scholarly journals Bacterial microbiota similarity between predators and prey in a blue tit trophic network

2021 ◽  
Author(s):  
Hélène Dion-Phénix ◽  
Anne Charmantier ◽  
Christophe de Franceschi ◽  
Geneviève Bourret ◽  
Steven W. Kembel ◽  
...  
Keyword(s):  
Spatial Scales ◽  
Trophic Levels ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
16S Rrna Gene Sequences ◽  
Blue Tit ◽  
Trophic Networks ◽  
Bacterial Microbiota ◽  
Trophic Network ◽  
Blue Tits

AbstractTrophic networks are composed of many organisms hosting microbiota that interact with their hosts and with each other. Yet, our knowledge of the factors driving variation in microbiota and their interactions in wild communities is limited. To investigate the relation among host microbiota across a trophic network, we studied the bacterial microbiota of two species of primary producers (downy and holm oaks), a primary consumer (caterpillars), and a secondary consumer (blue tits) at nine sites in Corsica. To quantify bacterial microbiota, we amplified 16S rRNA gene sequences in blue tit feces, caterpillars, and leaf samples. Our results showed that hosts from adjacent trophic levels had a more similar bacterial microbiota than hosts separated by two trophic levels. Our results also revealed a difference between bacterial microbiota present on the two oak species, and among leaves from different sites. The main drivers of bacterial microbiota variation within each trophic level differed across spatial scales, and sharing the same tree or nest box increased similarity in bacterial microbiota for caterpillars and blue tits. This study quantifies host microbiota interactions across a three-level trophic network and illustrates how the factors shaping bacterial microbiota composition vary among different hosts.

scholarly journals Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction

2018 ◽  
Vol 5 (5) ◽  
pp. 180041 ◽  
Author(s):  
Muriel Dietrich ◽  
Teresa Kearney ◽  
Ernest C. J. Seamark ◽  
Janusz T. Paweska ◽  
Wanda Markotter
Keyword(s):  
Disease Ecology ◽  
High Throughput Sequencing ◽  
Natural Infection ◽  
Pathogen Transmission ◽  
Comparative Approach ◽  
Seasonal Reproduction ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Infection Dynamics ◽  
Bacterial Microbiota

Seasonal reproduction is a period of extreme physiological and behavioural changes, yet we know little about how it may affect host microbial communities (i.e. microbiota) and pathogen transmission. Here, we investigated shifts of the bacterial microbiota in saliva, urine and faeces during the seasonal reproduction of bats in South Africa, and test for an interaction in shedding patterns of both bacterial ( Leptospira ) and viral (adeno- and herpesviruses) agents. Based on a comparative approach in two cave-dwelling bat species and high-throughput sequencing of the 16S rRNA gene, we demonstrated a clear signature in microbiota changes over the reproduction season, consistent across the multiple body habitats investigated, and associated with the sex, age and reproductive condition of bats. We observed in parallel highly dynamic shedding patterns for both bacteria and viruses, but did not find a significant association between viral shedding and bacterial microbiota composition. Indeed, only Leptospira shedding was associated with alterations in both the diversity and composition of the urinary microbiota. These results illustrate how seasonal reproduction in bats substantially affects microbiota composition and infection dynamics, and have broad implications for the understanding of disease ecology in important reservoir hosts, such as bats.

The Effect of Holder Pasteurization on the Diversity of the Human Milk Bacterial Microbiota Using High-Throughput DNA Sequencing

2021 ◽  
pp. 089033442110119
Author(s):  
Igrid García-González ◽  
Karina Corona-Cervantes ◽  
Fernando Hernández-Quiroz ◽  
Loan Edel Villalobos-Flores ◽  
Flor Galván-Rodríguez ◽  
...  
Keyword(s):  
Human Milk ◽  
Bacterial Diversity ◽  
High Throughput ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Sequencing Data ◽  
Cross Sectional ◽  
Milk Samples ◽  
Bacterial Microbiota ◽  
Before And After

Background Human milk is the best food for infants; however, when breastfeeding is not possible, pasteurized milk from human milk banks is the best alternative. Little has been reported about variations in the bacterial microbiota composition of human milk after pasteurization. Research aim To characterize and compare the bacterial microbiota composition and diversity within human milk among Mexican mothers before and after the Holder pasteurization process. Methods: A cross-sectional, observational, and comparative design was used. The effect of the pasteurization process on the bacterial composition and diversity of human milk samples of donors ( N = 42) from a public milk bank was assessed before and after pasteurization by high throughput deoxyribonucleic acid sequencing of V3-16S rRNA gene libraries. Sequencing data were examined using the Quantitative Insights into Microbial Ecology software and Phyloseq in R environment. Results A varied community of bacteria was found in both raw and pasteurized human milk. The bacterial diversity of the milk samples was increased by the pasteurization, where some thermoduric bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were more abundant. The source tracker analysis indicated that at most 1.0% of bacteria may have come from another source, showing the safety of the process used to treat milk samples. Conclusion The pasteurization process increased the bacterial diversity. We selected taxa capable of surviving the process, which could proliferate after the treatment without being a risk for infants.

scholarly journals The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile

2020 ◽  
Vol 8 (5) ◽  
pp. 677 ◽  
Author(s):  
Monique J. T. Crobach ◽  
Quinten R. Ducarmon ◽  
Elisabeth M. Terveer ◽  
Celine Harmanus ◽  
Ingrid M. J. G. Sanders ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Clostridioides Difficile ◽  
Bacterial Microbiota ◽  
Differential Abundance Analysis ◽  
Gut Microbiota Composition ◽  
Eubacterium Hallii

Gut microbiota composition in patients with Clostridioides difficile colonization is not well investigated. We aimed to identify bacterial signatures associated with resistance and susceptibility to C. difficile colonization (CDC) and infection (CDI). Therefore, gut microbiota composition from patients with CDC (n = 41), with CDI (n = 41), and without CDC (controls, n = 43) was determined through 16S rRNA gene amplicon sequencing. Bacterial diversity was decreased in CDC and CDI patients (p < 0.01). Overall microbiota composition was significantly different between control, CDC, and CDI patients (p = 0.001). Relative abundance of Clostridioides (most likely C. difficile) increased stepwise from controls to CDC and CDI patients. In addition, differential abundance analysis revealed that CDI patients’ gut microbiota was characterized by significantly higher relative abundance of Bacteroides and Veillonella than CDC patients and controls. Control patients had significantly higher Eubacterium hallii and Fusicatenibacter abundance than colonized patients. Network analysis indicated that Fusicatenibacter was negatively associated with Clostridioides in CDI patients, while Veillonella was positively associated with Clostridioides in CDC patients. Bacterial microbiota diversity decreased in both CDC and CDI patients, but harbored a distinct microbiota. Eubacterium hallii and Fusicatenibacter may indicate resistance against C. difficile colonization and subsequent infection, while Veillonella may indicate susceptibility to colonization and infection by C. difficile.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

2018 ◽  
Vol 41 (3) ◽  
pp. 255-264 ◽  
Author(s):  
J. Abraham Pérez-Pérez ◽  
David Espinosa-Victoria ◽  
Hilda V. Silva-Rojas ◽  
Lucía López-Reyes
Keyword(s):  
Bacterial Diversity ◽  
Digestive Tract ◽  
Bacterial Species ◽  
Brain Heart Infusion ◽  
Rrna Gene ◽  
Eisenia Foetida ◽  
Bacterial Isolates ◽  
Bacterial Microbiota ◽  
Decomposition Of Organic Matter ◽  
Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

scholarly journals New Chitosan-Degrading Strains That Produce Chitosanases Similar to ChoA of Mitsuaria chitosanitabida

2005 ◽  
Vol 71 (9) ◽  
pp. 5138-5144 ◽  
Author(s):  
ChoongSoo Yun ◽  
Daiki Amakata ◽  
Yasuhiro Matsuo ◽  
Hideyuki Matsuda ◽  
Makoto Kawamukai
Keyword(s):  
Southern Hybridization ◽  
Glycosyl Hydrolase ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Glycosyl Hydrolase Family ◽  
Broad Variety ◽  
Hydrolase Family ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

ABSTRACT The betaproteobacterium Mitsuaria chitosanitabida (formerly Matsuebacter chitosanotabidus) 3001 produces a chitosanase (ChoA) that is classified in glycosyl hydrolase family 80. While many chitosanase genes have been isolated from various bacteria to date, they show limited homology to the M. chitosanitabida 3001 chitosanase gene (choA). To investigate the phylogenetic distribution of chitosanases analogous to ChoA in nature, we identified 67 chitosan-degrading strains by screening and investigated their physiological and biological characteristics. We then searched for similarities to ChoA by Western blotting and Southern hybridization and selected 11 strains whose chitosanases showed the most similarity to ChoA. PCR amplification and sequencing of the chitosanase genes from these strains revealed high deduced amino acid sequence similarities to ChoA ranging from 77% to 99%. Analysis of the 16S rRNA gene sequences of the 11 selected strains indicated that they are widely distributed in the β and γ subclasses of Proteobacteria and the Flavobacterium group. These observations suggest that the ChoA-like chitosanases that belong to family 80 occur widely in a broad variety of bacteria.

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

scholarly journals Modulation of Saliva Microbiota through Prebiotic Intervention in HIV-Infected Individuals

Nutrients ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1346 ◽  
Author(s):  
Nuria Jiménez-Hernández ◽  
Sergio Serrano-Villar ◽  
Alba Domingo ◽  
Xavier Pons ◽  
Alejandro Artacho ◽  
...  
Keyword(s):  
Hiv Infection ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Microbiota Composition ◽  
Hiv Status ◽  
T Helper ◽  
Immunodeficiency Virus ◽  
Salivary Microbiota ◽  
Rrna Gene Sequencing

Human immunodeficiency virus (HIV) infection is characterized by an early depletion of the mucosal associated T helper (CD4+) cells that impair the host immunity and impact the oral and gut microbiomes. Although, the HIV-associated gut microbiota was studied in depth, few works addressed the dysbiosis of oral microbiota in HIV infection and, to our knowledge, no studies on intervention with prebiotics were performed. We studied the effect of a six-week-long prebiotic administration on the salivary microbiota in HIV patients and healthy subjects. Also, the co-occurrence of saliva microorganisms in the fecal bacteria community was explored. We assessed salivary and feces microbiota composition using deep 16S ribosomal RNA (rRNA) gene sequencing with Illumina methodology. At baseline, the different groups shared the same most abundant genera, but the HIV status had an impact on the saliva microbiota composition and diversity parameters. After the intervention with prebiotics, we found a drastic decrease in alpha diversity parameters, as well as a change of beta diversity, without a clear directionality toward a healthy microbiota. Interestingly, we found a differential response to the prebiotics, depending on the initial microbiota. On the basis of 100% identity clustering, we detected saliva sequences in the feces datasets, suggesting a drag of microorganisms from the upper to the lower gastrointestinal tract.

scholarly journals Distribution and recombination of Wolbachia endosymbionts in Korean coleopteran insects

2019 ◽  
Vol 43 (1) ◽  
Author(s):  
Gilsang Jeong ◽  
Taeman Han ◽  
Haechul Park ◽  
Soyeon Park ◽  
Pureum Noh
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Surface Protein ◽  
Rrna Gene ◽  
Infection Frequency ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Endosymbiotic Bacteria ◽  
Molecular Machinery ◽  
Broad Scale

Abstract Background Wolbachia are among the most prevalent endosymbiotic bacteria and induce reproductive anomalies in various invertebrate taxa. The bacterium has huge impacts on host reproductive biology, immunity, evolution, and molecular machinery. However, broad-scale surveys of Wolbachia infections at the order scale, including the order Coleoptera, are limited. In this study, we investigated the Wolbachia infection frequency in 201 Coleopteran insects collected in Korea. Results A total of 26 species (12.8%) belonging to 11 families harbored Wolbachia. The phylogenetic trees of based on partial 16S rRNA gene sequences and partial Wolbachia surface protein (wsp) gene sequences were largely incongruent to that of their hosts. This result confirms that Wolbachia evolved independently from their hosts, Conclusion Phylogenetic trees suggest that complex horizontal gene transfer and recombination events occurred within and between divergent Wolbachia subgroups.

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