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 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.

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 Spatially-resolved correlative microscopy and microbial identification reveals dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment

2020 ◽  
Author(s):  
Jeffrey Marlow ◽  
Rachel Spietz ◽  
Keun-Young Kim ◽  
Mark Ellisman ◽  
Peter Girguis ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Community Members ◽  
Marsh Sediment ◽  
Anabolic Activity ◽  
Salt Marsh Sediment ◽  
Rrna Gene Sequencing ◽  
And Function

AbstractCoastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were embedded and analyzed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ∼60% in the top cm to 10-25% between 2-7 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase, and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.Statement of SignificanceMicroscale spatial relationships dictate critical aspects of a microbiome’s inner workings and emergent properties, such as evolutionary pathways, niche development, and community structure and function. However, many commonly used methods in microbial ecology neglect this parameter – obscuring important microbe-microbe and microbe-mineral interactions – and instead employ bulk-scale methodologies that are incapable of resolving these intricate relationships.This benchmark study presents a compelling new approach for exploring the anabolic activity of a complex microbial community by mapping the precise spatial configuration of anabolically active organisms within mineralogically heterogeneous sediment through in situ incubation, resin embedding, and correlative fluorescence and electron microscopy. In parallel, active organisms were identified through fluorescence-activated cell sorting and 16S rRNA gene sequencing, enabling a powerful interpretive framework connecting location, identity, activity, and putative biogeochemical roles of microbial community members.We deploy this novel approach in salt marsh sediment, revealing quantitative insights into the fundamental principles that govern the structure and function of sediment-hosted microbial communities. In particular, at different sediment horizons, we observed striking changes in the proportion of anabolically active cells, the identities of the most prominent active community members, and the nature of microbe-mineral affiliations. Improved approaches for understanding microscale ecosystems in a new light, such as those presented here, reveal environmental parameters that promote or constrain metabolic activity and clarify the impact that microbial communities have on our world.

scholarly journals Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions

2021 ◽  
Author(s):  
A. Shore ◽  
R. D. Day ◽  
J. A. Stewart ◽  
C.A. Burge
Keyword(s):  
Ocean Acidification ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Ph Gradient ◽  
Rrna Gene ◽  
Seawater Ph ◽  
Coral Health ◽  
And Function ◽  
The Impact

Ocean acidification (OA) threatens the growth and function of coral reef ecosystems. A key component to coral health is the microbiome, but little is known about the impact of OA on coral microbiomes. A submarine CO2 vent at Maug Island in the Northern Marianas Islands provides a natural pH gradient to investigate coral responses to long-term OA conditions. Three coral species (Pocillopora eydouxi, Porites lobata, and Porites rus) were sampled from three sites where mean seawater pH is 8.04, 7.98, and 7.94. We characterized coral bacterial communities (using 16S rRNA gene sequencing) and determined pH of the extracellular calcifying fluid (ECF) (using skeletal boron isotopes) across the seawater pH gradient. Bacterial communities of both Porites species stabilized (decreases in community dispersion) with decreased seawater pH, coupled with large increases in the abundance of Endozoicomonas, an endosymbiont. P. lobata experienced a significant decrease in ECF pH near the vent, whereas P. rus experienced a trending decrease in ECF pH near the vent. By contrast, Pocillopora exhibited bacterial community destabilization (increases in community dispersion), with significant decreases in Endozoicomonas abundance, while its ECF pH remained unchanged across the pH gradient. Our study shows that OA has multiple consequences on Endozoicomonas abundance and suggests that Endozoicomonas abundance may be an indicator of coral response to OA. We reveal an interesting dichotomy between two facets of coral physiology (regulation of bacterial communities and regulation of calcification), highlighting the importance of multidisciplinary approaches to understanding coral health and function in a changing ocean. IMPORTANCE Ocean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e. calcification) and disrupting associated bacterial communities. Coral-associated bacteria are important for host health, but it remains unclear how coral-associated bacterial communities will respond to future OA conditions. We document changes in coral-associated bacterial communities and changes to calcification physiology with long-term exposure to decreases in seawater pH that are environmentally relevant under mid-range IPCC emission scenarios (0.1 pH units). We also find species-specific responses that may reflect different responses to long-term OA. In Pocillopora, calcification physiology was highly regulated despite changing seawater conditions. In Porites spp., changes in bacterial communities do not reflect a breakdown of coral-bacterial symbiosis. Insights into calcification and host-microbe interactions are critical to predicting the health and function of different coral taxa to future OA conditions.

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.

scholarly journals Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age

2021 ◽  
Author(s):  
Yumiko Okamoto ◽  
Natsumi Ichinohe ◽  
Cheolwoon Woo ◽  
Sung-Yong Han ◽  
Hyeong-Hoo Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Lutra Lutra ◽  
Rrna Gene ◽  
Baseline Information ◽  
The Difference ◽  
Rrna Gene Sequencing ◽  
And Function

AbstractUnderstanding the gut microbiota characteristics of endangered species such as the Eurasian otter (Lutra lutra), especially in their early stages of life, could be essential for improving their management and ex situ conservation strategies. Here, we analyzed the gut microbiota diversity, composition, and function of captive Eurasian otters at different ages using high-throughput 16S rRNA gene sequencing. We found that: (1) Clostridiaceae was abundant in all age stages; (2) Lactococcus in cubs is thought to predominate for digesting milk; (3) bacteria associated with amino acid metabolism increase with age, while bacteria associated with carbohydrate metabolism decrease with age, which is likely due to decrease in dietary carbohydrate content (e.g., milk) and increase in dietary protein contents (e.g., fishes) with age; and (4) fish-related bacteria were detected in feces of healthy adults and juveniles. Overall, the gut microbiota of captive Eurasian otters was taxonomically and functionally different by age, which is thought to be attributed to the difference in the diet in their life stages. This study provided baseline information regarding the gut microbiota of Eurasian otters for the first time and contributes to improvement in their management in captivity.

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.

scholarly journals Altered Gut Microbiota Associated with Hemorrhage in Chronic Radiation Proctitis

2020 ◽  
Author(s):  
Liangzhe Liu ◽  
Bingcheng Chen ◽  
Chaoyun Chen ◽  
Chen Ding ◽  
Nana Xiao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Radiation Proctitis ◽  
Rrna Gene ◽  
Chronic Radiation Proctitis ◽  
Chronic Radiation ◽  
Pelvic Cancer ◽  
Metagenomic Study ◽  
Rrna Gene Sequencing ◽  
And Function

Abstract Background: Pelvic cancer radiotherapy may cause chronic radiation proctitis (CRP) that adversely affects patient’s quality of life. Here, we aimed to characterize the gut microbiota of CRP patients and reveal the association of dysbiosis and hematochezia. A comparative metagenomic study of CRP with and without hematochezia was conducted by 16S rRNA gene sequencing. Results: Different patterns of dysbiosis were observed in CRP patients with and without hematochezia. The abundance of Bacteroides was higher in CRP patients without hematochezia. The Verrucomicrobia phylum was enriched while the compositions of the Enterobacteriales family and the Porphyromonadaceae genus were relatively lower in the microbiota of CRP patients with hematochezia. PICRUSt analysis suggested that the expression of Fe-S protein, Glutathione peroxidase and Glutaredoxin-related protein were increased, indicating an exacerbated inflammation state in hematochezia patients. Conclusions: This study provides new insight to the altered composition and function of gut microbiota in patients with hematochezia, implying the link of CRP symptom and bacterial ecosystem on rectal epithelial layer.

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