Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition

2017 ◽  
Vol 20 (1) ◽  
pp. 214-227 ◽  
Author(s):  
Jessy Praet ◽  
Anneleen Parmentier ◽  
Regula Schmid-Hempel ◽  
Ivan Meeus ◽  
Guy Smagghe ◽  
...  
Keyword(s):  
Species Diversity ◽  
Gut Microbiota ◽  
Large Scale ◽  
Bacterial Species ◽  
Pathogen Inhibition ◽  
Large Scale Cultivation

Metagenomic profiling of gut microbiota in urban and rural rats: A comparative study

2021 ◽  
Author(s):  
Rafig GURBANOV ◽  
Uygar KABAOĞLU ◽  
Tuba YAĞCI
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Gut Microbiota ◽  
Bacterial Species ◽  
Rattus Rattus ◽  
Food Sources ◽  
Control Group ◽  
Laboratory Rats ◽  
Food Variety ◽  
Wild Rats

Abstract Mammals have a symbiotic relationship with various microorganisms called microbiota throughout their lives. These microorganisms are known to affect the host's physiology, health, and even mental balance. In the harbor of the densest and most diverse microorganisms in mammals, the curved structure of the intestines and their rich nutrient content are effective. The development of the gut microbiota is regulated by a complex interaction between host and environmental factors, including diet and lifestyle. Herein, it is aimed to elucidate the changes in the gut microbiota of rats living in urban and rural habitats. All taxonomic changes in the gut microbiota of wild rats belonging to Rattus rattus species caught from urban and rural areas of Western Anatolian (Bilecik province) were examined comparatively by 16S rRNA next-generation sequencing technique. Laboratory rats were used as a control group for comparison. Thus, 2000 different bacterial species were identified in gut microbiota. According to the Shannon and Simpsons values ​​calculated, laboratory rats showed the highest species diversity. When the similarities of microbiota profiles were compared with the principal coordinate analysis (PcoA), bacterial populations showed variability among different habitats. The comparison of species richness between the groups with the species rarefaction technique revealed higher species richness in all wild rats, especially in the rural habitat, compared to laboratory rats. Food sources were determined as the most important factor contributing to species richness and diversity. While the increased food variety boosted species richness, species diversity was increased due to the diminished food variety.

scholarly journals Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives

Parasitology ◽  
2017 ◽  
Vol 145 (5) ◽  
pp. 543-562 ◽  
Author(s):  
M. KOSOY ◽  
C. MCKEE ◽  
L. ALBAYRAK ◽  
Y. FOFANOV
Keyword(s):  
Species Diversity ◽  
Large Scale ◽  
Bacterial Species ◽  
Molecular Data ◽  
Current Status ◽  
Animal Tissues ◽  
Complete Understanding ◽  
Bacterial Systematics ◽  
Vector Borne ◽  
Animal Hosts

SUMMARYGrowing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genusBartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.

scholarly journals Gut microbial structural variations as determinants of human bile acid metabolism

2021 ◽  
Author(s):  
Daoming Wang ◽  
Marwah Doestzada ◽  
Lianmin Chen ◽  
Sergio Andreu-Sánchez ◽  
Inge C.L. van den Munckhof ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Association Analysis ◽  
Large Scale ◽  
Bacterial Species ◽  
Bile Acid Metabolism ◽  
Fat Absorption ◽  
Structural Variations ◽  
Human Bile ◽  
Intestinal Fat Absorption ◽  
The Impact

Bile acids (BAs) facilitate intestinal fat absorption and act as important signaling molecules in host-gut microbiota crosstalk. BA-metabolizing pathways in the microbial community have been identified, but how the highly variable genomes of gut bacteria interact with host BA metabolism remains largely unknown. We characterized 8,282 structural variants (SVs) of 55 bacterial species in the gut microbiomes of 1,437 individuals from two Dutch cohorts and performed a systematic association study with 39 plasma BA parameters. Both variations in SV-based continuous genetic makeup and discrete subspecies showed correlations with BA metabolism. Metagenome-wide association analysis identified 797 replicable associations between bacterial SVs and BAs and SV regulators that mediate the effects of lifestyle factors on BA metabolism. This is the first large-scale microbial genetic association analysis to demonstrate the impact of bacterial SVs on human BA composition, and highlights the potential of targeting gut microbiota to regulate BA metabolism through lifestyle intervention.

scholarly journals Strain inheritance and neonatal gut microbiota development: a meta-analysis

2020 ◽  
Author(s):  
Daniel Podlesny ◽  
W. Florian Fricke
Keyword(s):  
Gut Microbiota ◽  
Large Scale ◽  
Meta Analysis ◽  
Bacterial Species ◽  
First Year ◽  
Delivery Mode ◽  
Older Children ◽  
Strain Transfer ◽  
Comprehensive Picture ◽  
First Year Of Life

ABSTRACTAs many inflammatory and metabolic disorders have been associated with structural deficits of the human gut microbiota, the principles and mechanisms that govern its initialization and development are of considerable scientific interest and clinical relevance. However, our current understanding of the developing gut microbiota dynamics remains incomplete. We carried out a large-scale, comprehensive meta-analysis of over 1900 available metagenomic shotgun samples from neonates, infants, adolescents, and their families, using our recently introduced SameStr program for strain-level microbiota profiling and the detection of microbial strain transfer and persistence. We found robust associations between gut microbiota composition and age, as well as delivery mode which was measurable for up to two years of life. C-section was associated with increased relative abundances of non-gut species and delayed transition from a predominantly oxygen-tolerant to intolerant microbial community. Unsupervised networks based on shared strain profiles generated family-specific clusters connecting infants, their siblings, parents and grandparents and, in one case, suggested strain transfer between neonates from the same hospital ward, but could also be used to identify potentially mislabeled metagenome samples. Following birth, larger quantities of strains were shared between vaginally born infants and their mothers compared to C-section infants, which further persisted throughout the first year of life and belonged to the same bacterial species as strains that were shared between adults and their parents. Irrespective of delivery type, older children shared strains with their mothers and fathers and, into adulthood, could be accurately distinguished from unrelated sample pairs. Prominent gut commensal bacteria were both among frequently transferred (e.g. Bacteroides and Sutterella) and newly acquired taxa (e.g. Blautia, Faecalibacterium, and Ruminococcus). Our meta-analysis presents a more detailed and comprehensive picture of the highly dynamic neonatal and infant gut microbiota development than previous studies and presents evidence for taxonomic and functional compositional differences early in life between infants born naturally or by C-section, which persist well into adolescence.

Substrate use prioritization by a coculture of five species of gut bacteria fed mixtures of arabinoxylan, xyloglucan, β-glucan, and pectin

2020 ◽  
Author(s):  
Y Liu ◽  
AL Heath ◽  
B Galland ◽  
N Rehrer ◽  
L Drummond ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Fiber ◽  
Plant Cell Wall ◽  
Bacterial Species ◽  
Short Chain ◽  
Emergent Properties ◽  
Human Gut ◽  
Fermentation Products ◽  
Plant Polysaccharides ◽  
Human Gut Microbiota

© 2020 American Society for Microbiology. Dietary fiber provides growth substrates for bacterial species that belong to the colonic microbiota of humans. The microbiota degrades and ferments substrates, producing characteristic short-chain fatty acid profiles. Dietary fiber contains plant cell wall-associated polysaccharides (hemicelluloses and pectins) that are chemically diverse in composition and structure. Thus, depending on plant sources, dietary fiber daily presents the microbiota with mixtures of plant polysaccharides of various types and complexity. We studied the extent and preferential order in which mixtures of plant polysaccharides (arabinoxylan, xyloglucan, β-glucan, and pectin) were utilized by a coculture of five bacterial species (Bacteroides ovatus, Bifidobacterium longum subspecies longum, Megasphaera elsdenii, Ruminococcus gnavus, and Veillonella parvula). These species are members of the human gut microbiota and have the biochemical capacity, collectively, to degrade and ferment the polysaccharides and produce short-chain fatty acids (SCFAs). B. ovatus utilized glycans in the order β-glucan, pectin, xyloglucan, and arabinoxylan, whereas B. longum subsp. longum utilization was in the order arabinoxylan, arabinan, pectin, and β-glucan. Propionate, as a proportion of total SCFAs, was augmented when polysaccharide mixtures contained galactan, resulting in greater succinate production by B. ovatus and conversion of succinate to propionate by V. parvula. Overall, we derived a synthetic ecological community that carries out SCFA production by the common pathways used by bacterial species for this purpose. Systems like this might be used to predict changes to the emergent properties of the gut ecosystem when diet is altered, with the aim of beneficially affecting human physiology. This study addresses the question as to how bacterial species, characteristic of the human gut microbiota, collectively utilize mixtures of plant polysaccharides such as are found in dietary fiber. Five bacterial species with the capacity to degrade polymers and/or produce acidic fermentation products detectable in human feces were used in the experiments. The bacteria showed preferential use of certain polysaccharides over others for growth, and this influenced their fermentation output qualitatively. These kinds of studies are essential in developing concepts of how the gut microbial community shares habitat resources, directly and indirectly, when presented with mixtures of polysaccharides that are found in human diets. The concepts are required in planning dietary interventions that might correct imbalances in the functioning of the human microbiota so as to support measures to reduce metabolic conditions such as obesity.

Modulation of Gut Microbiota through Dietary Phytochemicals as a Novel Anti-infective Strategy

2020 ◽  
Vol 17 (4) ◽  
pp. 498-506 ◽  
Author(s):  
Pavan K. Mujawdiya ◽  
Suman Kapur
Keyword(s):  
Microbial Community ◽  
Quorum Sensing ◽  
Population Density ◽  
Gut Microbiota ◽  
Biofilm Formation ◽  
Chemical Interaction ◽  
Bacterial Species ◽  
Critical Role ◽  
Bacterial Cells ◽  
Gut Microbes

: Quorum Sensing (QS) is a phenomenon in which bacterial cells communicate with each other with the help of several low molecular weight compounds. QS is largely dependent on population density, and it triggers when the concentration of quorum sensing molecules accumulate in the environment and crosses a particular threshold. Once a certain population density is achieved and the concentration of molecules crosses a threshold, the bacterial cells show a collective behavior in response to various chemical stimuli referred to as “auto-inducers”. The QS signaling is crucial for several phenotypic characteristics responsible for bacterial survival such as motility, virulence, and biofilm formation. Biofilm formation is also responsible for making bacterial cells resistant to antibiotics. : The human gut is home to trillions of bacterial cells collectively called “gut microbiota” or “gut microbes”. Gut microbes are a consortium of more than 15,000 bacterial species and play a very crucial role in several body functions such as metabolism, development and maturation of the immune system, and the synthesis of several essential vitamins. Due to its critical role in shaping human survival and its modulating impact on body metabolisms, the gut microbial community has been referred to as “the forgotten organ” by O`Hara et al. (2006) [1]. Several studies have demonstrated that chemical interaction between the members of bacterial cells in the gut is responsible for shaping the overall microbial community. : Recent advances in phytochemical research have generated a lot of interest in finding new, effective, and safer alternatives to modern chemical-based medicines. In the context of antimicrobial research various plant extracts have been identified with Quorum Sensing Inhibitory (QSI) activities among bacterial cells. This review focuses on the mechanism of quorum sensing and quorum sensing inhibitors isolated from natural sources.

scholarly journals JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Cong Li ◽  
Qiuyi Shen ◽  
Xiang Cai ◽  
Danni Lai ◽  
Lingshang Wu ◽  
...  
Keyword(s):  
Large Scale ◽  
Plant Immunity ◽  
Expression Patterns ◽  
Protein Domain ◽  
Functional Identification ◽  
Necrotrophic Pathogen ◽  
Southern Blight ◽  
Meja Treatment ◽  
Sclerotium Delphinii ◽  
Large Scale Cultivation

Abstract Background Dendrobium catenatum belongs to the Orchidaceae, and is a precious Chinese herbal medicine. In the past 20 years, D. catenatum industry has developed from an endangered medicinal plant to multi-billion dollar grade industry. The necrotrophic pathogen Sclerotium delphinii has a devastating effection on over 500 plant species, especially resulting in widespread infection and severe yield loss in the process of large-scale cultivation of D. catenatum. It has been widely reported that Jasmonate (JA) is involved in plant immunity to pathogens, but the mechanisms of JA-induced plant resistance to S. delphinii are unclear. Results In the present study, the role of JA in enhancing D. catenatum resistance to S. delphinii was investigated. We identified 2 COI1, 13 JAZ, and 12 MYC proteins in D. catenatum genome. Subsequently, systematic analyses containing phylogenetic relationship, gene structure, protein domain, and motif architecture of core JA pathway proteins were conducted in D. catenatum and the newly characterized homologs from its closely related orchid species Phalaenopsis equestris and Apostasia shenzhenica, along with the well-investigated homologs from Arabidopsis thaliana and Oryza sativa. Public RNA-seq data were investigated to analyze the expression patterns of D. catenatum core JA pathway genes in various tissues and organs. Transcriptome analysis of MeJA and S. delphinii treatment showed exogenous MeJA changed most of the expression of the above genes, and several key members, including DcJAZ1/2/5 and DcMYC2b, are involved in enhancing defense ability to S. delphinii in D. catenatum. Conclusions The findings indicate exogenous MeJA treatment affects the expression level of DcJAZ1/2/5 and DcMYC2b, thereby enhancing D. catenatum resistance to S. delphinii. This research would be helpful for future functional identification of core JA pathway genes involved in breeding for disease resistance in D. catenatum.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

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