scholarly journals Microbiome structure of ecologically important bioeroding sponges (family Clionaidae): The role of host phylogeny and environmental plasticity

2020 ◽  
Author(s):  
Oriol Sacristán-Soriano ◽  
Xavier Turon ◽  
Malcolm Hill
Keyword(s):  
Coral Reef ◽  
Florida Keys ◽  
16S Rrna Gene Sequencing ◽  
Future Research ◽  
Rrna Gene ◽  
Potential Threat ◽  
Bacterial Phyla ◽  
Rare Biosphere ◽  
Excavating Sponges ◽  
Species Specific

AbstractThe potential of increased bioerosion by excavating sponges in future environmental scenarios represents a potential threat to coral reef structure and function. If we are to predict changes to coral reef habitats, it is important to understand the biology of these sponges. Little is known about prokaryotic associations in excavating sponges despite the fact that evidence indicates they contribute to the sponge growth through their heterotrophic metabolism and may even act as microborers. Here, we provide the first detailed description of the microbial community of multiple bioeroding sponges from the Clionaidae family (Cliona varians, C. tumula, C. delitrix, Spheciospongia vesparium, Cervicornia cuspidifera) collected in inshore and offshore coral reefs in the Florida Keys. A total of 6,811 prokaryote OTUs identified using 16S rRNA gene sequencing was detected in the samples studied, including ambient water, belonging to 39 bacterial phyla and 3 archaeal phyla. The microbiomes of species harboring Symbiodinium (Cliona varians, C. tumula, Cervicornia cuspidifera) and the azooxanthellate S. vesparium were dominated by Alphaproteobacteria that represented from 83 to 96% of total sequences. These clionaid sponges presented species-specific core microbiomes, with 4 OTUs being shared by all sponge samples, albeit with species-specific enrichments. The microbiomes of C. varians and S. vesparium were stable but showed certain plasticity between offshore and inshore reefs. The distantly related Cliona delitrix does not harbor Symbiodinium, and had a microbiome dominated by Gammaproteobacteria, which represented 82% of all sequences. Most of the sponge-exclusive OTUs are found in low abundance and belong to the “rare biosphere” category, highlighting the potential importance of these microbes in the ecology of the holobiont. Sponge microbiomes may enhance functional redundancy for the sponge holobiont and allow it to respond to shifting environments over much short time scales than evolutionary change would permit. This work establishes the basis for future research to explore how microbial shifts in bioeroding sponges contribute to bioerosion in the face of a changing environment.

scholarly journals Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
O. H. Oduaran ◽  
F. B. Tamburini ◽  
V. Sahibdeen ◽  
R. Brewster ◽  
F. X. Gómez-Olivé ◽  
...  
Keyword(s):  
South African ◽  
Gut Microbiome ◽  
Geographical Location ◽  
16S Rrna Gene Sequencing ◽  
Overweight And Obesity ◽  
Future Research ◽  
Epidemiological Transition ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Targeted Interventions

Abstract Background Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. Results We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = − 4.7). Conclusions Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.

scholarly journals Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

2008 ◽  
Vol 74 (17) ◽  
pp. 5422-5428 ◽  
Author(s):  
Mostafa S. Elshahed ◽  
Noha H. Youssef ◽  
Anne M. Spain ◽  
Cody Sheik ◽  
Fares Z. Najar ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Tall Grass ◽  
Data Set ◽  
Bacterial Phyla ◽  
Rare Biosphere ◽  
Soil Bacterial ◽  
Close Relatives ◽  
Taxonomic Groups

ABSTRACT Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

scholarly journals Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

2020 ◽  
Author(s):  
Connie A. Rojas ◽  
Santiago A. Ramírez-Barahona ◽  
Kay E. Holekamp ◽  
Kevin. R. Theis
Keyword(s):  
Gut Microbiota ◽  
Host Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phylogenetic Relatedness ◽  
Host Phylogeny ◽  
Host Ecology ◽  
Herbivore Species ◽  
Rrna Gene Sequencing ◽  
Species Specific

AbstractThe gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host dietary guild in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders. We found that gut microbiotas were highly species-specific, and that host family accounted for more variation in the gut microbiota (35%) than did host dietary guild (14%). Overall, similarity among gut microbiotas increased with host phylogenetic relatedness (r=0.73), yet this relationship was not apparent among seven closely related Bovid host species (r=0.21 NS). In bovids, host dietary guild explained twice as much variation in the gut microbiota as did host species. Lastly, we found that the gut microbiotas of herbivores residing in southwest Kenya closely resemble those of conspecifics from central Kenya, suggesting that regardless of variability in host local habitat, hosts consistently provide microbes with similar niches for colonization. Overall, our findings suggest that host phylogeny may structure the gut microbiota at broad taxonomic scales, but that host ecology may be more influential in shaping the gut microbiotas of closely related host species.

scholarly journals Dynamic changes in intestinal microbiota in young forest musk deer during weaning

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8923
Author(s):  
Yimeng Li ◽  
Minghui Shi ◽  
Tianxiang Zhang ◽  
Xin Hu ◽  
Baofeng Zhang ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Relative Abundance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Musk Deer ◽  
Dynamic Changes ◽  
Linear Discriminant ◽  
Bacterial Phyla ◽  
Young Forest ◽  
Rrna Gene Sequencing

Weaning is an important event for all mammals, including young forest musk deer. However, weaning stress may cause intestinal microbiota-related disorders. Therefore, high-throughput 16S rRNA gene sequencing was applied to study the dynamic changes in intestinal microbiota during pre-weaning (10 days before weaning) and post-weaning (10 days after weaning) in 15 young forest musk deer. We saw that intestinal microbiota diversity in the post-weaning period was significantly higher than that in the pre-weaning period. The most dominant bacterial phyla were similar in the two groups (Firmicutes, Bacteroidetes and Verrucomicrobia). Meanwhile, we applied Linear discriminant analysis effect size (LefSe) to identify the most differentially microbial taxa in the pre-weaning and post-weaning groups. In the post-weaning forest musk deer, the relative abundance of Actinobacteria, Spirochaetes, Ruminococcaceae_UCG-005, Treponema and Prevotella was higher than in the pre-weaning group. However, higher relative abundance of the phyla Bacteroidetes was found in the pre-weaning group compared with that in the post-weaning group. In summary, this research provides a theoretical foundation for the dynamics of young forest musk deer intestinal microbiota during the weaning transition, which may benefit in understanding the growth and health of forest musk deer.

scholarly journals Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves

2020 ◽  
Vol 8 (7) ◽  
pp. 981 ◽  
Author(s):  
Yaoyue Wang ◽  
Qingmiao Shen ◽  
Shu Zhong ◽  
Yulin Chen ◽  
Yuxin Yang
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Rumen Fermentation ◽  
Control Group ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Mulberry Leaves ◽  
Serum Biochemical ◽  
Cashmere Goats ◽  
Rrna Gene Sequencing ◽  
Biochemical Indices

Mulberry leaves, which have high nutritional value, have not been fully utilized. Few research systems have indicated whether mulberry leaves can replace traditional feed ingredients in goats. In this study, we investigated the effects of feeding white cashmere goats ensiled (Group E) or sun-dried mulberry leaves (Group S) on changes in ruminal microbial communities, rumen fermentation parameters and serum biochemical indices. The control group (Group C) received a typical total mixed ration (TMR). 16S rRNA gene sequencing revealed 209 genera belonging to 19 bacterial phyla dominated by Firmicutes and Bacteroidetes. Only the relative abundances of Erysipelotrichaceae_UCG-009 were significantly different among the three groups (p < 0.05). Physiological and biochemical findings revealed that only the serum leptin concentrations were significantly decreased when mulberry leaves were added to the diets (p < 0.05). Correlation analysis revealed that Ruminococcus_2 were significantly positively correlated with the butyrate concentration. These findings suggested that supplementation with mulberry leaves only induced minor changes in the abovementioned indicators, implying that the rumen fermentation status was still stable after adding mulberry leaves to the diets.

scholarly journals The gastric microbiota in patients with Crohn’s disease; a preliminary study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jerzy Ostrowski ◽  
Maria Kulecka ◽  
Iwona Zawada ◽  
Natalia Żeber-Lubecka ◽  
Agnieszka Paziewska ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Pairwise Comparison ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Abundant Otus ◽  
Significant Difference ◽  
H Pylori ◽  
Gastric Microbiota

AbstractThe gastric microbiota in Crohn’s disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.

scholarly journals Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16s rRNA gene sequencing and LC/MS-based metabolomics

2020 ◽  
Author(s):  
Yan Hua ◽  
Heqin cao ◽  
Jiao Wang ◽  
Fengping He ◽  
Guangshun Jiang
Keyword(s):  
Gut Microbiota ◽  
North China ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Bacterial Phyla ◽  
Metabolic Phenotypes ◽  
Rrna Gene Sequencing ◽  
First Time

Abstract Background: Gut microbes significantly contribute to nutrient digestion and absorption, intestinal health and immunity, and are essential for the survival and environmental adaptation of wild animals. However, there are few studies on the gut microbiota of captive and wild North China leopard (Panthera pardus japonensis). Results: A total of 10 mainly bacterial phyla were identified in the fecal microbiota of North China leopard, Lachnoclostridium (p = 0.003), Peptoclostridium (p = 0.005), Bacteroides (p =0.008), Fusobacterium (p = 0.017) and Collinsella (p = 0.019) were significantly higher than those of wild North China leopard. Distinct differences in the fecal metabolic phenotypes of captive and wild North China leopard were found, such as content of l-methionine, n-acetyl-l-tyrosine, pentadecanoic acid and oleic acid. Differentially abundant gut microbes were associated with fecal metabolites, especially the bacteria in Firmicutes and Bacteroidetes, involved in the metabolism of N-acetyl-L-alanine and D-quinovose.Conclusion: This study reports for the first time the differences in gut microbiota abundance between captive and wild North China leopard, as well as significant differences in fecal metabolic phenotypes between two groups.

scholarly journals Ecological relevance of abundant and rare taxa in a high-diverse elastic hypersaline microbial mat, using a small-scale sampling

2021 ◽  
Author(s):  
Laura Espinosa-Asuar ◽  
Camila Monroy ◽  
David Madrigal-Trejo ◽  
Marisol Navarro ◽  
Jazmin Sanchez ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Chihuahuan Desert ◽  
Biotic Interactions ◽  
16S Rrna Gene Sequencing ◽  
Biological Properties ◽  
Microbial Mat ◽  
Small Scale ◽  
Rrna Gene ◽  
Rare Taxa ◽  
Rare Biosphere

We evaluated the microbial diversity and metabolomic signatures of a hypersaline elastic microbial mat from Cuatro Cienegas Basin (CCB) in the Chihuahuan Desert of Coahuila, Mexico. We collected ten samples within a small scale (1.5-meters transect) and found a high microbial diversity through NGS-based ITS and 16S rRNA gene sequencing. A very low number of taxa were abundant and shared between all sites, whereas the rare biosphere was more phylogenetically diverse (FPD index) and phylogenetically disperse (PSC index) than the abundant taxa for both analyzed libraries. In regard to potential biotic interactions (Pearson analysis), there were more positive correlations than negative. We also found a distinctive metabolomic signature for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties. Together, these results reveal cohesive, diverse and fluctuating microbial communities, where abundant and rare taxa appear to have different ecological roles.

scholarly journals Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria

2021 ◽  
Author(s):  
Michelle M McKnight ◽  
Josh D Neufeld
Keyword(s):  
Microbial Communities ◽  
Ammonia Oxidation ◽  
16S Rrna Gene Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ammonia Oxidizer ◽  
Future Research ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.

scholarly journals The Devils Hole pupfish gut microbiome and its potential role in paradoxical anaerobism

2019 ◽  
Author(s):  
Shrikant S Bhute ◽  
Brisa Escobedo ◽  
Mina Haider ◽  
Yididya Mekonen ◽  
Dafhner Ferrer ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Critical Role ◽  
16S Rrna Gene Sequencing ◽  
Wide Distribution ◽  
Control Group ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Bacterial Phyla ◽  
Devils Hole

Abstract Background The Devils Hole Pupfish ( Cyprinodon diabolis ) frequently enters paradoxical anaerobism in response to endogenously produced or exogenously supplied ethanol in a dose-dependent manner. To decipher the role of the gut microbiota in ethanol-associated paradoxical anaerobism, gut microbial communities were depleted using a cocktail of antibiotics and profiled using 16S rRNA gene sequencing. Results Compared to the control group (n=12), microbiota-depleted fish (n=11) spent more time in paradoxical anaerobism. Our analysis indicated that the bacterial phyla Proteobacteria , Fusobacteria , Bacteroidetes , Firmicutes , Actinobacteria , Patescibacteria , and Dependentiae dominated the pupfish gut, which is consistent with other fish gut microbiota. Although the gut microbial communities with and without antibiotic treatment were similarly diverse, they were distinct and the greatest contribution to the dissimilarity (27.38%) was the common fish commensal Cetobacterium . We speculate that Cetobacterium , a primary fermenter, also consumes ethanol through secondary fermentation via an alcohol dehydrogenase and therefore regulates the transition from paradoxical anaerobism to aerobic respiration in fish. Conclusions This study reports the first characterization of gut microbial communities of critically endangered pupfish and suggests the microbiome may play a critical role in regulating metabolic strategies that are critical for survival in extremes of temperature and oxygen concentration. Given the wide distribution and abundance of Cetobacterium in warm-water fishes, this process may be of broad importance, and suggests that the microbiome be carefully considered for both conservation and aquaculture.

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