Profiling the microbial community of a Triassic halite deposit in Northern Ireland: an environment with significant potential for biodiscovery

ABSTRACT Kilroot salt mine, a Triassic halite deposit located in County Antrim, Northern Ireland, is the only permanent hypersaline environment on the island of Ireland. In this study, the microbiome of this unstudied environment was profiled for the first time using conventional and enhanced culturing techniques, and culture independent metagenomic approaches. Using both conventional isolation plates and iChip devices, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained, based on 16S rRNA gene sequencing. The archaeal isolates were similar to those previously isolated from other ancient halite deposits, and as expected, numerous genera were identified in the metagenome which were not represented among the culturable isolates. Preliminary screening of a selection of isolates from this environment identified antimicrobial activities against a panel of clinically important bacterial pathogens from 15 of the bacterial isolates and one of the archaea. This, alongside previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be a new, untapped source of of chemical diversity with high biodiscovery potential.

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Rhodomyrtus tomentosa Fruit Extract and Skin Microbiota: A Focus on C. acnes Phylotypes in Acne Subjects

Cosmetics ◽

10.3390/cosmetics7030053 ◽

2020 ◽

Vol 7 (3) ◽

pp. 53 ◽

Cited By ~ 1

Author(s):

Sandie Gervason ◽

Isabelle Metton ◽

Elodie Gemrot ◽

Edwige Ranouille ◽

Gilbert Skorski ◽

...

Keyword(s):

Active Ingredient ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Skin Microbiome ◽

Skin Microbiota ◽

Cutibacterium Acnes ◽

Culture Independent ◽

Rrna Gene Sequencing ◽

Abundant Genus ◽

Rhodomyrtus Tomentosa

Knowing that Rhodomyrtus tomentosa is known to have antibacterial effects, this study investigated the skin microbiota with a focus on Cutibacterium acnes (C. acnes) phylotypes in subjects with acne, and determined microbiota changes after 28 days of treatment with berries Rhodomyrtus tomentosa as an active ingredient (RT). Skin swabs from seventeen acne subjects were collected and the skin microbiome was analyzed using 16S rRNA gene sequencing. A culture-independent next-generation sequencing (NGS)-based SLST (single-locus sequence typing) approach was aimed at evaluating RT extract effects on C. acnes phylotype repartition. Clinical evaluations (lesion counts) were performed at baseline (D0) and after 28 days (D28) of twice-daily application of the RT active ingredient. We determined: (1) the skin microbiota at D0 was dominated by Actinobacteria followed by Firmicutes and Proteobacteria; (2) at the genus level, Cutibacterium was the most abundant genus followed by Staphylococcus and Corynebacterium; (3) C. acnes was the major species in terms of mean abundance, followed by Staphylococcus epidermidis (S. epidermidis) and Staphylococcus hominis (S. hominis); and (4) phylotype IA1 was most represented, with a predominance of SLST type A1, followed by phylotypes II, IB, IA2, IC, and III. After 28 days of RT extract treatment, phylotype repartition were modified with a decrease in abundance (approximately 4%) of phylotype IA1 and an increase in phylotype II and III. Cutibacterium granulosum (C. granulosum) abundance also decreased. Reduction of retentional and inflammatory lesions was also noted only after RT treatment; thus, RT extract acts as a microbiota-regulating agent.

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Assessment and Characterization of Xylanolytic Bacteria Isolated from the Gut of Microtermes Obesi for Biomass Pretreatment

10.21203/rs.3.rs-282399/v1 ◽

2021 ◽

Author(s):

Iram Batool ◽

Falak Sher Khan ◽

Muhammad Awais ◽

Dawood Ahmed ◽

Sami Ullah Khan ◽

...

Keyword(s):

Corn Stover ◽

Rice Straw ◽

16S Rrna Gene Sequencing ◽

Major Constituent ◽

Rrna Gene ◽

Bacterial Isolates ◽

Cotton Stalk ◽

Termite Gut ◽

Chemical Pretreatments ◽

Rrna Gene Sequencing

Abstract The aim of current research was to examine the potential for the production of hemicelluloses degrading enzymes from bacteria harbor in termite gut. The research was also focused on the conversion of lignocellulosic biomass (Corn stover, rice straw and cotton stalk) into fermentable sugars by using enzymes from the bacterial isolates. The bacterial isolates from termite gut were screened for their ability to degrade xylan that is the major constituent of hemicelluloses. Two bacterial isolates were chosen and identified by 16S rRNA gene sequencing. Both isolates TGB9 and TGB10 belong to Bacillus geneus. The isolates have shown higher xylan degrading activity at 50 oC and optimum pH was 6.0. Xylanases from isolate TGB9 and TGB10 were utilized for sccharification of agricultural substrates (stover, rice straw and cotton stalk). As a result higher contents of reducing sugars were observed from corn stover. Xylanases from isolate TGB9 produced higher yields of reducing sugar than isolate TGB10. A comparative study was also performed among chemical pretreatment and xylanases from bacterial isolates. For this purpose agricultural substrates were also treated with H2SO4 and NaOH. Xylanases produced by TGB9 and TGB10 released higher content of sugar from agricultural substrates than chemical pretreatments. So it is concluded that termite gut have bacteria that can hydrolyze hemicelluloses more efficiently than chemicals.

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Phylogenetic and Chemical Diversity of Three Chemotypes of Bloom-Forming Lyngbya Species (Cyanobacteria: Oscillatoriales) from Reefs of Southeastern Florida

Applied and Environmental Microbiology ◽

10.1128/aem.02656-08 ◽

2009 ◽

Vol 75 (9) ◽

pp. 2879-2888 ◽

Cited By ~ 40

Author(s):

Koty Sharp ◽

Karen E. Arthur ◽

Liangcai Gu ◽

Cliff Ross ◽

Genelle Harrison ◽

...

Keyword(s):

16S Rrna Gene Sequencing ◽

Chemical Diversity ◽

Biologically Active ◽

Rrna Gene ◽

Broward County ◽

Free Living ◽

Genetic Components ◽

Rrna Gene Sequencing ◽

Southern Florida ◽

Cyanobacterial Genus

ABSTRACTThe cyanobacterial genusLyngbyaincludes free-living, benthic, filamentous cyanobacteria that form periodic nuisance blooms in lagoons, reefs, and estuaries.Lyngbyaspp. are prolific producers of biologically active compounds that deter grazers and help blooms persist in the marine environment. Here, our investigations reveal the presence of three distinctLyngbyaspecies on nearshore reefs in Broward County, FL, sampled in 2006 and 2007. With a combination of morphological measurements, molecular biology techniques, and natural products chemistry, we associated these threeLyngbyaspecies with three distinctLyngbyachemotypes. One species, identified asLyngbyacf.confervoidesvia morphological measurements and 16S rRNA gene sequencing, produces a diverse array of bioactive peptides and depsipeptides. Our results indicate that the other twoLyngbyaspecies produce either microcolins A and B or curacin D and dragonamides C and D. Results from screening for the biosynthetic capacity for curacin production among the threeLyngbyachemotypes in this study correlated that capacity with the presence of curacin D. Our work on these bloom-formingLyngbyaspecies emphasizes the significant phylogenetic and chemical diversity of the marine cyanobacteria on southern Florida reefs and identifies some of the genetic components of those differences.

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Chitinolytic bacteria in the intestinal tract of Japanese coastal fishes

Canadian Journal of Microbiology ◽

10.1139/w06-082 ◽

2006 ◽

Vol 52 (12) ◽

pp. 1158-1163 ◽

Cited By ~ 19

Author(s):

Shiro Itoi ◽

Toshihiro Okamura ◽

Yuki Koyama ◽

Haruo Sugita

Keyword(s):

16S Rrna ◽

Intestinal Tract ◽

Intestinal Bacteria ◽

16S Rrna Gene Sequencing ◽

Colloidal Chitin ◽

Rrna Gene ◽

Bacterial Isolates ◽

Coastal Fish ◽

Chitinolytic Bacteria ◽

Rrna Gene Sequencing

Intestinal bacteria from several coastal fish species were screened on 1/20 PYBG medium containing 0.2% colloidal chitin, and 361 bacteria capable of decomposing colloidal chitin were isolated. These isolates were subsequently screened on media containing either 0.5% α-chitin or 0.5% β-chitin resulting in the identification of 31 α-chitinolytic and 275 β-chitinolytic bacterial isolates. Partial 16S rRNA gene sequencing was carried out and homology searches of the resultant sequences against the DDBJ, EMBL, and GenBank databases revealed that the majority (99%) of the chitinolytic bacteria isolated belonged to the Vibrionaceae. Phylogenetic analysis using a Bayesian approach showed that the α-chitinolytic bacteria belonging to the Vibrionaceae formed a separate cluster from the non-α-chitinolytic bacteria in the Vibrionaceae.Key words: chitinolytic bacteria, 16S rRNA, α-chitin, coastal fish, intestinal bacteria.

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Estructura de la comunidad bacteriana en diferentes tejidos de Lobatus gigas silvestres (Linnaeus, 1758) de la Reserva de Biosfera Seaflower del Caribe

Bulletin of Marine and Coastal Research ◽

10.25268/bimc.invemar.2018.47.2.746 ◽

2018 ◽

Vol 47 (2) ◽

Author(s):

Mónica Marcela Higuita-Valencia ◽

Olga Inés Montoya Campuzano ◽

Edna Judith Márquez Fernández ◽

Claudia Ximena Moreno Herrera

Keyword(s):

Biosphere Reserve ◽

16S Rrna Gene Sequencing ◽

Reproductive Rate ◽

Rrna Gene ◽

Bacterial Populations ◽

Microbiological Methods ◽

Culture Independent ◽

Total Dna ◽

Rrna Gene Sequencing ◽

Genetic Profiles

The microbial diversity of Lobatus gigas has not been thoroughly studied despite of them is a specie endangered. Knowledge of microbiota may help to improve the conservation and cultivation of this species. The objective of this study was to evaluate the bacterial populationsassociated with the gonad and the gut compartments of the wild endangered L. gigas from the Caribbean Seaflower Biosphere Reserve, using microbiological methods and culture-independent molecular tools. The genetic profiles of the bacterial populations were generated and Temporal Temperature Gradient Electrophoresis (TTGE) was used to compare them with total DNA. A genetic and statistical analysis of the bacterial communities revealed a low level of diversity in gonad tissue based on the number of bands detected using TTGE. In addition, statistical differences in bacterial community structure were found between the foregut and hindgut tissue of L. gigas. The dominant phylogenetic affiliations of the gonad bacteria, as determined using 16S rRNA gene sequencing, belong to Ralstonia (50%). The possible involvement of this genus in the reproduction and development of the conch is discussed. On the other hand, the bacterial phylotypes from foregut and hindgut included members of Alphaproteobactera (12.5%), Betaproteobacteria (12.5%), Gammaproteobacteria (12.5%), Bacilli (31.25%), Clostridia (6.25%), Actinobacteria (6.25%), Mollicutes (6.25%) and Deinococci (6.25%) classes. Knowing the composition of the gonad and foregut and hindgut bacteria of L. gigas is the first step toward exploring the proper management of this species, as well as provides useful information to future researches that allow a better understanding of the role of these bacterial populations in the health and reproductive rate of L. gigas.

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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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Beyond Archaea: The Table Salt Bacteriome

Frontiers in Microbiology ◽

10.3389/fmicb.2021.714110 ◽

2021 ◽

Vol 12 ◽

Author(s):

Leila Satari ◽

Alba Guillén ◽

Adriel Latorre-Pérez ◽

Manuel Porcar

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Halophilic Bacteria ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Culturable Bacteria ◽

Table Salt ◽

Culture Independent ◽

Rrna Gene Sequencing ◽

Marine Salt

Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.

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Bacterial growth in saturated and eutectic solutions of magnesium sulphate and potassium chlorate with relevance to Mars and the ocean worlds

International Journal of Astrobiology ◽

10.1017/s1473550418000502 ◽

2019 ◽

Vol 18 (6) ◽

pp. 502-509 ◽

Cited By ~ 3

Author(s):

Jonathan M. Wilks ◽

Fei Chen ◽

Benton C. Clark ◽

Mark A. Schneegurt

Keyword(s):

Microbial Growth ◽

Freezing Point ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Bacterial Isolates ◽

Near Surface ◽

Iron Sulphate ◽

High Concentrations ◽

Rrna Gene Sequencing ◽

Hygroscopic Salts

AbstractLiquid water on Mars might be created by deliquescence of hygroscopic salts or by permafrost melts, both potentially forming saturated brines. Freezing point depression allows these heavy brines to remain liquid in the near-surface environment for extended periods, perhaps as eutectic solutions, at the lowest temperatures and highest salt concentrations where ices and precipitates do not form. Perchlorate and chlorate salts and iron sulphate form brines with low eutectic temperatures and may persist under Mars near-surface conditions, but are chemically harsh at high concentrations and were expected to be incompatible with life, while brines of common sulphate salts on Mars may be more suitable for microbial growth. Microbial growth in saturated brines also may be relevant beyond Mars, to the oceans of Ceres, Enceladus, Europa and Pluto. We have previously shown strong growth of salinotolerant bacteria in media containing 2M MgSO4 heptahydrate (~50% w/v) at 25°C. Here we extend those observations to bacterial isolates from Basque Lake, BC and Hot Lake, WA, that grow well in saturated MgSO4 medium (67%) at 25°C and in 50% MgSO4 medium at 4°C (56% would be saturated). Psychrotolerant, salinotolerant microbes isolated from Basque Lake soils included Halomonas and Marinococcus, which were identified by 16S rRNA gene sequencing and characterized phenetically. Eutectic liquid medium constituted by 43% MgSO4 at −4°C supported copious growth of these psychrotolerant Halomonas isolates, among others. Bacterial isolates also grew well at the eutectic for K chlorate (3% at −3°C). Survival and growth in eutectic solutions increases the possibility that microbes contaminating spacecraft pose a contamination risk to Mars. The cold brines of sulphate and (per)chlorate salts that may form at times on Mars through deliquescence or permafrost melt have now been demonstrated to be suitable microbial habitats, should appropriate nutrients be available and dormant cells become vegetative.

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Comprehensive Understanding of the Bacterial Populations and Metabolites Profile of Fermented Feed by 16S rRNA Gene Sequencing and Liquid Chromatography–Mass Spectrometry

Metabolites ◽

10.3390/metabo9100239 ◽

2019 ◽

Vol 9 (10) ◽

pp. 239

Author(s):

Wei Jin ◽

Zheng Zhang ◽

Kun Zhu ◽

Yanfeng Xue ◽

Fei Xie ◽

...

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Antimicrobial Activities ◽

Rrna Gene ◽

Liquid Chromatography Mass Spectrometry ◽

Bacterial Populations ◽

Fermented Feed ◽

Rrna Gene Sequencing

The comprehensive bacterial populations and metabolites profile in fermented feed is unclear, which may have significant effects on the stability of fermented feed quality and animal gut health. In this study, 16S rRNA gene sequencing and liquid chromatography–mass spectrometry were used to explore the bacterial populations and metabolites profile in the fermented feed incubated with probiotics (MF) or without probiotics (SF). The probiotics were a combination of Lactobacillus salivarius, Bacillus subtilis, and Saccharomyces cerevisiae. The pH and lactic acid levels were higher in MF than in SF (P < 0.05), while the total volatile fatty acid content was lower (P < 0.05). Interestingly, after fermentation, the most abundant bacterial genus in MF was Enterococcus, rather than the added probiotics Lactobacillus or Bacillus. Weissella and a few potential pathogens (Enterobacter, Escherichia-Shigella, and Pantoea) were dominant in SF (P < 0.05). Metabolomics analysis identified 32 different metabolites in the two types of fermented feed. These metabolites enriched in MF, such as maleic acid, phenylacetic acid, ethyl linoleate, dihomo-gamma-linolenic acid, and L-theanine had potential antimicrobial activities. Conclusively, the addition of probiotics enriched a few potentially beneficial microbes and small molecular compounds with antimicrobial activities, and inhibited the potential pathogens in fermented feed.

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Microbiological and Metagenomic Characterization of a Retail Delicatessen Galotyri-Like Fresh Acid-Curd Cheese Product

Fermentation ◽

10.3390/fermentation7020067 ◽

2021 ◽

Vol 7 (2) ◽

pp. 67

Author(s):

John Samelis ◽

Agapi I. Doulgeraki ◽

Vasiliki Bikouli ◽

Dimitrios Pappas ◽

Athanasia Kakouri

Keyword(s):

Lactococcus Lactis ◽

Streptococcus Thermophilus ◽

16S Rrna Gene Sequencing ◽

Lactobacillus Delbrueckii ◽

Rrna Gene ◽

Sequencing Analysis ◽

Viable Cells ◽

Culture Independent ◽

Rrna Gene Sequencing

This study evaluated the microbial quality, safety, and ecology of a retail delicatessen Galotyri-like fresh acid-curd cheese traditionally produced by mixing fresh natural Greek yogurt with ‘Myzithrenio’, a naturally fermented and ripened whey cheese variety. Five retail cheese batches (mean pH 4.1) were analyzed for total and selective microbial counts, and 150 presumptive isolates of lactic acid bacteria (LAB) were characterized biochemically. Additionally, the most and the least diversified batches were subjected to a culture-independent 16S rRNA gene sequencing analysis. LAB prevailed in all cheeses followed by yeasts. Enterobacteria, pseudomonads, and staphylococci were present as <100 viable cells/g of cheese. The yogurt starters Streptococcus thermophilus and Lactobacillus delbrueckii were the most abundant LAB isolates, followed by nonstarter strains of Lactiplantibacillus, Lacticaseibacillus, Enterococcus faecium, E. faecalis, and Leuconostoc mesenteroides, whose isolation frequency was batch-dependent. Lactococcus lactis isolates were sporadic, except for one cheese batch. However, Lactococcus lactis, Enterobacteriaceae, Vibrionaceae, Salinivibrio, and Shewanellaceae were detected at fairly high relative abundances culture-independently, despite the fact that their viable counts in the cheeses were low or undetectable. Metagenomics confirmed the prevalence of S. thermophilus and Lb. delbrueckii. Overall, this delicatessen Galotyri-like cheese product was shown to be a rich pool of indigenous nonstarter LAB strains, which deserve further biotechnological investigation.

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