@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},
pmid = {31830061},
issn = {1932-6203},
mesh = {Adolescent ; Adult ; Chlamydia Infections/immunology/*microbiology ; Chlamydia trachomatis/genetics/immunology/isolation & purification ; DNA, Bacterial/isolation & purification ; Female ; Humans ; Microbiota/genetics/*immunology ; Pregnancy ; Pregnancy Complications, Infectious/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trichomonas Vaginitis/immunology/*microbiology ; Trichomonas vaginalis/genetics/immunology/isolation & purification ; Vagina/*microbiology ; Young Adult ; },
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.},
}

Adolescent
Adult
Chlamydia Infections/immunology/*microbiology
Chlamydia trachomatis/genetics/immunology/isolation & purification
DNA, Bacterial/isolation & purification
Female
Humans
Microbiota/genetics/*immunology
Pregnancy
Pregnancy Complications, Infectious/immunology/*microbiology
RNA, Ribosomal, 16S/genetics
Trichomonas Vaginitis/immunology/*microbiology
Trichomonas vaginalis/genetics/immunology/isolation & purification
Vagina/*microbiology
Young Adult

@article {pmid31818595,
year = {2020},
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 = {711},
number = {},
pages = {135067},
doi = {10.1016/j.scitotenv.2019.135067},
pmid = {31818595},
issn = {1879-1026},
mesh = {Biodegradation, Environmental ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S ; Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; },
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.},
}

Biodegradation, Environmental
*Microbiota
Plant Roots
RNA, Ribosomal, 16S
Rhizosphere
Soil
*Soil Microbiology
Soil Pollutants

@article {pmid31739640,
year = {2019},
author = {Liang, YX and Wen, P and Wang, Y and OuYang, DM and Wang, D and Chen, YZ and Song, Y and Deng, J and Sun, YM and Wang, H},
title = {The Constipation-Relieving Property of d-Tagatose by Modulating the Composition of Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {20},
number = {22},
pages = {},
pmid = {31739640},
issn = {1422-0067},
support = {2016YFE0106000//National Key R&D Program of China/ ; No. 2019B020211002//Key Area R&D Program of Guangdong Province/ ; 201804020077//Science and Technology Planning Project of Guangzhou City/ ; 2019SCAUGH03//International Cooperation Program of SCAU/ ; 2017//Project Supported by Guangdong Province Universities and Colleges Pearl River Scholar Funded Scheme/ ; },
mesh = {Animals ; Biodiversity ; Constipation/drug therapy ; Defecation/drug effects ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Transit/drug effects ; Hexoses/*pharmacology ; Metagenomics ; Mice ; Neurotransmitter Agents/blood ; Prebiotics ; RNA, Ribosomal, 16S ; },
abstract = {d-tagatose, a monosaccharide as well as a dietary supplement, has been reported as having a wide range of applicability in the food industry, however, the prebiotic activity, anticonstipation effects, and related mechanisms are still unclear. In this study, using the loperamide-induced constipation Kunming mice as the animal model, the effects of d-tagatose for the prevention of constipation were evaluated by gastrointestinal transit experiment and defecation experiment. Furthermore, the underlying mechanism was clarified by evaluating the change of the biochemical indicators and analyzing 16S rRNA amplicon of gut microbiota among the different mice groups. The results showed that the gastrointestinal transit rate, fecal number, and weight in six hours were significantly enhanced after the administration of d-tagatose. In addition, d-tagatose significantly increased the serum levels of acetylcholine (Ach) and substance P (SP), whereas the serum levels of nitric oxide (NO) were significantly decreased. Moreover, the 16S rRNA sequencing analysis revealed that the changes in the gut microbiota caused by constipation were restored by d-tagatose treatment. In conclusion, this study indicated that the administration of d-tagatose as a dietary supplement can effectively prevent and relieve constipation in Kunming mice, and it is a promising prebiotic candidate with constipation-relieving properties.},
}

Animals
Biodiversity
Constipation/drug therapy
Defecation/drug effects
Gastrointestinal Microbiome/*drug effects
Gastrointestinal Transit/drug effects
Hexoses/*pharmacology
Metagenomics
Mice
Neurotransmitter Agents/blood
Prebiotics
RNA, Ribosomal, 16S

@article {pmid31605691,
year = {2020},
author = {Dubinsky, V and Reshef, L and Bar, N and Keizer, D and Golan, N and Rabinowitz, K and Godny, L and Yadgar, K and Zonensain, K and Tulchinsky, H and Gophna, U and Dotan, I},
title = {Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.},
journal = {Gastroenterology},
volume = {158},
number = {3},
pages = {610-624.e13},
doi = {10.1053/j.gastro.2019.10.001},
pmid = {31605691},
issn = {1528-0012},
mesh = {Adult ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Bacteria/*drug effects/genetics/isolation & purification ; Ciprofloxacin/pharmacology/therapeutic use ; Cytokines/metabolism ; Drug Resistance, Bacterial/*drug effects/genetics ; Feces/chemistry/*microbiology ; Female ; Gastrointestinal Microbiome/drug effects ; HT29 Cells/metabolism ; Humans ; Leukocyte L1 Antigen Complex/analysis ; Male ; Metagenomics ; Metronidazole/therapeutic use ; Middle Aged ; Point Mutation ; Pouchitis/*drug therapy/*microbiology ; Prospective Studies ; Recurrence ; Treatment Outcome ; Virulence Factors/metabolism ; Young Adult ; },
abstract = {BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic-dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis.

METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent-acute pouchitis (n = 6), chronic pouchitis and Crohn's-like disease of the pouch (n = 27), normal pouch from patient with ulcerative colitis (n = 10), and normal pouch from patient with familial adenomatous polyposis (n = 6). Fecal samples (n = 234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow-up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by HT-29 intestinal epithelial cells.

RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics; however, 89% of those who completed a 4-week course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae, but also beneficial species, such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to nonrelated antibiotics, including extended-spectrum beta-lactamases.

CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of an antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.},
}

Adult
Anti-Bacterial Agents/pharmacology/*therapeutic use
Bacteria/*drug effects/genetics/isolation & purification
Ciprofloxacin/pharmacology/therapeutic use
Cytokines/metabolism
Drug Resistance, Bacterial/*drug effects/genetics
Feces/chemistry/*microbiology
Female
Gastrointestinal Microbiome/drug effects
HT29 Cells/metabolism
Humans
Leukocyte L1 Antigen Complex/analysis
Male
Metagenomics
Metronidazole/therapeutic use
Middle Aged
Point Mutation
Pouchitis/*drug therapy/*microbiology
Prospective Studies
Recurrence
Treatment Outcome
Virulence Factors/metabolism
Young Adult

@article {pmid31319276,
year = {2019},
author = {Harvey, E and Rose, K and Eden, JS and Lawrence, A and Doggett, SL and Holmes, EC},
title = {Identification of diverse arthropod associated viruses in native Australian fleas.},
journal = {Virology},
volume = {535},
number = {},
pages = {189-199},
doi = {10.1016/j.virol.2019.07.010},
pmid = {31319276},
issn = {1096-0341},
mesh = {Animals ; Australia ; *Biodiversity ; Gene Expression Profiling ; Insect Vectors/virology ; Metagenomics ; Phylogeny ; RNA Viruses/*classification/genetics/*isolation & purification ; Siphonaptera/*virology ; },
abstract = {Fleas are important vectors of zoonotic disease. However, little is known about the natural diversity and abundance of flea viruses, particularly in the absence of disease associations, nor the evolutionary relationships among those viruses found in different parasitic vector species. Herein, we present the first virome scale study of fleas, based on the meta-transcriptomic analysis of 52 fleas collected along the eastern coast of Australia. Our analysis revealed 18 novel RNA viruses belonging to nine viral families with diverse genome organizations, although the majority (72%) possessed single-stranded positive-sense genomes. Notably, a number of the viruses identified belonged to the same phylogenetic groups as those observed in ticks sampled at the same locations, although none were likely associated with mammalian infection. Overall, we identified high levels of genomic diversity and abundance of viruses in the flea species studied, and established that fleas harbor viruses similar to those seen to other vectors.},
}

Animals
Australia
*Biodiversity
Gene Expression Profiling
Insect Vectors/virology
Metagenomics
Phylogeny
RNA Viruses/*classification/genetics/*isolation & purification
Siphonaptera/*virology

@article {pmid30981666,
year = {2019},
author = {Wang, JJ and Zhang, RQ and Zhai, QY and Liu, JC and Li, N and Liu, WX and Li, L and Shen, W},
title = {Metagenomic analysis of gut microbiota alteration in a mouse model exposed to mycotoxin deoxynivalenol.},
journal = {Toxicology and applied pharmacology},
volume = {372},
number = {},
pages = {47-56},
doi = {10.1016/j.taap.2019.04.009},
pmid = {30981666},
issn = {1096-0333},
mesh = {Animals ; Bacteria/*drug effects/genetics/metabolism ; Cecum/*drug effects/microbiology ; DNA, Bacterial/*genetics ; Dysbiosis ; Feces/microbiology ; *Food Microbiology ; Gastrointestinal Microbiome/*drug effects ; *Genome, Bacterial ; Metagenomics/*methods ; Mice ; Trichothecenes/*toxicity ; },
abstract = {As one of the most prevalent contaminants in animal and human food, the deleterious effects of trichothecene mycotoxin deoxynivalenol (DON) warrant extensive investigation. Here, to assess the effects of DON exposure to the populations of gut microbiota, four-weeks-old mice were exposed to different doses (1.0 and 5.0 mg/kg) of DON every two days for 14 days. The contents of the cecum were then collected for DNA extraction and metagenomic shotgun sequencing, in order to detect alterations of the gut microbiota. We found that the average body weight and daily gain in the high dose DON treated group decreased. Metagenomic analysis demonstrated that the relative abundance of Firmicutes in the low and Bacteroidetes in the high dose groups increased compared to that in the untreated control group. Moreover, using gene calling and functional annotation, we found that large numbers of biosynthesis and degradation dependent populations were altered. As a result, metabolism pathways including sphingolipid, protein digestion/absorption, and lipoic acid pathways in the high dose DON exposed group dramatically fluctuated in comparison to the control and low dose groups. In addition, metagenomic binning identified ten microbiota genome drafts, with high levels of completeness, that further explain the DON-induced intestinal toxicity. Our findings suggested that DON exposure significantly impacted the microbiota community in the mouse, causing biosynthesis and degradation damage and metabolism pathway disorders.},
}

Animals
Bacteria/*drug effects/genetics/metabolism
Cecum/*drug effects/microbiology
DNA, Bacterial/*genetics
Dysbiosis
Feces/microbiology
*Food Microbiology
Gastrointestinal Microbiome/*drug effects
*Genome, Bacterial
Metagenomics/*methods
Mice
Trichothecenes/*toxicity

@article {pmid30342317,
year = {2019},
author = {Zhou, S and Wang, Z and He, F and Qiu, H and Wang, Y and Wang, H and Zhou, J and Zhou, J and Cheng, G and Zhou, W and Xu, R and Wang, M},
title = {Association of serum bilirubin in newborns affected by jaundice with gut microbiota dysbiosis.},
journal = {The Journal of nutritional biochemistry},
volume = {63},
number = {},
pages = {54-61},
doi = {10.1016/j.jnutbio.2018.09.016},
pmid = {30342317},
issn = {1873-4847},
mesh = {Bifidobacterium/genetics ; Bilirubin/*blood ; Breast Feeding ; Case-Control Studies ; Child, Preschool ; Cholestasis/blood/microbiology ; Dysbiosis/*blood/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Jaundice, Neonatal/*blood/microbiology ; Male ; },
abstract = {BACKGROUND AND AIMS: Breast milk jaundice (BMJ) is common and benign, but neonatal cholestasis (NC) is rare and not benign, so early differentiation between NC and non-NC jaundice is important and may facilitate diagnosis and treatment. Gut microbiota plays an important role in enterohepatic circulation, which in turn plays an important role in the secretion of bilirubin. We aimed to determine the composition of gut microbiota in patients with NC and BMJ, and to identify the gut microbiota composition associated with NC and BMJ.

METHODS: Data on age, gender, delivery, feeding mode, serum total bilirubin, direct bilirubin, and liver function were collected for NC patients, BMJ patients and healthy controls, respectively. Shotgun metagenomic sequencing and metagenome-wide association were performed.

RESULTS: Forty NC patients, 16 patients affected by BMJ, and 14 healthy controls (CON) without jaundice were enrolled. A significant increase in species richness, especially Bacteroides, was found in NC patients. The abundances of potentially pathogenic species and KEGG orthologies (KOs) of virulence factor genes were positively correlated with serum bilirubin level. The abundances of nine species of Bifidobacterium and three KOs of galactose metabolism were significantly decreased in the jaundice group (NC and BMJ) and were negatively correlated with serum bilirubin level.

CONCLUSIONS: The gut microbiota in NC patients is characterized by a significant increase in species richness, possibly due to the proliferation of potentially pathogenic species. Additionally, the gut microbiota in jaundice patients is characterized by a decreased abundance of Bifidobacterium. Decreased Bifidobacterium has been associated with elevated bilirubin and abnormal gut microbiota galactose metabolic pathway. Further, ten bacteria species were identified as potential biomarker of jaundice.

KEY POINTS: Question Is there any alteration of gut microbiotain neonatal cholestasis patients? Does gut microbiota have any involvement in the occurrence of neonatal cholestasis or breast milk jaundice? Findings The alteration of gut microbiota in neonatal cholestasis patients mainly manifested as a significant increase in species richness and an increased abundance of potentially pathogenic species, while the main manifestation in jaundice patients was a significant decrease in Bifidobacterium which may be involved in the metabolism of bilirubin through the galactose metabolic pathway. Meaning The results suggest that an imbalance of gut microbiota exist in neonatal cholestasis and breast milk jaundice patients, primarily in the form of a substantial reduction in the abundance of Bifidobacterium, suggesting the possibility of intervention treatment for neonatal cholestasis and breast milk jaundice by supplementing probiotics.},
}

Bifidobacterium/genetics
Bilirubin/*blood
Breast Feeding
Case-Control Studies
Child, Preschool
Cholestasis/blood/microbiology
Dysbiosis/*blood/microbiology
Female
*Gastrointestinal Microbiome/genetics
Humans
Infant
Infant, Newborn
Jaundice, Neonatal/*blood/microbiology
Male

@article {pmid31726738,
year = {2019},
author = {Liang, YN and Yu, JG and Zhang, DB and Zhang, Z and Ren, LL and Li, LH and Wang, Z and Tang, ZS},
title = {Indigo Naturalis Ameliorates Dextran Sulfate Sodium-Induced Colitis in Mice by Modulating the Intestinal Microbiota Community.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {22},
pages = {},
pmid = {31726738},
issn = {1420-3049},
support = {81803951//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Biopsy ; Colitis/drug therapy/*etiology/metabolism/*pathology ; Cytokines/metabolism ; Dextran Sulfate/*adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Immunohistochemistry ; Indigo Carmine/chemistry/*pharmacology ; Inflammation Mediators/metabolism ; Intestinal Mucosa/drug effects/metabolism/microbiology/pathology ; Metagenomics ; Mice ; Molecular Structure ; RNA, Ribosomal, 16S ; },
abstract = {Indigo naturalis (IN) is a traditional Chinese medicine, named Qing-Dai, which is extracted from indigo plants and has been used to treat patients with inflammatory bowel disease (IBD) in China and Japan. Though there are notable effects of IN on colitis, the mechanisms remain elusive. Regarding the significance of alterations of intestinal flora related to IBD and the poor water solubility of the blue IN powder, we predicted that the protective action of IN on colitis may occur through modifying gut microbiota. To investigate the relationships of IN, colitis, and gut microbiomes, a dextran sulfate sodium (DSS)-induced mice colitis model was tested to explore the protective effects of IN on macroscopic colitis symptoms, the histopathological structure, inflammation cytokines, and gut microbiota, and their potential functions. Sulfasalazine (SASP) was used as the positive control. Firstly, because it was a mixture, the main chemical compositions of indigo and indirubin in IN were detected by ultra-performance liquid chromatography (UPLC). The clinical activity score (CAS), hematoxylin and eosin (H&E) staining results, and enzyme-linked immunosorbent assay (ELISA) results in this study showed that IN greatly improved the health conditions of the tested colitis mice, ameliorated the histopathological structure of the colon tissue, down-regulated pro-inflammatory cytokines, and up-regulated anti-inflammatory cytokines. The results of 16S rDNA sequences analysis with the Illumina MiSeq platform showed that IN could modulate the balance of gut microbiota, especially by down-regulating the relative quantity of Turicibacter and up-regulating the relative quantity of Peptococcus. The therapeutic effect of IN may be closely related to the anaerobic gram-positive bacteria of Turicibacter and Peptococcus. The inferred metagenomes from 16S data using PICRUSt demonstrated that decreased metabolic genes, such as through biosynthesis of siderophore group nonribosomal peptides, non-homologous end-joining, and glycosphingolipid biosynthesis of lacto and neolacto series, may maintain microbiota homeostasis during inflammation from IN treatment in DSS-induced colitis.},
}

Animals
Biopsy
Colitis/drug therapy/*etiology/metabolism/*pathology
Cytokines/metabolism
Dextran Sulfate/*adverse effects
Disease Models, Animal
Gastrointestinal Microbiome/*drug effects
Immunohistochemistry
Indigo Carmine/chemistry/*pharmacology
Inflammation Mediators/metabolism
Intestinal Mucosa/drug effects/metabolism/microbiology/pathology
Metagenomics
Mice
Molecular Structure
RNA, Ribosomal, 16S

@article {pmid31195972,
year = {2019},
author = {Smith, BJ and Miller, RA and Ericsson, AC and Harrison, DC and Strong, R and Schmidt, TM},
title = {Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {130},
pmid = {31195972},
issn = {1471-2180},
support = {U01 AG022307/AG/NIA NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; U01 AG022308/AG/NIA NIH HHS/United States ; U01 AG022303/AG/NIA NIH HHS/United States ; P30 AG024824/AG/NIA NIH HHS/United States ; },
mesh = {Acarbose/*pharmacology ; Animals ; Bacteria/*classification/drug effects/isolation & purification ; Case-Control Studies ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; Female ; Fermentation/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Longevity/*drug effects ; Male ; Mice ; Phylogeny ; Proportional Hazards Models ; },
abstract = {BACKGROUND: Treatment with the α-glucosidase inhibitor acarbose increases median lifespan by approximately 20% in male mice and 5% in females. This longevity extension differs from dietary restriction based on a number of features, including the relatively small effects on weight and the sex-specificity of the lifespan effect. By inhibiting host digestion, acarbose increases the flux of starch to the lower digestive system, resulting in changes to the gut microbiota and their fermentation products. Given the documented health benefits of short-chain fatty acids (SCFAs), the dominant products of starch fermentation by gut bacteria, this secondary effect of acarbose could contribute to increased longevity in mice. To explore this hypothesis, we compared the fecal microbiome of mice treated with acarbose to control mice at three independent study sites.

RESULTS: Microbial communities and the concentrations of SCFAs in the feces of mice treated with acarbose were notably different from those of control mice. At all three study sites, the bloom of a single bacterial taxon was the most obvious response to acarbose treatment. The blooming populations were classified to the largely uncultured Bacteroidales family Muribaculaceae and were the same taxonomic unit at two of the three sites. Propionate concentrations in feces were consistently elevated in treated mice, while the concentrations of acetate and butyrate reflected a dependence on study site. Across all samples, Muribaculaceae abundance was strongly correlated with propionate and community composition was an important predictor of SCFA concentrations. Cox proportional hazards regression showed that the fecal concentrations of acetate, butyrate, and propionate were, together, predictive of mouse longevity even while controlling for sex, site, and acarbose.

CONCLUSION: We observed a correlation between fecal SCFAs and lifespan in mice, suggesting a role of the gut microbiota in the longevity-enhancing properties of acarbose. Treatment modulated the taxonomic composition and fermentation products of the gut microbiome, while the site-dependence of the responses illustrate the challenges facing reproducibility and interpretation in microbiome studies. These results motivate future studies exploring manipulation of the gut microbial community and its fermentation products for increased longevity, testing causal roles of SCFAs in the observed effects of acarbose.},
}

Acarbose/*pharmacology
Animals
Bacteria/*classification/drug effects/isolation & purification
Case-Control Studies
Fatty Acids, Volatile/metabolism
Feces/chemistry/microbiology
Female
Fermentation/*drug effects
Gastrointestinal Microbiome/*drug effects
Longevity/*drug effects
Male
Mice
Phylogeny
Proportional Hazards Models

@article {pmid31738795,
year = {2019},
author = {Cheong, HC and Yap, PSX and Chong, CW and Cheok, YY and Lee, CYQ and Tan, GMY and Sulaiman, S and Hassan, J and Sabet, NS and Looi, CY and Gupta, R and Arulanandam, B and AbuBakar, S and Teh, CSJ and Chang, LY and Wong, WF},
title = {Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224658},
pmid = {31738795},
issn = {1932-6203},
mesh = {Academic Medical Centers ; Adult ; Bacteria, Anaerobic/immunology/isolation & purification ; Cervix Uteri/*microbiology ; Chlamydia Infections/complications/immunology/*microbiology ; Chlamydia trachomatis/*isolation & purification/pathogenicity ; Cohort Studies ; DNA, Bacterial/genetics/isolation & purification ; Female ; Host-Pathogen Interactions/immunology ; Humans ; Infertility/immunology/*microbiology ; Malaysia ; Metagenomics ; Microbiota/genetics/*immunology ; Outpatient Clinics, Hospital ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {The cervical microbiota constitutes an important protective barrier against the invasion of pathogenic microorganisms. A disruption of microbiota within the cervical milieu has been suggested to be a driving factor of sexually transmitted infections. These include Chlamydia trachomatis which frequently causes serious reproductive sequelae such as infertility in women. In this study, we profiled the cervical microbial composition of a population of 70 reproductive-age Malaysian women; among which 40 (57.1%) were diagnosed with genital C. trachomatis infection, and 30 (42.8%) without C. trachomatis infection. Our findings showed a distinct compositional difference between the cervical microbiota of C. trachomatis-infected subjects and subjects without C. trachomatis infection. Specifically, significant elevations of mostly strict and facultative anaerobes such as Streptococcus, Megasphaera, Prevotella, and Veillonella in the cervical microbiota of C. trachomatis-positive women were detected. The results from the current study highlights an interaction of C. trachomatis with the environmental microbiome in the endocervical region.},
}

Academic Medical Centers
Adult
Bacteria, Anaerobic/immunology/isolation & purification
Cervix Uteri/*microbiology
Chlamydia Infections/complications/immunology/*microbiology
Chlamydia trachomatis/*isolation & purification/pathogenicity
Cohort Studies
DNA, Bacterial/genetics/isolation & purification
Female
Host-Pathogen Interactions/immunology
Humans
Infertility/immunology/*microbiology
Malaysia
Metagenomics
Microbiota/genetics/*immunology
Outpatient Clinics, Hospital
RNA, Ribosomal, 16S/genetics
Young Adult

@article {pmid31719228,
year = {2019},
author = {Kuntal, BK and Mande, SS},
title = {Visual exploration of microbiome data.},
journal = {Journal of biosciences},
volume = {44},
number = {5},
pages = {},
pmid = {31719228},
issn = {0973-7138},
mesh = {Metagenomics ; *Microbiota ; },
abstract = {A dramatic increase in large-scale cross-sectional and temporal-level metagenomic experiments has led to an improved understanding of the microbiome and its role in human well-being. Consequently, a plethora of analytical methods has been developed to decipher microbial biomarkers for various diseases, cluster different ecosystems based on microbial content, and infer functional potential of the microbiome as well as analyze its temporal behavior. Development of user-friendly visualization methods and frameworks is necessary to analyze this data and infer taxonomic and functional patterns corresponding to a phenotype. Thus, new methods as well as application of pre-existing ones has gained importance in recent times pertaining to the huge volume of the generated microbiome data. In this review, we present a brief overview of some useful visualization techniques that have significantly enriched microbiome data analytics.},
}

Metagenomics
*Microbiota

@article {pmid31719221,
year = {2019},
author = {Chaudhari, D and Dhotre, D and Agarwal, D and Gondhali, A and Nagarkar, A and Lad, V and Patil, U and Juvekar, S and Sinkar, V and Shouche, Y},
title = {Understanding the association between the human gut, oral and skin microbiome and the Ayurvedic concept of prakriti.},
journal = {Journal of biosciences},
volume = {44},
number = {5},
pages = {},
pmid = {31719221},
issn = {0973-7138},
mesh = {Female ; Humans ; Intestines/*microbiology ; Male ; *Medicine, Ayurvedic ; *Microbiota ; Mouth/*microbiology ; Skin/*microbiology ; },
abstract = {Ayurveda is one of the ancient systems of medicine which is widely practised as a personalized scientific approach towards the general wellness. Ayurvedic prakriti is broadly defined as the phenotypes which are determined on the basis of physical, psychological and physiological traits irrespective of their social, ethnic, dietary and geographical stature. Prakriti is the constitution of a person, which comprises vata, pitta, and kapha and is a key determinant of how one individual is different from the other. Human microbiome is considered the 'latest discovered' human organ and microbiome research reiterates the fundamental principles of Ayurveda for creating a healthy gut environment by maintaining the individual-specific microbiome. Hence, it is important to understand the association of human microbiome with the Ayurvedic prakriti of an individual. Here, we provide a comprehensive analysis of human microbiome from the gut, oral and skin samples of healthy individuals (n=18) by 16S rRNA gene-based metagenomics using standard QIIME pipeline. In the three different prakriti samples differential abundance of Bacteroides, Desulfovibrio, Parabacteroides, Slackia, and Succinivibrio was observed in the gut microbiome. Analysis also revealed prakriti-specific presence of Mogibacterium, Propionibacterium, Pyramidobacter, Rhodococcus in the kapha prakriti individuals Planomicrobium, Hyphomicrobium, Novosphingobium in the pitta prakriti individuals and Carnobacterium, Robiginitalea, Cetobacterium, Psychrobacter in the vata prakriti individuals. Similarly, the oral and skin microbiome also revealed presence of prakriti-specific differential abundance of diverse bacterial genera. Prakriti-specific presence of bacterial taxa was recorded and only 42% microbiome in the oral samples and 52% microbiome in the skin samples were shared. Bacteria known for preventing gut inflammation by digesting the resistant starch were abundant in the pitta prakriti individuals, who are more prone to develop gut-inflammation-related disorders. In summary, human gut, oral and skin microbiome showed presence or high abundance of few bacterial taxa across three prakriti types, suggesting their specific physiological importance.},
}

Female
Humans
Intestines/*microbiology
Male
*Medicine, Ayurvedic
*Microbiota
Mouth/*microbiology
Skin/*microbiology

@article {pmid30885294,
year = {2019},
author = {Prodan, A and Levin, E and Nieuwdorp, M},
title = {Does disease start in the mouth, the gut or both?.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {30885294},
issn = {2050-084X},
mesh = {Bacteria ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract ; Metagenomics ; *Microbiota ; Mouth ; },
abstract = {Oral bacteria colonize the gut more frequently than previously thought.},
}

Bacteria
*Gastrointestinal Microbiome
*Gastrointestinal Tract
Metagenomics
*Microbiota
Mouth

@article {pmid32179734,
year = {2020},
author = {Mas-Lloret, J and Obón-Santacana, M and Ibáñez-Sanz, G and Guinó, E and Pato, ML and Rodriguez-Moranta, F and Mata, A and García-Rodríguez, A and Moreno, V and Pimenoff, VN},
title = {Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {92},
pmid = {32179734},
issn = {2052-4463},
mesh = {*Colon ; Cross-Sectional Studies ; *Feces ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {The gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300 k reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.},
}

*Colon
Cross-Sectional Studies
*Feces
Female
Gastrointestinal Microbiome/*genetics
High-Throughput Nucleotide Sequencing
Humans
Male
Metagenomics
RNA, Ribosomal, 16S/*genetics

@article {pmid31635933,
year = {2019},
author = {Ray, KJ and Cotter, SY and Arzika, AM and Kim, J and Boubacar, N and Zhou, Z and Zhong, L and Porco, TC and Keenan, JD and Lietman, TM and Doan, T},
title = {High-throughput sequencing of pooled samples to determine community-level microbiome diversity.},
journal = {Annals of epidemiology},
volume = {39},
number = {},
pages = {63-68},
pmid = {31635933},
issn = {1873-2585},
support = {K08 EY026986/EY/NEI NIH HHS/United States ; K08 EY026986/EY/NEI NIH HHS/United States ; },
mesh = {Administration, Oral ; Anti-Bacterial Agents/*administration & dosage ; Azithromycin/*administration & dosage ; Bacteria/classification/*drug effects/genetics/isolation & purification ; Biodiversity ; Child, Preschool ; Female ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Niger ; Placebos/administration & dosage ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {PURPOSE: Community-level interventions in cluster randomized controlled trials may alter the gut microbiome of individuals. The current method of estimating community diversities uses microbiome data obtained from multiple individual's specimens. Here we propose randomly pooling a number of microbiome samples from the same community into one sample before sequencing to estimate community-level microbiome diversity.

METHODS: We design and analyze an experiment to compare community microbiome diversity (gamma-diversity) estimates derived from 16S rRNA gene sequencing of 1) individually sequenced specimens vs. 2) pooled specimens collected from a community. Pool sizes of 10, 20, and 40 are considered. We then compare the gamma-estimates using Pearson's correlation as well as using Bland and Altman agreement analysis for three established diversity indices including richness, Simpson's and Shannon's.

RESULTS: The gamma-diversity estimates are highly correlated, with most being statistically significant. All correlations between all three diversity estimates are significant in the 10-pooled data. Pools comprising 40 specimens are closest to the line of agreement, but all pooled samples and individual samples fall within the 95% limits of agreement.

CONCLUSIONS: Pooling microbiome samples before DNA amplification and metagenomics sequencing to estimate community-level diversity is a viable measure to consider in population-level association research studies.},
}

Administration, Oral
Anti-Bacterial Agents/*administration & dosage
Azithromycin/*administration & dosage
Bacteria/classification/*drug effects/genetics/isolation & purification
Biodiversity
Child, Preschool
Female
Gastrointestinal Microbiome/*drug effects
Gastrointestinal Tract/*microbiology
High-Throughput Nucleotide Sequencing/*methods
Humans
Infant
Infant, Newborn
Male
Metagenomics/*methods
Microbiota/*genetics
Niger
Placebos/administration & dosage
RNA, Ribosomal, 16S/*genetics
Sequence Analysis, DNA

@article {pmid31990909,
year = {2020},
author = {Kordy, K and Gaufin, T and Mwangi, M and Li, F and Cerini, C and Lee, DJ and Adisetiyo, H and Woodward, C and Pannaraj, PS and Tobin, NH and Aldrovandi, GM},
title = {Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0219633},
pmid = {31990909},
issn = {1932-6203},
support = {K12 HD052954/HD/NICHD NIH HHS/United States ; },
mesh = {Acinetobacter/genetics/isolation & purification ; Adolescent ; Adult ; *Bacterial Translocation ; Bifidobacterium breve/genetics/*isolation & purification ; Enterobacter/genetics/isolation & purification ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Intestines/*microbiology ; Mammary Glands, Human/*microbiology ; Metagenomics/methods ; Milk, Human/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Staphylococcus/genetics/isolation & purification ; Streptococcus/genetics/isolation & purification ; },
abstract = {Increasing evidence supports the importance of the breast milk microbiome in seeding the infant gut. However, the origin of bacteria in milk and the process of milk microbe-mediated seeding of infant intestine need further elucidation. Presumed sources of bacteria in milk include locations of mother-infant and mother-environment interactions. We investigate the role of mother-infant interaction on breast milk microbes. Shotgun metagenomics and 16S rRNA gene sequencing identified milk microbes of mother-infant pairs in breastfed infants and in infants that have never latched. Although breast milk has low overall biomass, milk microbes play an important role in seeding the infant gut. Breast milk bacteria were largely comprised of Staphylococcus, Streptococcus, Acinetobacter, and Enterobacter primarily derived from maternal areolar skin and infant oral sites in breastfeeding pairs. This suggests that the process of breastfeeding is a potentially important mechanism for propagation of breast milk microbes through retrograde flux via infant oral and areolar skin contact. In one infant delivered via Caesarian section, a distinct strain of Bifidobacteria breve was identified in maternal rectum, breast milk and the infant's stool potentially suggesting direct transmission. This may support the existence of microbial translocation of this anaerobic bacteria via the enteromammary pathway in humans, where maternal bacteria translocate across the maternal gut and are transferred to the mammary glands. Modulating sources of human milk microbiome seeding potentially imply opportunities to ultimately influence the development of the infant microbiome and health.},
}

Acinetobacter/genetics/isolation & purification
Adolescent
Adult
*Bacterial Translocation
Bifidobacterium breve/genetics/*isolation & purification
Enterobacter/genetics/isolation & purification
Female
Gastrointestinal Microbiome/genetics
Humans
Infant
Infant, Newborn
Intestines/*microbiology
Mammary Glands, Human/*microbiology
Metagenomics/methods
Milk, Human/*microbiology
Pregnancy
RNA, Ribosomal, 16S/genetics
Staphylococcus/genetics/isolation & purification
Streptococcus/genetics/isolation & purification

@article {pmid31124702,
year = {2019},
author = {Davis, A and Kohler, C and Alsallaq, R and Hayden, R and Maron, G and Margolis, E},
title = {Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass.},
journal = {BioTechniques},
volume = {66},
number = {6},
pages = {285-289},
doi = {10.2144/btn-2019-0016},
pmid = {31124702},
issn = {1940-9818},
mesh = {Bacteria/*genetics ; Bacterial Load ; DNA Contamination ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {A major challenge for microbiome studies is maintaining an even and accurate DNA extraction in the presence of samples with a wide range of bacterial content. Here we compare five DNA extraction methods using replicate stool samples that were diluted to create high and low biomass samples. Our results indicate greater variation in microbiome composition between high and low biomass samples than variation between methods. Many of the extraction methods had reduced yield from low biomass samples; however, our adapted plate column-based extraction method was evenly efficient and captured the largest number of high-quality reads. Based on these results, we have identified a DNA extraction method that ensures adequate yield in metagenomic microbiome studies that have samples with a broad range of bacterial content.},
}

Bacteria/*genetics
Bacterial Load
DNA Contamination
DNA, Bacterial/genetics/*isolation & purification
Feces/microbiology
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenomics/methods
*Microbiota
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/methods

@article {pmid31830070,
year = {2019},
author = {Khilyas, IV and Sorokina, AV and Elistratova, AA and Markelova, MI and Siniagina, MN and Sharipova, MR and Shcherbakova, TA and D'Errico, ME and Cohen, MF},
title = {Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225929},
pmid = {31830070},
issn = {1932-6203},
mesh = {Asbestos, Serpentine/*analysis ; Biodiversity ; Computational Biology/methods ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Minerals/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; *Soil Microbiology ; Spectrum Analysis ; },
abstract = {Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.},
}

Asbestos, Serpentine/*analysis
Biodiversity
Computational Biology/methods
Geologic Sediments/*chemistry/*microbiology
Metagenome
Metagenomics/methods
*Microbiota
Minerals/*analysis
Phylogeny
RNA, Ribosomal, 16S/genetics
Russia
*Soil Microbiology
Spectrum Analysis

@article {pmid31821372,
year = {2019},
author = {Osimani, A and Milanović, V and Roncolini, A and Riolo, P and Ruschioni, S and Isidoro, N and Loreto, N and Franciosi, E and Tuohy, K and Olivotto, I and Zarantoniello, M and Cardinali, F and Garofalo, C and Aquilanti, L and Clementi, F},
title = {Hermetia illucens in diets for zebrafish (Danio rerio): A study of bacterial diversity by using PCR-DGGE and metagenomic sequencing.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225956},
pmid = {31821372},
issn = {1932-6203},
mesh = {*Animal Feed ; Animals ; Bacteria/classification/genetics ; *Diptera/microbiology ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Microbial Viability ; RNA, Ribosomal, 16S ; Zebrafish/*physiology ; },
abstract = {In the present research, bacterial diversity was studied during a 6-month feeding trial utilizing zebrafish (Danio rerio) fed Hermetia illucens reared on different substrates with an emphasis on fish gut bacterial diversity. A polyphasic approach based on viable counting, PCR-DGGE and metagenomic 16S rRNA gene amplicon target sequencing was applied. Two different H. illucens groups were reared on coffee by-products (C) or a mixture of vegetables (S). Viable counts showed a wide variability based on substrate. PCR-DGGE and Illumina sequencing allowed the major and minor bacterial taxa to be detected. Both samples of larvae and their frass reared on the S substrate showed the highest richness and evenness of bacterial communities, whereas zebrafish (ZHC) fed H. illucens reared on substrate C and zebrafish (ZHS) fed H. illucens reared on substrate S had the lowest bacterial richness and evenness. A stimulating effect of bioactive compounds from coffee by-products on the occurrence of Lactobacillaceae and Leuconostoccaceae in H. illucens reared on substrate C has been hypothesized. Zebrafish gut samples originating from the two feeding trials showed complex microbial patterns in which Actinobacteria and Alteromonadales were always detected, irrespective of the diet used. Enterobacteriaceae in fish guts were more abundant in ZHS than in ZHC, thus suggesting an influence of the bioactive compounds (chlorogenic and caffeic acids) in the substrate on Enterobacteriaceae in fish guts. ZHC showed a higher abundance of Clostridia than did ZHS, which was likely explained by stimulating activity on the bacteria in this class by the bioactive compounds contained in H. illucens reared on substrate C. An influence of the microbiota of H. illucens or insect-derived bioactive compounds on the gut microbiota of zebrafish has been suggested. The presence of bacteria consistently associated with zebrafish guts has been found irrespective of the diet, thus attesting to the likely stability of the core fish microbiota.},
}

*Animal Feed
Animals
Bacteria/classification/genetics
*Diptera/microbiology
Gastrointestinal Microbiome
Metagenome
Metagenomics/methods
Microbial Viability
RNA, Ribosomal, 16S
Zebrafish/*physiology

@article {pmid31800638,
year = {2019},
author = {Choi, S and Lee, JG and Lee, AR and Eun, CS and Han, DS and Park, CH},
title = {Helicobacter pylori antibody and pepsinogen testing for predicting gastric microbiome abundance.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225961},
pmid = {31800638},
issn = {1932-6203},
mesh = {Adult ; Antibodies, Bacterial/*immunology ; Bacterial Load ; Comorbidity ; Female ; Helicobacter Infections/diagnosis/*immunology/*metabolism/*microbiology ; Helicobacter pylori/*immunology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Pepsinogen A/*metabolism ; Prognosis ; Serologic Tests ; Stomach Neoplasms/etiology ; },
abstract = {BACKGROUND: Although the high-throughput sequencing technique is useful for evaluating gastric microbiome, it is difficult to use clinically. We aimed to develop a predictive model for gastric microbiome based on serologic testing.

METHODS: This study was designed to analyze sequencing data obtained from the Hanyang University Gastric Microbiome Cohort, which was established initially to investigate gastric microbial composition according to the intragastric environment. We evaluated the relationship between the relative abundance of potential gastric cancer-associated bacteria (nitrosating/nitrate-reducing bacteria or type IV secretion system [T4SS] protein gene-contributing bacteria) and serologic markers (IgG anti-Helicobacter pylori [HP] antibody or pepsinogen [PG] levels).

RESULTS: We included 57 and 26 participants without and with HP infection, respectively. The relative abundance of nitrosating/nitrate-reducing bacteria was 4.9% and 3.6% in the HP-negative and HP-positive groups, respectively, while that of T4SS protein gene-contributing bacteria was 20.5% and 6.5% in the HP-negative and HP-positive groups, respectively. The relative abundance of both nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria increased exponentially as PG levels decreased. Advanced age (only for nitrosating/nitrate-reducing bacteria), a negative result of IgG anti-HP antibody, low PG levels, and high Charlson comorbidity index were associated with a high relative abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria. The adjusted coefficient of determination (R2) was 53.7% and 70.0% in the model for nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria, respectively.

CONCLUSION: Not only the negative results of IgG anti-HP antibody but also low PG levels were associated with a high abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria.},
}

Adult
Antibodies, Bacterial/*immunology
Bacterial Load
Comorbidity
Female
Helicobacter Infections/diagnosis/*immunology/*metabolism/*microbiology
Helicobacter pylori/*immunology
Humans
Male
Metagenome
Metagenomics/methods
*Microbiota
Middle Aged
Pepsinogen A/*metabolism
Prognosis
Serologic Tests
Stomach Neoplasms/etiology

@article {pmid31582523,
year = {2019},
author = {Sugimoto, Y and Camacho, FR and Wang, S and Chankhamjon, P and Odabas, A and Biswas, A and Jeffrey, PD and Donia, MS},
title = {A metagenomic strategy for harnessing the chemical repertoire of the human microbiome.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6471},
pages = {},
doi = {10.1126/science.aax9176},
pmid = {31582523},
issn = {1095-9203},
support = {DP2 AI124441/AI/NIAID NIH HHS/United States ; },
mesh = {Host Microbial Interactions/*genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Multigene Family ; Polyketides/chemistry/*metabolism ; },
abstract = {Extensive progress has been made in determining the effects of the microbiome on human physiology and disease, but the underlying molecules and mechanisms governing these effects remain largely unexplored. Here, we combine a new computational algorithm with synthetic biology to access biologically active small molecules encoded directly in human microbiome-derived metagenomic sequencing data. We discover that members of a clinically used class of molecules are widely encoded in the human microbiome and that they exert potent antibacterial activities against neighboring microbes, implying a possible role in niche competition and host defense. Our approach paves the way toward a systematic unveiling of the chemical repertoire encoded by the human microbiome and provides a generalizable platform for discovering molecular mediators of microbiome-host and microbiome-microbiome interactions.},
}

Host Microbial Interactions/*genetics
Humans
*Metagenome
Metagenomics/*methods
Microbiota/*genetics
Multigene Family
Polyketides/chemistry/*metabolism

@article {pmid31285347,
year = {2019},
author = {Johnston, ER and Hatt, JK and He, Z and Wu, L and Guo, X and Luo, Y and Schuur, EAG and Tiedje, JM and Zhou, J and Konstantinidis, KT},
title = {Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {30},
pages = {15096-15105},
pmid = {31285347},
issn = {1091-6490},
mesh = {Alaska ; Arctic Regions ; Carbon/*chemistry/metabolism ; Carbon Cycle ; Carbon Dioxide/*chemistry/metabolism ; Climate Change/statistics & numerical data ; Microbiota/*genetics ; *Models, Statistical ; Permafrost/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Temperature ; *Tundra ; },
abstract = {Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.},
}

Alaska
Arctic Regions
Carbon/*chemistry/metabolism
Carbon Cycle
Carbon Dioxide/*chemistry/metabolism
Climate Change/statistics & numerical data
Microbiota/*genetics
*Models, Statistical
Permafrost/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Soil/chemistry
*Soil Microbiology
Temperature
*Tundra

@article {pmid31285337,
year = {2019},
author = {Greenlon, A and Chang, PL and Damtew, ZM and Muleta, A and Carrasquilla-Garcia, N and Kim, D and Nguyen, HP and Suryawanshi, V and Krieg, CP and Yadav, SK and Patel, JS and Mukherjee, A and Udupa, S and Benjelloun, I and Thami-Alami, I and Yasin, M and Patil, B and Singh, S and Sarma, BK and von Wettberg, EJB and Kahraman, A and Bukun, B and Assefa, F and Tesfaye, K and Fikre, A and Cook, DR},
title = {Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {30},
pages = {15200-15209},
pmid = {31285337},
issn = {1091-6490},
mesh = {Biological Evolution ; Cicer/*microbiology ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mesorhizobium/classification/*genetics ; Metagenomics/methods ; Microbial Consortia/*genetics ; Nitrogen Fixation/physiology ; Phylogeny ; Phylogeography ; Soil/classification ; Soil Microbiology ; Symbiosis/genetics ; },
abstract = {Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.},
}

Biological Evolution
Cicer/*microbiology
Conjugation, Genetic
*Gene Transfer, Horizontal
*Genome, Bacterial
Mesorhizobium/classification/*genetics
Metagenomics/methods
Microbial Consortia/*genetics
Nitrogen Fixation/physiology
Phylogeny
Phylogeography
Soil/classification
Soil Microbiology
Symbiosis/genetics

@article {pmid31238873,
year = {2019},
author = {Somerville, V and Lutz, S and Schmid, M and Frei, D and Moser, A and Irmler, S and Frey, JE and Ahrens, CH},
title = {Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {143},
pmid = {31238873},
issn = {1471-2180},
mesh = {Bacteria/classification/*virology ; Bacteriophages/*genetics/*physiology ; Biodiversity ; Cheese/microbiology ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genome, Bacterial ; Lactobacillus delbrueckii/genetics ; Lactobacillus helveticus/genetics ; *Metagenome ; Metagenomics ; Microbiota/*genetics/*physiology ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruyère and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii.

RESULTS: Two NWCs from Swiss Gruyère producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats.

CONCLUSIONS: Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.},
}

Bacteria/classification/*virology
Bacteriophages/*genetics/*physiology
Biodiversity
Cheese/microbiology
Clustered Regularly Interspaced Short Palindromic Repeats
Genome, Bacterial
Lactobacillus delbrueckii/genetics
Lactobacillus helveticus/genetics
*Metagenome
Metagenomics
Microbiota/*genetics/*physiology
Plasmids
RNA, Ribosomal, 16S/genetics
Whole Genome Sequencing

@article {pmid31141224,
year = {2019},
author = {Suzuki, TA and Phifer-Rixey, M and Mack, KL and Sheehan, MJ and Lin, D and Bi, K and Nachman, MW},
title = {Host genetic determinants of the gut microbiota of wild mice.},
journal = {Molecular ecology},
volume = {28},
number = {13},
pages = {3197-3207},
pmid = {31141224},
issn = {1365-294X},
support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; R01 GM127468/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/*classification ; Biodiversity ; Exome ; *Gastrointestinal Microbiome ; Genetics, Population ; Genome-Wide Association Study ; Host Microbial Interactions/*genetics ; Humans ; Linear Models ; Mice/*microbiology ; Models, Genetic ; Multivariate Analysis ; North America ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Identifying a common set of genes that mediate host-microbial interactions across populations and species of mammals has broad relevance for human health and animal biology. However, the genetic basis of the gut microbial composition in natural populations remains largely unknown outside of humans. Here, we used wild house mouse populations as a model system to ask three major questions: (a) Does host genetic relatedness explain interindividual variation in gut microbial composition? (b) Do population differences in the microbiota persist in a common environment? (c) What are the host genes associated with microbial richness and the relative abundance of bacterial genera? We found that host genetic distance is a strong predictor of the gut microbial composition as characterized by 16S amplicon sequencing. Using a common garden approach, we then identified differences in microbial composition between populations that persisted in a shared laboratory environment. Finally, we used exome sequencing to associate host genetic variants with microbial diversity and relative abundance of microbial taxa in wild mice. We identified 20 genes that were associated with microbial diversity or abundance including a macrophage-derived cytokine (IL12a) that contained three nonsynonymous mutations. Surprisingly, we found a significant overrepresentation of candidate genes that were previously associated with microbial measurements in humans. The homologous genes that overlapped between wild mice and humans included genes that have been associated with traits related to host immunity and obesity in humans. Gene-bacteria associations identified in both humans and wild mice suggest some commonality to the host genetic determinants of gut microbial composition across mammals.},
}

Animals
Animals, Wild/microbiology
Bacteria/*classification
Biodiversity
Exome
*Gastrointestinal Microbiome
Genetics, Population
Genome-Wide Association Study
Host Microbial Interactions/*genetics
Humans
Linear Models
Mice/*microbiology
Models, Genetic
Multivariate Analysis
North America
Polymorphism, Single Nucleotide
RNA, Ribosomal, 16S/genetics

@article {pmid30971183,
year = {2019},
author = {Kurilshikov, A and van den Munckhof, ICL and Chen, L and Bonder, MJ and Schraa, K and Rutten, JHW and Riksen, NP and de Graaf, J and Oosting, M and Sanna, S and Joosten, LAB and van der Graaf, M and Brand, T and Koonen, DPY and van Faassen, M and , and Slagboom, PE and Xavier, RJ and Kuipers, F and Hofker, MH and Wijmenga, C and Netea, MG and Zhernakova, A and Fu, J},
title = {Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk.},
journal = {Circulation research},
volume = {124},
number = {12},
pages = {1808-1820},
doi = {10.1161/CIRCRESAHA.118.314642},
pmid = {30971183},
issn = {1524-4571},
mesh = {Adult ; Aged ; Cardiovascular Diseases/*epidemiology/genetics/*metabolism ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metabolome/*physiology ; Middle Aged ; Netherlands/epidemiology ; Obesity/*epidemiology/genetics/*metabolism ; Phenotype ; Prospective Studies ; Risk Factors ; },
abstract = {RATIONALE: Altered gut microbial composition has been linked to cardiovascular diseases (CVDs), but its functional links to host metabolism and immunity in relation to CVD development remain unclear.

OBJECTIVES: To systematically assess functional links between the microbiome and the plasma metabolome, cardiometabolic phenotypes, and CVD risk and to identify diet-microbe-metabolism-immune interactions in well-documented cohorts.

METHODS AND RESULTS: We assessed metagenomics-based microbial associations between 231 plasma metabolites and microbial species and pathways in the population-based LLD (Lifelines DEEP) cohort (n=978) and a clinical obesity cohort (n=297). After correcting for age, sex, and body mass index, the gut microbiome could explain ≤11.1% and 16.4% of the variation in plasma metabolites in the population-based and obesity cohorts, respectively. Obese-specific microbial associations were found for lipid compositions in the VLDL, IDL, and LDL lipoprotein subclasses. Bacterial L-methionine biosynthesis and a Ruminococcus species were associated to cardiovascular phenotypes in obese individuals, namely atherosclerosis and liver fat content, respectively. Integration of microbiome-diet-inflammation analysis in relation to metabolic risk score of CVD in the population cohort revealed 48 microbial pathways associated to CVD risk that were largely independent of diet and inflammation. Our data also showed that plasma levels rather than fecal levels of short-chain fatty acids were relevant to inflammation and CVD risk.

CONCLUSIONS: This study presents the largest metagenome-based association study on plasma metabolism and microbiome relevance to diet, inflammation, CVD risk, and cardiometabolic phenotypes in both population-based and clinical obesity cohorts. Our findings identified novel bacterial species and pathways that associated to specific lipoprotein subclasses and revealed functional links between the gut microbiome and host health that provide a basis for developing microbiome-targeted therapy for disease prevention and treatment.},
}

Adult
Aged
Cardiovascular Diseases/*epidemiology/genetics/*metabolism
Cohort Studies
Female
Gastrointestinal Microbiome/*physiology
Humans
Male
Metabolome/*physiology
Middle Aged
Netherlands/epidemiology
Obesity/*epidemiology/genetics/*metabolism
Phenotype
Prospective Studies
Risk Factors

@article {pmid30683748,
year = {2019},
author = {Burkert, A and Douglas, TA and Waldrop, MP and Mackelprang, R},
title = {Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {7},
pages = {},
pmid = {30683748},
issn = {1098-5336},
mesh = {Actinobacteria/genetics/isolation & purification ; Alaska ; Bacillaceae/genetics/isolation & purification ; Carbon/metabolism ; Clostridiaceae/genetics/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Ecology ; Freezing ; Metagenomics ; Microbiota/genetics/*physiology ; Permafrost/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Spores, Bacterial/physiology ; Temperature ; },
abstract = {Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous "relic" DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCE Permafrost soils store more than half of Earth's soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171-179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.},
}

Actinobacteria/genetics/isolation & purification
Alaska
Bacillaceae/genetics/isolation & purification
Carbon/metabolism
Clostridiaceae/genetics/isolation & purification
DNA, Bacterial/genetics/isolation & purification
Ecology
Freezing
Metagenomics
Microbiota/genetics/*physiology
Permafrost/*microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Soil/*chemistry
*Soil Microbiology
Spores, Bacterial/physiology
Temperature

@article {pmid30658977,
year = {2019},
author = {Li, Y and Pinto-Tomás, AA and Rong, X and Cheng, K and Liu, M and Huang, Y},
title = {Population Genomics Insights into Adaptive Evolution and Ecological Differentiation in Streptomycetes.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {7},
pages = {},
pmid = {30658977},
issn = {1098-5336},
mesh = {Adaptation, Physiological/*genetics ; Animals ; Biodiversity ; *Ecology ; Ecosystem ; *Evolution, Molecular ; Gene Flow ; Genes, Bacterial ; Genetic Variation ; Genome-Wide Association Study ; Genotype ; Homologous Recombination ; Insecta/microbiology ; *Metagenomics ; Multigene Family/genetics ; N-Acetylneuraminic Acid/metabolism ; Organic Chemicals/metabolism ; Phylogeny ; Polymorphism, Single Nucleotide ; Soil Microbiology ; Streptomyces/classification/*genetics/isolation & purification/*physiology ; Water Microbiology ; },
abstract = {Deciphering the genomic variation that represents microevolutionary processes toward species divergence is key to understanding microbial speciation, which has long been under debate. Streptomycetes are filamentous bacteria that are ubiquitous in nature and the richest source of antibiotics; however, their speciation processes remain unknown. To tackle this issue, we performed a comprehensive population genomics analysis on Streptomyces albidoflavus residing in different habitats and with a worldwide distribution and identified and characterized the foundational changes within the species. We detected three well-defined phylogenomic clades, of which clades I and III mainly contained free-living (soil/marine) and insect-associated strains, respectively, and clade II had a mixed origin. By performing genome-wide association studies (GWAS), we identified a number of genetic variants associated with free-living or entomic (denoting or relating to insects) habitats in both the accessory and core genomes. These variants contributed collectively to the population structure and had annotated or confirmed functions that likely facilitate differential adaptation of the species. In addition, we detected higher levels of homologous recombination within each clade and in the free-living group than within the whole species and in the entomic group. A subset of the insect-associated strains (clade III) showed a relatively independent evolutionary trajectory with more symbiosis-favorable genes but little genetic interchange with the other lineages. Our results demonstrate that ecological adaptation promotes genetic differentiation in S. albidoflavus, suggesting a model of ecological speciation with gene flow in streptomycetes.IMPORTANCE Species are the fundamental units of ecology and evolution, and speciation leads to the astounding diversity of life on Earth. Studying speciation is thus of great significance to understand, protect, and exploit biodiversity, but it is a challenge in the microbial world. In this study, using population genomics, we placed Streptomyces albidoflavus strains in a spectrum of speciation and showed that the genetic differences between phylogenomic clusters evolved mainly by environmental selection and gene-specific sweeps. These findings highlight the role of ecology in structuring recombining bacterial species, making a step toward a deeper understanding of microbial speciation. Our results also raise concerns of an underrated microbial diversity at the intraspecies level, which can be utilized for mining of ecologically relevant natural products.},
}

Adaptation, Physiological/*genetics
Animals
Biodiversity
*Ecology
Ecosystem
*Evolution, Molecular
Gene Flow
Genes, Bacterial
Genetic Variation
Genome-Wide Association Study
Genotype
Homologous Recombination
Insecta/microbiology
*Metagenomics
Multigene Family/genetics
N-Acetylneuraminic Acid/metabolism
Organic Chemicals/metabolism
Phylogeny
Polymorphism, Single Nucleotide
Soil Microbiology
Streptomyces/classification/*genetics/isolation & purification/*physiology
Water Microbiology

@article {pmid31420693,
year = {2019},
author = {Carabeo-Pérez, A and Guerra-Rivera, G and Ramos-Leal, M and Jiménez-Hernández, J},
title = {Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems.},
journal = {Applied microbiology and biotechnology},
volume = {103},
number = {23-24},
pages = {9379-9390},
doi = {10.1007/s00253-019-10052-5},
pmid = {31420693},
issn = {1432-0614},
mesh = {Anaerobiosis ; *Metagenome ; Metagenomics/*methods ; Methane/metabolism ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sewage ; },
abstract = {Microbial metagenome analysis has proven its usefulness to investigate the microbiomes present in technical engineered ecosystems such as anaerobic digestion systems. The analysis of the total microbial genomic DNA allows the detailed determination of both the microbial community structure and its functionality. In addition, it enables to study the response of the microbiome to alterations in technical process parameters. Strategies of functional microbial networks to face abiotic stressors, e.g., resistance, resilience, and reorganization, can be evaluated with respect to overall process optimization. The objective of this paper is to review the main metagenomic tools used for effective studies on anaerobic digestion systems in monitoring the dynamic of the microbiomes, as well as the factors that have been identified so far as limiting the metagenomic studies in this ecosystems.},
}

Anaerobiosis
*Metagenome
Metagenomics/*methods
Methane/metabolism
Microbiota/*genetics
RNA, Ribosomal, 16S/genetics
Sewage

@article {pmid31240835,
year = {2019},
author = {Weng, YJ and Gan, HY and Li, X and Huang, Y and Li, ZC and Deng, HM and Chen, SZ and Zhou, Y and Wang, LS and Han, YP and Tan, YF and Song, YJ and Du, ZM and Liu, YY and Wang, Y and Qin, N and Bai, Y and Yang, RF and Bi, YJ and Zhi, FC},
title = {Correlation of diet, microbiota and metabolite networks in inflammatory bowel disease.},
journal = {Journal of digestive diseases},
volume = {20},
number = {9},
pages = {447-459},
doi = {10.1111/1751-2980.12795},
pmid = {31240835},
issn = {1751-2980},
support = {81790632//National Natural Science Foundation for Key Programs of China/ ; 2015AA020702//National High Technology Research and Development Program of China (863 Program)/ ; },
mesh = {Adult ; Biopsy ; Body Mass Index ; Case-Control Studies ; *Diet ; Dysbiosis/complications ; Feces/microbiology ; Female ; *Food Preferences ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/metabolism/*microbiology/pathology ; Intestinal Mucosa/microbiology/pathology ; Male ; Metabolic Networks and Pathways/physiology ; Metagenomics ; Middle Aged ; Nutrition Assessment ; Young Adult ; },
abstract = {OBJECTIVES: Microbiota dysbiosis in inflammatory bowel disease (IBD) has been widely reported. The gut microbiota connect diet to the metabolism by producing small molecules via diverse metabolic pathways. In this study we aimed to investigate the dietary preferences of IBD patients, and to explore the interactions among gut microbiota composition, dietary components, and metabolites in relation to IBD.

METHODS: Dietary preferences of IBD patients (including those with ulcerative colitis [UC] and Crohn's disease [CD]) and health controls were investigated, and their gut microbiota were analyzed using 16S rRNA gene sequencing and metagenomic analyses of fecal and biopsy samples. The metabolite profiles of the samples were then analyzed using gas and liquid chromatography-mass spectrometry analyses.

RESULTS: The daily intake of folic acid, niacin, vitamins C and D, calcium, and selenium differed significantly between patients with IBD and healthy controls. A decrease in long-chain (such as arachidic, and oleic acid) and medium-chain fatty acids (sebacic acid and isocaproic acid) as well as bile acid was observed in patients with IBD. Compared with healthy controls, 22 microbial species (including Sulfolobus acidocaldarius, and Clostridium clostridioforme CAG132) in the UC group and 37 microbial species (such as Bacteroides fragilis and Fusobacterium nucleatum) in the CD group were found to be correlated to diet and metabolites. Bacteroides fragilis was enriched in patients with IBD and associated with multi-nutrients, and 21 metabolites including 25-hydroxyvitamin D3 and taurolithocholic acid.

CONCLUSIONS: This study provides an interaction network to identify key micronutrients, microbiota components and metabolites that contribute to IBD.},
}

Adult
Biopsy
Body Mass Index
Case-Control Studies
*Diet
Dysbiosis/complications
Feces/microbiology
Female
*Food Preferences
*Gastrointestinal Microbiome
Humans
Inflammatory Bowel Diseases/metabolism/*microbiology/pathology
Intestinal Mucosa/microbiology/pathology
Male
Metabolic Networks and Pathways/physiology
Metagenomics
Middle Aged
Nutrition Assessment
Young Adult

@article {pmid31109865,
year = {2019},
author = {Takahashi, Y and Park, J and Hosomi, K and Yamada, T and Kobayashi, A and Yamaguchi, Y and Iketani, S and Kunisawa, J and Mizuguchi, K and Maeda, N and Ohshima, T},
title = {Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing.},
journal = {Journal of oral biosciences},
volume = {61},
number = {2},
pages = {120-128},
doi = {10.1016/j.job.2019.03.003},
pmid = {31109865},
issn = {1880-3865},
mesh = {Bacteria ; Humans ; Japan ; *Microbiota ; *Mouth Neoplasms ; RNA, Ribosomal, 16S ; },
abstract = {OBJECTIVES: It is important to determine the cause of increasing oral cancer occurrence and mortality rates in Japan, because the mortality rate has recently decreased in other developed countries. The impact of microbiota in carcinogenesis, especially in the digestive tract has been reported. This study aimed to clarify the relationship between oral cancer and oral microbiota in Japanese patients.

METHODS: DNA was extracted from salivary samples of 60 oral cancer patients and 80 non-cancer individuals as controls. We performed metagenomic analysis using 16S rRNA amplicon sequencing. Statistical analysis in this study was performed using R (version 3.5.0).

RESULTS: Oral cancer patients showed higher α-diversity compared to the control group, and the β-diversity between the two groups differed significantly. Further, there was a significant difference in the abundance ratio of bacterial genera between the two groups. Peptostreptococcus, Fusobacterium, Alloprevotella, and Capnocytophaga were more abundant in the cancer group compared to the control, whereas Rothia and Haemophilus were less abundant (p < 0.01). A negative correlation in the microbiota composition was confirmed between the operational taxonomic units (OTU) of genus Rothia and T-stage progression using the TNM classification method. We performed logistic regression analysis to investigate the impact factor for the oral cancer group, and the result showed that Chao 1 index and sex are statistically significant variables.

CONCLUSIONS: In this study, we observed an increased bacterial diversity in oral cancer patients and found distribution changes for some bacteria.},
}

Bacteria
Humans
Japan
*Microbiota
*Mouth Neoplasms
RNA, Ribosomal, 16S

@article {pmid30747106,
year = {2019},
author = {Schmidt, TS and Hayward, MR and Coelho, LP and Li, SS and Costea, PI and Voigt, AY and Wirbel, J and Maistrenko, OM and Alves, RJ and Bergsten, E and de Beaufort, C and Sobhani, I and Heintz-Buschart, A and Sunagawa, S and Zeller, G and Wilmes, P and Bork, P},
title = {Extensive transmission of microbes along the gastrointestinal tract.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {30747106},
issn = {2050-084X},
support = {ERC-AdG-669830//H2020 European Research Council/International ; 669830/ERC_/European Research Council/International ; 661019//H2020 Marie Skłodowska-Curie Actions/International ; de.NBI #031A537B//German Network for Bioinformatics Infrastructure/International ; CORE/15/BM/10404093//Fonds National de la Recherche Luxembourg/International ; de.NBI #031A537B//German Network Bioinformatics/International ; },
mesh = {Bacteria/*classification/*genetics ; Cluster Analysis ; Feces/microbiology ; Humans ; Intestine, Large/*microbiology ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; Saliva/microbiology ; },
abstract = {The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.},
}

Bacteria/*classification/*genetics
Cluster Analysis
Feces/microbiology
Humans
Intestine, Large/*microbiology
Metagenomics
*Microbiota
Mouth/*microbiology
Saliva/microbiology

@article {pmid30404941,
year = {2019},
author = {Morand, A and Cornu, F and Dufour, JC and Tsimaratos, M and Lagier, JC and Raoult, D},
title = {Human Bacterial Repertoire of the Urinary Tract: a Potential Paradigm Shift.},
journal = {Journal of clinical microbiology},
volume = {57},
number = {3},
pages = {},
pmid = {30404941},
issn = {1098-660X},
mesh = {Bacteria/classification/genetics/growth & development/pathogenicity ; Bacterial Physiological Phenomena ; *Biodiversity ; Dysbiosis ; Gastrointestinal Microbiome ; Humans ; Microbiota ; Urinary Tract/*microbiology ; Urinary Tract Infections/microbiology ; Urine/*microbiology ; },
abstract = {The aim of this article is to review the human repertoire of bacteria in urine already described by culture and metagenomic techniques and published in the literature. Our study led us to compare this repertoire with other available human repertoires. We followed automatic and manual bibliographical methods and found 562 bacterial species reported in the literature as part of the human urinary microbiota. Of the 562 species, 322 were described only by culture, 101 by both culture and metagenomics, and 139 only by metagenomics. A total of 352 species (62.6%) have been associated with at least one case report of human infection, of which 225 (40.0%) have been described as causative agents of urinary tract infection. The urinary tract bacterial repertoire contains 21.4% of the known prokaryotic diversity associated with human beings (464 species in common), and it shares 23.6% species with the human gut microbiota (350 species in common, 62.3% of the urine species). The urinary repertoire shares a significant difference in aerointolerant species compared with those of the gut microbiota (100/562 [17.8%] and 505/1,484 [34.0%], respectively; P < 0.001; odds ratio [OR] = 9.0 [7.0 to 11.4]). Studies using high-throughput sequencing show a higher proportion of aerointolerant bacteria in urine (74/240 [30.8%]) than studies using culture techniques (40/423 [9.5%]). Most pathogenic bacteria are part of the commensal human urinary tract bacteria, and their pathogenicity may occur following any imbalance of this microbiota. The restoration of urinary tract health can occur following a fecal transplantation. The potential gut origin of the human bacterial microbiota has to be explored.},
}

Bacteria/classification/genetics/growth & development/pathogenicity
Bacterial Physiological Phenomena
*Biodiversity
Dysbiosis
Gastrointestinal Microbiome
Humans
Microbiota
Urinary Tract/*microbiology
Urinary Tract Infections/microbiology
Urine/*microbiology

@article {pmid30058291,
year = {2019},
author = {Bahram, M and Anslan, S and Hildebrand, F and Bork, P and Tedersoo, L},
title = {Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.},
journal = {Environmental microbiology reports},
volume = {11},
number = {4},
pages = {487-494},
pmid = {30058291},
issn = {1758-2229},
support = {ERC-AdG-669830/ERC_/European Research Council/International ; PUT1399//Estonian Research Council/International ; PUT1317//Estonian Research Council/International ; },
mesh = {Archaea/*classification/genetics ; DNA Primers/*genetics ; DNA, Archaeal/genetics ; *Environmental Microbiology ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately.},
}

Archaea/*classification/genetics
DNA Primers/*genetics
DNA, Archaeal/genetics
*Environmental Microbiology
Metagenomics
Microbiota/genetics
Phylogeny
RNA, Ribosomal, 16S/*genetics

@article {pmid32105997,
year = {2020},
author = {Dias, MF and da Rocha Fernandes, G and Cristina de Paiva, M and Christina de Matos Salim, A and Santos, AB and Amaral Nascimento, AM},
title = {Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings.},
journal = {Water research},
volume = {174},
number = {},
pages = {115630},
doi = {10.1016/j.watres.2020.115630},
pmid = {32105997},
issn = {1879-2448},
mesh = {Anti-Bacterial Agents ; *Drinking Water ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota ; },
abstract = {Aquatic ecosystems harbor a vast pool of antibiotic resistance genes (ARGs), which can suffer mutation, recombination and selection events. Here, we explored the diversity of ARGs, virulence factors and the bacterial community composition in water samples before (surface raw water, RW) and after (disinfected water, DW) drinking water conventional treatment, as well as in tap water (TW) and ultrafiltration membranes (UM, recovered from hemodialysis equipment) through metagenomics. A total of 852 different ARGs were identified, 21.8% of them only in RW, which might reflect the impact of human activities on the river at the sampling point. Although a similar resistance profile has been observed between the samples, significant differences in the frequency of clinically relevant antibiotic classes (penam and peptide) were identified. Resistance determinants to last resort antibiotics, including sequences related to mcr, optrA and poxtA and clinically relevant beta-lactamase genes (i.e. blaKPC, blaGES, blaIMP, blaVIM, blaSPM and blaNDM) were detected. 830 coding sequences (CDSs - related to 217 different ARGs) were embedded in contigs associated with mobile genetic elements, specially plasmids, of which 68% in RW, DW and TW, suggesting the importance of water environments in resistance dissemination. Shifts in bacterial pathogens genera were observed, such as a significant increase in Mycobacterium after treatment and distribution. In UM, the potentially pathogenic genus Halomonas predominated. Its draft genome was closely related to H. stevensii, hosting mainly multidrug efflux pumps. These results broaden our understanding of the global ARGs diversity and stress the importance of tracking the ever-expanding environmental resistome.},
}

Anti-Bacterial Agents
*Drinking Water
Drug Resistance, Microbial
Genes, Bacterial
Humans
Metagenomics
*Microbiota

@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},
pmid = {31825995},
issn = {1932-6203},
mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Crohn Disease/*microbiology ; Humans ; Metagenomics/*methods ; Microbiota ; Mouth Neoplasms/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Software ; Time Factors ; },
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.},
}

Bacteria/*classification/*genetics
*Biodiversity
Crohn Disease/*microbiology
Humans
Metagenomics/*methods
Microbiota
Mouth Neoplasms/*microbiology
Phylogeny
RNA, Ribosomal, 16S/*genetics
Sequence Analysis, DNA
Software
Time Factors

@article {pmid31703093,
year = {2019},
author = {Kato, S and Hirai, M and Ohkuma, M and Suzuki, K},
title = {Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224888},
pmid = {31703093},
issn = {1932-6203},
mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Carbon/metabolism ; Metabolic Networks and Pathways ; *Metabolome ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Nitrogen/metabolism ; Phylogeny ; },
abstract = {Rocky outcrops covered with thick Fe and Mn oxide coatings, which are known as ferromanganese (Fe-Mn) crusts, are commonly found on slopes of aged seamounts in bathyal and abyssal zones. Although the presence of diverse microorganisms on these Fe-Mn crusts has been reported, little is known about their metabolism. Here, we report the metabolic potential of the microbial community in an abyssal crust collected in the Takuyo-Daigo Seamount, in the north-western Pacific. We performed shotgun metagenomic sequencing of the Fe-Mn crust, and detected putative genes involved in dissolution and precipitation of Fe and Mn, nitrification, sulfur oxidation, carbon fixation, and decomposition of organics in the metagenome. In addition, four metagenome-assembled genomes (MAGs) of abundant members in the microbial community were recovered from the metagenome. The MAGs were affiliated with Thaumarchaeota, Alphaproteobacteria, and Gammaproteobacteria, and were distantly related to previously reported genomes/MAGs of cultured and uncultured species. Putative genes involved in the above reactions were also found in the crust MAGs. Our results suggest that crust microbial communities play a role in biogeochemical cycling of C, N, S, Fe, and Mn, and imply that they contribute to the growth of Fe-Mn crusts.},
}

Archaea/classification/genetics
Bacteria/classification/genetics
Carbon/metabolism
Metabolic Networks and Pathways
*Metabolome
*Metagenome
*Metagenomics/methods
*Microbiota
Nitrogen/metabolism
Phylogeny

@article {pmid31291462,
year = {2019},
author = {Liu, Y and Ajami, NJ and El-Serag, HB and Hair, C and Graham, DY and White, DL and Chen, L and Wang, Z and Plew, S and Kramer, J and Cole, R and Hernaez, R and Hou, J and Husain, N and Jarbrink-Sehgal, ME and Kanwal, F and Ketwaroo, G and Natarajan, Y and Shah, R and Velez, M and Mallepally, N and Petrosino, JF and Jiao, L},
title = {Dietary quality and the colonic mucosa-associated gut microbiome in humans.},
journal = {The American journal of clinical nutrition},
volume = {110},
number = {3},
pages = {701-712},
pmid = {31291462},
issn = {1938-3207},
support = {I01 CX001430/CX/CSRD VA/United States ; K07 CA181480/CA/NCI NIH HHS/United States ; },
mesh = {Aged ; Bacteria/*classification ; Colon/*microbiology ; Computational Biology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Diet/*standards ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Despite tremendous interest in modulating the microbiome to improve health, the association between diet and the colonic mucosa-associated gut microbiome in healthy individuals has not been examined.

OBJECTIVE: To investigate the associations between Healthy Eating Index (HEI)-2005 and the colonic mucosa-associated microbiota.

METHODS: In this cross-sectional observational study, we analyzed bacterial community composition and structure using 16S rRNA gene (V4 region) sequencing of 97 colonic mucosal biopsies obtained endoscopically from different colon segments of 34 polyp-free participants. Dietary consumption was ascertained using an FFQ. Differences in α- and β-diversity and taxonomic relative abundances between the higher and lower score of total HEI and its components were compared, followed by multivariable analyses.

RESULTS: The structure of the microbiota significantly differed by the scores for total HEI, total and whole fruits (HEI 1 and HEI 2), whole grains (HEI 6), milk products and soy beverages (HEI 7), and solid fat, alcohol, and added sugar (HEI 12). A lower score for total HEI and HEIs 2, 7, and 12 was associated with significantly lower richness. A lower score for total HEI was associated with significantly reduced relative abundance of Parabacteroides, Roseburia, and Subdoligranulum but higher Fusobacterium. A lower score for HEI 2 was associated with lower Roseburia but higher Bacteroides. A lower score for HEI 7 was associated with lower Faecalibacterium and Fusobacterium but higher Bacteroides. A lower score for HEI 12 was associated with lower Subdoligranulum but higher Escherichia and Fusobacterium (false discovery rate-adjusted P values <0.05). The findings were confirmed by multivariate analysis. Less abundant bacteria such as Alistipes, Odoribacter, Bilophila, and Tyzzerella were also associated with dietary quality.

CONCLUSIONS: A lower score for total HEI-2005 was significantly associated with reduced relative abundance of potentially beneficial bacteria but increased potentially harmful bacteria in the colonic mucosa of endoscopically normal individuals.},
}

Aged
Bacteria/*classification
Colon/*microbiology
Computational Biology
Cross-Sectional Studies
DNA, Bacterial/genetics
Diet/*standards
Female
*Gastrointestinal Microbiome
Humans
Intestinal Mucosa/*microbiology
Male
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid31091181,
year = {2019},
author = {Joyce, A and McCarthy, CGP and Murphy, S and Walsh, F},
title = {Antibiotic resistomes of healthy pig faecal metagenomes.},
journal = {Microbial genomics},
volume = {5},
number = {5},
pages = {},
pmid = {31091181},
issn = {2057-5858},
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/isolation & purification ; Cluster Analysis ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial ; Humans ; Ireland ; Metagenome/*genetics ; Metagenomics ; Swine ; },
abstract = {Antibiotic resistance reservoirs within food-producing animals are thought to be a risk to animal and human health. This study describes the minimum natural resistome of pig faeces as the bacteria are under no direct antibiotic selective pressure. The faecal resistome of 257 different genes comprised 56 core and 201 accessory resistance genes. The genes present at the highest relative abundances across all samples were tetW, tetQ, tet44, tet37, tet40, mefA, aadE, ant(9)-1, ermB and cfxA2. This study characterized the baseline resistome, the microbiome composition and the metabolic components described by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in healthy pig faeces, without antibiotic selective pressures. The microbiome hierarchical analysis resulted in a cluster tree with a highly similar pattern to that of the accessory resistome cluster tree. Functional capacity profiling identified genes associated with horizontal gene transfer. We identified a statistically significant positive correlation between the total antibiotic resistome and suggested indicator genes, which agree with using these genes as indicators of the total resistomes. The correlation between total resistome and total microbiome in this study was positive and statistically significant. Therefore, the microbiome composition influenced the resistome composition. This study identified a core and accessory resistome present in a cohort of healthy pigs, in the same conditions without antibiotics. It highlights the presence of antibiotic resistance in the absence of antibiotic selective pressure and the variability between animals even under the same housing, food and living conditions. Antibiotic resistance will remain in the healthy pig gut even when antibiotics are not used. Therefore, the risk of antibiotic resistance transfer from animal faeces to human pathogens or the environment will remain in the absence of antibiotics.},
}

Animals
Anti-Bacterial Agents/*pharmacology
Bacteria/classification/drug effects/genetics/isolation & purification
Cluster Analysis
Drug Resistance, Bacterial/genetics
Drug Resistance, Microbial/*genetics
Feces/*microbiology
Gastrointestinal Microbiome/drug effects/genetics
Gastrointestinal Tract/microbiology
Gene Transfer, Horizontal
Genes, Bacterial/genetics
Genome, Bacterial
Humans
Ireland
Metagenome/*genetics
Metagenomics
Swine

@article {pmid32157464,
year = {2020},
author = {Casalone, E and Cavalieri, D and Daly, G and Vitali, F and Perito, B},
title = {Propolis hosts a diversemicrobial community.},
journal = {World journal of microbiology & biotechnology},
volume = {36},
number = {3},
pages = {50},
pmid = {32157464},
issn = {1573-0972},
support = {prot.2012RCEZWH_001//Programmi di Ricerca di Rilevante Interesse Nazionale (PRIN) 2012/ ; },
mesh = {Animals ; Anti-Infective Agents/pharmacology ; Bacteria/*classification/drug effects/isolation & purification ; Bees ; DNA, Ribosomal/genetics ; Fungi/*classification/drug effects/isolation & purification ; Gastrointestinal Microbiome ; Microbial Sensitivity Tests ; *Microbiota/drug effects ; Phylogeny ; Propolis/*pharmacology ; },
abstract = {Despite the deep knowledge of the honey bee (Apis mellifera) gut microbiome, information on the microbial communities of other hive components is still scarce. Propolis originates from a natural resinous mixture that honeybees collect from different plants sources and modify; it is used mainly to ensure the hygiene of the hive. By virtue of its antimicrobial properties, propolis has been considered relatively aseptic, yet its ability to harbor microorganisms has not been previously investigated. In this study we report the first description of the diversity of the microbial community of propolis by both targeted-metagenomics analysis and cultivation. We demonstrated that propolis hosts a variety of microbial strains belonging to taxa already described in other hive components. Some of them are cultivable in standard laboratory conditions, and show metabolic characteristics compatible with their persistence in different physiological states inside propolis. Isolated bacteria produce antimicrobials against Gram-negative and Gram-positive bacteria, and entomopathogenic fungi, with different spectra of inhibition. Metagenomics analysis shows the presence of bacteria and fungi with great potential to outcompete potentially harmful microorganisms. These findings suggest that the characterized microbiota could contribute to the overall antimicrobial properties of propolis and to its ecological role as "disinfectant" within the hive.},
}

Animals
Anti-Infective Agents/pharmacology
Bacteria/*classification/drug effects/isolation & purification
Bees
DNA, Ribosomal/genetics
Fungi/*classification/drug effects/isolation & purification
Gastrointestinal Microbiome
Microbial Sensitivity Tests
*Microbiota/drug effects
Phylogeny
Propolis/*pharmacology

@article {pmid31751342,
year = {2019},
author = {Eckstrom, K and Barlow, JW},
title = {Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0219807},
pmid = {31751342},
issn = {1932-6203},
mesh = {Animal Feed/*microbiology ; Animals ; *Composting ; Drug Resistance, Bacterial/genetics ; Farms ; Food Microbiology ; Humans ; Metagenome ; Metagenomics ; Microbiota/*genetics ; *Poultry ; Refuse Disposal ; Risk Assessment ; Vermont ; },
abstract = {Food waste diversion and composting, either mandated or voluntary, are growing alternatives to traditional waste disposal. An acceptable source of agricultural feed and composting material, methane-emitting food residuals, including post-consumer food scraps, are diverted from landfills allowing recapture of nutrients that would otherwise be lost. However, risk associated with the transfer of antimicrobial resistant bacteria (ARB), antibiotic resistance genes (ARGs), or pathogens from food waste is not well characterized. Using shotgun metagenomic sequencing, ARGs, microbial content, and associated virulence factors were successfully identified across samples from an integrated poultry farm that feeds post-consumer food waste. A total of 495 distinct bacterial species or sub-species, 50 ARGs, and 54 virulence gene sequences were found. ARG sequences related to aminoglycoside, tetracycline, and macrolide resistance were most prominent, while most virulence gene sequences were related to transposon or integron activity. Microbiome content was distinct between on-farm samples and off-farm food waste collection sites, with a reduction in pathogens throughout the composting process. While most samples contained some level of resistance, only 3 resistance gene sequences occurred in both on- and off-farm samples and no multidrug resistance (MDR) gene sequences persisted once on the farm. The risk of incorporating novel or multi-drug resistance from human sources appears to be minimal and the practice of utilizing post-consumer food scraps as feed for poultry and composting material may not present a significant risk for human or animal health. Pearson correlation and co-inertia analysis identified a significant interaction between resistance and virulence genes (P = 0.05, RV = 0.67), indicating that ability to undergo gene transfer may be a better marker for ARG risk than presence of specific bacterial species. This work expands the knowledge of ARG fate during food scrap animal feeding and composting and provides a methodology for reproducible analysis.},
}

Animal Feed/*microbiology
Animals
*Composting
Drug Resistance, Bacterial/genetics
Farms
Food Microbiology
Humans
Metagenome
Metagenomics
Microbiota/*genetics
*Poultry
Refuse Disposal
Risk Assessment
Vermont

@article {pmid31697678,
year = {2019},
author = {Srivathsan, A and Nagarajan, N and Meier, R},
title = {Boosting natural history research via metagenomic clean-up of crowdsourced feces.},
journal = {PLoS biology},
volume = {17},
number = {11},
pages = {e3000517},
pmid = {31697678},
issn = {1545-7885},
mesh = {Animals ; Bacteria ; Biodiversity ; Conservation of Natural Resources ; Crowdsourcing ; Feces/chemistry/microbiology/parasitology ; Gastrointestinal Microbiome ; *Mammals ; Metagenome ; *Metagenomics ; Natural History/*methods ; Sequence Analysis, DNA ; },
abstract = {Biodiversity is in crisis due to habitat destruction and climate change. The conservation of many noncharismatic species is hampered by the lack of data. Yet, natural history research-a major source of information on noncharismatic species-is in decline. We here suggest a remedy for many mammal species, i.e., metagenomic clean-up of fecal samples that are "crowdsourced" during routine field surveys. Based on literature data, we estimate that this approach could yield natural history information for circa 1,000 species within a decade. Metagenomic analysis would simultaneously yield natural history data on diet and gut parasites while enhancing our understanding of host genetics, gut microbiome, and the functional interactions between traditional and new natural history data. We document the power of this approach by carrying out a "metagenomic clean-up" on fecal samples collected during a single night of small mammal trapping in one of Alfred Wallace's favorite collecting sites.},
}

Animals
Bacteria
Biodiversity
Conservation of Natural Resources
Crowdsourcing
Feces/chemistry/microbiology/parasitology
Gastrointestinal Microbiome
*Mammals
Metagenome
*Metagenomics
Natural History/*methods
Sequence Analysis, DNA

@article {pmid31437575,
year = {2019},
author = {Li, A and Wang, Y and Pei, L and Mehmood, K and Li, K and Qamar, H and Iqbal, M and Waqas, M and Liu, J and Li, J},
title = {Influence of dietary supplementation with Bacillus velezensis on intestinal microbial diversity of mice.},
journal = {Microbial pathogenesis},
volume = {136},
number = {},
pages = {103671},
doi = {10.1016/j.micpath.2019.103671},
pmid = {31437575},
issn = {1096-1208},
mesh = {Animals ; Bacillus/*growth & development/isolation & purification ; Cattle/microbiology ; Cecum/microbiology ; Diet/*methods ; Duodenum/microbiology ; *Gastrointestinal Microbiome ; Ileum/microbiology ; Jejunum/microbiology ; Metagenomics ; Mice ; Probiotics/*administration & dosage ; Tibet ; },
abstract = {Yaks are an aboriginal breed of the Qinghai-Tibet plateau (3000 m), which are highly adaptable to cold and hypoxic environments. It is noticed that hypoxia and hypothermia can induce changes in intestinal microbial structure in animals. Increasing evidences suggested that probiotics supplementation can improve the balance of gut microbiota of animals. However, so far, very few studies have emphasized on the probiotics isolated from yaks in the Qinghai-Tibet Plateau. Therefore, a potential probiotic strain Bacillus velezensis was isolated from yaks. In the present study, a total of 18 Kunming mice (15-18 g) were equally distributed into two groups; control and probiotic treated groups (1 × 109 CFU/day). During the experimental period, all the mice from both groups were given standard normal diet ad libitum. At the end of the experiment, mice were euthanized and the intestines (duodenum, jejunum, ileum, and cecum) were removed for high-throughput sequencing. The results demonstrated that Bacillus velezensis supplementation showed beneficial effects on the gut microbiota of mice. Specifically, Bacillus velezensis supplementation increased the population of Lactobacillus and Ruminococcus in the duodenum, and Candidatus Arthromitus in the jejunum. Additionally, Acinetobacter in the duodenum and Helicobacter in the cecum were decreased after feeding Bacillus velezensis. Altogether, these findings suggested that Bacillus velezensis isolated from Tibetan yaks can improve gut microbiota of mice.},
}

Animals
Bacillus/*growth & development/isolation & purification
Cattle/microbiology
Cecum/microbiology
Diet/*methods
Duodenum/microbiology
*Gastrointestinal Microbiome
Ileum/microbiology
Jejunum/microbiology
Metagenomics
Mice
Probiotics/*administration & dosage
Tibet

@article {pmid31265324,
year = {2019},
author = {Dao, MC and Belda, E and Prifti, E and Everard, A and Kayser, BD and Bouillot, JL and Chevallier, JM and Pons, N and Le Chatelier, E and Ehrlich, SD and Doré, J and Aron-Wisnewsky, J and Zucker, JD and Cani, PD and Clément, K},
title = {Akkermansia muciniphila abundance is lower in severe obesity, but its increased level after bariatric surgery is not associated with metabolic health improvement.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {317},
number = {3},
pages = {E446-E459},
doi = {10.1152/ajpendo.00140.2019},
pmid = {31265324},
issn = {1522-1555},
mesh = {Adult ; *Bariatric Surgery ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Glucose Tolerance Test ; Health Status ; Homeostasis ; Humans ; Insulin Resistance ; Longitudinal Studies ; Middle Aged ; Obesity, Morbid/metabolism/*microbiology/*surgery ; Prospective Studies ; Treatment Outcome ; *Verrucomicrobia ; Young Adult ; },
abstract = {The gut bacterial species Akkermansia muciniphila is associated with a healthier clinical profile. The purpose of this study was to determine the association between A. muciniphila and glucose homeostasis in patients undergoing bariatric surgery (BS): gastric banding (GB) or Roux-en-Y gastric bypass (RYGB). This nonrandomized prospective study included 65 women with severe obesity. Longitudinal analysis included subjects for whom A. muciniphila data were available at follow-up [1, 3, and 12 mo; GB (n = 10) or RYGB (n = 11)]. Glucose homeostasis markers were measured under fasting conditions (glucose, insulin, and HbA1c) or during an oral glucose tolerance test. Fecal microbiota was analyzed using shotgun metagenomics, and A. muciniphila relative abundance was assessed with 16S rRNA quantitative PCR. A. muciniphila relative abundance was significantly lower in severe obesity [mean body mass index, 45.7 kg/m2 (SD 5.4)] than in moderate obesity [33.2 kg/m2 (SD 3.8)] but not associated with glucose homeostasis markers. A significant increase in A. muciniphila relative abundance after RYGB was not correlated with metabolic improvement. Baseline A. muciniphila abundance was correlated with bacterial gene richness and was highest in the high-richness Ruminococcaceae enterotype. A. muciniphila increased in relative abundance after BS in patients with low baseline A. muciniphila abundance, especially those with a Bacteroides type 2 enterotype classification. Although decreased in severe obesity, relative abundance of A. muciniphila was not associated with glucose homeostasis before or after BS. A certain level of A. muciniphila abundance might be required to observe a beneficial link to health. The severity of obesity and gut dysbiosis may partly explain the discrepancy with previous findings in less obese populations.},
}

Adult
*Bariatric Surgery
Dysbiosis
Feces/microbiology
Female
*Gastrointestinal Microbiome
Glucose/metabolism
Glucose Tolerance Test
Health Status
Homeostasis
Humans
Insulin Resistance
Longitudinal Studies
Middle Aged
Obesity, Morbid/metabolism/*microbiology/*surgery
Prospective Studies
Treatment Outcome
*Verrucomicrobia
Young Adult

@article {pmid30737349,
year = {2019},
author = {Tuttle, RN and Demko, AM and Patin, NV and Kapono, CA and Donia, MS and Dorrestein, P and Jensen, PR},
title = {Detection of Natural Products and Their Producers in Ocean Sediments.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {8},
pages = {},
pmid = {30737349},
issn = {1098-5336},
mesh = {Bacteria/genetics/*metabolism ; Biological Products/chemistry/*isolation & purification ; Drug Discovery ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Metabolome ; Metabolomics ; Metagenome ; Microbiota/physiology ; Micromonosporaceae/metabolism ; Multigene Family ; *Oceans and Seas ; Seawater/microbiology ; },
abstract = {Thousands of natural products have been identified from cultured microorganisms, yet evidence of their production in the environment has proven elusive. Technological advances in mass spectrometry, combined with public databases, now make it possible to address this disparity by detecting compounds directly from environmental samples. Here, we used adsorbent resins, tandem mass spectrometry, and next-generation sequencing to assess the metabolome of marine sediments and its relationship to bacterial community structure. We identified natural products previously reported from cultured bacteria, providing evidence they are produced in situ, and compounds of anthropogenic origin, suggesting this approach can be used as an indicator of environmental impact. The bacterial metabolite staurosporine was quantified and shown to reach physiologically relevant concentrations, indicating that it may influence sediment community structure. Staurosporine concentrations were correlated with the relative abundance of the staurosporine-producing bacterial genus Salinispora and production confirmed in strains cultured from the same location, providing a link between compound and candidate producer. Metagenomic analyses revealed numerous biosynthetic gene clusters related to indolocarbazole biosynthesis, providing evidence for noncanonical sources of staurosporine and a path forward to assess the relationships between natural products and the organisms that produce them. Untargeted environmental metabolomics circumvents the need for laboratory cultivation and represents a promising approach to understanding the functional roles of natural products in shaping microbial community structure in marine sediments.IMPORTANCE Natural products are readily isolated from cultured bacteria and exploited for useful purposes, including drug discovery. However, these compounds are rarely detected in the environments from which the bacteria are obtained, thus limiting our understanding of their ecological significance. Here, we used environmental metabolomics to directly assess chemical diversity in marine sediments. We identified numerous metabolites and, in one case, isolated strains of bacteria capable of producing one of the compounds detected. Coupling environmental metabolomics with community and metagenomic analyses provides opportunities to link compounds and producers and begin to assess the complex interactions mediated by specialized metabolites in marine sediments.},
}

Bacteria/genetics/*metabolism
Biological Products/chemistry/*isolation & purification
Drug Discovery
Geologic Sediments/microbiology
High-Throughput Nucleotide Sequencing
Metabolome
Metabolomics
Metagenome
Microbiota/physiology
Micromonosporaceae/metabolism
Multigene Family
*Oceans and Seas
Seawater/microbiology

@article {pmid29984552,
year = {2019},
author = {Gulliver, D and Lipus, D and Ross, D and Bibby, K},
title = {Insights into microbial community structure and function from a shallow, simulated CO2 -leakage aquifer demonstrate microbial selection and adaptation.},
journal = {Environmental microbiology reports},
volume = {11},
number = {3},
pages = {338-351},
doi = {10.1111/1758-2229.12675},
pmid = {29984552},
issn = {1758-2229},
mesh = {Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; Biodiversity ; Carbon Cycle/genetics ; Carbon Dioxide/analysis/*metabolism ; Chemoautotrophic Growth/genetics ; Groundwater/chemistry/*microbiology ; Metagenomics ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/analysis/*metabolism ; },
abstract = {Geological carbon storage is likely to be a part of a comprehensive strategy to minimize the atmospheric release of carbon dioxide (CO2), raising concerns that injected CO2 will leak into overlying freshwater aquifers. CO2(aq) leakage may impact the dominant microbial community responsible for important ecosystem functions such as nutrient cycling, metal cycling and carbon conversion. Here, we examined the impact of an experimental in situ CO2 -leakage on a freshwater aquifer microbial community. High-throughput 16S rRNA gene sequencing demonstrated lower microbial diversity in freshwater wells with CO2 concentrations above 1.15 g l-1 . Metagenomic sequencing and population genome binning were used to evaluate the metabolic potential of microbial populations across four CO2 exposed samples and one control sample. Population genome binning resulted in the recovery and annotation of three metagenome assembled genomes (MAGs). Two of the MAGs, most closely related to Curvibacter and Sulfuricurvum, had the functional capacity for CO2 utilization via carbon fixation coupled to sulfur and iron oxidation. The third draft genome was an Archaea, most closely related to Methanoregula, characterized by the metabolic potential for methanogenesis. Together, these findings show that CO2 leakage in a freshwater aquifer poses a strong selection, driving both microbial community structure and metabolic function.},
}

Archaea/classification/genetics/isolation & purification/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism
Biodiversity
Carbon Cycle/genetics
Carbon Dioxide/analysis/*metabolism
Chemoautotrophic Growth/genetics
Groundwater/chemistry/*microbiology
Metagenomics
Microbiota/genetics/*physiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Water Pollutants, Chemical/analysis/*metabolism

@article {pmid29929823,
year = {2018},
author = {Schott, C and Weigt, SS and Turturice, BA and Metwally, A and Belperio, J and Finn, PW and Perkins, DL},
title = {Bronchiolitis obliterans syndrome susceptibility and the pulmonary microbiome.},
journal = {The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation},
volume = {37},
number = {9},
pages = {1131-1140},
pmid = {29929823},
issn = {1557-3117},
support = {F30 HL137267/HL/NHLBI NIH HHS/United States ; R01 HL138628/HL/NHLBI NIH HHS/United States ; },
mesh = {Adult ; Aged ; Bronchiolitis Obliterans/*microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Disease Susceptibility ; Female ; Follow-Up Studies ; Humans ; Lung/*microbiology ; *Lung Transplantation ; Male ; *Microbiota ; Middle Aged ; Syndrome ; },
abstract = {BACKGROUND: Lung transplantation outcomes remain complicated by bronchiolitis obliterans syndrome (BOS), a major cause of mortality and retransplantation for patients. A variety of factors linking inflammation and BOS have emerged, meriting further exploration of the microbiome as a source of inflammation. In this analysis, we determined features of the pulmonary microbiome associated with BOS susceptibility.

METHODS: Bronchoalveolar lavage (BAL) samples were collected from 25 patients during standard of care bronchoscopies before BOS onset. Microbial DNA was isolated from BAL fluid and prepared for metagenomics shotgun sequencing. Patient microbiomes were phenotyped using k-means clustering and compared to determine effects on BOS-free survival.

RESULTS: Clustering identified 3 microbiome phenotypes: Actinobacteria dominant (AD), mixed, and Proteobacteria dominant. AD microbiomes, distinguished by enrichment with Gram-positive organisms, conferred reduced odds and risks for patients to develop acute rejection and BOS compared with non-AD microbiomes. These findings were independent of treatment models. Microbiome findings were correlated with BAL cell counts and polymorphonuclear cell percentages.

CONCLUSIONS: In some populations, features of the microbiome may be used to assess BOS susceptibility. Namely, a Gram-positive enriched pulmonary microbiome may predict resilience to BOS.},
}

Adult
Aged
Bronchiolitis Obliterans/*microbiology
Bronchoalveolar Lavage Fluid/microbiology
Disease Susceptibility
Female
Follow-Up Studies
Humans
Lung/*microbiology
*Lung Transplantation
Male
*Microbiota
Middle Aged
Syndrome

@article {pmid32193245,
year = {2020},
author = {Valdés, N and Gonzalez, A and Garcia, V and Tello, M},
title = {Analysis of the Microbiome of Rainbow Trout (Oncorhynchus mykiss) Exposed to the Pathogen Flavobacterium psychrophilum 10094.},
journal = {Microbiology resource announcements},
volume = {9},
number = {12},
pages = {},
doi = {10.1128/MRA.01562-19},
pmid = {32193245},
issn = {2576-098X},
abstract = {Rainbow trout that were resistant or susceptible to Flavobacterium psychrophilum infection were compared with respect to their microbial composition by using 16S rRNA V3-V4 sequencing. The differences occurred in gills, where resistant fish displayed a greater abundance of the phylum Proteobacteria and a smaller proportion of Firmicutes relative to those of susceptible fish.},
}

@article {pmid31761556,
year = {2020},
author = {Sousa, STP and Cabral, L and Lacerda-Júnior, GV and Noronha, MF and Ottoni, JR and Sartoratto, A and Oliveira, VM},
title = {Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds.},
journal = {Ecotoxicology and environmental safety},
volume = {189},
number = {},
pages = {109974},
doi = {10.1016/j.ecoenv.2019.109974},
pmid = {31761556},
issn = {1090-2414},
mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Dioxygenases/genetics ; Gene Library ; Geologic Sediments/*microbiology ; Hydrocarbons, Aromatic/*metabolism ; *Metagenome ; Metagenomics ; Microbiota ; Mixed Function Oxygenases/genetics ; *Petroleum Pollution ; },
abstract = {Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metagenomic fosmid library was carried out to evaluate the functional and taxonomic diversity of genes involved in aromatic compounds degradation in oil-impacted mangrove sediments. In addition, activity-based approach and gas chromatography were used to assess the degradation potential of fosmid clones. Results indicated that AH degradation genes, such as monooxygenases and dioxygenases, were grouped into the following categories: anaerobic degradation of aromatic compounds (20.34%), metabolism of central aromatic intermediates (35.40%) and peripheral pathways for catabolism of aromatic compounds (22.56%). Taxonomic affiliation of genes related to aromatic compounds metabolism revealed the prevalence of the classes Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. Aromatic hydrocarbons (phenol, naphthalene, phenanthrene, pyrene and benzopyrene) were used as the only carbon source to screen clones with degradation potential. Of the 2500 clones tested, 48 showed some respiratory activity in at least one of the five carbon sources used. The hydrocarbon degradation ability of the top ten fosmid clones was confirmed by GC-MS. Further, annotation of assembled metagenomic fragments revealed ORFs corresponding to proteins and functional domains directly or indirectly involved in the aromatic compound metabolism, such as catechol 2,3-dioxygenase and ferredoxin oxidoreductase. Finally, these data suggest that the indigenous mangrove sediment microbiota developed essential mechanisms towards ecosystem remediation of petroleum hydrocarbon impact.},
}

Bacteria/genetics/metabolism
Biodegradation, Environmental
Dioxygenases/genetics
Gene Library
Geologic Sediments/*microbiology
Hydrocarbons, Aromatic/*metabolism
*Metagenome
Metagenomics
Microbiota
Mixed Function Oxygenases/genetics
*Petroleum Pollution

@article {pmid30206336,
year = {2019},
author = {Seck, EH and Senghor, B and Merhej, V and Bachar, D and Cadoret, F and Robert, C and Azhar, EI and Yasir, M and Bibi, F and Jiman-Fatani, AA and Konate, DS and Musso, D and Doumbo, O and Sokhna, C and Levasseur, A and Lagier, JC and Khelaifia, S and Million, M and Raoult, D},
title = {Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans.},
journal = {International journal of obesity (2005)},
volume = {43},
number = {4},
pages = {862-871},
doi = {10.1038/s41366-018-0201-3},
pmid = {30206336},
issn = {1476-5497},
mesh = {Adult ; Case-Control Studies ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Global Health ; Humans ; Inflammation/etiology/*microbiology/physiopathology ; Male ; Obesity/etiology/*microbiology/physiopathology ; RNA, Ribosomal, 16S/genetics ; Refractometry ; Sodium Chloride, Dietary/*adverse effects ; },
abstract = {BACKGROUND/OBJECTIVES: High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored.

METHODS/SUBJECTS: We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by taxonogenomics and their genome sequenced.

RESULTS: Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut.

CONCLUSIONS: High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.},
}

Adult
Case-Control Studies
Feces/*microbiology
Female
Gastrointestinal Microbiome/*genetics
Global Health
Humans
Inflammation/etiology/*microbiology/physiopathology
Male
Obesity/etiology/*microbiology/physiopathology
RNA, Ribosomal, 16S/genetics
Refractometry
Sodium Chloride, Dietary/*adverse effects

@article {pmid31521614,
year = {2019},
author = {Yamada, T and Hino, S and Iijima, H and Genda, T and Aoki, R and Nagata, R and Han, KH and Hirota, M and Kinashi, Y and Oguchi, H and Suda, W and Furusawa, Y and Fujimura, Y and Kunisawa, J and Hattori, M and Fukushima, M and Morita, T and Hase, K},
title = {Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis.},
journal = {EBioMedicine},
volume = {48},
number = {},
pages = {513-525},
pmid = {31521614},
issn = {2352-3964},
mesh = {Adult ; Animals ; Biomarkers ; Butyrates/metabolism ; Case-Control Studies ; Female ; Gastrointestinal Microbiome ; *Homeostasis ; Humans ; *Immunity, Mucosal ; Inflammatory Bowel Diseases/etiology/metabolism/pathology ; Intestinal Mucosa/*immunology/*metabolism ; Male ; Metagenome ; Metagenomics ; Mice ; Middle Aged ; Mucins/*metabolism ; Polysaccharides/*metabolism ; Symbiosis ; },
abstract = {BACKGROUND: The dysbiosis of gut microbiota has been implicated in the pathogenesis of inflammatory bowel diseases; however, the underlying mechanisms have not yet been elucidated. Heavily glycosylated mucin establishes a first-line barrier against pathogens and serves as a niche for microbial growth.

METHODS: To elucidate relationships among dysbiosis, abnormal mucin utilisation, and microbial metabolic dysfunction, we analysed short-chain fatty acids (SCFAs) and mucin components in stool samples of 40 healthy subjects, 49 ulcerative colitis (UC) patients, and 44 Crohn's disease (CD) patients from Japan.

FINDINGS: Levels of n-butyrate were significantly lower in stools of both CD and UC patients than in stools of healthy subjects. Correlation analysis identified seven bacterial species positively correlated with n-butyrate levels; the major n-butyrate producer, Faecalibacterium prausnitzii, was particularly underrepresented in CD patients, but not in UC patients. In UC patients, there were inverse correlations between mucin O-glycan levels and the production of SCFAs, such as n-butyrate, suggesting that mucin O-glycans serve as an endogenous fermentation substrate for n-butyrate production. Indeed, mucin-fed rodents exhibited enhanced n-butyrate production, leading to the expansion of RORgt+Treg cells and IgA-producing cells in colonic lamina propria. Microbial utilisation of mucin-associated O-glycans was significantly reduced in n-butyrate-deficient UC patients.

INTERPRETATION: Mucin O-glycans facilitate symbiosynthesis of n-butyrate by gut microbiota. Abnormal mucin utilisation may lead to reduced n-butyrate production in UC patients. FUND: Japan Society for the Promotion of Science, Health Labour Sciences Research Grant, AMED-Crest, AMED, Yakult Foundation, Keio Gijuku Academic Development Funds, The Aashi Grass Foundation, and The Canon Foundation.},
}

Adult
Animals
Biomarkers
Butyrates/metabolism
Case-Control Studies
Female
Gastrointestinal Microbiome
*Homeostasis
Humans
*Immunity, Mucosal
Inflammatory Bowel Diseases/etiology/metabolism/pathology
Intestinal Mucosa/*immunology/*metabolism
Male
Metagenome
Metagenomics
Mice
Middle Aged
Mucins/*metabolism
Polysaccharides/*metabolism
Symbiosis

@article {pmid32185431,
year = {2020},
author = {Pentimone, I and Colagiero, M and Rosso, LC and Ciancio, A},
title = {Omics applications: towards a sustainable protection of tomato.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-020-10500-7},
pmid = {32185431},
issn = {1432-0614},
abstract = {Transcriptome data and gene expression analysis have a huge potential in the study of multiple relationships involving plants, pathogens, and pests, including the interactions with beneficial microorganisms such as endophytes or other functional groups. Next-generation sequencing (NGS) and other recent long-read-based sequencing approaches (i.e., nanopore and others) provide unprecedented tools allowing the fast identification of plant information processing systems, in situ and in real time, fundamental for crop management and pest regulation. Other -omics approaches such as metagenomics and metatranscriptomics allow high-resolution insights on the rhizosphere ecology. They may highlight key factors affecting belowground biodiversity or processes, modulating the expression of stress-responsive pathways. The application of miRNAs and other small RNAs is a relatively new field of application, with enormous potential for the selective activation of defense pathways. However, limitations concerning the stability of the RNA molecules and their effective delivery must be overcome.},
}

@article {pmid32184999,
year = {2020},
author = {Moore, G and Tessler, M and Cunningham, SW and Betancourt, J and Harbert, R},
title = {Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.},
journal = {Ecology and evolution},
volume = {10},
number = {5},
pages = {2530-2544},
doi = {10.1002/ece3.6082},
pmid = {32184999},
issn = {2045-7758},
abstract = {Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.},
}

@article {pmid31668006,
year = {2019},
author = {Lugli, GA and Milani, C and Mancabelli, L and Turroni, F and van Sinderen, D and Ventura, M},
title = {A microbiome reality check: limitations of in silico-based metagenomic approaches to study complex bacterial communities.},
journal = {Environmental microbiology reports},
volume = {11},
number = {6},
pages = {840-847},
doi = {10.1111/1758-2229.12805},
pmid = {31668006},
issn = {1758-2229},
support = {15/JP-HDHL/3280//Joint Programming Initiative A healthy diet for a healthy life/International ; //Ministero dell'Istruzione, dell'Università e della Ricerca/International ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; //University of Parma/International ; },
mesh = {Animals ; Computational Biology/*methods ; Feces/microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; },
abstract = {In recent years, whole shotgun metagenomics (WSM) of complex microbial communities has become an established technology to perform compositional analyses of complex microbial communities, an approach that is heavily reliant on bioinformatic pipelines to process and interpret the generated raw sequencing data. However, the use of such in silico pipelines for the microbial taxonomic classification of short sequences may lead to significant errors in the compositional outputs deduced from such sequencing data. To investigate the ability of such in silico pipelines, we employed two commonly applied bioinformatic tools, i.e., MetaPhlAn2 and Kraken2 together with two metagenomic data sets originating from human and animal faecal samples. By using these bioinformatic programs that taxonomically classify WSM data based on marker genes, we observed a trend to depict a lower complexity of the microbial communities. Here, we assess the limitations of the most commonly employed bioinformatic pipelines, i.e., MetaPhlAn2 and Kraken2, and based on our findings, we propose that such analyses should ideally be combined with experimentally based microbiological validations.},
}

Animals
Computational Biology/*methods
Feces/microbiology
Humans
Metagenomics/*methods
*Microbiota

@article {pmid31573138,
year = {2019},
author = {McLean, AHC and Godfray, HCJ and Ellers, J and Henry, LM},
title = {Host relatedness influences the composition of aphid microbiomes.},
journal = {Environmental microbiology reports},
volume = {11},
number = {6},
pages = {808-816},
pmid = {31573138},
issn = {1758-2229},
support = {NBAF708//Natural Environment Research Council/International ; NE/M018016/1//Natural Environment Research Council/International ; VICI 865.12.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; },
mesh = {Animals ; Aphids/classification/*microbiology ; Bacteria/classification/genetics ; *Host Microbial Interactions ; Metagenomics ; *Microbiota ; },
abstract = {Animals are host to a community of microbes, collectively referred to as their microbiome, that can play a key role in their hosts' biology. The bacterial endosymbionts of insects have a particularly strong influence on their hosts, but despite their importance we still know little about the factors that influence the composition of insect microbial communities. Here, we ask: what is the relative importance of host relatedness and host ecology in structuring symbiont communities of diverse aphid species? We used next-generation sequencing to compare the microbiomes of 46 aphid species with known host plant affiliations. We find that relatedness between aphid species is the key factor explaining the microbiome composition, with more closely related aphid species housing more similar bacterial communities. Endosymbionts dominate the microbial communities, and we find a novel bacterium in the genus Sphingopyxis that is associated with numerous aphid species feeding exclusively on trees. The influence of ecology was less pronounced than that of host relatedness. Our results suggest that co-adaptation between insect species and their facultative symbionts is a more important determinant of symbiont species presence in aphids than shared ecology of hosts.},
}

Animals
Aphids/classification/*microbiology
Bacteria/classification/genetics
*Host Microbial Interactions
Metagenomics
*Microbiota

@article {pmid31634343,
year = {2019},
author = {Diakite, A and Dubourg, G and Dione, N and Afouda, P and Bellali, S and Ngom, II and Valles, C and Million, M and Levasseur, A and Cadoret, F and Lagier, JC and Raoult, D},
title = {Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0223543},
pmid = {31634343},
issn = {1932-6203},
mesh = {Adult ; Bacteria/classification/genetics ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metagenome ; *Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Molecular approaches have long led to the assumption that the human gut microbiota is dominated by uncultivable bacteria. The recent advent of large-scale culturing methods, and in particular that of culturomics have demonstrated that these prokaryotes can in fact be cultured. This is increasing in a dramatic manner the repertoire of commensal microbes inhabiting the human gut. Following eight years of culturomics approach applied on more than 900 samples, we propose herein a remake of the pioneering study applying a dual approach including culturomics and metagenomics on a cohort of 8 healthy specimen. Here we show that culturomics enable a 20% higher richness when compared to molecular approaches by culturing 1 archaeal species and 494 bacterial species of which 19 were new taxa. Species discovered as a part of previous culturomics studies represent 30% of the cultivated isolates, while sequences derived from these new taxa enabled to increase by 22% the bacterial richness retrieved by metagenomics. Overall, 67% of the total reads generated were covered by cultured isolates, significantly reducing the hidden content of sequencing methods compared to the pioneering study. By redefining culture conditions to recover microbes previously considered fastidious, there are greater opportunities than ever to eradicate metagenomics dark matter.},
}

Adult
Bacteria/classification/genetics
Female
*Gastrointestinal Microbiome
Humans
Male
*Metagenome
*Metagenomics
Middle Aged
RNA, Ribosomal, 16S
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

@article {pmid31576454,
year = {2019},
author = {Alibrahim, A and Al-Gharabally, D and Mahmoud, H and Dittrich, M},
title = {Proto-dolomite formation in microbial consortia dominated by Halomonas strains.},
journal = {Extremophiles : life under extreme conditions},
volume = {23},
number = {6},
pages = {765-781},
pmid = {31576454},
issn = {1433-4909},
support = {PR17-12SL-10//Kuwait Foundation for the Advancement of Sciences/ ; },
mesh = {Calcium Carbonate ; *Halomonas ; Kuwait ; Magnesium ; *Microbial Consortia ; },
abstract = {Microbes can be found in hypersaline environments forming diverse populations with complex ecological interactions. Microbes in such environments were found to be involved in the formation of minerals including dolomite, a mineral of economic importance and whose origin has been long-debated. Various reports on in vitro experiments using pure cultures provided evidence for the microbial role in dolomite formation. However, culturing experiments have been limited in scope and do not fully address the possible interactions of the naturally occurring microbial communities; consequently, the ability of microbes as a community to form dolomite has been investigated in this study. Our experiments focused on examining the microbial composition by culturing aerobic heterotrophs from the top hypersaline sediments of Al-Khiran sabkha in Kuwait, a modern dolomite-forming environment. The objectives of this study were to assess the ability of two microbial consortia to form dolomite using enrichment culture experiments, mineralogy, and metagenomics. Proto-dolomite was formed by a microbial community dominated by Halomonas strains whereby degradation of the extracellular polymeric substances (EPS) was observed and the pH changed from 7.00 to 8.58. Conversely, proto-dolomite was not observed within a microbial community dominated by Clostridiisalibacter in which EPS continuously accumulated and the pH slightly changed from 7.00 to 7.29.},
}

Calcium Carbonate
*Halomonas
Kuwait
Magnesium
*Microbial Consortia

@article {pmid31529842,
year = {2019},
author = {Caguazango, JC and Pazos, ÁJ},
title = {Microbiota according to gastric topography in patients with low or high risk of gastric cancer in Nariño, Colombia.},
journal = {Biomedica : revista del Instituto Nacional de Salud},
volume = {39},
number = {Supl. 2},
pages = {157-171},
doi = {10.7705/biomedica.v39i4.4520},
pmid = {31529842},
issn = {0120-4157},
mesh = {Adult ; Aged ; Colombia/epidemiology ; Female ; Gastric Mucosa/microbiology/pathology ; Gastritis/epidemiology/*microbiology ; Gastritis, Atrophic/epidemiology/microbiology ; *Gastrointestinal Microbiome ; Helicobacter Infections/epidemiology/microbiology ; Helicobacter pylori/genetics/isolation & purification ; Humans ; Male ; Metaplasia ; Middle Aged ; Pyloric Antrum/microbiology ; Ribotyping ; Risk ; Stomach/*microbiology ; Stomach Neoplasms/*epidemiology ; },
}

Adult
Aged
Colombia/epidemiology
Female
Gastric Mucosa/microbiology/pathology
Gastritis/epidemiology/*microbiology
Gastritis, Atrophic/epidemiology/microbiology
*Gastrointestinal Microbiome
Helicobacter Infections/epidemiology/microbiology
Helicobacter pylori/genetics/isolation & purification
Humans
Male
Metaplasia
Middle Aged
Pyloric Antrum/microbiology
Ribotyping
Risk
Stomach/*microbiology
Stomach Neoplasms/*epidemiology

@article {pmid30728065,
year = {2019},
author = {Johnson, ME and Franks, JM and Cai, G and Mehta, BK and Wood, TA and Archambault, K and Pioli, PA and Simms, RW and Orzechowski, N and Arron, S and Whitfield, ML},
title = {Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression in systemic sclerosis skin.},
journal = {Arthritis research & therapy},
volume = {21},
number = {1},
pages = {49},
pmid = {30728065},
issn = {1478-6362},
support = {T32 LM012204/LM/NLM NIH HHS/United States ; W81XWH-14-1-0224//U.S. Department of Defense/International ; },
mesh = {Adult ; Aged ; Bacteria/classification/genetics ; Biopsy ; Cohort Studies ; Dysbiosis/*genetics ; Female ; Gene Expression Profiling ; Humans ; Inflammation/*genetics/microbiology/pathology ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Population Dynamics ; Scleroderma, Systemic/*genetics/microbiology/pathology ; Skin/*metabolism/microbiology/pathology ; Time Factors ; },
abstract = {BACKGROUND: Infectious agents have long been postulated to be disease triggers for systemic sclerosis (SSc), but a definitive link has not been found. Metagenomic analyses of high-throughput data allows for the unbiased identification of potential microbiome pathogens in skin biopsies of SSc patients and allows insight into the relationship with host gene expression.

METHODS: We examined skin biopsies from a diverse cohort of 23 SSc patients (including lesional forearm and non-lesional back samples) by RNA-seq. Metagenomic filtering and annotation was performed using the Integrated Metagenomic Sequencing Analysis (IMSA). Associations between microbiome composition and gene expression were analyzed using single-sample gene set enrichment analysis (ssGSEA).

RESULTS: We find the skin of SSc patients exhibits substantial changes in microbial composition relative to controls, characterized by sharp decreases in lipophilic taxa, such as Propionibacterium, combined with increases in a wide range of gram-negative taxa, including Burkholderia, Citrobacter, and Vibrio.

CONCLUSIONS: Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression. These data provide a comprehensive portrait of the SSc skin microbiome and its association with local gene expression, which mirrors the molecular changes in lesional skin.},
}

Adult
Aged
Bacteria/classification/genetics
Biopsy
Cohort Studies
Dysbiosis/*genetics
Female
Gene Expression Profiling
Humans
Inflammation/*genetics/microbiology/pathology
Male
Metagenomics/methods
Microbiota/*genetics
Middle Aged
Population Dynamics
Scleroderma, Systemic/*genetics/microbiology/pathology
Skin/*metabolism/microbiology/pathology
Time Factors

@article {pmid30590603,
year = {2019},
author = {Mansbach, JM and Hasegawa, K and Piedra, PA and Avadhanula, V and Petrosino, JF and Sullivan, AF and Espinola, JA and Camargo, CA},
title = {Haemophilus-Dominant Nasopharyngeal Microbiota Is Associated With Delayed Clearance of Respiratory Syncytial Virus in Infants Hospitalized for Bronchiolitis.},
journal = {The Journal of infectious diseases},
volume = {219},
number = {11},
pages = {1804-1808},
pmid = {30590603},
issn = {1537-6613},
support = {UH3 OD023253/OD/NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R01 AI134940/AI/NIAID NIH HHS/United States ; R01 AI127507/AI/NIAID NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; },
mesh = {Bronchiolitis/*microbiology ; Female ; Haemophilus/*growth & development ; Hospitalization ; Humans ; Infant ; Male ; *Microbiota ; Nasopharynx/microbiology/virology ; Respiratory Syncytial Virus Infections/virology ; Respiratory Syncytial Virus, Human/*immunology ; Viral Load ; },
abstract = {The relation of nasopharyngeal microbiota to the clearance of respiratory syncytial virus (RSV) in infants hospitalized for bronchiolitis is not known. In a multicenter cohort, we found that 106 of 557 infants (19%) hospitalized with RSV bronchiolitis had the same RSV subtype 3 weeks later (ie, delayed clearance of RSV). Using 16S ribosomal RNA gene sequencing and a clustering approach, infants with a Haemophilus-dominant microbiota profile at hospitalization were more likely than those with a mixed profile to have delayed clearance, after adjustment for 11 factors, including viral load. Nasopharyngeal microbiota composition is associated with delayed RSV clearance.},
}

Bronchiolitis/*microbiology
Female
Haemophilus/*growth & development
Hospitalization
Humans
Infant
Male
*Microbiota
Nasopharynx/microbiology/virology
Respiratory Syncytial Virus Infections/virology
Respiratory Syncytial Virus, Human/*immunology
Viral Load

@article {pmid30336176,
year = {2019},
author = {Brusaferro, A and Cavalli, E and Farinelli, E and Cozzali, R and Principi, N and Esposito, S},
title = {Gut dysbiosis and paediatric Crohn's disease.},
journal = {The Journal of infection},
volume = {78},
number = {1},
pages = {1-7},
doi = {10.1016/j.jinf.2018.10.005},
pmid = {30336176},
issn = {1532-2742},
mesh = {Autophagy ; Child ; Crohn Disease/*microbiology/physiopathology/therapy ; *Dysbiosis ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; Probiotics/therapeutic use ; },
abstract = {OBJECTIVES: The main objective of this manuscript is to discuss our present knowledge of the relationships between dysbiosis and paediatric Crohn's disease (CD). The therapeutic role of the methods currently used to re-establish normal gut microbiota composition is also analysed.

METHODS: PubMed was used to search for all of the studies published from January 2008 to June 2018 using the key words: "Crohn's disease" and "gut dysbiosis" or "microbiota" or "microbioma" or "probiotic" and "children" or "paediatric". More than 100 articles were found, but only those published in English or providing evidence-based data were included in the evaluation.

RESULTS: Gut microbiota are primary actors in CD's pathogenesis. The new techniques developed in metagenomics allow us to reveal new details of microbiota composition in healthy subjects and CD patients, and to elucidate the link between microbiota and numerous pathologies, such as obesity, allergies and type 1 diabetes mellitus.

CONCLUSION: Discoveries on the role of gut microbiota could potentially disclose new therapeutic options for CD treatment and improve the existing therapies. Further studies are needed to facilitate the diagnosis and tailor the therapy of a pathology that is an increasing burden on public health.},
}

Autophagy
Child
Crohn Disease/*microbiology/physiopathology/therapy
*Dysbiosis
Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Humans
Metagenomics
Probiotics/therapeutic use

@article {pmid31703372,
year = {2019},
author = {Gowers, GF and Vince, O and Charles, JH and Klarenberg, I and Ellis, T and Edwards, A},
title = {Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition.},
journal = {Genes},
volume = {10},
number = {11},
pages = {},
pmid = {31703372},
issn = {2073-4425},
support = {BB/K006290/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Electric Power Supplies ; *Expeditions ; Ice Cover/*microbiology ; Iceland ; *Metagenome ; Metagenomics/instrumentation/*methods ; *Microbiota ; Nanopore Sequencing/instrumentation/*methods ; *Solar Energy ; },
abstract = {Microbial communities in remote locations remain under-studied. This is particularly true on glaciers and icecaps, which cover approximately 11% of the Earth's surface. The principal reason for this is the inaccessibility of most of these areas due to their extreme isolation and challenging environmental conditions. While remote research stations have significantly lowered the barrier to studying the microbial communities on icecaps, their use has led to a bias for data collection in the near vicinity of these institutions. Here, miniaturisation of a DNA sequencing lab suitable for off-grid metagenomic studies is demonstrated. Using human power alone, this lab was transported across Europe's largest ice cap (Vatnajökull, Iceland) by ski and sledge. After 11 days of unsupported polar-style travel, a metagenomic study of a geothermal hot spring gorge was conducted on the remote northern edge of the ice cap. This tent-based metagenomic study resulted in over 24 h of Nanopore sequencing, powered by solar power alone. This study demonstrates the ability to conduct DNA sequencing in remote locations, far from civilised resources (mechanised transport, external power supply, internet connection, etc.), whilst greatly reducing the time from sample collection to data acquisition.},
}

Electric Power Supplies
*Expeditions
Ice Cover/*microbiology
Iceland
*Metagenome
Metagenomics/instrumentation/*methods
*Microbiota
Nanopore Sequencing/instrumentation/*methods
*Solar Energy

@article {pmid31484222,
year = {2019},
author = {Ewart, KM and Johnson, RN and Ogden, R and Joseph, L and Frankham, GJ and Lo, N},
title = {Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species.},
journal = {Molecular ecology resources},
volume = {19},
number = {6},
pages = {1578-1592},
doi = {10.1111/1755-0998.13082},
pmid = {31484222},
issn = {1755-0998},
support = {//Australian Government Research Training Program Scholarship/ ; //Birdlife Australia, Stuart Leslie Bird Research Award/ ; //Australian Museum Foundation/ ; //University of Sydney Merit Award/ ; //University of Sydney Industry and Community Engagement Seed Fund/ ; 16//Australian Museum/ ; 02//Australian Museum/ ; },
mesh = {Animals ; Cockatoos/*genetics ; DNA/genetics ; DNA Fragmentation ; Endangered Species ; Genetic Variation/genetics ; Genome/*genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Museums ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA/methods ; Specimen Handling/methods ; },
abstract = {Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq™). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.},
}

Animals
Cockatoos/*genetics
DNA/genetics
DNA Fragmentation
Endangered Species
Genetic Variation/genetics
Genome/*genetics
Genomics/methods
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Museums
Polymorphism, Single Nucleotide/*genetics
Sequence Analysis, DNA/methods
Specimen Handling/methods

@article {pmid31379089,
year = {2019},
author = {Marquina, D and Esparza-Salas, R and Roslin, T and Ronquist, F},
title = {Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches.},
journal = {Molecular ecology resources},
volume = {19},
number = {6},
pages = {1516-1530},
pmid = {31379089},
issn = {1755-0998},
support = {642241//European Union's Horizon 2020/ ; 2014-05901//Swedish Research Council/ ; },
mesh = {Animals ; Arthropods/*genetics ; Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; DNA Primers/genetics ; Ethanol/chemistry ; Metagenomics/methods ; Soil ; },
abstract = {DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers - COI and 16S - and three different sampling methods: (a) homogenized Malaise trap samples (homogenate), (b) preservative ethanol from the same samples, and (c) soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is significantly different from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol while strong and large taxa are overrepresented in homogenate. For soil samples, highly degenerate COI primers pick up large amounts of nontarget DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in molecular operational taxonomic unit (MOTU) content was found between the trap and the soil samples. Our results demonstrate that none of the tested sampling approaches is satisfactory on its own. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.},
}

Animals
Arthropods/*genetics
Biodiversity
DNA/genetics
DNA Barcoding, Taxonomic/methods
DNA Primers/genetics
Ethanol/chemistry
Metagenomics/methods
Soil

@article {pmid31349392,
year = {2019},
author = {Seeber, PA and McEwen, GK and Löber, U and Förster, DW and East, ML and Melzheimer, J and Greenwood, AD},
title = {Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes.},
journal = {Molecular ecology resources},
volume = {19},
number = {6},
pages = {1486-1496},
doi = {10.1111/1755-0998.13069},
pmid = {31349392},
issn = {1755-0998},
support = {SAW-2015-IZW-1 440//Leibniz Gemeinschaft/ ; },
mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/genetics ; Ecosystem ; Environmental DNA/*genetics ; Environmental Monitoring/methods ; Genome, Mitochondrial/genetics ; Hybridization, Genetic/*genetics ; Mammals ; Metagenomics/methods ; Namibia ; Nucleic Acid Hybridization/*genetics ; Tanzania ; Water ; },
abstract = {Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA-based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water-limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus-specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non-African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over-representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100-fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.},
}

Animals
Biodiversity
DNA, Mitochondrial/genetics
Ecosystem
Environmental DNA/*genetics
Environmental Monitoring/methods
Genome, Mitochondrial/genetics
Hybridization, Genetic/*genetics
Mammals
Metagenomics/methods
Namibia
Nucleic Acid Hybridization/*genetics
Tanzania
Water

@article {pmid30240894,
year = {2019},
author = {Allaband, C and McDonald, D and Vázquez-Baeza, Y and Minich, JJ and Tripathi, A and Brenner, DA and Loomba, R and Smarr, L and Sandborn, WJ and Schnabl, B and Dorrestein, P and Zarrinpar, A and Knight, R},
title = {Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {17},
number = {2},
pages = {218-230},
pmid = {30240894},
issn = {1542-7714},
support = {K08 DK102902/DK/NIDDK NIH HHS/United States ; },
mesh = {Computational Biology/*methods ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Individuality ; Metabolomics/*methods ; Metagenomics/*methods ; *Microbiota ; },
abstract = {Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.},
}

Computational Biology/*methods
*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Humans
Individuality
Metabolomics/*methods
Metagenomics/*methods
*Microbiota

@article {pmid32153535,
year = {2020},
author = {Stokke, R and Reeves, EP and Dahle, H and Fedøy, AE and Viflot, T and Lie Onstad, S and Vulcano, F and Pedersen, RB and Eijsink, VGH and Steen, IH},
title = {Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {249},
doi = {10.3389/fmicb.2020.00249},
pmid = {32153535},
issn = {1664-302X},
abstract = {Deep-sea hydrothermal vents are amongst the most extreme environments on Earth and represent interesting targets for marine bioprospecting and biodiscovery. The microbial communities in hydrothermal vents are often dominated by chemolithoautotrophs utilizing simple chemical compounds, though the full extent of their heterotrophic abilities is still being explored. In the bioprocessing industry, where degradation of complex organic materials often is a major challenge, new microbial solutions are heavily needed. To meet these needs, we have developed novel in situ incubators and tested if deployment of recalcitrant materials from fish farming and wood-pulping industries introduced changes in the microbial community structure in hot marine hydrothermal sediments. The incubation chambers were deployed in sediments at the Bruse vent site located within the Jan Mayen vent field for 1 year, after which the microbial populations in the chambers were profiled by 16S rRNA Ion Torrent amplicon sequencing. A total of 921 operational taxonomic units (OTUs) were assigned into 74 different phyla where differences in community structure were observed depending on the incubated material, chamber depth below the sea floor and/or temperature. A high fraction of putative heterotrophic microbial lineages related to cultivated members within the Thermotogales were observed. However, considerable fractions of previously uncultivated and novel Thermotogales and Bacteroidetes were also identified. Moreover, several novel lineages (e.g., members within the DPANN superphylum, unidentified archaeal lineages, unclassified Thermoplasmatales and Candidatus division BRC-1 bacterium) of as-yet uncultivated thermophilic archaea and bacteria were identified. Overall, our data illustrate that amendment of hydrothermal vent communities by in situ incubation of biomass induces shifts in community structure toward increased fractions of heterotrophic microorganisms. The technologies utilized here could aid in subsequent metagenomics-based enzyme discovery for diverse industries.},
}

@article {pmid31635158,
year = {2019},
author = {Guo, W and Mishra, S and Wang, C and Zhang, H and Ning, R and Kong, F and Zeng, B and Zhao, J and Li, Y},
title = {Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca).},
journal = {Genes},
volume = {10},
number = {10},
pages = {},
pmid = {31635158},
issn = {2073-4425},
mesh = {Amylases/metabolism ; Animals ; Animals, Wild/microbiology/physiology ; Animals, Zoo/*microbiology/physiology ; Diet ; Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; *Metagenome ; RNA, Ribosomal, 16S ; Ursidae/*microbiology/physiology ; },
abstract = {Captive breeding has been used as an effective approach to protecting endangered animals but its effect on the gut microbiome and the conservation status of these species is largely unknown. The giant panda is a flagship species for the conservation of wildlife. With integrated efforts including captive breeding, this species has been recently upgraded from "endangered" to "vulnerable" (IUCN 2016). Since a large proportion (21.8%) of their global population is still captive, it is critical to understand how captivity changes the gut microbiome of these pandas and how such alterations to the microbiome might affect their future fitness and potential impact on the ecosystem after release into the wild. Here, we use 16S rRNA (ribosomal RNA) marker gene sequencing and shotgun metagenomics sequencing to demonstrate that the fecal microbiomes differ substantially between wild and captive giant pandas. Fecal microbiome diversity was significantly lower in captive pandas, as was the diversity of functional genes. Additionally, captive pandas have reduced functional potential for cellulose degradation but enriched metabolic pathways for starch metabolism, indicating that they may not adapt to a wild diet after being released into the wild since a major component of their diet in the wild will be bamboo. Most significantly, we observed a significantly higher level of amylase activity but a lower level of cellulase activity in captive giant panda feces than those of wild giant pandas, shown by an in vitro experimental assay. Furthermore, antibiotic resistance genes and virulence factors, as well as heavy metal tolerance genes were enriched in the microbiomes of captive pandas, which raises a great concern of spreading these genes to other wild animals and ecosystems when they are released into a wild environment. Our results clearly show that captivity has altered the giant panda microbiome, which could have unintended negative consequences on their adaptability and the ecosystem during the reintroduction of giant pandas into the wild.},
}

Amylases/metabolism
Animals
Animals, Wild/microbiology/physiology
Animals, Zoo/*microbiology/physiology
Diet
Drug Resistance, Bacterial
*Gastrointestinal Microbiome
*Metagenome
RNA, Ribosomal, 16S
Ursidae/*microbiology/physiology

@article {pmid31494301,
year = {2019},
author = {Li, L and Wang, F and Liu, Y and Gu, F},
title = {Intestinal microbiota dysbiosis in children with recurrent respiratory tract infections.},
journal = {Microbial pathogenesis},
volume = {136},
number = {},
pages = {103709},
doi = {10.1016/j.micpath.2019.103709},
pmid = {31494301},
issn = {1096-1208},
mesh = {Bacteria/classification/isolation & purification ; Child ; Dysbiosis/*complications ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; ROC Curve ; Recurrence ; Respiratory Tract Infections/*complications ; },
abstract = {BACKGROUND: The impact of the gut microbiota on recurrent respiratory tract infection (RRTI) remains to be fully elucidated.

METHODS: To characterize the gut microbiota in patients with RRTI, fecal samples from 26 patients with RRTI and 23 healthy volunteers were profiled using the Illumina MiSeq platform. Beta diversity (Principal Component Analysis (PCA), Principal Co-ordinates Analysis (PCoA), Non-metric multidimensional scaling (NMDS)) analysis showed that the bacterial community structure segregated differently between the RRTI and control groups.

RESULTS: Results from alpha diversity analysis revealed lower microbiota diversity in samples from RRTI patients than in normal controls. Taxonomic analysis illustrated that the abundance of six phyla (Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Tenericutes) and four genera (Enterococcus, Faecalibacterium, Bifidobacterium, Eubacterium were significantly different between these two groups. In addition, Enterococcus (P < 0.001) was more enriched in the RRTI group, whereas the abundances of Eubacterium (P < 0.001), Faecalibacterium (0.01 < P < 0.05) and Bifidobacterium (0.01 < P < 0.05) were reduced in the RRTI group compared to those in the normal control group. The performance of the model was assessed using ROC analysis, and Enterococcus, Eubacterium and Bifidobacterium achieved AUC values of 0.860, 0.820, and 0.689, respectively.

CONCLUSIONS: These results provide fundamental evidence in support of intestinal microbiota dysbiosis in children with RRTI.},
}

Bacteria/classification/isolation & purification
Child
Dysbiosis/*complications
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Male
Metagenomics
ROC Curve
Recurrence
Respiratory Tract Infections/*complications

@article {pmid30285475,
year = {2020},
author = {Afshari, R and Pillidge, CJ and Dias, DA and Osborn, AM and Gill, H},
title = {Cheesomics: the future pathway to understanding cheese flavour and quality.},
journal = {Critical reviews in food science and nutrition},
volume = {60},
number = {1},
pages = {33-47},
doi = {10.1080/10408398.2018.1512471},
pmid = {30285475},
issn = {1549-7852},
mesh = {Cheese/*analysis/microbiology ; Computational Biology ; *Food Microbiology ; Metagenomics ; *Microbiota ; Taste ; },
abstract = {Cheese is a fermented dairy product, harboring diverse microbial communities (microbiota) that change over time and vary depending on the type of cheese and their respective starter and adjunct cultures. These microorganisms play a crucial role in determining the flavor, quality and safety of the final product. Exploring the composition of cheese microbiota and the underlying molecular mechanisms involved in cheese ripening has been the subject of many studies. Recent advances in next generation sequencing (NGS) methods and the development of sophisticated bioinformatics tools have provided deeper insights into the composition and potential functionality of cheese microbiota far beyond the information provided by culture-dependent methods. These advances, which include rRNA gene amplicon sequencing and metagenomics, have been complemented and expanded in recent years by the application of metatranscriptomics, metaproteomics and metabolomics. This paper reviews studies in which application of these meta-omics technologies has led to a better understanding of the microbial composition and functionality of cheese and highlights opportunities by which the integration of outputs from diverse multi-omics analytical platforms (cheesomics) could be used in the future to advance our knowledge of the cheese ripening process and identify biomarkers for predicting cheese flavor, quality, texture and safety, and bioactive metabolites with potential to influence human health.},
}

Cheese/*analysis/microbiology
Computational Biology
*Food Microbiology
Metagenomics
*Microbiota
Taste

@article {pmid31596877,
year = {2019},
author = {Allegrini, M and Gomez, EDV and Smalla, K and Zabaloy, MC},
title = {Suppression treatment differentially influences the microbial community and the occurrence of broad host range plasmids in the rhizosphere of the model cover crop Avena sativa L.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0223600},
pmid = {31596877},
issn = {1932-6203},
mesh = {Archaea/genetics ; Avena/drug effects/*microbiology ; DNA Barcoding, Taxonomic ; Glycerol/*analogs & derivatives/pharmacology ; Glycine/*analogs & derivatives/pharmacology ; Herbicides/*pharmacology ; Mesorhizobium/genetics ; *Metagenome ; Metagenomics ; Microbiota/*drug effects/genetics ; *Rhizosphere ; },
abstract = {Cover crop suppression with glyphosate-based herbicides (GBHs) represents a common agricultural practice. The objective of this study was to compare rhizospheric microbial communities of A. sativa plants treated with a GBH relative to the mechanical suppression (mowing) in order to assess their differences and the potential implications for soil processes. Samples were obtained at 4, 10, 17 and 26 days post-suppression. Soil catabolic profiling and DNA-based methods were applied. At 26 days, higher respiration responses and functional diversity indices (Shannon index and catabolic evenness) were observed under glyphosate suppression and a neat separation of catabolic profiles was detected in multivariate analysis. Sarcosine and Tween 20 showed the highest contribution to this separation. Metabarcoding revealed a non-significant effect of suppression method on either alpha-diversity metrics or beta-diversity. Conversely, differences were detected in the relative abundance of specific bacterial taxa. Mesorhizobium sequences were detected in higher relative abundance in glyphosate-treated plants at the end of the experiment while the opposite trend was observed for Gaiella. Quantitative PCR of amoA gene from ammonia-oxidizing archaea showed a lower abundance under GBH suppression again at 26 days, while ammonia-oxidizing bacteria remained lower at all sampling times. Broad host range plasmids IncP-1β and IncP-1ε were exclusively detected in the rhizosphere of glyphosate-treated plants at 10 days and at 26 days, respectively. Overall, our study demonstrates differential effects of suppression methods on the abundance of specific bacterial taxa, on the physiology and mobile genetic elements of microbial communities while no differences were detected in taxonomic diversity.},
}

Archaea/genetics
Avena/drug effects/*microbiology
DNA Barcoding, Taxonomic
Glycerol/*analogs & derivatives/pharmacology
Glycine/*analogs & derivatives/pharmacology
Herbicides/*pharmacology
Mesorhizobium/genetics
*Metagenome
Metagenomics
Microbiota/*drug effects/genetics
*Rhizosphere

@article {pmid31509535,
year = {2019},
author = {King, CH and Desai, H and Sylvetsky, AC and LoTempio, J and Ayanyan, S and Carrie, J and Crandall, KA and Fochtman, BC and Gasparyan, L and Gulzar, N and Howell, P and Issa, N and Krampis, K and Mishra, L and Morizono, H and Pisegna, JR and Rao, S and Ren, Y and Simonyan, V and Smith, K and VedBrat, S and Yao, MD and Mazumder, R},
title = {Baseline human gut microbiota profile in healthy people and standard reporting template.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0206484},
pmid = {31509535},
issn = {1932-6203},
support = {I01 BX003732/BX/BLRD VA/United States ; R01 AA023146/AA/NIAAA NIH HHS/United States ; R01 CA236591/CA/NCI NIH HHS/United States ; U01 CA230690/CA/NCI NIH HHS/United States ; UL1 TR000075/TR/NCATS NIH HHS/United States ; },
mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; },
abstract = {A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. This list can be expanded to 863 organisms if closely related proteomes are considered. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual's microbiome to the growing knowledgebase of "normal" microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and their abundances, this study also generated a collection of assembled contiguous sequences (contigs) of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI's Short Read Archive.},
}

Feces/microbiology
*Gastrointestinal Microbiome
Humans
*Metagenome
*Metagenomics/methods

@article {pmid31490939,
year = {2019},
author = {Danczak, RE and Johnston, MD and Kenah, C and Slattery, M and Wilkins, MJ},
title = {Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0221694},
pmid = {31490939},
issn = {1932-6203},
mesh = {Arsenic/*metabolism ; Bacteria/classification/genetics/metabolism ; Groundwater/*microbiology ; Iron/metabolism ; Metagenomics ; Microbiota ; *Phylogeny ; Sulfates/metabolism ; },
abstract = {Despite the importance of microbial activity in mobilizing arsenic in groundwater aquifers, the phylogenetic distribution of contributing microbial metabolisms is understudied. Groundwater samples from Ohio aquifers were analyzed using metagenomic sequencing to identify functional potential that could drive arsenic cycling, and revealed mechanisms for direct (i.e., Ars system) and indirect (i.e., iron reduction) arsenic mobilization in all samples, despite differing geochemical conditions. Analyses of 194 metagenome-assembled genomes (MAGs) revealed widespread functionality related to arsenic mobilization throughout the bacterial tree of life. While arsB and arsC genes (components of an arsenic resistance system) were found in diverse lineages with no apparent phylogenetic bias, putative aioA genes (aerobic arsenite oxidase) were predominantly identified in Methylocystaceae MAGs. Both previously described and undescribed respiratory arsenate reduction potential via arrA was detected in Betaproteobacteria, Deltaproteobacteria, and Nitrospirae MAGs, whereas sulfate reduction potential was primarily limited to members of the Deltaproteobacteria and Nitrospirae. Lastly, iron reduction potential was detected in the Ignavibacteria, Deltaproteobacteria, and Nitrospirae. These results expand the phylogenetic distribution of taxa that may play roles in arsenic mobilization in subsurface systems. Specifically, the Nitrospirae are a much more functionally diverse group than previously assumed and may play key biogeochemical roles in arsenic-contaminated ecosystems.},
}

Arsenic/*metabolism
Bacteria/classification/genetics/metabolism
Groundwater/*microbiology
Iron/metabolism
Metagenomics
Microbiota
*Phylogeny
Sulfates/metabolism

@article {pmid31465520,
year = {2019},
author = {Karmacharya, D and Manandhar, P and Manandhar, S and Sherchan, AM and Sharma, AN and Joshi, J and Bista, M and Bajracharya, S and Awasthi, NP and Sharma, N and Llewellyn, B and Waits, LP and Thapa, K and Kelly, MJ and Vuyisich, M and Starkenburg, SR and Hero, JM and Hughes, J and Wultsch, C and Bertola, L and Fountain-Jones, NM and Sinha, AK},
title = {Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0221868},
pmid = {31465520},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Nepal ; Tigers/*metabolism ; },
abstract = {Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities.},
}

Animals
Biodiversity
*Gastrointestinal Microbiome
*Metabolomics/methods
Metagenome
Metagenomics/methods
Nepal
Tigers/*metabolism

@article {pmid31202277,
year = {2019},
author = {Soverini, M and Turroni, S and Biagi, E and Brigidi, P and Candela, M and Rampelli, S},
title = {HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {496},
pmid = {31202277},
issn = {1471-2164},
mesh = {Animals ; Fungi/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Mycobiome/*genetics ; *Software ; },
abstract = {BACKGROUND: Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component.

RESULTS: HumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and > 10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies.

CONCLUSIONS: Although blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing.},
}

Animals
Fungi/*genetics
High-Throughput Nucleotide Sequencing
Humans
Metagenomics/*methods
Mycobiome/*genetics
*Software

@article {pmid32132981,
year = {2020},
author = {Song, D and Zhang, Y and Liu, J and Zhong, H and Zheng, Y and Zhou, S and Yu, M and Todd, JD and Zhang, XH},
title = {Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {157},
doi = {10.3389/fmicb.2020.00157},
pmid = {32132981},
issn = {1664-302X},
abstract = {The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples-dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments.},
}

@article {pmid31741368,
year = {2019},
author = {Fiore, JR and Di Stefano, M and Greco, P and Elnour, MO and Alwazzeh, MJ and Santantonio, T},
title = {The absence of culturable bacteria from at term placentae from HIV-negative and positive women argues against a placental unique microbiota.},
journal = {Minerva ginecologica},
volume = {71},
number = {6},
pages = {476-477},
doi = {10.23736/S0026-4784.19.04474-5},
pmid = {31741368},
issn = {1827-1650},
mesh = {Bacteria ; Female ; *HIV Infections ; Humans ; Metagenomics ; *Microbiota ; Placenta ; Pregnancy ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; },
}

Bacteria
Female
*HIV Infections
Humans
Metagenomics
*Microbiota
Placenta
Pregnancy
RNA, Ribosomal, 16S
Real-Time Polymerase Chain Reaction

@article {pmid31533707,
year = {2019},
author = {Willmann, M and Vehreschild, MJGT and Biehl, LM and Vogel, W and Dörfel, D and Hamprecht, A and Seifert, H and Autenrieth, IB and Peter, S},
title = {Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {76},
doi = {10.1186/s12915-019-0692-y},
pmid = {31533707},
issn = {1741-7007},
mesh = {Anti-Bacterial Agents/*adverse effects/therapeutic use ; Ciprofloxacin/*adverse effects/therapeutic use ; Cohort Studies ; *Drug Resistance, Microbial/drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial/drug effects ; Germany ; Humans ; Longitudinal Studies ; Metagenomics/methods ; Plasmids/*drug effects ; Trimethoprim, Sulfamethoxazole Drug Combination/*adverse effects/therapeutic use ; },
abstract = {BACKGROUND: The selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, and there is an urgent need to develop a more quantitative knowledge base that can enable predictions of the impact of individual antibiotics on the human gut microbiome and resistome.

RESULTS: Using shotgun metagenomics, we quantified changes in the gut microbiome in two cohorts of hematological patients receiving prophylactic antibiotics; one cohort was treated with ciprofloxacin in a hospital in Tübingen and the other with cotrimoxazole in a hospital in Cologne. Analyzing this rich longitudinal dataset, we found that gut microbiome diversity was reduced in both treatment cohorts to a similar extent, while effects on the gut resistome differed. We observed a sharp increase in the relative abundance of sulfonamide antibiotic resistance genes (ARGs) by 148.1% per cumulative defined daily dose of cotrimoxazole in the Cologne cohort, but not in the Tübingen cohort treated with ciprofloxacin. Through multivariate modeling, we found that factors such as individual baseline microbiome, resistome, and plasmid diversity; liver/kidney function; and concurrent medication, especially virostatic agents, influence resistome alterations. Strikingly, we observed different effects on the plasmidome in the two treatment groups. There was a substantial increase in the abundance of ARG-carrying plasmids in the cohort treated with cotrimoxazole, but not in the cohort treated with ciprofloxacin, indicating that cotrimoxazole might contribute more efficiently to the spread of resistance.

CONCLUSIONS: Our study represents a step forward in developing the capability to predict the effect of individual antimicrobials on the human microbiome and resistome. Our results indicate that to achieve this, integration of the individual baseline microbiome, resistome, and mobilome status as well as additional individual patient factors will be required. Such personalized predictions may in the future increase patient safety and reduce the spread of resistance.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT02058888 . Registered February 10 2014.},
}

Anti-Bacterial Agents/*adverse effects/therapeutic use
Ciprofloxacin/*adverse effects/therapeutic use
Cohort Studies
*Drug Resistance, Microbial/drug effects/genetics
Gastrointestinal Microbiome/*drug effects
Genes, Bacterial/drug effects
Germany
Humans
Longitudinal Studies
Metagenomics/methods
Plasmids/*drug effects
Trimethoprim, Sulfamethoxazole Drug Combination/*adverse effects/therapeutic use

@article {pmid31504055,
year = {2019},
author = {Scheifler, M and Ruiz-Rodríguez, M and Sanchez-Brosseau, S and Magnanou, E and Suzuki, MT and West, N and Duperron, S and Desdevises, Y},
title = {Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0221475},
pmid = {31504055},
issn = {1932-6203},
mesh = {Animals ; Apicomplexa/genetics ; Arthropods/genetics ; Ascomycota/genetics ; *Biodiversity ; Ciliophora/genetics ; DNA Barcoding, Taxonomic/methods ; Fishes/microbiology/*parasitology ; Gills/microbiology/parasitology ; Intestines/microbiology/parasitology ; *Metagenome ; Metagenomics/methods ; Nematoda/genetics ; Skin/microbiology/parasitology ; Symbiosis ; },
abstract = {Next-generation sequencing methods are increasingly used to identify eukaryotic, unicellular and multicellular symbiont communities within hosts. In this study, we analyzed the non-specific reads obtained during a metabarcoding survey of the bacterial communities associated to three different tissues collected from 13 wild Mediterranean teleost fish species. In total, 30 eukaryotic genera were identified as putative parasites of teleosts, associated to skin mucus, gills mucus and intestine: 2 ascomycetes, 4 arthropods, 2 cnidarians, 7 nematodes, 10 platyhelminthes, 4 apicomplexans, 1 ciliate as well as one order in dinoflagellates (Syndiniales). These results highlighted that (1) the metabarcoding approach was able to uncover a large spectrum of symbiotic organisms associated to the fish species studied, (2) symbionts not yet identified in several teleost species were putatively present, (3) the parasitic diversity differed markedly across host species and (4) in most cases, the distribution of known parasitic genera within tissues is in accordance with the literature. The current work illustrates the large insights that can be gained by making maximum use of data from a metabarcoding approach.},
}

Animals
Apicomplexa/genetics
Arthropods/genetics
Ascomycota/genetics
*Biodiversity
Ciliophora/genetics
DNA Barcoding, Taxonomic/methods
Fishes/microbiology/*parasitology
Gills/microbiology/parasitology
Intestines/microbiology/parasitology
*Metagenome
Metagenomics/methods
Nematoda/genetics
Skin/microbiology/parasitology
Symbiosis

@article {pmid31240449,
year = {2019},
author = {Huang, J and Ran, Y and Pradhan, S and Yan, W and Dai, Y},
title = {Investigation on Microecology of Hair Root Fungi in Androgenetic Alopecia Patients.},
journal = {Mycopathologia},
volume = {184},
number = {4},
pages = {505-515},
pmid = {31240449},
issn = {1573-0832},
mesh = {Adult ; Alopecia/*microbiology ; *Dysbiosis ; Female ; Fungi/*classification/genetics/*isolation & purification ; Hair Follicle/*microbiology ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; *Microbiota ; Microscopy ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: This study focused on the differences in hairy root fungal microecology between androgenetic alopecia patients and healthy individuals.

METHODS: Light microscopy was used to observe the morphology of hairy roots. Morphological observations were also performed in the positive specimens using scanning electron microscopy and transmission electron microscopy. The high-throughput sequencing method was used to detect the fungal microecology of hairy roots at different sites. Moreover, the comparison of fungal loads of Malassezia in different group and scalp area were tested by PCR.

RESULTS: The fungi in the hair root observed by optical microscopy are mainly Malassezia yeast. The positive rate of Malassezia in the hair loss group (60%) was higher than that in the control group (40%). The detection efficiency of Malassezia examined by scanning electron microscopy was higher than that by light microscopy. Results acquired from high-throughput molecular sequencing of fungi suggested that Ascomycota was the dominant species, whereas in the occipital hair roots of the control group Basidiomycota was the dominant species in the hair loss group. Malassezia followed by Trichosporon were the most abundant fungal genera. The changes in abundance at the top and occipital region of the control group were more significant than those of the genus Fusarium, followed by Epicoccum and Malassezia. The load of Malassezia located on calvaria in the alopecia group was significantly higher than that in the control group. In the alopecia group, the load of Malassezia on the scalp was higher than that on the occipital region. The load of Malassezia globosa and Malassezia restricta in the hair loss group was higher on calvaria and occipital areas.

CONCLUSION: Malassezia had a positive correlation with the incidence of androgenic alopecia.},
}

Adult
Alopecia/*microbiology
*Dysbiosis
Female
Fungi/*classification/genetics/*isolation & purification
Hair Follicle/*microbiology
Healthy Volunteers
High-Throughput Nucleotide Sequencing
Humans
Male
Metagenomics
*Microbiota
Microscopy
Polymerase Chain Reaction

@article {pmid30645723,
year = {2019},
author = {},
title = {Profile of Dr. Fuwen Wei.},
journal = {Science China. Life sciences},
volume = {62},
number = {2},
pages = {165-167},
doi = {10.1007/s11427-019-9468-8},
pmid = {30645723},
issn = {1869-1889},
mesh = {Adaptation, Physiological ; Animals ; *Conservation of Natural Resources ; History, 20th Century ; History, 21st Century ; Humans ; Metagenomics ; Microbiota/genetics ; Ursidae/microbiology/physiology ; Zoology/*education ; },
}

Adaptation, Physiological
Animals
*Conservation of Natural Resources
History, 20th Century
History, 21st Century
Humans
Metagenomics
Microbiota/genetics
Ursidae/microbiology/physiology
Zoology/*education

@article {pmid30588567,
year = {2019},
author = {Wei, F and Wu, Q and Hu, Y and Huang, G and Nie, Y and Yan, L},
title = {Conservation metagenomics: a new branch of conservation biology.},
journal = {Science China. Life sciences},
volume = {62},
number = {2},
pages = {168-178},
doi = {10.1007/s11427-018-9423-3},
pmid = {30588567},
issn = {1869-1889},
mesh = {Animals ; Animals, Wild/*microbiology/physiology ; Biological Coevolution ; Conservation of Natural Resources/*trends ; Humans ; *Metagenomics ; Microbiota/genetics/*physiology ; },
abstract = {Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.},
}

Animals
Animals, Wild/*microbiology/physiology
Biological Coevolution
Conservation of Natural Resources/*trends
Humans
*Metagenomics
Microbiota/genetics/*physiology

@article {pmid31607556,
year = {2019},
author = {Tett, A and Huang, KD and Asnicar, F and Fehlner-Peach, H and Pasolli, E and Karcher, N and Armanini, F and Manghi, P and Bonham, K and Zolfo, M and De Filippis, F and Magnabosco, C and Bonneau, R and Lusingu, J and Amuasi, J and Reinhard, K and Rattei, T and Boulund, F and Engstrand, L and Zink, A and Collado, MC and Littman, DR and Eibach, D and Ercolini, D and Rota-Stabelli, O and Huttenhower, C and Maixner, F and Segata, N},
title = {The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.},
journal = {Cell host & microbe},
volume = {26},
number = {5},
pages = {666-679.e7},
pmid = {31607556},
issn = {1934-6069},
support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; /ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 DK103358/DK/NIDDK NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; },
mesh = {Diet ; Ethiopia ; Feces/microbiology ; Fossils/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Ghana ; Humans ; Prevotella/*classification/*genetics/isolation & purification ; Tanzania ; },
abstract = {Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.},
}

Diet
Ethiopia
Feces/microbiology
Fossils/*microbiology
Gastrointestinal Microbiome/*genetics
Genetic Variation
Genome, Bacterial/*genetics
Ghana
Humans
Prevotella/*classification/*genetics/isolation & purification
Tanzania

@article {pmid31318946,
year = {2019},
author = {Gaona, O and Gómez-Acata, ES and Cerqueda-García, D and Neri-Barrios, CX and Falcón, LI},
title = {Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0219982},
doi = {10.1371/journal.pone.0219982},
pmid = {31318946},
issn = {1932-6203},
mesh = {Animals ; Chiroptera/*physiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Geography ; Male ; Metagenome ; Metagenomics/methods ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Reproduction ; },
abstract = {In this study we analyzed the microbiota composition of fecal samples from the lesser-long nosed bat Leptonycteris yerbabuenae in different reproductive stages (juveniles and adult bats of both sexes as well as pregnant and lactating females). The V4 region of the 16s rRNA gene from 33 individuals was analyzed using alpha and beta diversity metrics. We found that microbiota diversity (expressed in Amplicon Sequence Variants) is higher in pregnant and lactating females. The microbiota of the juveniles and non-reproductive adults was dominated by Gammaproteobacteria and Firmicutes. Reproductive females had a much more diverse microbiota, with a significant increase in phyla such as Bacteroidetes and Alphaproteobacteria. There was no difference in fecal microbiota diversity between pregnant and lactating females and juveniles and non-reproductive adults. Results suggest that differences in microbiota diversity are related to reproduction. We infer that males maintain stable microbiota composition because they do not undergo the large physiological changes that females do during reproduction and maintain a more specialized diet throughout all life stages.},
}

Animals
Chiroptera/*physiology
Feces/*microbiology
Female
*Gastrointestinal Microbiome
Geography
Male
Metagenome
Metagenomics/methods
Pregnancy
RNA, Ribosomal, 16S/genetics
*Reproduction

@article {pmid31310635,
year = {2019},
author = {Tan, Z and Dong, W and Ding, Y and Ding, X and Zhang, Q and Jiang, L},
title = {Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0219868},
doi = {10.1371/journal.pone.0219868},
pmid = {31310635},
issn = {1932-6203},
mesh = {Animals ; Computational Biology/methods ; Coronavirus Infections/*veterinary ; Feces/*virology ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Molecular Sequence Annotation ; Phylogeny ; *Porcine epidemic diarrhea virus ; RNA, Ribosomal, 16S/genetics ; Swine ; Swine Diseases/*virology ; },
abstract = {Diarrhea, caused by porcine epidemic diarrhea virus (PEDV), is a catastrophic gastrointestinal disease among suckling piglets, with high infectivity, morbidity, and mortality, causing huge economic losses to the pig industry. In the present study, we investigated the different microbiota from the cecal mucosa and cecal contents between healthy and PEDV-infected piglets. High-throughput 16S rRNA gene sequencing was performed to explore differences. The results revealed that microbial dysbiosis by PEDV infection occurred in the cecal mucosa and contents of suckling piglets at each microbial taxonomic level. The abundance of pathogenic bacteria associated with diseases, including diarrhea, was increased. The abundance of Fusobacterium was 26.71% and 33.91% in cecal mucosa and contents of PEDV-infected group, respectively, whereas that in the healthy groups was 17.85% and 9.88%. The proportion of Proteobacteria in the infected groups was relatively high (24.67% and 22.79%, respectively), whereas that in the healthy group was 13.13% and 11.34% in the cecal mucosa and contents, respectively. Additionally, the proportion of Bacteroidetes in the healthy group (29.89%, 37.32%) was approximately twice that of the PEDV-infected group (15.50%, 15.39%). "Nitrate reduction", "Human pathogens diarrhea", "Human pathogens gastroenteritis", "Nitrite respiration", and "Nitrite ammonification" were the enriched functional annotation terms in the PEDV-infected groups. Porcine epidemic diarrhea virus infection increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria in the cecal mucosa and contents of suckling piglets. Our findings suggest that determining the intestinal microbiota might provide a promising method to prevent PEDV and open a new avenue for future research.},
}

Animals
Computational Biology/methods
Coronavirus Infections/*veterinary
Feces/*virology
*Gastrointestinal Microbiome
Metagenome
Metagenomics/methods
Molecular Sequence Annotation
Phylogeny
*Porcine epidemic diarrhea virus
RNA, Ribosomal, 16S/genetics
Swine
Swine Diseases/*virology

@article {pmid31249397,
year = {2019},
author = {Schirmer, M and Garner, A and Vlamakis, H and Xavier, RJ},
title = {Microbial genes and pathways in inflammatory bowel disease.},
journal = {Nature reviews. Microbiology},
volume = {17},
number = {8},
pages = {497-511},
pmid = {31249397},
issn = {1740-1534},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; },
mesh = {Bacterial Adhesion ; Biological Factors/metabolism ; Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Humans ; Immunologic Factors/metabolism ; Inflammatory Bowel Diseases/*pathology/*physiopathology ; *Microbiota ; T-Lymphocytes, Regulatory/*immunology ; Th17 Cells/*immunology ; },
abstract = {Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). Studies of treatment-naive patients have identified microbial taxa associated with disease course and treatment efficacy. To gain a mechanistic understanding of how the microbiome affects gastrointestinal health, we need to move from census to function. Bacteria, including those that adhere to epithelial cells as well as several Clostridium species, can alter differentiation of T helper 17 cells and regulatory T cells. Similarly, microbial products such as short-chain fatty acids and sphingolipids also influence immune responses. Metagenomics and culturomics have identified strains of Ruminococcus gnavus and adherent invasive Escherichia coli that are linked to IBD and gut inflammation. Integrated analysis of multiomics data, including metagenomics, metatranscriptomics and metabolomics, with measurements of host response and culturomics, have great potential in understanding the role of the microbiome in IBD. In this Review, we highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.},
}

Bacterial Adhesion
Biological Factors/metabolism
Gastrointestinal Microbiome
*Host-Pathogen Interactions
Humans
Immunologic Factors/metabolism
Inflammatory Bowel Diseases/*pathology/*physiopathology
*Microbiota
T-Lymphocytes, Regulatory/*immunology
Th17 Cells/*immunology

@article {pmid31127248,
year = {2019},
author = {Woyke, T},
title = {Beyond the census of human gut dwellers.},
journal = {Nature reviews. Microbiology},
volume = {17},
number = {7},
pages = {401},
doi = {10.1038/s41579-019-0220-7},
pmid = {31127248},
issn = {1740-1534},
mesh = {*Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; },
}

*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Humans
Metagenomics/*methods
*Microbiota

@article {pmid31143925,
year = {2019},
author = {Hundsdoerfer, AK and Lee, KM and Kitching, IJ and Mutanen, M},
title = {Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths.},
journal = {Genome biology and evolution},
volume = {11},
number = {8},
pages = {2136-2150},
doi = {10.1093/gbe/evz113},
pmid = {31143925},
issn = {1759-6653},
mesh = {Animals ; *Evolution, Molecular ; *Genome ; Metagenomics/*methods ; Moths/*classification/*genetics ; Phylogeny ; *Polymorphism, Single Nucleotide ; Species Specificity ; },
abstract = {The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of "when do nondiscrete entities become distinct, mutually exclusive evolutionary units"? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.},
}

Animals
*Evolution, Molecular
*Genome
Metagenomics/*methods
Moths/*classification/*genetics
Phylogeny
*Polymorphism, Single Nucleotide
Species Specificity

@article {pmid31073691,
year = {2019},
author = {Bersanelli, M and Santoni, M and Ticinesi, A and Buti, S},
title = {The Urinary Microbiome and Anticancer Immunotherapy: The Potentially Hidden Role of Unculturable Microbes.},
journal = {Targeted oncology},
volume = {14},
number = {3},
pages = {247-252},
doi = {10.1007/s11523-019-00643-7},
pmid = {31073691},
issn = {1776-260X},
mesh = {Antineoplastic Agents, Immunological/*therapeutic use ; Bacteriuria/drug therapy/immunology/*microbiology ; Biomarkers/*urine ; Cell Cycle Checkpoints/*drug effects ; Humans ; Immunotherapy ; Microbiota/*drug effects ; Neoplasms/drug therapy/immunology/*microbiology ; Urinary Tract/drug effects/*microbiology ; },
abstract = {Several urinary disorders, including overactive bladder, urinary incontinence, and interstitial cystitis, are often characterized by negative urine cultures. The application of metagenomics (i.e., 16S rRNA microbial profiling or whole-genome shotgun sequencing) to urine samples has enabled the identification of previously undetected bacteria, contributing to the discovery and characterization of the urinary microbiome. The most frequent species isolated are Lactobacillus (15%), Corynebacterium (14.2%), Streptococcus (11.9%), Actinomyces (6.9%), and Staphylococcus (6.9%). Although several studies are emerging in this context, the role of urinary microbiota in the pathogenesis of infections and in tumor carcinogenesis remains unclear. Furthermore, data on the activity of gut microbiota in modulating sensitivity to immune checkpoint inhibitors in advanced cancer patients suggest that the influence of urinary microbiota on tumor response to anticancer therapy should also be investigated. Moreover, its possible relationship with tumor mutational burden, which is in turn correlated with response to immunotherapy, should be the focus of future studies. Of note, the effect of antibiotics on this complex scenario seems to deserve careful consideration.},
}

Antineoplastic Agents, Immunological/*therapeutic use
Bacteriuria/drug therapy/immunology/*microbiology
Biomarkers/*urine
Cell Cycle Checkpoints/*drug effects
Humans
Immunotherapy
Microbiota/*drug effects
Neoplasms/drug therapy/immunology/*microbiology
Urinary Tract/drug effects/*microbiology

@article {pmid30718047,
year = {2019},
author = {Zegarra-Ruiz, DF and Diehl, GE},
title = {Skin IL-17-Producing T Cells Support Repair 2!.},
journal = {Trends in immunology},
volume = {40},
number = {3},
pages = {177-179},
doi = {10.1016/j.it.2019.01.004},
pmid = {30718047},
issn = {1471-4981},
mesh = {Animals ; Cytokines/metabolism ; Humans ; Immunity, Cellular ; Mice ; Microbiota/*immunology ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Receptors, Antigen, T-Cell/metabolism ; Th2 Cells/*immunology ; *Wound Healing ; },
abstract = {In a recent study, Harrison et al. (Science 2019;363;eaat6280) report that RORγt-expressing skin commensal-specific T cells rapidly respond to tissue wounding by producing type 2 T helper cell (Th2) cytokines in mice. The cells constitutively coexpress GATA-3 and type 2 cytokine mRNAs that are translated after injury. These T cells act as sentinels, linking T cell receptor (TCR) recognition of commensals, tissue damage, and wound repair.},
}

Animals
Cytokines/metabolism
Humans
Immunity, Cellular
Mice
Microbiota/*immunology
Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
Receptors, Antigen, T-Cell/metabolism
Th2 Cells/*immunology
*Wound Healing

@article {pmid30424933,
year = {2019},
author = {Castillo-Álvarez, F and Marzo-Sola, ME},
title = {Disease of the holobiont, the example of multiple sclerosis.},
journal = {Medicina clinica},
volume = {152},
number = {4},
pages = {147-153},
doi = {10.1016/j.medcli.2018.08.019},
pmid = {30424933},
issn = {1578-8989},
mesh = {Animals ; Disease Models, Animal ; Encephalomyelitis, Autoimmune, Experimental/immunology/*microbiology/prevention & control ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Immunity, Cellular ; Male ; Multiple Sclerosis/*microbiology ; Sex Factors ; Symbiosis ; },
abstract = {In recent years there has been a revolution regarding the role of the microbiota in different diseases, most of them within the spectrum of inflammatory and autoimmune diseases, associated with the development of metagenomics and the concept of holobiont, a large organism together with its microbiota. Specifically, in Multiple Sclerosis, multiple evidence points to the role of the microbiota in experimental autoimmune encephalomyelitis, animal model of the disease, and several articles have been published in recent years about differences in intestinal microbiota among patients with multiple sclerosis and control subjects. We review in this article the concept of holobiont and the gut microbiota functions, as well as the evidence accumulated about the role of the microbiota in experimental autoimmune encephalomyelitis and multiple sclerosis. Nowadays, there is a lot of evidence showing the role of the microbiota in the genesis, prevention and treatment of experimental autoimmune encephalomyelitis based mainly on three immunological pillars, the Th1-Th17 / Th2 balance, the Treg cells and the humoral immunity. It is also well documented that there are differences in the microbiota of patients with MS that are associated with a different expression of genes related to inflammation.},
}

Animals
Disease Models, Animal
Encephalomyelitis, Autoimmune, Experimental/immunology/*microbiology/prevention & control
Female
Gastrointestinal Microbiome/genetics/*physiology
Humans
Immunity, Cellular
Male
Multiple Sclerosis/*microbiology
Sex Factors
Symbiosis

@article {pmid31602443,
year = {2019},
author = {Li, Q and Chen, H and Zhang, M and Wu, T and Liu, R},
title = {Altered short chain fatty acid profiles induced by dietary fiber intervention regulate AMPK levels and intestinal homeostasis.},
journal = {Food & function},
volume = {10},
number = {11},
pages = {7174-7187},
doi = {10.1039/c9fo01465a},
pmid = {31602443},
issn = {2042-650X},
mesh = {AMP-Activated Protein Kinases/genetics/*metabolism ; Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Dietary Fiber/*metabolism ; Fatty Acids, Volatile/chemistry/*metabolism ; Female ; *Gastrointestinal Microbiome ; Homeostasis ; Intestinal Mucosa/enzymology/*metabolism/microbiology ; Male ; Methylamines/blood ; Mice, Inbred C57BL ; Triglycerides/blood ; },
abstract = {The objective of this study was to investigate the effects of dietary intervention on intestinal microbiota-mediated change in short chain fatty acid (SCFA) profile and intestinal homeostasis. Sequencing of the 16S rDNA of gut bacteria, metagenomics, intestinal epithelial transcriptomics, and metabonomics were conducted. Results showed that the dietary interventions altered the microbiota composition of cecal digesta, microbiota-mediated metabolism, and the gene expression profile in intestinal epithelial cells. Compared with red meat-diet-fed mice, fiber-diet-fed mice presented a shift in the gut microbiome toward increased production of butanoate, which was accompanied by up-regulation of microbiota- and AMP-activated protein kinase (AMPK)-dependent gene expression and decrease in serum concentrations of trimethylamine N-oxide (TMAO), triglyceride (TG) and glucose (GLU). The results suggested a new regulatory mechanism via which butanoate and AMPK activation contributed to intestinal integrity and homeostasis by affecting metabolism, intestinal barrier function and transporter expression.},
}

AMP-Activated Protein Kinases/genetics/*metabolism
Animals
Bacteria/classification/genetics/isolation & purification/*metabolism
Dietary Fiber/*metabolism
Fatty Acids, Volatile/chemistry/*metabolism
Female
*Gastrointestinal Microbiome
Homeostasis
Intestinal Mucosa/enzymology/*metabolism/microbiology
Male
Methylamines/blood
Mice, Inbred C57BL
Triglycerides/blood