scholarly journals Novel microbiome dominated by Arcobacter during anoxic excurrent flow from an ocean blue hole in Andros Island, The Bahamas

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256305
Author(s):  
Deborah D. Iwanowicz ◽  
Robert B. Jonas ◽  
William B. Schill ◽  
Kay Marano-Briggs
Keyword(s):  
Water Column ◽  
Deep Penetration ◽  
Rrna Gene ◽  
Turbid Water ◽  
Microbial Composition ◽  
The Bahamas ◽  
Near Surface ◽  
Tidal Forces ◽  
Andros Island ◽  
Blue Holes

Andros Island, The Bahamas, composed of porous carbonate rock, has about 175 inland blue holes and over 50 known submerged ocean caves along its eastern barrier reef. These ocean blue holes can have both vertical and horizontal zones that penetrate under the island. Tidal forces drive water flow in and out of these caves. King Kong Cavern has a vertical collapse zone and a deep penetration under Andros Island that emits sulfidic, anoxic water and masses of thin, mucoid filaments ranging to meters in length and off-white turbid water during ebb flow. Our objective was to determine the microbial composition of this mucoid material and the unconsolidated water column turbidity based on the concept that they represent unique lithoautotrophic microbial material swept from the cave into the surrounding ocean. Bacterial DNA extracted from these filaments and surrounding turbid water was characterized using PCR that targeted a portion of the 16S rRNA gene. The genus Arcobacter dominated both the filaments and the water column above the cave entrance. Arcobacter nitrofigilis and Arcobacter sp. UDC415 in the mucoid filaments accounted for as much as 80% of mapped DNA reads. In the water column Arcobacter comprised from 65% to over 85% of the reads in the depth region from about 18 m to 34 m. Bacterial species diversity was much higher in surface water and in water deeper than 36 m than in the intermediate zone. Community composition indicates that ebb flow from the cavern influences the entire water column at least to within 6 m of the surface and perhaps the near surface as well.

scholarly journals Inland blue holes of The Bahamas – chemistry and biology in a unique aquatic environment

2020 ◽  
Vol 194 (2) ◽  
pp. 95-106
Author(s):  
Caroline Björnerås ◽  
Martin Škerlep ◽  
Raphael Gollnisch ◽  
Simon David Herzog ◽  
Gustaf Ekelund Ugge ◽  
...  
Keyword(s):  
Water Chemistry ◽  
Zooplankton Community ◽  
The Bahamas ◽  
Saline Groundwater ◽  
Reducing Conditions ◽  
Andros Island ◽  
Gobiomorus Dormitor ◽  
Lake Systems ◽  
Replicated Systems ◽  
Blue Holes

While lake systems in temperate regions have been extensively studied, tropical and subtropical systems have received less attention. Here, we describe the water chemistry and biota of ten inland blue holes on Andros Island, The Bahamas, representative of the morphological, abiotic, and biotic variation among Androsian inland blue holes. The majority of the studied blue holes were vertically stratified with oxic freshwater overlying anoxic saline groundwater of marine origin. Water chemistry (e.g.total phosphorus and nitrogen) in shallow waters was similar among blue holes, while turbidity and water color varied. Presence of hydrogen sulfide and reduced iron in and below the halocline indicate reducing conditions in all stratified blue holes. The biota above the halocline was also similar among blue holes with a few taxa dominating the phytoplankton community, and the zooplankton community consisting of copepods and rotifers. The Bahamas mosquitofish (Gambusia hubbsi) was present in all investigated blue holes, often accompanied by other small planktivorous fish, while the piscivorous bigmouth sleeper (Gobiomorus dormitor) was only present in some of the blue holes. Our field study reinforces that inland blue holes are highly interesting for biogeochemical research, and provide naturally replicated systems for evolu- tionary studies.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

scholarly journals Ingestion of probiotic (Lactobacillus helveticus and Bifidobacterium longum) alters intestinal microbial structure and behavioral expression following social defeat stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katherine A. Partrick ◽  
Anna M. Rosenhauer ◽  
Jérémie Auger ◽  
Amanda R. Arnold ◽  
Nicole M. Ronczkowski ◽  
...  
Keyword(s):  
Social Stress ◽  
Bifidobacterium Longum ◽  
Social Defeat ◽  
Lactobacillus Helveticus ◽  
Rrna Gene ◽  
Social Avoidance ◽  
Social Defeat Stress ◽  
Microbial Structure ◽  
Microbial Composition ◽  
Anti Inflammatory

AbstractSocial stress exacerbates anxious and depressive behaviors in humans. Similarly, anxiety- and depressive-like behaviors are triggered by social stress in a variety of non-human animals. Here, we tested whether oral administration of the putative anxiolytic probiotic strains Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 reduces the striking increase in anxiety-like behavior and changes in gut microbiota observed following social defeat stress in Syrian hamsters. We administered the probiotic at two different doses for 21 days, and 16S rRNA gene amplicon sequencing revealed a shift in microbial structure following probiotic administration at both doses, independently of stress. Probiotic administration at either dose increased anti-inflammatory cytokines IL-4, IL-5, and IL-10 compared to placebo. Surprisingly, probiotic administration at the low dose, equivalent to the one used in humans, significantly increased social avoidance and decreased social interaction. This behavioral change was associated with a reduction in microbial richness in this group. Together, these results demonstrate that probiotic administration alters gut microbial composition and may promote an anti-inflammatory profile but that these changes may not promote reductions in behavioral responses to social stress.

scholarly journals Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sesilje Weiss ◽  
David Taggart ◽  
Ian Smith ◽  
Kristofer M. Helgen ◽  
Raphael Eisenhofer
Keyword(s):  
Microbial Community ◽  
Reproductive Cycle ◽  
Tammar Wallaby ◽  
The Body ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Birth Canal ◽  
Gram Positive Bacteria ◽  
Rigorous Framework ◽  
The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

scholarly journals Ultrafine particles altered gut microbial population and metabolic profiles in a sex-specific manner in an obese mouse model

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kundi Yang ◽  
Mengyang Xu ◽  
Jingyi Cao ◽  
Qi Zhu ◽  
Monica Rahman ◽  
...  
Keyword(s):  
Ultrafine Particles ◽  
Microbial Population ◽  
Phosphate Buffer Solution ◽  
Biodiesel Fuel ◽  
Control Group ◽  
Obese Mouse ◽  
Rrna Gene ◽  
Obese Mice ◽  
Microbial Composition ◽  
Increased Risk

AbstractEmerging evidence has highlighted the connection between exposure to air pollution and the increased risk of obesity, metabolic syndrome, and comorbidities. Given the recent interest in studying the effects of ultrafine particle (UFP) on the health of obese individuals, this study examined the effects of gastrointestinal UFP exposure on gut microbial composition and metabolic function using an in vivo murine model of obesity in both sexes. UFPs generated from light-duty diesel engine combustion of petrodiesel (B0) and a petrodiesel/biodiesel fuel blend (80:20 v/v, B20) were administered orally. Multi-omics approaches, including liquid chromatography–mass spectrometry (LC–MS) based targeted metabolomics and 16S rRNA gene sequence analysis, semi-quantitatively compared the effects of 10-day UFP exposures on obese C57B6 mouse gut microbial population, changes in diversity and community function compared to a phosphate buffer solution (PBS) control group. Our results show that sex-specific differences in the gut microbial population in response to UFP exposure can be observed, as UFPs appear to have a differential impact on several bacterial families in males and females. Meanwhile, the alteration of seventy-five metabolites from the gut microbial metabolome varied significantly (ANOVA p < 0.05) across the PBS control, B0, and B20 groups. Multivariate analyses revealed that the fuel-type specific disruption to the microbial metabolome was observed in both sexes, with stronger disruptive effects found in females in comparison to male obese mice. Metabolic signatures of bacterial cellular oxidative stress, such as the decreased concentration of nucleotides and lipids and increased concentrations of carbohydrate, energy, and vitamin metabolites were detected. Furthermore, blood metabolites from the obese mice were differentially affected by the fuel types used to generate the UFPs (B0 vs. B20).

scholarly journals Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 472
Author(s):  
Yeong-Ji Oh ◽  
Ye-Rin Park ◽  
Jungil Hong ◽  
Do-Yup Lee
Keyword(s):  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Metabolic Phenotype ◽  
Rrna Gene ◽  
Functional Evaluation ◽  
Initial Condition ◽  
Microbial Composition ◽  
Light Emitting ◽  
Blue Led ◽  
Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

scholarly journals Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shenzheng Zeng ◽  
Sukontorn Khoruamkid ◽  
Warinphorn Kongpakdee ◽  
Dongdong Wei ◽  
Lingfei Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Well Being ◽  
Pacific White Shrimp ◽  
Shrimp Farming ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Water And Sediment ◽  
Surrounding Environment ◽  
Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

scholarly journals The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota

2021 ◽  
Vol 9 (2) ◽  
pp. 278
Author(s):  
Shen Jean Lim ◽  
Miriam Aguilar-Lopez ◽  
Christine Wetzel ◽  
Samia V. O. Dutra ◽  
Vanessa Bray ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Preterm Infant ◽  
Neonatal Intensive Care ◽  
Genetic Relatedness ◽  
Bovine Milk ◽  
Alpha Diversity ◽  
Neonatal Intensive Care Units ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Operational Taxonomic Units

The preterm infant gut microbiota is influenced by environmental, endogenous, maternal, and genetic factors. Although siblings share similar gut microbial composition, it is not known how genetic relatedness affects alpha diversity and specific taxa abundances in preterm infants. We analyzed the 16S rRNA gene content of stool samples, ≤ and >3 weeks postnatal age, and clinical data from preterm multiplets and singletons at two Neonatal Intensive Care Units (NICUs), Tampa General Hospital (TGH; FL, USA) and Carle Hospital (IL, USA). Weeks on bovine milk-based fortifier (BMF) and weight gain velocity were significant predictors of alpha diversity. Alpha diversity between siblings were significantly correlated, particularly at ≤3 weeks postnatal age and in the TGH NICU, after controlling for clinical factors. Siblings shared higher gut microbial composition similarity compared to unrelated individuals. After residualizing against clinical covariates, 30 common operational taxonomic units were correlated between siblings across time points. These belonged to the bacterial classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Erysipelotrichia, and Negativicutes. Besides the influence of BMF and weight variables on the gut microbial diversity, our study identified gut microbial similarities between siblings that suggest genetic or shared maternal and environmental effects on the preterm infant gut microbiota.

scholarly journals Numerical investigation of the Arctic ice-ocean boundary layer; implications for air-sea gas fluxes

2016 ◽  
Author(s):  
A. Bigdeli ◽  
B. Loose ◽  
S. T. Cole
Keyword(s):  
Sea Ice ◽  
Water Column ◽  
Mixed Layer ◽  
Mixed Layer Depth ◽  
The Arctic ◽  
Layer Depth ◽  
Near Surface ◽  
Resolution Model ◽  
Simplifying Assumptions ◽  
Vertical Spacing

Abstract. In ice-covered regions it can be challenging to determine air-sea exchange – for heat and momentum, but also for gases like carbon dioxide and methane. The harsh environment and relative data scarcity make it difficult to characterize even the physical properties of the ocean surface. Here, we seek a mechanistic interpretation for the rate of air-sea gas exchange (k) derived from radon-deficits. These require an estimate of the water column history extending 30 days prior to sampling. We used coarse resolution (36 km) regional configuration of the MITgcm with fine near surface vertical spacing (2 m) to evaluate the capability of the model to reproduce conditions prior to sampling. The model is used to estimate sea-ice velocity, concentration and mixed-layer depth experienced by the water column. We then compared the model results to existing field data including satellite, moorings and Ice-tethered profilers. We found that model-derived sea-ice coverage is 88 to 98 % accurate averaged over Beaufort Gyre, sea-ice velocities have 78 % correlation which resulted in 2 km/day error in 30 day trajectory of sea-ice. The model demonstrated the capacity to capture the broad trends in the mixed layer although with a bias and model water velocities showed only 29 % correlation with actual data. Overall, we find the course resolution model to be an inadequate surrogate for sparse data, however the simulation results are a slight improvement over several of the simplifying assumptions that are often made when surface ocean geochemistry, including the use of a constant mixed layer depth and a velocity profile that is purely wind-driven.

scholarly journals Ratio of Klebsiella/Bifidobacterium in early life correlates with later development of paediatric allergy

2017 ◽  
Vol 8 (5) ◽  
pp. 681-695 ◽  
Author(s):  
J.S.Y. Low ◽  
S.-E. Soh ◽  
Y.K. Lee ◽  
K.Y.C. Kwek ◽  
J.D. Holbrook ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Allergic Disease ◽  
Early Life ◽  
16S Rrna Gene Sequencing ◽  
Early Infancy ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Healthy Infants ◽  
Increased Risk ◽  
Paediatric Allergy

Several studies have reported that intestinal microbial colonisation patterns differ between non-allergic and allergic infants. However, the microbial signature underlying the pathogenesis of allergies remains unclear. We aim to gain insight into the development of the intestinal microbiota of healthy infants and infants who develop allergy in early life, and identify potential microbiota biomarkers of later allergic disease. Using a case-control design in a Chinese sub-cohort of a Singaporean birth cohort (GUSTO), we utilised 16S rRNA gene sequencing to assess intestinal microbial composition and diversity of 21 allergic and 18 healthy infants at 3 weeks, 3 months and 6 months of age, and correlated the microbiota with allergy at ages 18 and 36 months. Pronounced differences in intestinal microbiota composition between allergic and healthy infants were observed at 3 months of age. The intestine of healthy infants was colonised with higher abundance of commensal Bifidobacterium. Conversely, Klebsiella, an opportunistic pathogen, was significantly enriched in the allergic infants. Interestingly, infants with a high Klebsiella/Bifidobacterium (K/B) ratio (above the population median K/B ratio) at age 3 months had an odds ratio of developing allergy by 3 years of age of 9.00 (95% confidence interval 1.46-55.50) compared to those with low K/B ratio. This study demonstrated a relationship between the ratio of genera Klebsiella and Bifidobacterium during early infancy and development of paediatric allergy in childhood. Our study postulates that an elevated K/B ratio in early infancy could be a potential indicator of an increased risk of allergy development. This line of research might enable future intervention strategies in early life to prevent or treat allergy. Our study provides new insights into microbial signatures associated with childhood allergy, in particular, suggests that an elevated K/B ratio could be a potential early-life microbiota biomarker of allergic disease.

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