DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

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.

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Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits

Animals ◽

10.3390/ani11010031 ◽

2020 ◽

Vol 11 (1) ◽

pp. 31

Author(s):

Elisa Cotozzolo ◽

Paola Cremonesi ◽

Giulio Curone ◽

Laura Menchetti ◽

Federica Riva ◽

...

Keyword(s):

Digestive Tract ◽

Large Intestine ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Productive Performance ◽

Bacterial Populations ◽

Bacterial Microbiota ◽

Rrna Gene Sequencing

The microbiota is extremely important for the animal’s health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species, while the highest variability was found in the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.

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Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽

10.1128/msphere.00187-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 1

Author(s):

Shinya Kageyama ◽

Mikari Asakawa ◽

Toru Takeshita ◽

Yukari Ihara ◽

Shunsuke Kanno ◽

...

Keyword(s):

Oral Cavity ◽

Bacterial Diversity ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Oral Microbiota ◽

Bacterial Composition ◽

Content Type ◽

Operational Taxonomic Units ◽

Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

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Isolation, Characterization, and Identification of Bacterial Population from Textile and Tannery Effluents of Bangladesh

Bangladesh Journal of Microbiology ◽

10.3329/bjm.v29i2.28441 ◽

2016 ◽

Vol 29 (2) ◽

pp. 84-88

Author(s):

A Hakim ◽

S Hoque ◽

SM Ullah

Keyword(s):

Bacterial Population ◽

Bacterial Species ◽

Bacterial Count ◽

Rrna Gene ◽

Bacterial Isolates ◽

Tannery Effluents ◽

Bacterial Composition ◽

Degrading Bacteria ◽

Diagnostic Characteristics ◽

Metal Treatment

Ten effluent samples from two different sites located at Hazaribagh tannery belt and Dhaka EPZ, Savar were collected. This study aimed to compare the bacterial composition isolated from tannery and textile effluents and to investigate the occurrence of metal toxicity tolerant and dye degrading bacteria and to select the potential strains for the use in bioremediation. The average bacterial count of HT and DETDE varied in between 3.35×106 and 5.45×106 cfu/mL and 4.8×106 and 7.75×106cfu/mL, respectively. A total of 12 bacterial isolates were characterized as strains of Bacillus, Staphylococcus, and Pseudomonas. A few, however, were re-cultured on other recommended media for verification of diagnostic characteristics. Maximum numbers of bacterial species were isolated from textile effluent. The results showed that a Gram-positive bacillus with a yellow pigment was considered as a major group of the population. Among them three isolates were identified based on alignments of partial sequence of 16S rRNA gene. These are also being used in different wastewater and metal treatment plants all over the world.Bangladesh J Microbiol, Volume 29, Number 2, Dec 2012, pp 84-88

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Assessment of microbiological and residual antibiotics status in milk sold in Abeokuta, Ogun State. Nigeria

Turkish Journal of Agriculture - Food Science and Technology ◽

10.24925/turjaf.v6i6.642-651.1415 ◽

2018 ◽

Vol 6 (6) ◽

pp. 642

Author(s):

Flora Oluwafemi ◽

Bosede Folashade Oluwabamiwo ◽

Oluseyi Oluwajubelo Oluwatosin ◽

Olufunmilayo Ruth Akinrinade ◽

Adelodun Lawrence Kolapo

Keyword(s):

Bacterial Species ◽

Method Comparison ◽

Antibiotic Sensitivity ◽

Plate Count ◽

Diffusion Method ◽

Rrna Gene ◽

Antibiotic Residues ◽

Bacterial Isolates ◽

Powdered Milk ◽

Microbiological Methods

This study investigated the prevalence and concentration of antibiotic residues in twenty brands of milk. Determination and quantification of antibiotic residues was done using High Performance Liquid Chromatography. Aerobic plate count was carried out and the associated bacteria isolated. Identification of bacteria was done using standard microbiological methods. Molecular characterization and identification of bacterial isolates was done using 16S rRNA gene sequencing method. Antibiotic sensitivity was carried out on bacterial isolates using disc diffusion method. Plasmid profile of drug resistant isolates was done using alkaline analysis method. Comparison of means was done using Analysis of Variance. Antibiotic residues were detected in 10 (50%) of the 20 milk brands analyzed. The residual levels of tetracycline, oxytetracycline and chlortetracycline ranged between 5ng/kg and 1569ng/kg while none of the samples had doxycycline residues. The prevalence of tetracycline residues in evaporated milk brands and powdered milk samples were 100 and 23 % respectively. The aerobic plate counts ranged from 2.5 × 102 to 6.5 × 102 CFU∕mL for evaporated milk and 2.5 × 101 to 6.0 × 101 CFU∕mL for powdered milk. A total of ten bacterial species were isolated and identified. Susceptibility result showed that 95% of the isolates were sensitive to erythromycin, cefuroxime and gentamycin; 12.5% were resistant to tetracycline and ampicillin, 10% were resistant to ofloxacin and 7.5% to doxycycline and penicillin. Five of the bacterial isolates were resistant to more than one class of antibiotics. Resistant isolates subjected to plasmid profiling had detectable plasmids with estimated sizes between 120bp and 1000bp. The obtained results provide evidence that the presence of antibiotic residues in evaporated and powdered milk is an indication that the public is exposed to the harmful effects of the residues.

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Cultivable Microbial Diversity in Speleothems Using MALDI-TOF Spectrometry and DNA Sequencing from Krem Soitan, Krem Lawbah, Krem Mawpun, Khasi Hills, Meghalaya, India

10.21203/rs.3.rs-528486/v1 ◽

2021 ◽

Author(s):

Mudgil Devender ◽

Dhiraj Paul ◽

Sushmitha Baskar ◽

Ramanathan Baskar ◽

Yogesh S Shouche

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Bacterial Isolates ◽

Maldi Tof ◽

Rrna Gene Sequencing ◽

Culture Dependent

Abstract This study reports on the culturable microbial communities in caves from the Indian sub-continent. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. This approach helped to detect a number bacterial strains from the Indian caves. The microbial diversity in the Indian caves is inadequately characterized. The study aims to expand the current understanding of bacterial diversity in the speleothems from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. High microbial enumerations were observed on dilute nutrient agar (5.3 × 103 to 8.8 × 105) followed by M9 minimal medium (4 × 104 to 1.7 × 105) and R2A medium (1.0 × 104 to 5.7 × 105). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. 91% of the total bacterial diversity was dominated by Proteobacteria and Actinobacteria. The other important phyla detected include the Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%). At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. A culture-dependent approach was employed for elucidating the community structure colonizing the speleothems and wall deposits in the caves using MALDI-TOF and 16S rRNA gene sequencing. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.

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Bacterial diversity of soil samples from the western Himalayas, India

Canadian Journal of Microbiology ◽

10.1139/w09-011 ◽

2009 ◽

Vol 55 (5) ◽

pp. 564-577 ◽

Cited By ~ 38

Author(s):

Pooja Gangwar ◽

Syed Imteyaz Alam ◽

Sunita Bansod ◽

Lokendra Singh

Keyword(s):

Bacterial Diversity ◽

Bacterial Species ◽

Hydrolytic Enzymes ◽

Soil Samples ◽

Rrna Gene ◽

Organic Carbon Content ◽

Western Himalayas ◽

Bacterial Strains ◽

Culture Independent ◽

The One

High-altitude cold habitats of the Himalayas are little explored with respect to bacterial diversity. Diverse bacterial species and phylotypes obtained by culture-dependent and culture-independent approaches are reported here. Phylogenetic analysis and modulation of bacterial diversity with altitude and available organic carbon content are also described. Psychrophilic and psychrotolerant bacteria dominated the Himalayan habitats, accounting for 60% of the cultivated strains. Isolates produced one or more (up to five) hydrolytic enzymes, lipase being the one secreted by most strains (62%). Partial 16S rRNA gene sequences were obtained for 99 bacterial strains and 74 clones obtained from soil samples from the western Himalayas. Forty-five percent of cultured bacterial strains belonged to the Proteobacteria group with 39% belonging to γ-Proteobacteria. Firmicutes was the second most abundant class with 32% of the total isolates followed by Actinobacteria (16%) and Bacteroidetes (6%). Most of the strains belonged to the genus Bacillus (30%) followed by Pseudomonas (24%) and Arthrobacter (12%). In culture-independent studies, phylotypes belonging to the Proteobacteria were dominant (73%) with the majority being β-Proteobacteria (31%). The bacterial diversity exhibited an altitude gradient with a gradual decline in the number of genera with increase in altitude. The isolates exhibited close phylogenetic affinities to bacteria from other cold habitats.

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

Journal of Human Lactation ◽

10.1177/08903344211011946 ◽

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.

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Antimicrobial activity evaluation of frankincense oil in domestic water samples by 16s rRNA gene

Journal of Applied and Advanced Research ◽

10.21839/jaar.2017.v2i4.104 ◽

2017 ◽

Vol 2 (4) ◽

Author(s):

Saeed F R ◽

Al Kendi R ◽

Vijith Chandu

Keyword(s):

Antimicrobial Activity ◽

Bacterial Species ◽

Water System ◽

Morphological Characteristics ◽

Rrna Gene ◽

Water Tank ◽

Pseudomonas Sp ◽

Bacterial Isolates ◽

Domestic Water ◽

Minimum Effective Concentration

The domestic water system permits the growth and reproduction of bacterial species. The removal of such contaminants by the application of chemical disinfectants like chlorine may pose health risk. Therefore, the natural products are more favored to be investigated for its antimicrobial activity. The current study investigates the efficiency of frankincense oil as an antimicrobial agent on bacterial species isolated from the domestic water system. In the previous study, 15 bacterial species were isolated based on the colony morphological characteristics and prepared for identification. 16S rDNA gene was amplified using PCR for all bacterial isolates followed by sequencing and identification using BLAST. Thirteen bacterial isolates were identified and represented in Staphylococcus saprophhyticus, Bacillus pumilus, Bacillus safensis and Pseudomonas sp. and the last one showed more resistant to frankincense oil as the numbers increased with the treatment by 26% and 35%. Other species were either completely or partially eliminated. The results confirmed that the antimicrobial activity of frankincense oil against some bacterial species, mainly exist in storage tank. Pseudomonas sp. showed resistance to frankincense oil (10%) used in this study. In addition, Staphylococcus saprophhyticus is of a concern to human health, however, it showed sensitivity to frankincense oil and also, its presence in the water tank indicates hygiene issues of the household. The frankincense oil found to be a promising disinfectant, thus further analysis needed to specify the minimum effective concentration to be applied, also to find out whether it is cost effective to be used as a disinfectant.

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Diversity of Biofilm-Forming Bacteria in Chinnamuttom Harbor of Southeast India

Bioscience Biotechnology Research Communications ◽

10.21786/bbrc/14.4.61 ◽

2021 ◽

Vol 14 (4) ◽

pp. 1793-1799

Author(s):

P. Nithya

Keyword(s):

Surface Water ◽

Bacterial Species ◽

Ship Hull ◽

Rrna Gene ◽

Pseudomonas Sp ◽

Bacillus Sp ◽

Bacterial Isolates ◽

Four Seasons ◽

The Mean ◽

Marine Environmental

Biofilms are species rich, partially due to highly effective powers of diffusion of the microorganisms and have wide tolerance to marine environmental conditions. Characteristically, the first organisms to respond to and convalesce from stress. The present study aims to isolate and identify the biofilm forming bacterial species, collected from surface water and substratum of the ship hull for four seasons at Chinnamuttom fishing harbor, Southeast coast of India, during June 2015 to May 2016. Among the mean concentration of bacterial isolates of both water and substratum of the station, maximum in monsoon and minimum in summer seasons. Totally 16 isolates were obtained, based on the adherence property, 8 isolates from surface water and 8 isolates from substratum of the ship hull. The samples were plated on Zobell marine agar medium for bacterial isolates of study area. The isolates of Bacillus sp., Flavobacterium sp., Pseudomonas sp., Aeromonas sp., Micrococcus sp., Vibrio sp., Salmonella sp., Staphylococcus sp., Shegella sp., Klebsiella sp., Corynebacterium sp., Enterobacter sp., Chromohalobacter sp., Bacillus sp., Escherichia coli and Bacilus sp. were reported in all the seasons at study area. The major diverse bacterial isolates were further characterized through morphological and molecular identification. Based on 16S rRNA gene sequences. Biofilm bacterial isolates were confirmed as Bacillus sp., and Pseudomonas sp.

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Effect of the Mycorrhizosphere on the Genotypic and Metabolic Diversity of the Bacterial Communities Involved in Mineral Weathering in a Forest Soil

Applied and Environmental Microbiology ◽

10.1128/aem.00121-07 ◽

2007 ◽

Vol 73 (9) ◽

pp. 3019-3027 ◽

Cited By ~ 184

Author(s):

S. Uroz ◽

C. Calvaruso ◽

M. P. Turpault ◽

J. C. Pierrat ◽

C. Mustin ◽

...

Keyword(s):

Carbon Metabolism ◽

Mycorrhizal Fungi ◽

Bacterial Species ◽

Mineral Weathering ◽

Bulk Soil ◽

Rrna Gene ◽

Bacterial Isolates ◽

Bacterial Strains ◽

Gene Sequence Analysis ◽

Scleroderma Citrinum

ABSTRACT To date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. However, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. In this study, we characterized a collection of 61 bacterial strains isolated from Scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. The ability of bacteria to weather biotite was assessed with a new microplate bioassay that measures the pH and the quantity of iron released from this mineral. We showed that weathering bacteria occurred more frequently in the vicinity of S. citrinum than in the bulk soil. Moreover, the weathering efficacy of the mycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera Burkholderia, Collimonas, Pseudomonas, and Sphingomonas, and their carbon metabolism was characterized by the BIOLOG method. The most efficient isolates belonged to the genera Burkholderia and Collimonas. Multivariate analysis resulted in identification of three metabolic groups, one of which contained mainly bacterial isolates associated with S. citrinum and exhibiting high mineral-weathering potential. Therefore, our results support the hypothesis that by its carbon metabolism this fungus selects in the bulk soil reservoir a bacterial community with high weathering potential, and they also address the question of functional complementation between mycorrhizal fungi and bacteria in the ectomycorrhizal complex for the promotion of tree nutrition.

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