scholarly journals Sea anemone and clownfish microbiota diversity and variation during the initial steps of symbiosis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Natacha Roux ◽  
Raphaël Lami ◽  
Pauline Salis ◽  
Kévin Magré ◽  
Pascal Romans ◽  
...  
Keyword(s):  
Sea Water ◽  
16S Rrna Gene Sequencing ◽  
Sea Anemone ◽  
Rrna Gene ◽  
Natural Environments ◽  
Sea Anemones ◽  
Heteractis Magnifica ◽  
Sequencing Strategy ◽  
Rrna Gene Sequencing

AbstractClownfishes and sea anemones form an intriguing long-term association, but the mechanism underlying this symbiosis is not well understood. Since clownfishes seem to cover themselves with sea anemone mucus, we investigated the microbiomes of the two partners to search for possible shifts in their compositions. We used a 16S rRNA gene sequencing strategy to study the dynamics of the microbiota during the association between the clownfish Amphiprion ocellaris and its host Heteractis magnifica under laboratory conditions. The experiment conducted in aquaria revealed that both clownfish and sea anemone mucus had specific signatures compared to artificial sea water. The microbiomes of both species were highly dynamic during the initiation of the symbiosis and for up to seven days after contact. Three families of bacteria (Haliangiaceae, Pseudoalteromonadacae, Saprospiracae) were shared between the two organisms after symbiosis. Once the symbiosis had been formed, the clownfishes and sea anemone then shared some communities of their mucus microbiota. This study paves the way for further investigations to determine if similar microbial signatures exist in natural environments, whether such microbial sharing can be beneficial for both organisms, and whether the microbiota is implicated in the mechanisms that protect the clownfish from sea anemone stinging.

Occurrence of bacteria with technological and probiotic potential in Argentinian human breast-milk

2020 ◽  
pp. 1-18 ◽  
Author(s):  
S. Oddi ◽  
A. Binetti ◽  
P. Burns ◽  
A. Cuatrin ◽  
J. Reinheimer ◽  
...  
Keyword(s):  
Breast Milk ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Human Breast Milk ◽  
Raw 264.7 Macrophages ◽  
Probiotic Potential ◽  
Long Term Storage ◽  
Technological Potential ◽  
Rrna Gene Sequencing

Breast milk can be a source of potential probiotic bacteria, but the technological capacity of isolates obtained from this source is not always guaranteed. We aimed at isolating lactobacilli from breast milk samples collected in Argentina, focusing on isolates with functional and technological potential as probiotics. Fourteen Lactobacillus and one Bifidobacterium isolates were obtained from 164 samples donated by 104 mothers. The isolates preliminarily identified by MALDI-TOF, and then the identity was confirmed by partial 16S rRNA gene sequencing. Hydrophobicity was determined (hexadecane and xylene partition). The strains were also co-cultured with murine RAW 264.7 macrophages for screening the capacity to induce the anti-inflammatory cytokine interleukin (IL)-10. Hydrophobicity ranged from 7.4 and 95.9%. The strains Lactobacillus gasseri (70a and 70c) and Lactobacillus plantarum (73a and 73b) were the strains with a higher capacity to induce IL-10 production by macrophages. The technological application was evaluated by freezing dried in 10% lactose or 10% polydextrose. The survival was assessed after accelerated (37 °C, 4 weeks) or long-term (5 and 25 °C, 12 months) storage. Except for Lactobacillus gallinarum 94d, strains lost less than 1 Log10 order cfu/g after long-term (12 months) storage at 5 °C in lactose and polydextrose as protectants. A low correlation between survival to accelerated and long-term storage tests was observed. L. gasseri (70a and 70c) and L. plantarum (73a and 73b) deserve further studies as potential probiotics due to their capacity to induce IL-10 from murine macrophages and their hydrophobicity. In special, L. plantarum 73a was able to confer enhanced protection against Salmonella infection by promoting the immunity of the small intestine.

scholarly journals Diversity of siderophore-producing bacterial cultures from Carlsbad Caverns National Park caves, Carlsbad, New Mexico

2021 ◽  
Vol 83 (1) ◽  
pp. 29-43
Author(s):  
Tammi Duncan ◽  
Margaret Werner-Washburne ◽  
Diana Northup
Keyword(s):  
National Park ◽  
Ferric Iron ◽  
16S Rrna Gene Sequencing ◽  
Siderophore Production ◽  
Rrna Gene ◽  
Hydroxamate Siderophores ◽  
Rrna Gene Sequencing ◽  
And Function ◽  
Ferromanganese Deposits

Siderophores are microbially-produced ferric iron chelators. They are essential for microbial survival, but their presence and function for cave microorganisms have not been extensively studied. Siderophores are classified based on the common functional groups (catechols, hydroxamates, carboxylates, and mixed) that coordinate to ferric (Fe3+) iron. Cave environments are nutrient-limited and previous evidence suggests siderophore usage in carbonate caves. We hypothesize that siderophores are likely used as a mechanism in caves to obtain critical ferric iron. Cave bacteria were collected from long-term parent cultures (LT PC) or short-term parent cultures (ST PC) inoculated with ferromanganese deposits (FMD) and carbonate secondary minerals from Lechuguilla and Spider caves in Carlsbad Caverns National Park, NM. LT PC were incubated for 10−11 years to identify potential chemolithoheterotrophic cultures able to survive in nutrient-limited conditions. ST PC were incubated for 1−3 days to identify a broader diversity of cave isolates. A total of 170 LT and ST cultures, 18 pure and 152 mixed, were collected and used to classify siderophore production and type and to identify siderophore producers. Siderophore production was slow to develop (>10 days) in LT cultures with a greater number of weak siderophore producers in comparison to the ST cultures that produced siderophores in <10 days, with a majority of strong siderophore producers. Overall, 64% of the total cultures were siderophore producers, with the majority producing hydroxamate siderophores. Siderophore producers were classified into Proteobacteria (Alpha-, Beta-, or Gamma-), Actinobacteria, Bacteroidetes, and Firmicutes phyla using 16S rRNA gene sequencing. Our study supports our hypothesis that cave bacteria have the capability to produce siderophores in the subsurface to obtain critical ferric iron.

scholarly journals Long-Term Recovery of the Fecal Microbiome and Metabolome of Dogs with Steroid-Responsive Enteropathy

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2498
Author(s):  
Rachel Pilla ◽  
Blake C Guard ◽  
Amanda B Blake ◽  
Mark Ackermann ◽  
Craig Webb ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Elimination Diet ◽  
Rrna Gene ◽  
Fecal Microbiome ◽  
Rrna Gene Sequencing ◽  
One Year ◽  
Long Term Impact

The long-term impact of treatment of dogs with steroid-responsive enteropathy (SRE) on the fecal microbiome and metabolome has not been investigated. Therefore, this study aimed to evaluate the fecal microbiome and metabolome of dogs with SRE before, during, and following treatment with standard immunosuppressive therapy and an elimination diet. We retrospectively selected samples from 9 dogs with SRE enrolled in a previous clinical trial, which received treatment for 8 weeks, and had achieved remission as indicated by the post-treatment clinical scores. Long-term (1 year) samples were obtained from a subset (5/9) of dogs. Samples from 13 healthy dogs were included as controls (HC). We evaluated the microbiome using 16S rRNA sequencing and qPCR. To evaluate the recovery of gut function, we measured fecal metabolites using an untargeted approach. While improvement was observed for some bacterial taxa after 8 weeks of treatment, several bacterial taxa remained significantly different from HC. Seventy-five metabolites were altered in dogs with SRE, including increased fecal amino acids and vitamins, suggesting malabsorption as a component of SRE. One year after treatment, however, all bacterial species were evaluated by qPCR and 16S rRNA gene sequencing, and all but thirteen metabolites were no longer different from healthy controls.

Community structure of microbes in natural environments

2018 ◽  
Author(s):  
David L. Kirchman
Keyword(s):  
Community Structure ◽  
16S Rrna ◽  
Deep Ocean ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Natural Environments ◽  
Viral Lysis ◽  
Structure Information ◽  
Rrna Gene Sequencing ◽  
Biochemical Testing

Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.

scholarly journals Long-term recovery of the fecal microbiome and metabolome of dogs with steroid-responsive enteropathy

2021 ◽  
Author(s):  
Rachel Pilla ◽  
Blake Guard ◽  
Amanda B Blake ◽  
Mark Ackermann ◽  
Craig Webb ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Elimination Diet ◽  
Rrna Gene ◽  
Fecal Microbiome ◽  
Rrna Gene Sequencing ◽  
One Year ◽  
Long Term Impact

The long-term impact of treatment of dogs with steroid-responsive enteropathy (SRE) on the fe-cal microbiome and metabolome has not been investigated. Therefore, this study aimed to evaluate the fecal microbiome and metabolome of dogs with SRE before, during, and following treatment with standard immunosuppressive therapy and an elimination diet. We retrospec-tively selected samples from 9 dogs with SRE enrolled in a previous clinical trial, which received treatment for 8 weeks, and had achieved remission as indicated by the post-treatment clinical scores. Long-term (1 year) samples were obtained from a subset (5/9) of dogs. Samples from 13 healthy dogs were included as controls (HC). We evaluated the microbiome using 16S rRNA sequencing and qPCR. To evaluate the recovery of gut function, we measured fecal metabolites using an untargeted approach. While improvement was observed for some bacterial taxa after 8 weeks of treatment, several bacterial taxa remained significantly different from HC. Seven-ty-five metabolites were altered in dogs with SRE, including increased fecal amino acids and vitamins, suggesting malabsorption as a component of SRE. One year after treatment, however, all bacterial species evaluated by qPCR and 16S rRNA gene sequencing, and all but thirteen me-tabolites were no longer different from healthy controls.

scholarly journals Gut Microbiota and Metabolome Alterations Associated with Chinese Monks’ Practice

2022 ◽  
Author(s):  
Tingting Qiao ◽  
Ganghua Lu ◽  
Zhongwei Lv ◽  
Dan Li ◽  
Chengyou Jia ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Flora ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Rrna Gene Sequencing ◽  
And Function ◽  
Mental Events ◽  
The Relationship

Abstract BackgroundThe practices of monks mainly include long-term vegetarianism and meditation, which are likely to fundamentally influence the gut microbiota and fecal metabolites. We aim to study the relationship between the practices of Chinese monks and gut microbiotas and metabolites.MethodsTwenty-four monks and forty-eight omnivorous controls (never meditated) were included. The microbiotas of all samples were profiled by 16S rRNA gene sequencing, and the metabolomes were examined by nontargeted LC–MS metabolomics. Twenty-four monks were divided into the H group and the L group according to the median time of practice, and microbiota and metabolite analyses were carried out in the two groups.ResultsMicrobial communities and metabolites were decreased in monks. Bacteroidetes was increased in monks, while the Firmicutes, Actinobacteria, and Firmicutes/Bacteroidetes ratios were decreased. At the genus level, Faecalibacterium, Lachnospira, Roseburia, norank_f__Lachnospiraceae, etc. were higher in monks, while Blautia, Eubacterium__hallii_group, Bifidobacteria, etc. were lower (all p < 0.05). Most identical KEGG categories in both Tax4Fun and PICRUSt2 were related to metabolism (6/8, 75.0%). Most higher abundance genera were positively correlated with higher abundance metabolites in monks, indicating that intestinal flora significantly affects intestinal metabolic function. Lipids and lipid-like molecules were the major differential metabolites (VIP >2, p < 0.05) in the two groups. L-dopa plays an important role in many metabolic pathways in monks. Prevotella_9 was enriched in the L group, while norank_f__Lachnospiraceae was enriched in the H group. DG (16:0/18:0/0:0) was highly expressed in the H group and participated in sixteen KEGG functional pathways as well as many immune-related KEGG enrichment pathways.ConclusionThe monks' lifestyle practices of vegetarianism and meditation have the potential to modulate human metabolism and function by affecting the gut microbial composition and metabolites. The appropriate practice of monks makes the intestine younger and increases immunity, but long-term practice may cause adverse physical and mental events.

Alterations of gut microbiome in patients with type 2 diabetes mellitus who had undergone cholecystectomy

2021 ◽  
Vol 320 (1) ◽  
pp. E113-E121
Author(s):  
Bin Wei ◽  
Yakun Wang ◽  
Shoukui Xiang ◽  
Yan Jiang ◽  
Rong Chen ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Stool Samples ◽  
Rrna Gene Sequencing ◽  
And Function ◽  
New Onset

The gut microbiome of long-term T2DM patients who had undergone cholecystectomy and age- and/or sex-matched subjects of new-onset and long-term T2DM without cholecystectomy was assessed using 16S rRNA gene sequencing in stool samples. The findings suggest that, cholecystectomy could partially alleviate long-term diabetes-induced dysbiosis of gut microbiome composition and function.

scholarly journals The Chronic Effect of Transgenic Maize Line with mCry1Ac or maroACC Gene on Ileal Microbiota Using a Hen Model

2019 ◽  
Vol 7 (3) ◽  
pp. 92 ◽  
Author(s):  
Liang Chen ◽  
Ruqing Zhong ◽  
Lilan Zhang ◽  
Hongfu Zhang
Keyword(s):  
Laying Hens ◽  
16S Rrna Gene Sequencing ◽  
Transgenic Maize ◽  
Rrna Gene ◽  
Maize Line ◽  
Chronic Effect ◽  
Bt Maize ◽  
Rrna Gene Sequencing ◽  
Dietary Treatments

The experiment was to determine the chronic effects of two transgenic maize lines that contained the mCry1Ac gene from the Bacillus thuringiensis strain (BT) and the maroACC gene from Agrobacterium tumefaciens strain (CC), respectively, on ileal microbiota of laying hens. Seventy-two laying hens were randomly assigned to one of the three dietary treatments for 12 weeks, as follows: (1) nontransgenic near-isoline maize-based diet (CT diet), (2) BT maize-based diet (BT diet), and (3) CC maize-based diet (CC diet). Ileum histological examination did not indicate a chronic effect of two transgenic maize diets. Few differences were observed in any bacterial taxa among the treatments that used high-throughput 16S rRNA gene sequencing. The only differences that were observed for bacterial genera were that Bifidobacterium belong within the Bifidobacteriaceae family tended to be greater (p = 0.114) abundant in hens fed the transgenic maize-based diet than in hens fed the CT diet. Birds that consumed the CC maize diet tended to have less abundance (p = 0.135) of Enterobacteriaceae family in the ileum than those that consumed the CT maize diet. These results indicate the lack of adverse effects of the BT maize and the CC maize lines on the ileal microbiota of hens for long term and provide important data regarding biosafety assessment of the transgenic maize lines.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 &#181;mol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

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