic use before understanding their climatic impacts.},
}

@article {pmid31824656,
year = {2019},
author = {Barton, W and O'Sullivan, O and Cotter, PD},
title = {Metabolic phenotyping of the human microbiome.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {},
doi = {10.12688/f1000research.19481.1},
pmid = {31824656},
issn = {2046-1402},
abstract = {The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.},
}

@article {pmid31824573,
year = {2019},
author = {Zhu, Q and Jiang, X and Zhu, Q and Pan, M and He, T},
title = {Graph Embedding Deep Learning Guides Microbial Biomarkers' Identification.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {1182},
doi = {10.3389/fgene.2019.01182},
pmid = {31824573},
issn = {1664-8021},
abstract = {The microbiome-wide association studies are to figure out the relationship between microorganisms and humans, with the goal of discovering relevant biomarkers to guide disease diagnosis. However, the microbiome data is complex, with high noise and dimensions. Traditional machine learning methods are limited by the models' representation ability and cannot learn complex patterns from the data. Recently, deep learning has been widely applied to fields ranging from text processing to image recognition due to its efficient flexibility and high capacity. But the deep learning models must be trained with enough data in order to achieve good performance, which is impractical in reality. In addition, deep learning is considered as black box and hard to interpret. These factors make deep learning not widely used in microbiome-wide association studies. In this work, we construct a sparse microbial interaction network and embed this graph into deep model to alleviate the risk of overfitting and improve the performance. Further, we explore a Graph Embedding Deep Feedforward Network (GEDFN) to conduct feature selection and guide meaningful microbial markers' identification. Based on the experimental results, we verify the feasibility of combining the microbial graph model with the deep learning model, and demonstrate the feasibility of applying deep learning and feature selection on microbial data. Our main contributions are: firstly, we utilize different methods to construct a variety of microbial interaction networks and combine the network via graph embedding deep learning. Secondly, we introduce a feature selection method based on graph embedding and validate the biological meaning of microbial markers. The code is available at https://github.com/MicroAVA/GEDFN.git.},
}

@article {pmid31824493,
year = {2019},
author = {Michel-Todó, L and Reche, PA and Bigey, P and Pinazo, MJ and Gascón, J and Alonso-Padilla, J},
title = {In silico Design of an Epitope-Based Vaccine Ensemble for Chagas Disease.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {2698},
doi = {10.3389/fimmu.2019.02698},
pmid = {31824493},
issn = {1664-3224},
abstract = {Trypanosoma cruzi infection causes Chagas disease, which affects 7 million people worldwide. Two drugs are available to treat it: benznidazole and nifurtimox. Although both are efficacious against the acute stage of the disease, this is usually asymptomatic and goes undiagnosed and untreated. Diagnosis is achieved at the chronic stage, when life-threatening heart and/or gut tissue disruptions occur in ~30% of those chronically infected. By then, the drugs' efficacy is reduced, but not their associated high toxicity. Given current deficiencies in diagnosis and treatment, a vaccine to prevent infection and/or the development of symptoms would be a breakthrough in the management of the disease. Current vaccine candidates are mostly based on the delivery of single antigens or a few different antigens. Nevertheless, due to the high biological complexity of the parasite, targeting as many antigens as possible would be desirable. In this regard, an epitope-based vaccine design could be a well-suited approach. With this aim, we have gone through publicly available databases to identify T. cruzi epitopes from several antigens. By means of a computer-aided strategy, we have prioritized a set of epitopes based on sequence conservation criteria, projected population coverage of Latin American population, and biological features of their antigens of origin. Fruit of this analysis, we provide a selection of CD8+ T cell, CD4+ T cell, and B cell epitopes that have <70% identity to human or human microbiome protein sequences and represent the basis toward the development of an epitope-based vaccine against T. cruzi.},
}

@article {pmid31824467,
year = {2019},
author = {Cárdenas, CA and Font, A and Steinert, G and Rondon, R and González-Aravena, M},
title = {Temporal Stability of Bacterial Communities in Antarctic Sponges.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2699},
doi = {10.3389/fmicb.2019.02699},
pmid = {31824467},
issn = {1664-302X},
abstract = {Marine sponges host dense, diverse, and species-specific microbial communities around the globe; however, most of the current knowledge is restricted to species from tropical and temperate waters. Only recently, some studies have assessed the microbiome of a few Antarctic sponges; however, contrary to low mid-latitude sponges, the knowledge about temporal (stability) patterns in the bacterial communities of Antarctic sponges is absent. Here, we studied the temporal patterns of bacterial communities in the Antarctic sponges Mycale (Oxymycale) acerata, Isodictya sp., Hymeniacidon torquata, and Tedania (Tedaniopsis) wellsae that were tagged in situ and monitored during three austral summers over a 24-month period. By using amplicon sequencing of the bacterial 16S rRNA gene we found that the microbiome differed between species. In general, bacterial communities were dominated by gammaproteobacterial OTUs; however, M. acerata showed the most distinct pattern, being dominated by a single betaproteobacterial OTU. The analysis at OTU level (defined at 97% sequence similarity) showed a highly stable bacterial community through time, despite the abnormal seawater temperatures (reaching 3°C) and rates of temperature increase of 0.15°C day-1 recorded in austral summer 2017. Sponges were characterized by a small core bacterial community that accounted for a high percentage of the abundance. Overall, no consistent changes in core OTU abundance were recorded for all studied species, confirming a high temporal stability of the microbiome. In addition, predicted functional pathway profiles showed that the most abundant pathways among all sponges belonged mostly to metabolism pathway groups (e.g., amino acid, carbohydrate, energy, and nucleotide). The predicted functional pathway patterns differed among the four sponge species. However, no clear temporal differences were detected supporting what was found in terms of the relatively stable composition of the bacterial communities.},
}

@article {pmid31824464,
year = {2019},
author = {Han, Q and Jiang, Y and Brandt, BW and Yang, J and Chen, Y and Buijs, MJ and Crielaard, W and Cheng, L and Deng, D},
title = {Regrowth of Microcosm Biofilms on Titanium Surfaces After Various Antimicrobial Treatments.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2693},
doi = {10.3389/fmicb.2019.02693},
pmid = {31824464},
issn = {1664-302X},
abstract = {Objectives: Our aim of this work was to investigate the regrowth of implant-related biofilms after various antimicrobial treatments in vitro. Methods: Saliva-derived microcosm biofilms were grown on titanium discs in an active attachment model. Treatments including hydrogen peroxide (HP), citric acid (CA), chlorhexidine (CHX), and distilled water (control), at different concentrations, were applied to 2-day biofilms for 1 or 5 min. The viability, lactic acid production, and composition of the biofilms were followed for 3 days. The biofilm composition was analyzed by 16S rDNA amplicon sequencing. Results: The short treatments of CA, CHX, and HP resulted in a 2-3 log reduction in biofilm viability and lactic acid production immediately. However, both parameters returned to the pre-treatment level within 2 days due to biofilm regrowth. The alpha diversity of the regrown biofilms in antimicrobial-treated groups tended to decrease, whereas the diversity of those in water-treated group increased. The composition of the regrown biofilms altered compared to those before treatments. Streptococcus and Enterobacteriaceae were enriched in the regrown biofilms. Conclusions: Although the antimicrobial treatments were efficient, the multi-species biofilms were indeed able to regrow within 2 days. The regrown biofilms display an altered microbial diversity and composition, which in the oral cavity may lead to an aggressive infection.},
}

@article {pmid31824463,
year = {2019},
author = {Freitag, TL and Hartikainen, A and Jouhten, H and Sahl, C and Meri, S and Anttila, VJ and Mattila, E and Arkkila, P and Jalanka, J and Satokari, R},
title = {Minor Effect of Antibiotic Pre-treatment on the Engraftment of Donor Microbiota in Fecal Transplantation in Mice.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2685},
doi = {10.3389/fmicb.2019.02685},
pmid = {31824463},
issn = {1664-302X},
abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) and is also considered a potential treatment for a wide range of intestinal and systemic diseases. FMT corrects the microbial dysbiosis associated with rCDI, and the engraftment of donor microbiota is likely to play a key role in treatment efficacy. For disease indications other than rCDI, FMT treatment efficacy has been moderate. This may be partly due to stronger resilience of resident host microbiota in patients who do not suffer from rCDI. In rCDI, patients typically have undergone several antibiotic treatments prior to FMT, depleting the microbiota. In this study, we addressed the effect of broad-spectrum antibiotics (Ab) as a pre-treatment to FMT on the engraftment of donor microbiota in recipients. We conducted a pre-clinical study of FMT between two healthy mouse strains, Balb/c as donors and C57BL/6 as recipients, to perform FMT within the same species and to mimic interindividual FMT between human donors and patients. Microbiota composition was assessed with high-throughput 16S rDNA amplicon sequencing. The microbiota of Balb/c and C57BL/6 mice differed significantly, which allowed for the assessment of microbiota transplantation from the donor strain to the recipient. Our results showed that Ab-treatment depleted microbiota in C57BL/6 recipient mice prior to FMT. The diversity of microbiota did not recover spontaneously to baseline levels during 8 weeks after Ab-treatment, but was restored already at 2 weeks in mice receiving FMT. Interestingly, pre-treatment with antibiotics prior to FMT did not increase the overall similarity of the recipient's microbiota to that of the donor's, as compared with mice receiving FMT without Ab-treatment. Pre-treatment with Ab improved the establishment of only a few donor-derived taxa, such as Bifidobacterium, in the recipients, thus having a minor effect on the engraftment of donor microbiota in FMT. In conclusion, pre-treatment with broad-spectrum antibiotics did not improve the overall engraftment of donor microbiota, but did improve the engraftment of specific taxa. These results may inform future therapeutic studies of FMT.},
}

@article {pmid31824456,
year = {2019},
author = {Hu, W and Strom, NB and Haarith, D and Chen, S and Bushley, KE},
title = {Seasonal Variation and Crop Sequences Shape the Structure of Bacterial Communities in Cysts of Soybean Cyst Nematode.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2671},
doi = {10.3389/fmicb.2019.02671},
pmid = {31824456},
issn = {1664-302X},
abstract = {Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is the number 1 pathogen of the important economic crop soybean. Bacteria represent potential biocontrol agents of the SCN, but few studies have characterized the dynamics of bacterial communities associated with cysts under different crop rotation sequences. The bacterial communities in SCN cysts in a long-term soybean-corn crop rotation experiment were investigated over 2 years. The crop sequences included long-term soybean monoculture (Ss), years 1-5 of soybean following 5 years corn (S1-S5), years 1 and 2 of corn following 5 years soybean (C1 and C2), and soybean-corn annual rotation (Sa and Ca). The bacterial 16S rRNA V4 region was amplified from DNA isolated from SCN cysts collected in spring at planting, midseason (2 months later), and fall at harvest and sequenced on the Illumina MiSeq platform. The SCN cyst microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidetes, and Verrucomicrobia. The bacterial community composition was influenced by both crop sequence and season. Although differences by crop sequence were not significant in the spring of each year, bacterial communities in cysts from annual rotation (Sa and Ca) or crop sequences of early years of monoculture following a 5-year rotation of the alternate crop (S1 and C1) became rapidly differentiated by crop over a single growing season. In the fall, genera of cyst bacteria associated with soybean crop sequences included Rhizobacter, Leptothrix, Cytophaga, Chitinophaga, Niastella, Streptomyces, and Halangium. The discovery of diverse bacterial taxa in SCN cysts and their dynamics across crop rotation sequences provides invaluable information for future development of biological control of the SCN.},
}

@article {pmid31824176,
year = {2019},
author = {Tao, Z and Zhang, L and Zhang, Q and Lv, T and Chen, R and Wang, L and Huang, Z and Hu, L and Liao, Q},
title = {The Pathogenesis Of Streptococcus anginosus In Aerobic Vaginitis.},
journal = {Infection and drug resistance},
volume = {12},
number = {},
pages = {3745-3754},
doi = {10.2147/IDR.S227883},
pmid = {31824176},
issn = {1178-6973},
abstract = {Background: Aerobic vaginitis (AV) is a newly defined type of bacterial vaginitis, but its pathogenesis is not yet clear. Streptococcus anginosus appears as an emerging pathogen in recent case reports, and colonizes in vagina of patients with AV. In this study, we investigate the pathogenesis of S. anginosus in AV.

Materials and methods: (1) We collected 41 vaginal specimens from 21 healthy, fertile women with normal vaginal flora (NM), 10 with bacterial vaginosis (BV) and 10 with AV; their microbiome structure was analysed by 16S rRNA gene sequencing. (2) S. anginosus and vaginal epithelial cells were cocultured in vitro, and cytotoxicity was tested by an LDH kit. (3) The S. anginosus virulence gene sag was knocked out, and the cytotoxicity of the mutant in vaginal epithelial cells was tested.

Results: (1) The microbiome structure of AV was dramatically different from that of BV and NM. The predominant genera of the three groups were Streptococcus spp., Gardnerella spp. and Lactobacillus spp. Streptococcus spp. were significantly more abundant in AV than in BV (95% CI [0.1391, 0.8676], P<0.01) and NM (95% CI [0.1391, 0.8676], P<0.01). (2) S. anginosus was the dominant species in AV (95% CI [0.04672, 0.1097], P<0.01). (3) The mean cytotoxicity of S. anginosus in vaginal epithelial cells was 58.34% for the wild type (WT) and 16.43% for the mutant; this difference was significant (95% CI [-60.55, -23.28], P<0.01).

Conclusion: S. anginosus was the predominant microorganism in patients with AV in our study. S. anginosus caused vaginal epithelial cell lysis, indicating that S. anginosus is an AV pathogen. The S. anginosus virulence gene sag is vital for vaginal epithelial cell lysis.},
}

@article {pmid31823916,
year = {2019},
author = {Singh, S and Verma, N and Taneja, N},
title = {The human gut resistome: Current concepts & future prospects.},
journal = {The Indian journal of medical research},
volume = {150},
number = {4},
pages = {345-358},
doi = {10.4103/ijmr.IJMR_1979_17},
pmid = {31823916},
issn = {0971-5916},
abstract = {The human gut is home to a myriad of organisms. While some are harmless commensals, others are transient, pathogenic flora. The gut microbiome is composed of diverse bacterial flora, and apart from playing a major role in protecting from various infectious and non-infectious diseases, it plays an important role in resistance to antimicrobials. The collection of genes or genetic material that confers antimicrobial resistance constitutes the gut resistome, and it may involve the pathogens or commensals of the intestinal tract. The diversity of this gut resistome is influenced by various environmental factors including the diet and antibiotic exposure. This review highlights the recent concepts pertaining to the human gut resistome, factors affecting it, how it impacts human health and diseases, methods to study the resistome and potential therapeutic approaches.},
}

@article {pmid31823811,
year = {2019},
author = {Maqsood, R and Rodgers, R and Rodriguez, C and Handley, SA and Ndao, IM and Tarr, PI and Warner, BB and Lim, ES and Holtz, LR},
title = {Discordant transmission of bacteria and viruses from mothers to babies at birth.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {156},
doi = {10.1186/s40168-019-0766-7},
pmid = {31823811},
issn = {2049-2618},
support = {MD-FR-2013-292//Children's Discovery Institute (US)/ ; BOC 388999//March of Dimes Foundation (US)/ ; 2017076//Doris Duke Charitable Foundation (US)/ ; R00 DK107923/DK/NIDDK NIH HHS/United States ; 5P30 DK052574/DK/NIDDK NIH HHS/United States ; Start up funding//Arizona State University/ ; UH3AI083265/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The earliest microbial colonizers of the human gut can have life-long consequences for their hosts. Precisely how the neonatal gut bacterial microbiome and virome are initially populated is not well understood. To better understand how the maternal gut microbiome influences acquisition of the infant gut microbiome, we studied the early life bacterial microbiomes and viromes of 28 infant twin pairs and their mothers.

RESULTS: Infant bacterial and viral communities more closely resemble those of their related co-twin than unrelated infants. We found that 63% of an infant's bacterial microbiome can be traced to their mother's gut microbiota. In contrast, only 15% of their viral communities are acquired from their mother. Delivery route did not determine how much of the bacterial microbiome or virome was shared from mother to infant. However, bacteria-bacteriophage interactions were altered by delivery route.

CONCLUSIONS: The maternal gut microbiome significantly influences infant gut microbiome acquisition. Vertical transmission of the bacterial microbiome is substantially higher compared to vertical transmission of the virome. However, the degree of similarity between the maternal and infant gut bacterial microbiome and virome did not vary by delivery route. The greater similarity of the bacterial microbiome and virome between twin pairs than unrelated twins may reflect a shared environmental exposure. Thus, differences of the inter-generation transmissibility at birth between the major kingdoms of microbes indicate that the foundation of these microbial communities are shaped by different rules. Video Abstract.},
}

@article {pmid31823713,
year = {2019},
author = {Chen, PY and Cripps, AW and West, NP and Cox, AJ and Zhang, P},
title = {A correlation-based network for biomarker discovery in obesity with metabolic syndrome.},
journal = {BMC bioinformatics},
volume = {20},
number = {Suppl 6},
pages = {477},
doi = {10.1186/s12859-019-3064-2},
pmid = {31823713},
issn = {1471-2105},
abstract = {BACKGROUND: Obesity is associated with chronic activation of the immune system and an altered gut microbiome, leading to increased risk of chronic disease development. As yet, no biomarker profile has been found to distinguish individuals at greater risk of obesity-related disease. The aim of this study was to explore a correlation-based network approach to identify existing patterns of immune-microbiome interactions in obesity.

RESULTS: The current study performed correlation-based network analysis on five different datasets obtained from 11 obese with metabolic syndrome (MetS) and 12 healthy weight men. These datasets included: anthropometric measures, metabolic measures, immune cell abundance, serum cytokine concentration, and gut microbial composition. The obese with MetS group had a denser network (total number of edges, n = 369) compared to the healthy network (n = 299). Within the obese with MetS network, biomarkers from the immune cell abundance group was found to be correlated to biomarkers from all four other datasets. Conversely in the healthy network, immune cell abundance was only correlated with serum cytokine concentration and gut microbial composition. These observations suggest high involvement of immune cells in obese with MetS individuals. There were also three key hubs found among immune cells in the obese with MetS networks involving regulatory T cells, neutrophil and cytotoxic cell abundance. No hubs were present in the healthy network.

CONCLUSION: These results suggest a more complex interaction of inflammatory markers in obesity, with high connectivity of immune cells in the obese with MetS network compared to the healthy network. Three key hubs were identified in the obese with MetS network, involving Treg, neutrophils and cytotoxic cell abundance. Compared to a t-test, the network approach offered more meaningful results when comparing obese with MetS and healthy weight individuals, demonstrating its superiority in exploratory analysis.},
}

@article {pmid31823248,
year = {2019},
author = {Dignard, C and Leibler, JH},
title = {Recent Research on Occupational Animal Exposures and Health Risks: A Narrative Review.},
journal = {Current environmental health reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s40572-019-00253-5},
pmid = {31823248},
issn = {2196-5412},
abstract = {PURPOSE OF REVIEW: In the last year, an increasing number of studies have reported on methicillin-resistant Staphylococcus aureus (MRSA) transmission in Africa and Asia and in migrant workers. We reviewed original research on occupational health and safety of animal workers published from January 1, 2018, through June 30, 2019, with a targeted focus on infectious disease studies published in these populations.

RECENT FINDINGS: Studies focused on occupational exposures to infectious agents, dust and allergens, pesticides, and occupational injury. Research on zoonotic MRSA used whole genome-sequencing technologies to evaluate transmission in Africa and Asia. Swine worker exposure to porcine coronavirus and emerging influenza A viruses was documented in China. 16s RNA amplicon sequencing identified distinct microbiota compositions in households with active animal farmers. Multiple bioaerosol exposures were assessed for industrial dairy workers. Occupational injury studies highlighted the struggles of Latino animal workers in the USA. These studies highlighted the global expansion of zoonotic antibiotic resistance and identified novel occupational zoonoses of concern. The integration of microbiome assessment and compound mixtures into the evaluation of dust and endotoxin exposures for animal workers marks a new direction for this work.},
}

@article {pmid31823133,
year = {2019},
author = {Borges, ED and Berteli, TS and Reis, TF and Silva, AS and Vireque, AA},
title = {Microbial contamination in assisted reproductive technology: source, prevalence, and cost.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10815-019-01640-5},
pmid = {31823133},
issn = {1573-7330},
abstract = {Even the strictest laboratories and clinics are prone to the occurrence of microbial contamination. In the case of in vitro fertilization (IVF) research and practice facilities, the number of possible sources is particularly vast. In addition to ambient air, personnel, and non-sterilized materials, follicular fluid and semen from patients are a very common gateway for a diverse range of bacteria and fungi into embryo cultures. Even so, reports of contamination cases are rare, what leads many clinics to see the issue as a negligible risk. Microbiological contamination may result in the demise of the patient's embryos, leading to additional costs to both the patient and the clinics. Regardless of financial loss, emotional costs, and stress levels during IVF are highly distressing. Other worrisome consequences include DNA fragmentation, poor-quality embryos, early pregnancy loss or preterm birth, and possible long-term damages that need further investigation. In this review, we aimed to shed a light on the issue that we consider largely underestimated and to be the underlying cause of poor IVF outcomes in many cases. We also discuss the composition of the microbiome and how its interaction with the reproductive tract of IVF-seeking patients might influence their outcomes. In conclusion, we urge clinics to more rigorously identify, register, and report contamination occurrences, and highlight the role of the study of the microbiome to improve overall results and safety of assisted reproduction.},
}

@article {pmid31823102,
year = {2019},
author = {Kaunitz, JD and Akiba, Y},
title = {Correction to: Control of Intestinal Epithelial Proliferation and Differentiation: The Microbiome, Enteroendocrine L Cells, Telocytes, Enteric Nerves, and GLP, Too.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-019-05987-8},
pmid = {31823102},
issn = {1573-2568},
abstract = {The original version of the article unfortunately contained an error in one of the sentences. The sentence, "Eventually, Dan Drucker in Pat Brubaker's laboratory convincingly demonstrated that GLP-2 is the proglucagon product controlling intestinal proliferation [19]," should read "Eventually, Dan Drucker convincingly demonstrated that GLP-2 is the proglucagon product controlling intestinal proliferation [19]."},
}

@article {pmid31822979,
year = {2019},
author = {Cao, W and Xiong, Y and Zhao, D and Tan, H and Qu, J},
title = {Bryophytes and the symbiotic microorganisms, the pioneers of vegetation restoration in karst rocky desertification areas in southwestern China.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10235-0},
pmid = {31822979},
issn = {1432-0614},
support = {31360041 and 31660052//National Natural Science Foundation of China/ ; [2014]01//2011 Collaboration Innovation Center Construction Program of Guizhou Province/ ; [2016]4003//High-level Innovation Talents Training Program of Guizhou Province/ ; },
abstract = {In karst rocky desertification areas, bryophytes coexist with algae, bacteria, and fungi on exposed calcareous rocks to form a bryophyte crust, which plays an irreplaceable role in the restoration of karst degraded ecosystems. We investigated the biodiversity of crust bryophytes in karst rocky desertification areas from Guizhou Province, China. A total of 145 species in 22 families and 56 genera were identified. According to frequency and coverage, seven candidate dominant mosses were screened out, and five drought-resistant indexes of them were measured. Hypnum leptothallum, Racopilum cuspidigerum, and Hyophila involuta have high drought adaptability. We explored the interactions between two dominant mosses (H. leptothallum, H. involuta) and the structure of microbial communities in three karst rocky desertification types. Microbial diversity and function analysis showed that both moss species and karst rocky desertification types affect microbial communities. Moss species much more strongly affected the diversity and changed the community composition of these microbial groups. Bacteria were more sensitive in the microbiome as their communities changed strongly between mosses and drought resistance factors. Moreover, several species of fungi and bacteria could be significantly associated with three drought-resistant indexes: Pro (free proline content), SOD (superoxide dismutase activity), and POD (peroxidase activity), which were closely related to the drought adaptability of mosses. Our results enforced the potential role of moss-associated microbes that are important components involved in the related biological processes when bryophytes adapted to arid habitats, or as one kind of promoters in the distribution pattern of early mosses succession in karst rocky desertification areas.},
}

@article {pmid31822775,
year = {2019},
author = {Chen, S and Zheng, Y and Zhou, Y and Guo, W and Tang, Q and Rong, G and Hu, W and Tang, J and Luo, H},
title = {Gut Dysbiosis with Minimal Enteritis Induced by High Temperature and Humidity.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18686},
doi = {10.1038/s41598-019-55337-x},
pmid = {31822775},
issn = {2045-2322},
support = {81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81673850//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {High temperature and humidity (HTH) can cause diarrhea owing to food and drinking water contamination. However, their direct effects on gut microbiota and gastrointestinal inflammation are unknown. This study aimed to investigate the effects of HTH and probiotics on the microbiome. Twenty-one male mice were randomly assigned to normal control (NC), HTH, and broad-spectrum probiotic-treated (PR) groups. HTH and PR groups were regularly housed at 30 ± 0.5 °C with humidity of 85-90% for eight consecutive weeks. A broad-spectrum probiotic was administrated to PR-group mice from day 50 to 56. Clinical signs were observed and gut microbiota were analyzed via 16 S rRNA-based functional metagenomics. Intestinal pathology and the expression of defensins and pro-inflammatory cytokines were also assessed. Mice in the HTH and PR groups gradually developed sticky or loose feces. The HTH group developed a distinct microbiota profile associated with augmented metabolism and human-like pathophysiologies upon suppression of environmental sensing. Pathological assays indicated minimal enteritis, increased bacterial translocation, and elevated intestinal pro-inflammatory cytokine levels. Thus, ambient HTH directly contributes to gut dysbiosis and minimal enteritis, whereas probiotics partially normalized the microbiota and ameliorated gut inflammation. This study provides novel insights into the pathogenesis of environment-associated diseases and offers a potential therapeutic approach.},
}

@article {pmid31822712,
year = {2019},
author = {Menon, RK and Gomez, A and Brandt, BW and Leung, YY and Gopinath, D and Watt, RM and Crielaard, W and Nelson, KE and Botelho, MG},
title = {Long-term impact of oral surgery with or without amoxicillin on the oral microbiome-A prospective cohort study.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18761},
doi = {10.1038/s41598-019-55056-3},
pmid = {31822712},
issn = {2045-2322},
abstract = {Routine postoperative antibiotic prophylaxis is not recommended for third molar extractions. However, amoxicillin still continues to be used customarily in several clinical practices worldwide to prevent infections. A prospective cohort study was conducted in cohorts who underwent third molar extractions with (group EA, n = 20) or without (group E, n = 20) amoxicillin (250 mg three times daily for 5 days). Further, a control group without amoxicillin and extractions (group C, n = 17) was included. Salivary samples were collected at baseline, 1-, 2-, 3-, 4-weeks and 3 months to assess the bacterial shift and antibiotic resistance gene changes employing 16S rRNA gene sequencing (Illumina-Miseq) and quantitative polymerase chain reaction. A further 6-month follow-up was performed for groups E and EA. Seven operational taxonomic units reported a significant change from baseline to 3 months for group EA (adjusted p < 0.05). No significant change in relative abundance of bacteria and β-lactamase resistance genes (TEM-1) was observed over 6 months for any group (adjusted p > 0.05). In conclusion, the salivary microbiome is resilient to an antibiotic challenge by a low-dose regimen of amoxicillin. Further studies evaluating the effect of routinely used higher dose regimens of amoxicillin on gram-negative bacteria and antibiotic resistance genes are warranted.},
}

@article {pmid31822687,
year = {2019},
author = {Eguíluz, VM and Salazar, G and Fernández-Gracia, J and Pearman, JK and Gasol, JM and Acinas, SG and Sunagawa, S and Irigoien, X and Duarte, CM},
title = {Scaling of species distribution explains the vast potential marine prokaryote diversity.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18710},
doi = {10.1038/s41598-019-54936-y},
pmid = {31822687},
issn = {2045-2322},
support = {MDM-2017-0711//Spanish State Research Agency/ ; FIS2016-80067-P//Agencia Estatal de Investigación/ ; },
abstract = {Global ocean expeditions have provided minimum estimates of ocean's prokaryote diversity, supported by apparent asymptotes in the number of prokaryotes with sampling effort, of about 40,000 species, representing <1% of the species cataloged in the Earth Microbiome Project, despite being the largest habitat in the biosphere. Here we demonstrate that the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.},
}

@article {pmid31822603,
year = {2019},
author = {Luter, HM and Whalan, S and Andreakis, N and Abdul Wahab, M and Botté, ES and Negri, AP and Webster, NS},
title = {The Effects of Crude Oil and Dispersant on the Larval Sponge Holobiont.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
doi = {10.1128/mSystems.00743-19},
pmid = {31822603},
issn = {2379-5077},
abstract = {Accidental oil spills from shipping and during extraction can threaten marine biota, particularly coral reef species which are already under pressure from anthropogenic disturbances. Marine sponges are an important structural and functional component of coral reef ecosystems; however, despite their ecological importance, little is known about how sponges and their microbial symbionts respond to petroleum products. Here, we use a systems biology-based approach to assess the effects of water-accommodated fractions (WAF) of crude oil, chemically enhanced water-accommodated fractions of crude oil (CWAF), and dispersant (Corexit EC9500A) on the survival, metamorphosis, gene expression, and microbial symbiosis of the abundant reef sponge Rhopaloeides odorabile in larval laboratory-based assays. Larval survival was unaffected by the 100% WAF treatment (107 μg liter-1 polycyclic aromatic hydrocarbon [PAH]), whereas significant decreases in metamorphosis were observed at 13% WAF (13.9 μg liter-1 PAH). The CWAF and dispersant treatments were more toxic, with decreases in metamorphosis identified at 0.8% (0.58 μg liter-1 PAH) and 1.6% (38 mg liter-1 Corexit EC9500A), respectively. In addition to the negative impact on larval settlement, significant changes in host gene expression and disruptions to the microbiome were evident, with microbial shifts detected at the lowest treatment level (1.6% WAF; 1.7 μg liter-1 PAH), including a significant reduction in the relative abundance of a previously described thaumarchaeal symbiont. The responsiveness of the R. odorabile microbial community to the lowest level of hydrocarbon treatment highlights the utility of the sponge microbiome as a sensitive marker for exposure to crude oils and dispersants.IMPORTANCE Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function.},
}

@article {pmid31822600,
year = {2019},
author = {Wang, L and Wu, J and Li, K and Sadd, BM and Guo, Y and Zhuang, D and Zhang, Z and Chen, Y and Evans, JD and Guo, J and Zhang, Z and Li, J},
title = {Dynamic Changes of Gut Microbial Communities of Bumble Bee Queens through Important Life Stages.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
doi = {10.1128/mSystems.00631-19},
pmid = {31822600},
issn = {2379-5077},
abstract = {Bumble bees are important pollinators in natural and agricultural ecosystems. Their social colonies are founded by individual queens, which, as the predominant reproductive females of colonies, contribute to colony function through worker production and fitness through male and new queen production. Therefore, queen health is paramount, but even though there has been an increasing emphasis on the role of gut microbiota for animal health, there is limited information on the gut microbial dynamics of bumble bee queens. Employing 16S rRNA amplicon sequencing and quantitative PCR, we investigate how the adult life stage and physiological state influence a queen's gut bacterial community diversity and composition in unmated, mated, and ovipositing queens of Bombus lantschouensis We found significant shifts in total gut microbe abundance and microbiota composition across queen states. There are specific compositional signatures associated with different stages, with unmated and ovipositing queens showing the greatest similarity in composition and mated queens being distinct. The bacterial genera Gilliamella, Snodgrassella, and Lactobacillus were relatively dominant in unmated and ovipositing queens, with Bifidobacterium dominant in ovipositing queens only. Bacillus, Lactococcus, and Pseudomonas increased following queen mating. Intriguingly, however, further analysis of unmated queens matching the mated queens in age showed that changes are independent of the act of mating. Our study is the first to explore the gut microbiome of bumble bee queens across key life stages from adult eclosion to egg laying and provides useful information for future studies of the function of gut bacteria in queen development and colony performance.IMPORTANCE Bumble bee queens undergo a number of biological changes as they transition through adult emergence, mating, overwintering, foraging, and colony initiation including egg laying. Therefore, they represent an important system to understand the link between physiological, behavioral, and environmental changes and host-associated microbiota. It is plausible that the bumble bee queen gut bacteria play a role in shaping the ability of the queen to survive environmental extremes and reproduce, due to long-established coevolutionary relationships between the host and microbiome members.},
}

@article {pmid31822562,
year = {2019},
author = {Simon, MC and Reinbeck, AL and Wessel, C and Heindirk, J and Jelenik, T and Kaul, K and Arreguin-Cano, J and Strom, A and Blaut, M and Bäckhed, F and Burkart, V and Roden, M},
title = {Distinct alterations of gut morphology and microbiota characterize accelerated diabetes onset in non-obese diabetic mice.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA119.010816},
pmid = {31822562},
issn = {1083-351X},
abstract = {The rising prevalence of type 1 diabetes (T1D) over the last decades has been linked to lifestyle changes, but the underlying mechanisms are largely unknown. Recent findings point to gut-associated mechanisms in the control of T1D pathogenesis. In non-obese diabetic (NOD) mice, a model of T1D, diabetes development accelerates after deletion of the Toll-like receptor 4 (TLR4). We hypothesized that altered intestinal functions contribute to metabolic alterations, which favor accelerated diabetes development in TLR4-deficient (TLR4-/-) NOD mice. In 70-90 days old normoglycemic (prediabetic) female NOD TLR4+/+ and NOD TLR4-/- mice, gut morphology and microbiome composition were analyzed. Parameters of lipid metabolism, glucose homeostasis and mitochondrial respiratory activity were measured in vivo and ex vivo. Compared to NOD TLR4+/+ mice, NOD TLR4-/- animals showed lower muscle mass of the small intestine, higher abundance of Bacteroidetes and lower Firmicutes in the large intestine, along with lower levels of circulating short-chain fatty acids (SCFA). These changes associated with higher body weight, hyperlipidemia and severe insulin and glucose intolerance, all occurring before the onset of diabetes. These mice also exhibited insulin resistance-related abnormalities of energy metabolism, such as lower total respiratory exchange rates and higher hepatic oxidative capacity. Distinct alterations of gut morphology and microbiota composition associated with reduction of circulating SCFA may contribute to metabolic disorders promoting the progression of insulin-deficient diabetes/T1D development.},
}

@article {pmid31822225,
year = {2019},
author = {Zeller-Simmerl, D},
title = {[Chronic Pelvic Pain Syndrome (CPPS) and Irritable Bowel Syndrome in Professional Overload].},
journal = {Praxis},
volume = {108},
number = {16},
pages = {1073-1078},
doi = {10.1024/1661-8157/a003339},
pmid = {31822225},
issn = {1661-8157},
abstract = {Chronic Pelvic Pain Syndrome (CPPS) and Irritable Bowel Syndrome in Professional Overload Abstract. Chronic pelvic floor pain syndrome (CPPS) and irritable bowel syndrome are exclusion diagnoses and are subsumed under somatoform disorders in ICD-10. The CPPS includes a variety of synonyms and is treated in an interdisciplinary manner. The causes are manifold and subject to the bio-psycho-social aspects. Often the chronic pain syndrome has its origin in a somatic cause that continues despite healing of the lesion, possibly due to mental comorbidities and social stressors. Irritable bowel syndrome has changed in recent years from a psychiatric illness to a somatic disorder. This is because of the findings in neurogastroenterology, knowledge of the microbiome, food intolerances and the gut-brain axis. In chronic pain syndromes, pain retention and enhancement are influenced by psychosocial aspects. Therefore, an interdisciplinary therapy makes sense.},
}

@article {pmid31821847,
year = {2019},
author = {Kuti, D and Winkler, Z and Horváth, K and Juhász, B and Paholcsek, M and Stágel, A and Gulyás, G and Czeglédi, L and Ferenczi, S and Kovács, KJ},
title = {Gastrointestinal (Non-systemic) Antibiotic Rifaximin Differentially Affects Chronic Stress-induced Changes in Colon Microbiome and Gut Permeability without Effect on Behavior.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2019.12.004},
pmid = {31821847},
issn = {1090-2139},
abstract = {Chronic stress is often accompanied by gastrointestinal symptoms, which might be due to stress-induced shift of gut microbiome to pathogenic bacteria. It has been hypothesized that stress alters gut permeability and results in mild endotoxemia which exaggerates HPA activity and contributes to anxiety and depression. To reveal the relationship between microbiome composition, stress-induced gastrointestinal functions and behavior, we treated chronically stressed mice with non-absorbable antibiotic, rifaximin. The "two hits" stress paradigm was used, where newborn mice were separated from their mothers for 3 hours daily as early life adversity (maternal separation, MS) and exposed to 4 weeks chronic variable stress (CVS) as adults. 16S rRNA based analysis of gut microbiome revealed increases of Bacteroidetes and Proteobacteria and more specifically, Clostridium species in chronically stressed animals. In mice exposed to MS+CVS, we found extenuation of colonic mucosa, increased bacterial translocation to mesenteric lymph node, elevation of plasma LPS levels and infiltration of F4/80 positive macrophages into the colon lamina propria. Chronically stressed mice displayed behavioral signs of anxiety-like behavior and neophobia. Rifaximin treatment decreased Clostridium concentration, gut permeability and LPS plasma concentration and increased colonic expression of tight junction proteins (TJP1,TJP2) and occludin. However, these beneficial effects of rifaximin in chronically stressed mice was not accompanied by positive changes in behavior. Our results suggest that non-absorbable antibiotic treatment alleviates stress-induced local pathologies, however, does not affect stress-induced behavior.},
}

@article {pmid31821833,
year = {2019},
author = {Golofast, B and Vales, K},
title = {The connection between microbiome and schizophrenia.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neubiorev.2019.12.011},
pmid = {31821833},
issn = {1873-7528},
abstract = {There has been an accumulation of knowledge about the human microbiome, some detailed investigations of the gastrointestinal microbiota and its functions, and the highlighting of complex interactions between the gut, the gut microbiota, and the central nervous system. That assumes the involvement of the microbiome in the pathogenesis of various CNS diseases, including schizophrenia. Given this information and the fact, that the gut microbiota is sensitive to internal and environmental influences, we have speculated that among the factors that influence the formation and composition of gut microbiota during life, possible key elements in the schizophrenia development chain are hidden where gut microbiota is a linking component. This article aims to describe and understand the developmental relationships between intestinal microbiota and the risk of developing schizophrenia.},
}

@article {pmid31821720,
year = {2019},
author = {Zhang, W and Keyhani, NO and Zhang, H and Cai, K and Xia, Y},
title = {Inhibitor of apoptosis-1 gene as a potential target for pest control and its involvement in immune regulation during fungal infection.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.5712},
pmid = {31821720},
issn = {1526-4998},
abstract = {BACKGROUND: Environmentally friendly insect management technologies, including RNAi and entomopathogenic fungi, have attracted increasing attention as options for pest control. Here, we sought to extend RNAi directed targeting of the inhibitor of apoptosis protein 1 (IAP1) gene to the locust, and to examine its relationship to immune responses and susceptibility to Metarhizium acridum, a locust specific fungal pathogen.

RESULTS: Expression of the locust LmIAP gene was induced in the hemolymph and fat body after M. acridum infection. RNAi directed silencing of locust LmIAP1 resulted in increased Caspase 3 activity, degeneration of the gut, and dose dependent mortality. Synergistic mortality was seen in RNAi-LmIAP/fungal co-infection experiments with the median survival time (MST) values decreasing from ~5 d for RNAi and M. acridum treatments alone, to 2.6 d for co-treatments. Reduced haemocyte numbers and antimicrobial peptide levels were seen in co-treated locusts, with changes in gut opportunistic pathogenic bacteria were seen between treatments. Enhanced fungal sporulation on co-treated insect cadavers was also compared with fungal infection alone.

CONCLUSIONS: Silencing of the locust LmIAP1 gene results in direct mortality and increases insect susceptibility to insect fungal pathogens in part by decreasing immunity and altering the gut microbiome. This article is protected by copyright. All rights reserved.},
}

@article {pmid31821689,
year = {2019},
author = {Mirshahi, F and Aqbi, HF and Cresswell, K and Saneshaw, M and Coleman, C and Jacobs, T and Idowu, MO and Dozmorov, M and Sanyal, AJ and Manjili, MH},
title = {Longitudinal studies can identify distinct inflammatory cytokines associated with the inhibition or progression of liver cancer.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1111/liv.14323},
pmid = {31821689},
issn = {1478-3231},
abstract = {BACKGROUND AND AIMS: Chronic diseases such as nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC) are associated with chronic inflammation. However, controversial reports as to the key cytokines involved in the process of chronic inflammation hinder development of targeted therapies for patients. This is because, chronic inflammatory process cannot be fully understood by studying the mechanisms of the disease in a short-term or isolated fashion. Understanding of the trend of inflammatory cytokines through longitudinal studies could provide a profound insight into the process of disease progression.

METHODS: We performed longitudinal analysis of inflammatory cytokines/chemokines and fecal microbiome dysbiosis associated with the diet-induced progression of NAFLD to HCC in Diet-Induced Animal Model Of Nonalcoholic fatty liver Disease (DIAMOND) comparing males and females since males show a higher incidence of these diseases than females do.

RESULTS: Longitudinal analyses revealed that a transient and timely increase in LIF and TMIP1 was associated with the inhibition of the progression of NAFLD to HCC in females. On the other hand, chronically increasing trends in CCL12, CCL17, CXCL9 and LIX/CXCL5 were associated with the promotion of the progression of NAFLD to HCC in males.

CONCLUSIONS: We provided empirical evidence that a methodological shift from snapshot observations to longitudinal data collection and analysis can provide a better understanding of chronic liver diseases.},
}

@article {pmid31821650,
year = {2019},
author = {DeCandia, AL and Brenner, LJ and King, JL and vonHoldt, BM},
title = {Ear mite infection is associated with altered microbial communities in genetically depauperate Santa Catalina Island foxes (Urocyon littoralis catalinae).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.15325},
pmid = {31821650},
issn = {1365-294X},
abstract = {The host-associated microbiome is increasingly recognized as a critical player in health and immunity. Recent studies have shown that disruption of commensal microbial communities can contribute to disease pathogenesis and severity. Santa Catalina Island foxes (Urocyon littoralis catalinae) present a compelling system in which to examine microbial dynamics in wildlife due to their depauperate genomic structure and extremely high prevalence of ceruminous gland tumors. Although the precise cause is yet unknown, infection with ear mites (Otodectes cynotis) has been linked to chronic inflammation, which is associated with abnormal cell growth and tumor development. Given the paucity of genomic variation in these foxes, other dimensions of molecular diversity, such as commensal microbes, may be critical to host response and disease pathology. We characterized the host-associated microbiome across six body sites of Santa Catalina Island foxes, and performed differential abundance testing between healthy and mite-infected ear canals. We found that mite infection was significantly associated with reduced microbial diversity and evenness, with the opportunistic pathogen Staphylococcus pseudintermedius dominating the ear canal community. These results suggest that secondary bacterial infection may contribute to the sustained inflammation associated with tumor development. As the emergence of antibiotic resistant strains remains a concern of the medical, veterinary, and conservation communities, uncovering high relative abundance of S. pseudintermedius provides critical insight into the pathogenesis of this complex system. Through use of culture-independent sequencing techniques, this study contributes to the broader effort of applying a more inclusive understanding of molecular diversity to questions within wildlife disease ecology.},
}

@article {pmid31821639,
year = {2019},
author = {Panicker, JN and Marcelissen, T and von Gontard, A and Vrijens, D and Abrams, P and Wyndaele, M},
title = {Bladder-bowel interactions: Do we understand pelvic organ cross-sensitization? International Consultation on Incontinence Research Society (ICI-RS) 2018.},
journal = {Neurourology and urodynamics},
volume = {38 Suppl 5},
number = {},
pages = {S25-S34},
doi = {10.1002/nau.24111},
pmid = {31821639},
issn = {1520-6777},
support = {//United Kingdom's Department of Health NIHR Biomedical Research Centres/ ; },
abstract = {AIMS: Mounting evidence from experimental animal and human studies suggests that cross-sensitization exists between different organs. Lower urinary tract (LUT) and bowel dysfunction commonly overlap, and the role of cross-sensitization between pelvic visceral organs is uncertain.

METHODS: At the International Consultation on Incontinence Research Society (ICI-RS) meeting in 2018, a panel of clinicians participated in a discussion on bladder and bowel interactions in the context of pelvic organ cross-sensitization.

RESULTS: Bladder and bowel problems commonly co-occur in adults and children across different disorders, and the mechanism responsible for overlapping dysfunction is uncertain in most instances. At a neuronal level, cross-sensitization occurs as a result of afferent signaling from the LUT and lower bowel through different central and peripheral mechanisms. Studies in animals and humans have demonstrated evidence for cross-organ sensitization following experimental inflammation or distension of the lower bowel, affecting the LUT. Nerve stimulation is an effective treatment for different functional LUT and bowel disorders, and whether this treatment may influence cross-organ sensitization remains uncertain. The role of physiologically dormant C-fibers, the bladder-gut-brain axis, and gut microbiome in cross-sensitization are speculative.

CONCLUSION: Recommendations for research were made to explore the role of cross-organ sensitization in the pathogenesis of co-occurring LUT and bowel dysfunction in humans.},
}

@article {pmid31821632,
year = {2019},
author = {Harding, C and Rantell, A and Cardozo, L and Jacobson, SK and Anding, R and Kirschner-Hermanns, R and Greenwell, T and Swamy, S and Malde, S and Abrams, P},
title = {How can we improve investigation, prevention and treatment for recurrent urinary tract infections - ICI-RS 2018.},
journal = {Neurourology and urodynamics},
volume = {38 Suppl 5},
number = {},
pages = {S90-S97},
doi = {10.1002/nau.24021},
pmid = {31821632},
issn = {1520-6777},
abstract = {BACKGROUND: Recurrent urinary tract infection (rUTI) is a chronic condition and has a significant impact on health-related quality of life. The commonly used definition for rUTI is greater than three episodes in a year or more than two in 6 months. Current diagnostic methods have been used worldwide for over five decades, despite well evidenced criticism. Enhanced culture techniques demonstrate that the microbiome of the bladder is far more complex than previously thought and begs a reappraisal of our current testing. Treatment of rUTI is based on a small number of antibiotic trials with some evidence showing a reduction in the number of positive cultures, but one must be cautious in interpreting the results and weigh against the risk of generation of antimicrobial resistance (AMR).

AIM: The International Consultation on Incontinence-Research Society think tank reviewed the literature with a view to improving investigation, prevention and treatment of rUTI.

METHODS: A multidisciplinary team of experts were invited to present evidence regarding the current diagnostic methods, recent advances related to bladder biome mapping and current treatment strategies, including antibiotic and nonantibiotic options. Current guidelines regarding antibiotic stewardship and concerns regarding AMR were discussed.

DISCUSSION: Outcome of the think tank discussions are summarised with a set of recommendations to inform future research. Particular consideration is given to bacterial survival in the bladder after treatment as well as defects in urothelial barrier function which may play a significant part in the failure to eradicate UTI.},
}

@article {pmid31821163,
year = {2019},
author = {Scudiero, O and Pero, R and Ranieri, A and Terracciano, D and Fimiani, F and Cesaro, A and Gentile, L and Leggiero, E and Laneri, S and Moscarella, E and Mazzaccara, C and Frisso, G and D'Alicandro, G and Limongelli, G and Pastore, L and Calabrò, P and Lombardo, B},
title = {Childhood obesity: an overview of laboratory medicine, exercise and microbiome.},
journal = {Clinical chemistry and laboratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1515/cclm-2019-0789},
pmid = {31821163},
issn = {1437-4331},
abstract = {In the last few years, a significant increase of childhood obesity incidence unequally distributed within countries and population groups has been observed, thus representing an important public health problem associated with several health and social consequences. Obese children have more than a 50% probability of becoming obese adults, and to develop pathologies typical of obese adults, that include type 2-diabetes, dyslipidemia and hypertension. Also environmental factors, such as reduced physical activity and increased sedentary activities, may also result in increased caloric intake and/or decreased caloric expenditure. In the present review, we aimed to identify and describe a specific panel of parameters in order to evaluate and characterize the childhood obesity status useful in setting up a preventive diagnostic approach directed at improving health-related behaviors and identifying predisposing risk factors. An early identification of risk factors for childhood obesity could definitely help in setting up adequate and specific clinical treatments.},
}

@article {pmid31821133,
year = {2019},
author = {Mathee, K and Cickovski, T and Deoraj, A and Stollstorff, M and Narasimhan, G},
title = {The gut microbiome and neuropsychiatric disorders: implications for attention deficit hyperactivity disorder (ADHD).},
journal = {Journal of medical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1099/jmm.0.001112},
pmid = {31821133},
issn = {1473-5644},
abstract = {Neuropsychiatric disorders (NPDs) such as depression, anxiety, bipolar disorder, autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) all relate to behavioural, cognitive and emotional disturbances that are ultimately rooted in disordered brain function. More specifically, these disorders are linked to various neuromodulators (i.e. serotonin and dopamine), as well as dysfunction in both cognitive and socio-affective brain networks. Increasing evidence suggests that the gut environment, and particularly the microbiome, plays a significant role in individual mental health. Although the presence of a gut-brain communication axis has long been established, recent studies argue that the development and regulation of this axis is dictated by the gut microbiome. Many studies involving both animals and humans have connected the gut microbiome with depression, anxiety and ASD. Microbiome-centred treatments for individuals with these same NPDs have yielded promising results. Despite its recent rise and underlying similarities to other NPDs, both biochemically and symptomatically, connections between the gut microbiome and ADHD currently lag behind those for other NPDs. We demonstrate that all evidence points to the importance of, and dire need for, a comprehensive and in-depth analysis of the role of the gut microbiome in ADHD, to deepen our understanding of a condition that affects millions of individuals worldwide.},
}

@article {pmid31821114,
year = {2019},
author = {Garrett, KA and Alcala-Briseno, R and Andersen, KF and Brawner, J and Choudhury, R and Delaquis, E and Fayette, J and Poudel, R and Purves, D and Rothschild, J and Small, I and Thomas-Sharma, S and Xing, Y},
title = {Effective altruism as an ethical lens on research priorities.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-05-19-0168-RVW},
pmid = {31821114},
issn = {0031-949X},
abstract = {Effective altruism is an ethical framework for identifying the greatest potential benefits from investments. Here we apply effective altruism concepts to maximize research benefits, in terms of priority stakeholders, pathosystems, and research questions and technologies. Priority stakeholders for research benefits may include smallholder farmers who have not yet attained the minimal standards of the UN Sustainable Development Goals; these farmers would often have the most to gain from better crop disease management, if their management problems are tractable. In wildlands, prioritization has been based on the risk of extirpating keystone species. Pathosystems may be prioritized based on yield and quality loss, and also factors such as whether replacement of efforts is unlikely, such as for orphan crops and orphan pathosystems. Research products that help build sustainable and resilient systems can be particularly beneficial. The "value of information" from research can be evaluated in epidemic networks and landscapes, to identify priority locations for both benefits to individuals and benefits to constrain regional epidemics. As decision-making becomes more consolidated and data more networked in digital agricultural systems, the range of ethical considerations expands. Low likelihood but high damage scenarios, such as generalist doomsday pathogens, may be research priorities because of the extreme cost if they were to occur. Regional microbiomes constitute a commons, and avoiding the 'tragedy of the microbiome commons' may depend on shifting research products from 'common pool goods' to 'public goods' or other categories. We provide suggestions for how individual researchers and funders may make altruism-driven research more effective.},
}

@article {pmid31820774,
year = {2019},
author = {Jiang, Y and Liu, Y and Gao, M and Xue, M and Wang, Z and Liang, H},
title = {Nicotinamide riboside alleviates alcohol-induced depression-like behaviours in C57BL/6J mice by altering the intestinal microbiota associated with microglial activation and BDNF expression.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9fo01780a},
pmid = {31820774},
issn = {2042-650X},
abstract = {The gut microbiota play an important role in many central nervous system diseases through the gut microbiota-brain axis. Recent studies suggest that nicotinamide riboside (NR) has neuroprotective properties. However, it is unknown whether NR can prevent or protect against alcohol-induced depression. Furthermore, it is unclear whether its therapeutic action involves changes in the composition of the gut microbiome. Here, we investigated the effects of NR in the mouse model of alcohol-induced depression. Treatment with NR improved the alcohol-induced depressive behaviour in mice. In addition, NR decreased the number of activated microglia in the hippocampus, and it reduced the levels of pro-inflammatory (IL-1β, IL-6, and TNF-α) and anti-inflammatory (IL-10 and TGF-β) cytokines in the brain of mice with alcohol-induced depression. Furthermore, NR significantly upregulated BDNF and diminished the inhibition of the AKT/GSK3β/β-catenin signalling pathway in the hippocampus of these mice. 16S rRNA sequencing revealed that, compared with control and NR-treated mice, the gut microbiome richness and composition were significantly altered in the depressed mice. Spearman's correlation analysis showed that differential gut bacterial genera correlated with the levels of inflammation-related cytokines and BDNF in the brain. After faecal microbiota transplantation, cognitive behaviours, microglial activity, levels of cytokines and BDNF, and activation state of the AKT/GSK3β/β-catenin signalling pathway (which is downstream of the BDNF receptor, TrkB) in recipient mice were similar to those in donor mice. Collectively, our findings show that NR dietary supplementation protects against alcohol-induced depression-like behaviours, possibly by altering the composition of the gut microbiota.},
}

@article {pmid31820171,
year = {2019},
author = {Chavira, A and Belda-Ferre, P and Kosciolek, T and Ali, F and Dorrestein, PC and Knight, R},
title = {The Microbiome and Its Potential for Pharmacology.},
journal = {Handbook of experimental pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1007/164_2019_317},
pmid = {31820171},
issn = {0171-2004},
abstract = {The human microbiota (the microscopic organisms that inhabit us) and microbiome (their genes) hold considerable potential for improving pharmacological practice. Recent advances in multi-"omics" techniques have dramatically improved our understanding of the constituents of the microbiome and their functions. The implications of this research for human health, including microbiome links to obesity, drug metabolism, neurological diseases, cancer, and many other health conditions, have sparked considerable interest in exploiting the microbiome for targeted therapeutics. Links between microbial pathways and disease states further highlight a rich potential for companion diagnostics and precision medicine approaches. For example, the success of fecal microbiota transplantation to treat Clostridium difficile infection has already started to redefine standard of care with a microbiome-directed therapy. In this review we briefly discuss the nature of human microbial ecosystems and with pathologies and biological processes linked to the microbiome. We then review emerging computational metagenomic, metabolomic, and wet lab techniques researchers are using today to learn about the roles host-microbial interactions have with respect to pharmacological purposes and vice versa. Finally, we describe how drugs affect the microbiome, how the microbiome can impact drug response in different people, and the potential of the microbiome itself as a source of new therapeutics.},
}

@article {pmid31820145,
year = {2019},
author = {Mutalib, M},
title = {Renal involvement in paediatric inflammatory bowel disease.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00467-019-04413-5},
pmid = {31820145},
issn = {1432-198X},
abstract = {Inflammatory bowel disease (IBD), which includes Crohn's disease, ulcerative colitis and inflammatory bowel disease unclassified, is a chronic inflammatory disorder that predominantly affects the gastrointestinal (GI) tract and has a rising incidence in both children and adults. Symptoms are caused by inappropriate inflammatory response triggered by interaction between the environment, gut microbiome and host immune system in a genetically susceptible individual. Extranintestinal manifestations of IBD are common and can affect any body system outside the gut; they can precede or run parallel to GI inflammation. Renal involvement in IBD is uncommon and can be part of extraintestinal manifestation or metabolic complications of IBD. Many medications used to treat IBD can cause renal damage. Renal manifestation in children with IBD can range from asymptomatic biochemical abnormalities to variable stages of renal impairment with significant morbidity and even mortality burden.},
}

@article {pmid31820107,
year = {2019},
author = {Wu, Y and Bible, PW and Long, S and Ming, WK and Ding, W and Long, Y and Wen, X and Li, X and Deng, X and Deng, Y and Guo, S and Doçi, CL and Wei, L and Chen, H and Wang, Z},
title = {Metagenomic analysis reveals gestational diabetes mellitus-related microbial regulators of glucose tolerance.},
journal = {Acta diabetologica},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00592-019-01434-2},
pmid = {31820107},
issn = {1432-5233},
support = {2015A030313198//Natural Science of Guangdong Province, China/ ; 17ykpy24//Youth cultivation project of Sun Yat-sen University, China/ ; 2012004//Clinical Medical Project 5010 of Sun Yat-sen University, China/ ; 81771606//National Natural Science Foundation of China/ ; 81571452//National Natural Science Foundation of China/ ; },
abstract = {AIMS: Recent studies have suggested a possible association between microbiota and gestational diabetes (GDM). However, the results are inconsistent. Our objective was to investigate further the relationship between GDM and microbiota and verify the potential microbial marker.

METHODS: Two complementary approaches were used for the demonstration. First, we compared the gut microbial composition of 23 GDM patients and 26 non-GDM ethnically Chinese Han pregnant women, by using whole-metagenome shotgun sequencing of their stool samples collected at the third trimester. Second, we used Q-PCR (quantitative polymerase chain reaction) to evaluate the gut microbial composition in the stool samples from another cohort of 150 Chinese pregnant women (113 Control and 37 GDM), to further confirm the potential microbial marker.

RESULTS: The gut microbiota of GDM women show lower albeit not statistically significant (p = 0.18) alpha diversity at the species level than non-GDM women. However, the species-level beta-diversity or between-sample diversity measured by Bray-Curtis distance shows significant differences (p < 2.2e-16) between the two groups. The species Bacteroides dorei positively correlated with both OGTT (oral glucose tolerance test) 0-Hour (p = 0.0099) and OGTT 1-Hour (p = 0.0070). There is a similar trend between Bacteroides sp. 3_1_33FAA and both OGTT 0-Hour (p = 0.014) and OGTT 1-Hour (p = 0.0101) response variables. The species Alistipes putredinis negatively correlated with OGTT 1-Hour (p = 0.0172) and OGTT 2-Hour (p = 0.0147). Q-PCR validation further confirmed the association between the glucose tolerance loci of Bacteroides dorei and OGTT response.

CONCLUSIONS: Gut microbiome is related to the diabetic status of Chinese women during pregnancy. Specific species such as Bacteroides dorei associate with glucose response and could be potential monitoring and therapeutic microbial markers for GDM.},
}

@article {pmid31820070,
year = {2019},
author = {Tyx, RE and Rivera, AJ and Keong, LM and Stanfill, SB},
title = {An exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10232-3},
pmid = {31820070},
issn = {1432-0614},
abstract = {Smokeless tobacco (ST) products are used worldwide and are a major public health concern. In addition to harmful chemicals found in these products, microbes found in ST products are believed to be responsible for generating harmful tobacco-specific nitrosamines (TSNAs), the most abundant carcinogens in ST. These microbes also contribute endotoxins and other pro-inflammatory components. A greater understanding of the microbial constituents in these products is sought in order to potentially link select design aspects or manufacturing processes to avoidable increases in harmful constituents. Previous studies looked primarily at bacterial constituents and had not differentiated between viable vs nonviable organisms, so in this study, we sought to use a dual metatranscriptomic and metagenomic analysis to see if differences exist. Using high-throughput sequencing, we observed that there were differences in taxonomic abundances between the metagenome and metatranscriptome, and in the metatranscriptome, we also observed an abundance of plant virus RNA not previously reported in DNA-only studies. We also found in the product tested, that there were no viable bacteria capable of metabolizing nitrate to nitrite. Therefore, the product tested would not be likely to increase TSNAs during shelf storage. We tested only a single product to date using the strategy presented here, but succeeded in demonstrating the value of using of these methods in tobacco products. These results present novel findings from the first combined metagenome and metatranscriptome of a commercial tobacco product.},
}

@article {pmid31819862,
year = {2019},
author = {Niina, A and Kibe, R and Suzuki, R and Yuchi, Y and Teshima, T and Matsumoto, H and Kataoka, Y and Koyama, H},
title = {Improvement in Clinical Symptoms and Fecal Microbiome After Fecal Microbiota Transplantation in a Dog with Inflammatory Bowel Disease.},
journal = {Veterinary medicine (Auckland, N.Z.)},
volume = {10},
number = {},
pages = {197-201},
doi = {10.2147/VMRR.S230862},
pmid = {31819862},
issn = {2230-2034},
abstract = {Purpose: Recently, fecal microbiota transplantation (FMT) has been tested in veterinary medicine as a treatment option for multiple gastrointestinal (GI) diseases, such as inflammatory bowel disease (IBD). However, there are no reports of changes in the microbial diversity of fecal microbiome after treatment with FMT in canine IBD cases. Moreover, little is known about the long-term efficacy and safety of FMT treatment for dogs. Herein, we present a case of canine intractable IBD treated with repeated, long-term FMT.

Patients and methods: The patient was a 10-year-old, neutered, male, 4-kg Toy Poodle with a prolonged history of vomiting and diarrhea. Fecal examination for pathogens was negative. Despite treatment with multiple antibacterial and antidiarrheal agents, the patient showed no improvement. Endoscopic mucus sampling diagnosed a case of lymphocytic-plasmacytic duodenitis, ie, idiopathic IBD. Eventually, we performed periodic, long-term fecal microbiota transplantation of fresh donor feces collected from a 4-year-old, 32.8-kg, neutered male Golden Retriever by rectal enema. Additionally, we performed 16S rRNA sequence analysis, before and after FMT, to evaluate the microbiome diversity.

Results: Fecal microbiome diversity after FMT resembled that of the healthy donor dog's fecal microbiome, before FMT, which led us to conclude that the fecal microbiome in our patient normalized with FMT. Moreover, the clinical symptoms improved remarkably with regard to the changes in the fecal microbiome. Additionally, we noted no observable side effects during FMT treatment.

Conclusion: This report indicates the efficacy and safety of long-term, periodic FMT for a case of canine IBD based on attenuation of clinical symptoms and changes in fecal microbiome diversity. Therefore, FMT could be chosen as a treatment option for IBD in canines in the future.},
}

@article {pmid31819070,
year = {2019},
author = {Weinberg, RP and Koledova, VV and Subramaniam, A and Schneider, K and Artamonova, A and Sambanthamurthi, R and Hayes, KC and Sinskey, AJ and Rha, C},
title = {Palm Fruit Bioactives augment expression of Tyrosine Hydroxylase in the Nile Grass Rat basal ganglia and alter the colonic microbiome.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18625},
doi = {10.1038/s41598-019-54461-y},
pmid = {31819070},
issn = {2045-2322},
abstract = {Tyrosine hydroxylase (TH) catalyzes the hydroxylation of L-tyrosine to L-DOPA. This is the rate-limiting step in the biosynthesis of the catecholamines - dopamine (DA), norepinephrine (NE), and epinephrine (EP). Catecholamines (CA) play a key role as neurotransmitters and hormones. Aberrant levels of CA are associated with multiple medical conditions, including Parkinson's disease. Palm Fruit Bioactives (PFB) significantly increased the levels of tyrosine hydroxylase in the brain of the Nile Grass rat (NGR), a novel and potentially significant finding, unique to PFB among known botanical sources. Increases were most pronounced in the basal ganglia, including the caudate-putamen, striatum and substantia nigra. The NGR represents an animal model of diet-induced Type 2 Diabetes Mellitus (T2DM), exhibiting hyperglycemia, hyperinsulinemia, and insulin resistance associated with hyperphagia and accelerated postweaning weight gain induced by a high-carbohydrate diet (hiCHO). The PFB-induced increase of TH in the basal ganglia of the NGR was documented by immuno-histochemical staining (IHC). This increase in TH occurred equally in both diabetes-susceptible and diabetes-resistant NGR fed a hiCHO. PFB also stimulated growth of the colon microbiota evidenced by an increase in cecal weight and altered microbiome. The metabolites of colon microbiota, e.g. short-chain fatty acids, may influence the brain and behavior significantly.},
}

@article {pmid31818878,
year = {2019},
author = {Choucair, I and Nemet, I and Li, L and Cole, MA and Skye, SM and Kirsop, JD and Fischbach, M and Gogonea, V and Brown, JM and Tang, WHW and Hazen, SL},
title = {Quantification of bile acids: A mass spectrometry platform for studying gut microbe connection to metabolic diseases.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {},
doi = {10.1194/jlr.RA119000311},
pmid = {31818878},
issn = {1539-7262},
abstract = {Bile acids (BAs) serve multiple biological functions, ranging from absorption of lipids and fat-soluble vitamins, to serving as signaling molecules through the direct activation of dedicated cellular receptors. Synthesized by both host and microbial pathways, BAs are increasingly appreciated to participate in the regulation of numerous pathways relevant to metabolic diseases including lipid and glucose metabolism, energy expenditure and inflammation, pathways relevant to metabolic diseases. Quantitative analyses of BAs in biological matrices can be problematic due to their unusual and diverse physicochemical properties, making optimization of a method that shows good accuracy, precision, efficiency of extraction, and minimized matrix effects across structurally distinct human and murine BAs challenging. Herein we develop and clinically validate a stable isotope dilution liquid chromatography-tandem mass spectrometry (LC/MS/MS) method for the quantitative analysis of numerous primary and secondary BAs in both human and mouse biological matrices. We also utilize this tool to investigate gut microbiota participation in generation of structurally specific BAs in both humans and mice. We examine circulating levels of specific BAs and in a clinical case-control study of age- and gender-matched type 2 diabetics (T2DM) versus non-diabetics. BAs whose circulating levels are associated with T2DM include numerous 12α-hydroxyl BAs (taurocholic acid, taurodeoxycholic acid, glycodeoxycholic acid, deoxycholic acid and 3-ketodeoxycholic acid), while taurohyodeoxycholic acid was negatively associated with diabetes. The LC/MS/MS based platform described should serve as a robust, high throughput investigative tool for studying the potential involvement of structurally specific BAs and the gut microbiome on both physiological and disease processes.},
}

@article {pmid31818666,
year = {2019},
author = {He, X and Qi, Z and Hou, H and Gao, J and Zhang, XX},
title = {Effects of chronic cadmium exposure at food limitation-relevant levels on energy metabolism in mice.},
journal = {Journal of hazardous materials},
volume = {},
number = {},
pages = {121791},
doi = {10.1016/j.jhazmat.2019.121791},
pmid = {31818666},
issn = {1873-3336},
abstract = {Cadmium (Cd) exposure has been implicated in the perturbation of energy metabolism and the development of cardiometabolic disease, but disease predisposition from chronic low-dose Cd exposure remains unclear. This study employed a mouse model to investigate the toxic effects of chronic Cd exposure at food limitation-relevant levels on energy metabolism and the associated liver and gut microbiome functions. Results showed that the Cd exposure induced the perturbation of energy metabolism in mice, evidenced by the alteration of various metabolites associated with the phosphorogen (adenosine triphosphate-creatine phosphate) system, tricarboxylic acid cycle, and lipid metabolism, as well as the increase of the cardiometabolic risk factor, triglyceride. Moreover, both liver and gut microbiome underwent marked structural/histological and functional alterations, prone to the onset of cardiometabolic disease following the Cd exposure. Certain hepatic transcription factors and gut microbes, specifically PPARα, SREBP1c, HNF4A and the Clostridiales_vadinBB60_group, were identified to be highly correlated with altered urinary metabolites, revealing potential toxicological interactions between the liver and gut microbiome, and energy metabolism. Our findings provide new insights into the progression of metabolic diseases induced by Cd exposure. We also propose a stricter Cd limitation in future food safety standards.},
}

@article {pmid31818660,
year = {2019},
author = {Liu, YJ and Qiao, NH and Diao, QY and Jing, Z and Vukanti, R and Dai, PL and Ge, Y},
title = {Thiacloprid exposure perturbs the gut microbiota and reduces the survival status in honeybees.},
journal = {Journal of hazardous materials},
volume = {},
number = {},
pages = {121818},
doi = {10.1016/j.jhazmat.2019.121818},
pmid = {31818660},
issn = {1873-3336},
abstract = {Honeybees (Apis mellifera) offer ecosystem services such as pollination, conservation of biodiversity, and provision of food. However, in recent years, the number of honeybee colonies is diminishing rapidly, which is probably linked to the wide use of neonicotinoid insecticides. Middle-aged honeybees were fed with 50% (w/v) sucrose solution containing 0, 0.2, 0.6, and 2.0 mg/L thiacloprid (a neonicotinoid insecticide) for up to 13 days, and on each day of exposure experiment, percentage survival, sucrose consumption, and bodyweight of honeybees were measured. Further, changes in honeybee gut microbial community were examined using next-generation 16S rDNA amplicon sequencing on day 1, 7, and 13 of the exposure. When compared to control-treatment, continuous exposure to high (0.6 mg/L) and very high (2.0 mg/L) concentrations of thiacloprid significantly reduced percentage survival of honeybees (p < 0.001) and led to dysbiosis of their gut microbial community on day 7 of the exposure. However, during subsequent developmental stages of middle-aged honeybees (i.e. on day 13), their gut microbiome recovered from dysbiosis that occurred previously due to thiacloprid exposure. Taken together, improper application of thiacloprid can cause loss of honeybee colonies, while the microbial gut community of honeybee is an independent variable in this process.},
}

@article {pmid31818598,
year = {2019},
author = {Nguyen, BT and Chen, QL and He, JZ and Hu, HW},
title = {Microbial regulation of natural antibiotic resistance: Understanding the protist-bacteria interactions for evolution of soil resistome.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {135882},
doi = {10.1016/j.scitotenv.2019.135882},
pmid = {31818598},
issn = {1879-1026},
abstract = {The emergence, evolution and spread of antibiotic resistance genes (ARGs) in the environment represent a global threat to human health. Our knowledge of antibiotic resistance in human-impacted ecosystems is rapidly growing with antibiotic use, organic fertilization and wastewater irrigation identified as key selection pressures. However, the importance of biological interactions, especially predation and competition, as a potential driver of antibiotic resistance in the natural environment with limited anthropogenic disturbance remains largely overlooked. Stress-affected bacteria develop resistance to maximize competition and survival, and similarly bacteria may develop resistance to fight stress under the predation pressure of protists, an essential component of the soil microbiome. In this article, we summarized the major findings for the prevalence of natural ARGs on our planet and discussed the potential selection pressures driving the evolution and development of antibiotic resistance in natural settings. This is the first article that reviewed the potential links between protists and the antibiotic resistance of bacteria, and highlighted the importance of predation by protists as a crucial selection pressure of antibiotic resistance in the absence of anthropogenic disturbance. We conclude that an improved ecological understanding of the protists-bacteria interactions and other biological relationships would greatly expand our ability to predict and mitigate the environmental antibiotic resistance under the context of global change.},
}

@article {pmid31818597,
year = {2019},
author = {Zadel, U and Nesme, J and Michalke, B and Vestergaard, G and Płaza, GA and Schröder, P and Radl, V and Schloter, M},
title = {Changes induced by heavy metals in the plant-associated microbiome of Miscanthus x giganteus.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {134433},
doi = {10.1016/j.scitotenv.2019.134433},
pmid = {31818597},
issn = {1879-1026},
abstract = {Miscanthus x giganteus is a high biomass producing plant with tolerance to heavy metals. This makes Miscanthus interesting to be used for phytoremediation of heavy metal contaminated areas coupled with energy production. Since plant performance in metal polluted areas is impaired, their growth and phytoremediation effect can be improved with bacterial assistance. To identify positive and negative responders of M. x giganteus associated microbiome influenced by Cd, Pb and Zn stress compared to non-contaminated controls, we designed a greenhouse experiment. Structure of the bacterial community in three rhizocompartments, namely rhizosphere, rhizoplane and root endosphere was analysed using an isolation independent molecular approach based on 16S rRNA gene barcoding. Furthermore, quantitative PCR (qPCR) was used for bacterial biomass estimation. Our results indicated that biomass and total bacterial diversity in rhizosphere, rhizoplane and root endosphere did not significantly change despite of substantial root uptake of heavy metals. Overall, we detected 6621 OTUs, from which 171 were affected by metal addition. Whereas Streptomyces and Amycolatopsis taxa were negatively affected by the heavy metal treatment in endosphere, taxa assigned to Luteolibacter in rhizosphere and rhizoplane (log2 fold change 1.9-4.1) and Micromonospora in endosphere (log2 fold change 10.2) were found to be significantly enriched and highly abundant (0.1-3.7% relative abundance) under heavy metal stress. Those taxa might be of key importance for M. x giganteus performance under heavy metal pollution and might be interesting candidates for the development of new bioinocula in the future to promote plant growth and phytoremediation in heavy metal contaminated soils.},
}

@article {pmid31818595,
year = {2019},
author = {Brereton, NJB and Gonzalez, E and Desjardins, D and Labrecque, M and Pitre, FE},
title = {Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {135067},
doi = {10.1016/j.scitotenv.2019.135067},
pmid = {31818595},
issn = {1879-1026},
abstract = {Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.},
}