scholarly journals Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elizabeth Fleming ◽  
Victor Pabst ◽  
Zoe Scholar ◽  
Ruoyun Xiong ◽  
Anita Y. Voigt ◽  
...  
Keyword(s):  
High Resolution ◽  
Gut Microbiota ◽  
Genetic Distance ◽  
Bacterial Species ◽  
Rapid Identification ◽  
Strain Level ◽  
Microbial Consortia ◽  
Metagenomic Sequencing ◽  
Ft Ir ◽  
Sample Set

Abstract Background Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exists at the subspecies, or strain, level. High-resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. High-throughput approaches are needed to acquire and identify the significant species- and strain-level diversity present in the oral, skin, and gut microbiome. Here, we describe and validate a streamlined workflow for cultivating dominant bacterial species and strains from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling. Results Of total genera discovered by either metagenomic sequencing or culturomics, our cultivation pipeline recovered between 18.1–44.4% of total genera identified. These represented a high proportion of the community composition reconstructed with metagenomic sequencing, ranging from 66.2–95.8% of the relative abundance of the overall community. Fourier-Transform Infrared spectroscopy (FT-IR) was effective in differentiating genetically distinct strains compared with whole-genome sequencing, but was less effective as a proxy for genetic distance. Conclusions Use of a streamlined set of conditions selected for cultivation of skin, oral, and gut microbiota facilitates recovery of dominant microbes and their strain variants from a relatively large sample set. FT-IR spectroscopy allows rapid differentiation of strain variants, but these differences are limited in recapitulating genetic distance. Our data highlights the strength of our cultivation and characterization pipeline, which is in throughput, comparisons with high-resolution genomic data, and rapid identification of strain variation.

scholarly journals Species and strain cultivation of skin, oral, and gut microbiota

2021 ◽  
Author(s):  
Elizabeth Fleming ◽  
Victor Pabst ◽  
Amelia Hoyt ◽  
Wei Zhou ◽  
Rachel Hardy ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Gut Microbiota ◽  
Strain Level ◽  
Microbial Consortia ◽  
Metagenomic Sequencing ◽  
Mechanistic Studies ◽  
Microbial Species ◽  
Human Microbiota

Genomics-driven discovery of microbial species have provided extraordinary insights into the biodiversity of human microbiota. High resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. Here, we describe and validate a streamlined workflow for cultivating microbes from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling.

scholarly journals Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus

2019 ◽  
Author(s):  
Feng Zhu ◽  
Yanmei Ju ◽  
Wei Wang ◽  
Qi Wang ◽  
Ruijin Guo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Validation Cohort ◽  
Bacterial Species ◽  
Metagenomic Sequencing ◽  
Operating Characteristics ◽  
Discovery Cohort ◽  
Peripheral Tissues ◽  
Functional Changes ◽  
Microbial Biomarkers

AbstractEmerging evidence has linked the gut microbiota to schizophrenia. However, the functional changes in the gut microbiota and the biological role of individual bacterial species in schizophrenia have not been explored systematically. Here, we characterized the gut microbiota in schizophrenia using shotgun metagenomic sequencing of feces from a discovery cohort of 90 drug-free patients and 81 controls, as well as a validation cohort of 45 patients taking antipsychotics and 45 controls. We screened 83 schizophrenia-associated bacterial species and constructed a classifier comprising 26 microbial biomarkers that distinguished patients from controls with a 0.896 area under the receiver operating characteristics curve (AUC) in the discovery cohort and 0.765 AUC in the validation cohort. Our analysis of fecal metagenomes revealed that schizophrenia-associated gut–brain modules included short-chain fatty acids synthesis, tryptophan metabolism, and synthesis/degradation of neurotransmitters including glutamate, γ-aminobutyric acid, and nitric oxide. The schizophrenia-enriched gut bacterial species include several oral cavity-resident microbes, such as Streptococcus vestibularis. We transplanted Streptococcus vestibularis into the gut of the mice with antibiotic-induced microbiota depletion to explore its functional role. We observed that this microbe transiently inhabited the mouse gut and this was followed by hyperactivity and deficit in social behaviors, accompanied with altered neurotransmitter levels in peripheral tissues. In conclusion, our study identified 26 schizophrenia-associated bacterial species representing potential microbial targets for future treatment, as well as gut–brain modules, some of which may give rise to new microbial metabolites involved in the development of schizophrenia.

scholarly journals Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sally L. Bornbusch ◽  
Rachel L. Harris ◽  
Nicholas M. Grebe ◽  
Kimberly Roche ◽  
Kristin Dimac-Stohl ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Microbial Consortia ◽  
Metagenomic Sequencing ◽  
Negative Consequences

Abstract Background Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases. Results Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups. Conclusions Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.

scholarly journals Distinct Actions of the Fermented Beverage Kefir on Host Behaviour, Immunity and Microbiome Gut-Brain Modules in the Mouse

2020 ◽  
Author(s):  
Marcel van de Wouw ◽  
Aaron M. Walsh ◽  
Fiona Crispie ◽  
Lucas van Leuven ◽  
Joshua M. Lyte ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Species ◽  
Fermented Foods ◽  
Dependent Manner ◽  
Metagenomic Sequencing ◽  
Metabolome Analysis ◽  
Repetitive Behaviour ◽  
Brain Physiology ◽  
Reward Seeking ◽  
Host Behaviour

Abstract Background Mounting evidence suggests a role for the gut microbiota in modulating brain physiology and behaviour through bi-directional communication along the gut-brain axis. As such, the gut microbiota represents a potential therapeutic target for influencing centrally-mediated events and host behaviour. It is thus notable that the fermented milk beverage kefir has recently been shown to modulate the composition of the gut microbiota in mice. It is unclear whether kefirs have differential effects on microbiota-gut-brain axis and whether they can modulate host behaviour per se.Methods To address this, two distinct kefirs (Fr1 and UK4) or unfermented milk control were administered to mice that underwent a battery of tests to characterise their behavioural phenotype. In addition, shotgun metagenomic sequencing of ileal, cecal and faecal matter was performed, as was faecal metabolome analysis. Finally, systemic immunity measures and gut serotonin levels were assessed. Statistical analysis was performed by ANOVA followed by Dunnett's post hoc test or Kruskal-Wallis test followed by Mann-Whitney U test.Results Fr1 ameliorated the stress-induced decrease in serotonergic signalling in the colon and reward-seeking behaviour in the saccharin preference test. On the other hand, UK4 decreased repetitive behaviour and ameliorated stress-induced deficits in reward-seeking behaviour. Furthermore, UK4 impaired long-term spatial learning, yet increased fear-dependent contextual memory. In the peripheral immune system, UK4 increased the prevalence of Treg cells and interleukin 10 levels, whereas Fr1 ameliorated the milk gavage stress-induced elevation in neutrophil levels and CXCL1 levels. Analysis of the gut microbiota revealed that both kefirs significantly changed the composition and functional capacity of the host microbiota, where specific bacterial species were changed in a kefir-dependent manner. Furthermore, both kefirs increased the capacity of the gut microbiota to produce GABA, which was linked to an increased prevalence in Lactobacillus reuteri.Conclusions Altogether, these data show that kefir can signal through the microbiota-gut-immune-brain axis and modulate host behaviour. In addition, different kefirs may direct the microbiota toward distinct immunological and behavioural modulatory effects. These results indicate that kefir can positively modulate the microbiota-gut-brain axis and support the broadening of the definition of psychobiotic to include fermented foods such as kefir.

scholarly journals Deep Investigating the Changes of Gut Microbiome and Its Correlation With the Shifts of Host Serum Metabolome Around Parturition in Sows

2021 ◽  
Vol 12 ◽  
Author(s):  
Hao Fu ◽  
Maozhang He ◽  
Jinyuan Wu ◽  
Yunyan Zhou ◽  
Shanlin Ke ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Late Pregnancy ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Functional Capacities

Parturition is a crucial event in the sow reproduction cycle, which accompanies by a series of physiological changes, including sex hormones, metabolism, and immunity. More and more studies have indicated the changes of the gut microbiota from pregnancy to parturition. However, what bacterial species and functional capacities of the gut microbiome are changed around parturition has been largely unknown, and the correlations between the changes of gut bacterial species and host metabolome were also uncovered. In this study, by combining 16S rRNA gene and shotgun metagenomic sequencing data, and the profiles of serum metabolome and fecal short-chain fatty acids (SCFAs), we investigated the changes of gut microbiome, serum metabolite features and fecal SCFAs from late pregnancy (LP) to postpartum (PO) stage. We found the significant changes of gut microbiota from LP to PO stage in both 16S rRNA gene sequencing and metagenomic sequencing analyses. The bacterial species from Lactobacillus, Streptococcus, and Clostridium were enriched at the LP stage, while the species from Bacteroides, Escherichia, and Campylobacter had higher abundances at the PO stage. Functional capacities of the gut microbiome were also significantly changed and associated with the shifts of gut bacteria. Untargeted metabolomic analyses revealed that the metabolite features related to taurine and hypotaurine metabolism, and arginine biosynthesis and metabolism were enriched at the LP stage, and positively associated with those bacterial species enriched at the LP stage, while the metabolite features associated with vitamin B6 and glycerophospholipid metabolism had higher abundances at the PO stage and were positively correlated with the bacteria enriched at the PO stage. Six kinds of SCFAs were measured in feces samples and showed higher concentrations at the LP stage. These results suggested that the changes of gut microbiome from LP to PO stage lead to the shifts of host lipid, amino acids and vitamin metabolism and SCFA production. The results from this study provided new insights for the changes of sow gut microbiome and host metabolism around parturition, and gave new knowledge for guiding the feeding and maternal care of sows from late pregnancy to lactation in the pig industry.

scholarly journals Gut microbes in healthy dogs have individualized responses to synbiotic supplementation that lead to increased abundances of probiotic strains: A randomized controlled trial

2020 ◽  
Author(s):  
Jirayu Tanprasertsuk ◽  
Aashish R Jha ◽  
Justin Shmalberg ◽  
LeeAnn M Perry ◽  
Heather Maughan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Controlled Trial ◽  
Bacterial Species ◽  
Gastrointestinal Symptoms ◽  
Healthy Population ◽  
Significant Shift ◽  
Metagenomic Sequencing ◽  
Β Diversity ◽  
Populations At Risk ◽  
Healthy Dogs

Abstract Background: Probiotics ameliorate gastrointestinal symptoms in dogs. However, the effect of probiotics in a healthy population, as well as factors contributing individualized responses, remains largely unknown. This trial examined gut microbiota (GM) and health outcomes in household dogs after synbiotic (SN) supplementation containing probiotics and inulin. Healthy dogs were randomized to receive SN (50 mg/d inulin and 20 billion total CFU/d of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples for GM profiling (metagenomic sequencing) at baseline and week 4 in both groups, and at week 6 in the SN group.Results: A significant shift (p<0.001) in β-diversity was observed in the SN (n=24), but not PL group (n=19), relative to baseline at week 4. Forty-five bacterial species, 43 (96%) of which were Lactobacillales, showed an increase in the abundances (≥2 fold change, adjusted p<0.05) at week 4. E. coli also decreased at week 4 in the SN group (2.8 folds, adjusted p<0.01). The altered taxa largely returned to baseline at week 6. The degree of changes in the β-diversity was associated with GM at baseline. Specifically, dogs with higher Proteobacteria and lower Lactobacillales responded more robustly to supplementation. Dogs fed SN tended to have lower diarrhea incidence (0% vs 16%, p=0.08).Conclusions: SN supplement had an impact on the change of gut microbiota in healthy household dogs as characterized with metagenomic sequencing. Findings warrant further investigation with longer duration or in populations at risk of gastrointestinal diseases. The magnitude of response to the supplement was associated with microbial profile at baseline. To our knowledge, this is the first study documenting such association that may provide a basis of personalized nutrition in companion dogs.

scholarly journals SO046REGULATION OF GUT MICROBIOTA AND HOST CO-METABOLISM BY POTASSIUM HOMEOSTASIS IN PATIENTS ON HEMODIALYSIS

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Dominic Raj ◽  
Bei Gao ◽  
Elizabeth Barrows ◽  
Muralidharan Jagadeesan ◽  
Richard Amdur ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Serum Potassium ◽  
Repeated Measures ◽  
Bacterial Species ◽  
Hemodialysis Patients ◽  
Diaminopimelic Acid ◽  
Metagenomic Sequencing ◽  
Microbial Composition ◽  
Potassium Homeostasis ◽  
The Impact

Abstract Background and Aims Gut microbiota composition is dysregulated in hemodialysis patients. However, the impact of potassium homeostasis on the gut microbiota and their metabolites has not been studied. Patiromer is a potassium binding polymer that exchanges calcium for potassium in the gastrointestinal (GI) tract, thereby increasing fecal potassium excretion and reducing serum potassium levels. Method In this non-randomized, open label, 3-period crossover trial with repeated measures within each period, we investigated the effect of 12 weeks of treatment with patiromer on the microbiome profile and microbiota-related metabolites in 27 hemodialysis patients using multi-omics integration of data from shotgun metagenomic sequencing and untargeted and targeted metabolomic profiling. Data from hemodialysis patients at baseline was first compared with individuals without kidney disease (n=20). Results We found that 18 bacterial species and 49 plasma chemical clusters were significantly different between patients and controls. Serum potassium decreased significantly from baseline (5.62±0.65 mEq/L) with patiromer treatment (4.80±0.46 meq/L) and increased during the post-treatment phase (5.45 ± 0.67 meq/L), (p&lt;0.001). Three bacterial species and one bacterial pathway were altered by patiromer. We identified 52 serum metabolites, which were significantly different in patients at baseline compared with controls, and were partially reversed with patiromer treatment. Specifically, the serum levels of polyphenols such as vanillic acid, gallic acid and benzoic acid, and other microbiota-related metabolites such as 2,6-diaminopimelic acid, 2-ketogluconic acid, indole-3-carboxaldehyde and 3-hydroxyphenylacetic acid were reduced by patiromer treatment. Conclusion Our study suggests that control of hyperkalemia by patiromer alters the gut microbial composition and host co-metabolism in hemodialysis patients.

scholarly journals Distinct Actions of the Fermented Beverage Kefir on Host Behaviour, Immunity and Microbiome Gut-Brain Modules in the Mouse

2020 ◽  
Author(s):  
Marcel van de Wouw ◽  
Aaron M. Walsh ◽  
Fiona Crispie ◽  
Lucas van Leuven ◽  
Joshua M. Lyte ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Lactobacillus Reuteri ◽  
Bacterial Species ◽  
Fermented Foods ◽  
Dependent Manner ◽  
Metagenomic Sequencing ◽  
Repetitive Behaviour ◽  
Brain Physiology ◽  
Reward Seeking ◽  
Host Behaviour

Abstract Background: Mounting evidence suggests a role for the gut microbiota in modulating brain physiology and behaviour through bi-directional communication along the gut-brain axis. As such, the gut microbiota represents a potential therapeutic target for influencing centrally-mediated events and host behaviour. It is thus notable that the fermented milk beverage kefir has recently been shown to modulate the composition of the gut microbiota in mice. It is unclear whether kefirs have differential effects on microbiota-gut-brain axis and whether they can modulate host behaviour per se. Methods: To address this, two distinct kefirs (Fr1 and UK4) or unfermented milk control were administered to mice that underwent a battery of tests to characterise their behavioural phenotype. In addition, shotgun metagenomic sequencing of ileal, cecal and faecal matter was performed, as was faecal metabolome analysis. Finally, systemic immunity measures and gut serotonin levels were assessed. Statistical analysis was performed by ANOVA followed by Dunnett's post hoc test or Kruskal-Wallis test followed by Mann-Whitney U test.Results: Fr1 ameliorated the stress-induced decrease in serotonergic signalling in the colon and reward-seeking behaviour in the saccharin preference test. On the other hand, UK4 decreased repetitive behaviour and ameliorated stress-induced deficits in reward-seeking behaviour. Furthermore, UK4 increased fear-dependent contextual memory, yet decreased milk gavage-induced improvements long-term spatial learning. In the peripheral immune system, UK4 increased the prevalence of Treg cells and interleukin 10 levels, whereas Fr1 ameliorated the milk gavage stress-induced elevation in neutrophil levels and CXCL1 levels. Analysis of the gut microbiota revealed that both kefirs significantly changed the composition and functional capacity of the host microbiota, where specific bacterial species were changed in a kefir-dependent manner. Furthermore, both kefirs increased the capacity of the gut microbiota to produce GABA, which was linked to an increased prevalence in Lactobacillus reuteri. Conclusions: Altogether, these data show that kefir can signal through the microbiota-gut-immune-brain axis and modulate host behaviour. In addition, different kefirs may direct the microbiota toward distinct immunological and behavioural modulatory effects. These results indicate that kefir can positively modulate specific aspects of the microbiota-gut-brain axis and support the broadening of the definition of psychobiotic to include kefir fermented foods.

scholarly journals StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

2021 ◽  
Author(s):  
Lucas R. van Dijk ◽  
Bruce J. Walker ◽  
Timothy J. Straub ◽  
Colin J. Worby ◽  
Alexandra Grote ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Species ◽  
Strain Level ◽  
Complex Mixtures ◽  
Metagenomic Sequencing ◽  
Nucleotide Level ◽  
Short Read ◽  
Relative Abundances ◽  
Strain Genome ◽  
Higher Sensitivity

AbstractHuman-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify nearest known references and find variants for multiple conspecific strains within a sample at relative abundances below 0.1% in typical metagenomic datasets.

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