The influence of diet on the microbiota of live-feed rotifers (Brachionus plicatilis) used in commercial fish larviculture

2020 ◽  
Vol 367 (2) ◽  
Author(s):  
Emre Turgay ◽  
Terje Marken Steinum ◽  
Kamil Mert Eryalçın ◽  
Remziye Eda Yardımcı ◽  
Süheyla Karataş
Keyword(s):  
Brachionus Plicatilis ◽  
Fish Larvae ◽  
Bacterial Species ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Fish Pathogens ◽  
Study Objective ◽  
Commercial Fish ◽  
Live Feed

ABSTRACT Live-feed is indispensable to commercial fish larviculture. However, high bacterial loads in rotifers could pose a biosecurity risk. While this may be true, live-feed associated bacteria could also be beneficial to fish larvae through improved feed utilization or pathogen inhibition following host microbiota modification. The study objective was to elucidate the largely unexplored microbiota of rotifers propagated on five different diets through bacterial community profiling by 16S rRNA gene amplicon sequencing. Investigated rotifer samples had a median observed alpha-diversity of 338 ± 87 bacterial species. Alpha- and Gamma-Proteobacteria dominated the rotifer microbiota followed by members of classes Flavobacteriia, Cytophagia, Mollicutes, Phycisphaerae and Bacteroidia. Different diets significantly altered the bacterial communities associated with rotifers according to PERMANOVA test results and beta dispersion calculations. A common core rotifer microbiome included 31 bacterial species present in relative abundances over 0.01%. We discuss the functional role of some microbiome members. Our data suggested the presence of several known fish pathogens in stock rotifers. However, we found no evidence for increased loads of these presumptive taxa in propagated live-feed rotifers during this field trial.

scholarly journals Changes in the Microbiome of Mariculture Feed Organisms after Treatment with a Potentially Probiotic Strain of Phaeobacter inhibens

2020 ◽  
Vol 86 (14) ◽  
Author(s):  
Karen K. Dittmann ◽  
Bastian Barker Rasmussen ◽  
Jette Melchiorsen ◽  
Eva C. Sonnenschein ◽  
Lone Gram ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Fish Larvae ◽  
Antagonistic Effect ◽  
Rrna Gene ◽  
Fish Pathogens ◽  
Content Type ◽  
Live Feed ◽  
The Impact ◽  
Phaeobacter Inhibens

ABSTRACT The Phaeobacter genus has been explored as probiotics in mariculture as a sustainable strategy for the prevention of bacterial infections. Its antagonistic effect against common fish pathogens is predominantly due to the production of the antibacterial compound tropodithietic acid (TDA), and TDA-producing strains have repeatedly been isolated from mariculture environments. Despite many in vitro trials targeting pathogens, little is known about its impact on host-associated microbiomes in mariculture. Hence, the purpose of this study was to investigate how the addition of a TDA-producing Phaeobacter inhibens strain affects the microbiomes of live feed organisms and fish larvae. We used 16S rRNA gene sequencing to characterize the bacterial diversity associated with live feed microalgae (Tetraselmis suecica), live feed copepod nauplii (Acartia tonsa), and turbot (Scophthalmus maximus) eggs/larvae. The microbial communities were unique to the three organisms investigated, and the addition of the probiotic bacterium had various effects on the diversity and richness of the microbiomes. The structure of the live feed microbiomes was significantly changed, while no effect was seen on the community structure associated with turbot larvae. The changes were seen primarily in particular taxa. The Rhodobacterales order was indigenous to all three microbiomes and decreased in relative abundance when P. inhibens was introduced in the copepod and turbot microbiomes, while it was unaffected in the microalgal microbiome. Altogether, the study demonstrates that the addition of P. inhibens in higher concentrations, as part of a probiotic regime, does not appear to cause major imbalances in the microbiome, but the effects were specific to closely related taxa. IMPORTANCE This work is an essential part of the risk assessment of the application of roseobacters as probiotics in mariculture. It provides insights into the impact of TDA-producing Phaeobacter inhibens on the commensal bacteria related to mariculture live feed and fish larvae. Also, the study provides a sequencing-based characterization of the microbiomes related to mariculture-relevant microalga, copepods, and turbot larvae.

scholarly journals Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert C. Kaplan ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
Martha L. Daviglus ◽  
...  
Keyword(s):  
Community Health ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Health Study ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Hispanic Community ◽  
The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

scholarly journals Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Zha ◽  
Fengping Liu ◽  
Zongxin Ling ◽  
Kevin Chang ◽  
Jiezuan Yang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Vital Role ◽  
Rrna Gene ◽  
Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

scholarly journals Gut microbiota composition is associated with narcolepsy type 1

2020 ◽  
Vol 7 (6) ◽  
pp. e896
Author(s):  
Alexandre Lecomte ◽  
Lucie Barateau ◽  
Pedro Pereira ◽  
Lars Paulin ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

scholarly journals Investigation of Age-Related Changes in the Skin Microbiota of Korean Women

2020 ◽  
Vol 8 (10) ◽  
pp. 1581
Author(s):  
Minseok Kim ◽  
Tansol Park ◽  
Jung Im Yun ◽  
Hye Won Lim ◽  
Na Rae Han ◽  
...  
Keyword(s):  
Age Groups ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Korean Women ◽  
Skin Microbiota ◽  
Microbial Distribution ◽  
Age Related ◽  
Age Related Changes

The microbiota of human skin is influenced by host and environmental factors. To determine if chronological age influences the composition of the skin microbiota on the forehead and hands, 73 Korean women were sorted into one of three age groups: (1) 10–29 years (n = 24), (2) 30–49 years (n = 21), and (3) 50–79 years (n = 28). From the 73 women, 146 skin samples (two skin sites per person) were collected. 16S rRNA gene amplicon sequencing was then conducted to analyze the skin microbiota. The overall microbial distribution varied on the forehead but was similar on the hands across the three age groups. In addition, the composition of the skin microbiota differed between the forehead and hands. Commensal microbiota, such as Streptococcus, Staphylococcus, Cutibacterium, and Corynebacterium, which contribute to maintaining skin health via dominant occupation, were affected by increasing age on forehead and hand skin. Alpha diversity indices increased significantly with age on forehead skin. This study indicates that older people may be more susceptible to pathogenic invasions due to an imbalanced skin microbiota resulting from age-related changes. The results of our study may help develop new strategies to rebalance skin microbiota shifted during aging.

scholarly journals Comparative Analysis of Fecal Microbiota Composition Between Rheumatoid Arthritis and Osteoarthritis Patients

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 748 ◽  
Author(s):  
Jin-Young Lee ◽  
Mohamed Mannaa ◽  
Yunkyung Kim ◽  
Jehun Kim ◽  
Geun-Tae Kim ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Stool Samples ◽  
Gut Microbiota Composition

The aim of this study was to investigate differences between the gut microbiota composition in patients with rheumatoid arthritis (RA) and those with osteoarthritis (OA). Stool samples from nine RA patients and nine OA patients were collected, and DNA was extracted. The gut microbiome was assessed using 16S rRNA gene amplicon sequencing. The structures and differences in the gut microbiome between RA and OA were analyzed. The analysis of diversity revealed no differences in the complexity of samples. The RA group had a lower Bacteroidetes: Firmicutes ratio than did the OA group. Lactobacilli and Prevotella, particularly Prevotella copri, were more abundant in the RA than in the OA group, although these differences were not statistically significant. The relative abundance of Bacteroides and Bifidobacterium was lower in the RA group. At the species level, the abundance of certain bacterial species was significantly lower in the RA group, such as Fusicatenibacter saccharivorans, Dialister invisus, Clostridium leptum, Ruthenibacterium lactatiformans, Anaerotruncus colihominis, Bacteroides faecichinchillae, Harryflintia acetispora, Bacteroides acidifaciens, and Christensenella minuta. The microbial properties of the gut differed between RA and OA patients, and the RA dysbiosis revealed results similar to those of other autoimmune diseases, suggesting that a specific gut microbiota pattern is related to autoimmunity.

scholarly journals Genome Sequence of the Psychrophilic Bacterium Tenacibaculum ovolyticum Strain da5A-8 Isolated from Deep Seawater

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Maki Teramoto ◽  
Zhenyu Zhai ◽  
Ayumi Komatsu ◽  
Keigo Shibayama ◽  
Masato Suzuki
Keyword(s):  
Genome Sequence ◽  
Gene Sequence ◽  
Virulence Genes ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Psychrophilic Bacterium ◽  
Fish Pathogen ◽  
Deep Seawater ◽  
Fish Pathogens ◽  
The 16S Rrna Gene

Some bacterial species of the genus Tenacibaculum , including Tenacibaculum ovolyticum , have been known as fish pathogens in the sea. So far, the only published genome sequence for this genus is for Tenacibaculum dicentrarchi , which could also be a fish pathogen. Strain da5A-8, showing 100% identity to the 16S rRNA gene sequence of T. ovolyticum DSM 18103 T , was isolated from seawater at a depth of 344 m in Kochi, Japan, and grew optimally at 10 to 20°C. The genome sequence of strain da5A-8 revealed the possible virulence genes commonly observed in the genus Tenacibaculum .

scholarly journals Compositional and functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

2018 ◽  
Author(s):  
Zongfu Hu ◽  
Xi CHEN ◽  
Jie CHANG ◽  
Jianhua YU ◽  
Qing TONG ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Amplicon Sequencing ◽  
Freshwater Snail ◽  
Gonadal Development ◽  
Growth Stages ◽  
Rrna Gene ◽  
16S Rrna Amplicon Sequencing ◽  
Radix Auricularia

Widely distributed across the world, the freshwater snail Radix auricularia plays an important role in freshwater systems. In this study, gut bacterial communities of R. auricularia were characterized using 16S rRNA amplicon sequencing, then intestinal bacteria were compared at different growth stages: adult snails (AS) (with complete gonadal development) and juvenile snails (JS) (with incomplete gonadal development). We obtained 251,072 high quality sequences which were clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria and Cyanobacteria, followed by Chloroflexi, Firmicutes, and Actinobacteria. Other bacterial species such as Tenericutes, Bacteroidetes, Fusobacteria and Verrucomicrobia were present to a lesser extent. 52 bacterial families and 55 genera were found in > 1% of each sample. A large number of species could not be successfully identified. 469 core OTUs were found to make up 39.38% of all OTUs and 88.38% of all sequences. Samples obtained from juvenile organisms possessed higher ratios of Ruminococcaceae, Subdoligranulum, and Faecalibacterium than adult species. Furthermore, 16S rRNA gene data was used to predict function, showing that genes related to metabolism and environmental information processing were rich in snail samples.

scholarly journals Exploring the bacterial community composition of soil from a tropical dry evergreen forest in Tamil Nadu, India

2021 ◽  
Author(s):  
Saptashwa Datta ◽  
Melvin S. Samuel ◽  
Ethiraj Selvarajan
Keyword(s):  
Bacterial Community ◽  
Tamil Nadu ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Evergreen Forest ◽  
Dry Evergreen Forest ◽  
Tropical Evergreen Forest ◽  
Tropical Dry Evergreen Forest

Abstract Metagenomics is a cutting edge omics technology that has been employed in various fields including novel product discovery, diagnostics, and pollutant monitoring. 16S metagenome amplicon sequencing is used for understanding the microbial diversity from various environments. Forest ecosystems have been known for the discovery of novel bacteria and also bacteria that produces novel compounds that are pharmaceutically and industrially relevant. In this study we try to show the bacterial community structure of the soil obtained from a tropical evergreen forest in India. We use 16s metagenomics sequencing and then follow it up with various analysis like alpha diversity analysis, to find out the dominant bacterial species found in these soils. Actinobacteria was found to be the most copmmonly found bacterial phylum followed by proteobacteria, firmicutes, chloroflexi, acidobacteria, verrucomicrobia, bacteroidetes, gemmatimonadetes, nitospirae and other unclassified organisms. Further studies can elucidate on the discovery of novel compounds from these bacteria.

scholarly journals Higher fiber complementary food alters Fecal microbiota composition and normalizes stool form in Malawian children: A randomized trial

2021 ◽  
Vol 21 (04) ◽  
pp. 17854-17875
Author(s):  
Edda Lungu ◽  
◽  
J Auger ◽  
A Piano ◽  
WJ Dahl ◽  
...  
Keyword(s):  
Dietary Intake ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Stool Frequency ◽  
Sub Saharan Africa ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Linear Discriminant ◽  
Stool Form

Dietary fiber favorably modulates gut microbiota and may be protective against diarrhea in sub-Saharan Africa where rates in infants and young children are high. Soybean hull is high in fiber and accessible in rural Africa; however, its use in complementary feeding has not been evaluated. The objective of this study was to determine the acceptability and feasibility of a soybean, soy hull fiber, and maize (SFM) blend food; the primary outcome was compliance to the feeding protocol. Secondary outcomes were stool form and frequency, fecal microbiota composition, growth and dietary intake. In a parallel, single-blind study, children 6-36 months of age from the Lilongwe district of Malawi were randomized to receive daily SFM (n=69) or maize only(n=10) porridge(phala) for 6 months. Anthropometrics were measured monthly, and compliance, stool frequency,and stool form, weekly. At baseline, 3-month,and 6-month (study end) time points, dietary intake (24-h recall) was assessed,and fecal samples were collected. Fecal DNA was analyzed by Real-Time polymerase chain reaction (PCR) for microbes of interest and 16S rRNA gene amplicon sequencing. Mothers accessed the acceptability and feasibility of the study foods at study end. Mothers reported excellent compliance to feeding the SFM porridge, rated it more acceptable than maize,and noted improved appetite, weight, and stool consistency of their children. Stool frequency at baseline (2±1 stools/d) was unchanged with intervention; however, there were significantly fewer diarrhea-type stools reported during study months 4-6 vs.1-3 for the SFM group, whereas no improvement was seen for the maize group. At study end, the fecal abundance ofAkkermansia muciniphila was enriched in children receiving the SFM, compared to maize (p<0.05), and a trend for increased Faecalibacterium prausnitzii (p=0.07) was seen. A comparison of fecal microbiota composition using linear discriminant analysis effect size (LEfSe)showed notable differences in numerous taxa in the SFM group compared to baseline, whereas the maize comparator exhibited fewer changes. Fiber intake was higher for the SFMgroup, compared to maize at 6 months (13.7±3.8 vs. 8.4±4.5 g/day, p<0.01). Weight-for-height and BMI-for-age Z-scores were significantly higher for the SFM group. In young Malawian children, feeding a blend of soybean, soy hulls and maize reduced diarrhea-type stools and increased the abundance of Akkermansia muciniphila, a bacterial species involved in maintaining intestinal health, and thus may provide a feasible means of improving wellness in children in resource-poor settings through the modulation of microbiota composition.

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