Probiotic Yeasts and Vibrio anguillarum Infection Modify the Microbiome of Zebrafish Larvae

The host microbiome plays an essential role in health and disease. Microbiome modification by pathogens or probiotics has been poorly explored especially in the case of probiotic yeasts. Next-generation sequencing currently provides the best tools for their characterization. Debaryomyces hansenii 97 (D. hansenii 97) and Yarrowia lipolytica 242 (Y. lipolytica 242) are yeasts that protect wildtype zebrafish (Danio rerio) larvae against a Vibrio anguillarum (V. anguillarum) infection, increasing their survival rate. We investigate the effect of these microorganisms on the microbiome and neutrophil response (inflammation) in zebrafish larvae line Tg(Bacmpx:GFP)i114. We postulated that preinoculation of larvae with yeasts would attenuate the intestinal neutrophil response and prevent modification of the larval microbiome induced by the pathogen. Microbiome study was performed by sequencing the V3-V4 region of the 16S rRNA gene and prediction of metabolic pathways by Piphillin in conventionally raised larvae. Survival and the neutrophil response were both evaluated in conventional and germ-free conditions. V. anguillarum infection resulted in higher neutrophil number in the intestinal area compared to non-infected larvae in both conditions. In germ-free conditions, infected larvae pre-inoculated with yeasts showed fewer neutrophil numbers than infected larvae. In both conditions, only D. hansenii 97 increased the survival of infected larvae. Beta diversity of the microbiota was modified by V. anguillarum and both yeasts, compared to non-inoculated larvae. At 3 days post-infection, V. anguillarum modified the relative abundance of 10 genera, and pre-inoculation with D. hansenii 97 and Y. lipolytica 242 prevented the modification of 5 and 6 of these genera, respectively. Both yeasts prevent the increase of Ensifer and Vogesella identified as negative predictors for larval survival (accounting for 40 and 27 of the variance, respectively). In addition, yeast pre-inoculation prevents changes in some metabolic pathways altered by V. anguillarum’s infection. These results suggest that both yeasts and V. anguillarum can shape the larval microbiota configuration in the early developmental stage of D. rerio. Moreover, modulation of key taxa or metabolic pathways of the larval microbiome by yeasts can be associated with the survival of infected larvae. This study contributes to the understanding of yeast–pathogen–microbiome interactions, although further studies are needed to elucidate the mechanisms involved.

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Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries

Nature Communications ◽

10.1038/s41467-021-22409-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Eric J. Raes ◽

Kristen Karsh ◽

Swan L. S. Sow ◽

Martin Ostrowski ◽

Mark V. Brown ◽

...

Keyword(s):

16S Rrna ◽

Metabolic Pathways ◽

Low Cost ◽

Marker Gene ◽

South Pacific ◽

Rrna Gene ◽

South Pacific Ocean ◽

Bacterial Marker ◽

Gene 16S Rrna ◽

Gene Data

AbstractGlobal oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.

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The Role of Cell Metabolism in Innate Immune Memory

Journal of Innate Immunity ◽

10.1159/000512280 ◽

2020 ◽

pp. 1-9

Author(s):

Anaisa Valido Ferreira ◽

Jorge Domiguéz-Andrés ◽

Mihai Gheorghe Netea

Keyword(s):

Metabolic Pathways ◽

Tricarboxylic Acid Cycle ◽

Cell Metabolism ◽

Innate Immune ◽

Immune Memory ◽

Functional Changes ◽

Trained Immunity ◽

Health And Disease

Immunological memory is classically attributed to adaptive immune responses, but recent studies have shown that challenged innate immune cells can display long-term functional changes that increase nonspecific responsiveness to subsequent infections. This phenomenon, coined <i>trained immunity</i> or <i>innate immune memory</i>, is based on the epigenetic reprogramming and the rewiring of intracellular metabolic pathways. Here, we review the different metabolic pathways that are modulated in trained immunity. Glycolysis, oxidative phosphorylation, the tricarboxylic acid cycle, amino acid, and lipid metabolism are interplaying pathways that are crucial for the establishment of innate immune memory. Unraveling this metabolic wiring allows for a better understanding of innate immune contribution to health and disease. These insights may open avenues for the development of future therapies that aim to harness or dampen the power of the innate immune response.

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Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

BioMed Research International ◽

10.1155/2014/480170 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Sonia Ciccazzo ◽

Alfonso Esposito ◽

Eleonora Rolli ◽

Stefan Zerbe ◽

Daniele Daffonchio ◽

...

Keyword(s):

High Altitude ◽

Developmental Stage ◽

Bacterial Communities ◽

Developmental Stages ◽

Gene Diversity ◽

Intergenic Spacer ◽

Intermediate Stage ◽

Plant Colonization ◽

Early Developmental Stage ◽

Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

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Diversity and Morphology of Members of the Phylum “Synergistetes” in Periodontal Health and Disease

Applied and Environmental Microbiology ◽

10.1128/aem.02763-08 ◽

2009 ◽

Vol 75 (11) ◽

pp. 3777-3786 ◽

Cited By ~ 57

Author(s):

S. R. Vartoukian ◽

R. M. Palmer ◽

W. G. Wade

Keyword(s):

Oral Health ◽

Oral Cavity ◽

Positive Sample ◽

Rrna Gene ◽

Fish Analysis ◽

Subgingival Plaque ◽

Pcr Cloning ◽

Human Oral Cavity ◽

Health And Disease

ABSTRACT Members of the phylum “Synergistetes” have frequently been detected in the human oral cavity at sites of dental disease, but they have rarely been detected in studies of oral health. Only two oral “Synergistetes” taxa are cultivable. The aims of this study were to investigate the diversity of “Synergistetes” in the oral cavity, to establish whether “Synergistetes” taxa are more strongly associated with periodontitis than with oral health, and to visualize unculturable “Synergistetes” in situ. Sixty samples (saliva, dental plaque, and mucosal swabs) were collected from five subjects with periodontitis and five periodontally healthy controls. Using phylum-specific 16S rRNA gene primers, “Synergistetes” were identified by PCR, cloning, and sequencing of 48 clones per PCR-positive sample. Subgingival plaque samples were labeled with probes targeting rRNA of unculturable oral “Synergistetes” using fluorescent in situ hybridization (FISH). Analysis of 1,664 clones revealed 12 “Synergistetes” operational taxonomic units (OTUs) at the 99% sequence identity level, 5 of which were novel. “Synergistetes” OTU 4.2 was found in significantly more subjects with periodontitis than controls (P = 0.048) and was more abundant in subgingival plaque at diseased sites than at healthy sites in subjects with periodontitis (P = 0.019) or controls (P = 0.019). FISH analysis revealed that unculturable oral “Synergistetes” cells were large curved bacilli. The human oral cavity harbors a diverse population of “Synergistetes.” “Synergistetes” OTU 4.2 is associated with periodontitis and may have a pathogenic role.

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OTUs clustering should be avoided for defining oral microbiome

10.1101/2021.08.09.455616 ◽

2021 ◽

Author(s):

Alba Regueira-Iglesias ◽

Lara Vazquez-Gonzalez ◽

Carlos Balsa-Castro ◽

Triana Blanco-Pintos ◽

Victor Manuel Arce ◽

...

Keyword(s):

Microbial Diversity ◽

Operational Taxonomic Unit ◽

Oral Bacteria ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

High Coverage ◽

Archaeal Species ◽

Health And Disease ◽

Similarity Relationships

This in silico investigation aimed to: 1) evaluate a set of primer pairs with high coverage, including those most commonly used in the literature, to find the different oral species with 16S rRNA gene amplicon similarity/identity (ASI) values ≥97%; and 2) identify oral species that may be erroneously clustered in the same operational taxonomic unit (OTU) and ascertain whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain amplicon sequence variants (ASVs) from the complete genomes of 186 bacterial and 135 archaeal species. For each primer, ASVs without mismatches were aligned using BLASTN and their similarity values were obtained. Finally, we selected ASVs from different species with an ASI value ≥97% that were covered 100% by the query sequences. For each primer, the percentage of species-level coverage with no ASI≥97% (SC-NASI≥97%) was calculated. Based on the SC-NASI≥97% values, the best primer pairs were OP_F053-KP_R020 for bacteria (65.05%), KP_F018-KP_R002 for archaea (51.11%), and OP_F114-KP_R031 for bacteria and archaea together (52.02%). Eighty percent of the oral-bacteria and oral-archaea species shared an ASI≥97% with at least one other taxa, including Campylobacter, Rothia, Streptococcus, and Tannerella, which played conflicting roles in the oral microbiota. Moreover, around a quarter and a third of these two-by-two similarity relationships were between species from different bacteria and archaea genera, respectively. Furthermore, even taxa from distinct families, orders, and classes could be grouped in the same cluster. Consequently, irrespective of the primer pair used, OTUs constructed with a 97% similarity provide an inaccurate description of oral-bacterial and oral-archaeal species, greatly affecting microbial diversity parameters. As a result, clustering by OTUs impacts the credibility of the associations between some oral species and certain health and disease conditions. This limits significantly the comparability of the microbial diversity findings reported in oral microbiome literature.

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Commensal and Opportunistic Bacteria Present in the Microbiota in Atlantic Cod (Gadus morhua) Larvae Differentially Alter the Hosts’ Innate Immune Responses

Microorganisms ◽

10.3390/microorganisms10010024 ◽

2021 ◽

Vol 10 (1) ◽

pp. 24

Author(s):

Ragnhild Inderberg Vestrum ◽

Torunn Forberg ◽

Birgit Luef ◽

Ingrid Bakke ◽

Per Winge ◽

...

Keyword(s):

Immune System ◽

Immune Responses ◽

Atlantic Cod ◽

Innate Immune ◽

Rrna Gene ◽

Innate Immune Responses ◽

Transcriptional Responses ◽

Gut Morphology ◽

Germ Free ◽

Opportunistic Bacteria

The roles of host-associated bacteria have gained attention lately, and we now recognise that the microbiota is essential in processes such as digestion, development of the immune system and gut function. In this study, Atlantic cod larvae were reared under germ-free, gnotobiotic and conventional conditions. Water and fish microbiota were characterised by 16S rRNA gene analyses. The cod larvae’s transcriptional responses to the different microbial conditions were analysed by a custom Agilent 44 k oligo microarray. Gut development was assessed by transmission electron microscopy (TEM). Water and fish microbiota differed significantly in the conventional treatment and were dominated by different fast-growing bacteria. Our study indicates that components of the innate immune system of cod larvae are downregulated by the presence of non-pathogenic bacteria, and thus may be turned on by default in the early larval stages. We see indications of decreased nutrient uptake in the absence of bacteria. The bacteria also influence the gut morphology, reflected in shorter microvilli with higher density in the conventional larvae than in the germ-free larvae. The fact that the microbiota alters innate immune responses and gut morphology demonstrates its important role in marine larval development.

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Consequences of Paternal Nutrition on Offspring Health and Disease

Nutrients ◽

10.3390/nu13082818 ◽

2021 ◽

Vol 13 (8) ◽

pp. 2818

Author(s):

Pauline Dimofski ◽

David Meyre ◽

Natacha Dreumont ◽

Brigitte Leininger-Muller

Keyword(s):

Metabolic Pathways ◽

Maternal Diet ◽

Disease Onset ◽

Adult Life ◽

Intermittent Fasting ◽

Low Protein ◽

Periconceptional Period ◽

Health And Disease ◽

Offspring Health ◽

The Impact

It is well established that the maternal diet during the periconceptional period affects the progeny’s health. A growing body of evidence suggests that the paternal diet also influences disease onset in offspring. For many years, sperm was considered only to contribute half of the progeny’s genome. It now appears that it also plays a crucial role in health and disease in offspring’s adult life. The nutritional status and environmental exposure of fathers during their childhood and/or the periconceptional period have significant transgenerational consequences. This review aims to describe the effects of various human and rodent paternal feeding patterns on progeny’s metabolism and health, including fasting or intermittent fasting, low-protein and folic acid deficient food, and overnutrition in high-fat and high-sugar diets. The impact on pregnancy outcome, metabolic pathways, and chronic disease onset will be described. The biological and epigenetic mechanisms underlying the transmission from fathers to their progeny will be discussed. All these data provide evidence of the impact of paternal nutrition on progeny health which could lead to preventive diet recommendations for future fathers.

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Toxicity of chlordane at early developmental stage of zebrafish

10.1101/119248 ◽

2017 ◽

Cited By ~ 1

Author(s):

Jingxuan Xiong

Keyword(s):

Early Stage ◽

Real Life ◽

Potential Effect ◽

Early Developmental Stage ◽

Dependent Manner ◽

Lower Survival Rate ◽

Zebrafish Larvae ◽

Hatching Time ◽

Early Developmental ◽

Dose Dependent

AbstractChlordane is highly toxic organochlorine pesticides that have been widely used throughout the world for decades and posing adverse effects on the environment. Contents detected in tissue and blood samples have resulted in a raising concern for their potential effects on wildlife and humans. In this study, we investigate the potential effect of chlordane on the development of zebrafish embryos. Zebrafish larvae were treated with different concentrations (0, 25, 50, 100, 200 ng/L) of chlordane from 12 hours postfertilization (hpf). Different early stage parameters were observed at 1, 2, 3 and 4 day post-fertilization (dpf). Chlordane-exposed zebrafish larvae appeared significant lower survival rate, developmental and hatching time delay and decreased embryo productivity. The heartbeat rate and blood flow were decreased in a dose dependent manner. These results suggested that exposure to real life of chlordane led to direct morphological and phenotypic changes and effects systems related to development and reproduction even in short-term manner.

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Yeasts Associated with Various Amazonian Native Fruits

Polish Journal of Microbiology ◽

10.33073/pjm-2020-027 ◽

2020 ◽

Vol 69 (3) ◽

pp. 251-261

Author(s):

CARLOS VEGAS ◽

AMPARO I. ZAVALETA ◽

PAMELA E. CANALES ◽

BRAULIO ESTEVE-ZARZOSO

Keyword(s):

Fragment Length Polymorphism ◽

Lipolytic Activity ◽

Debaryomyces Hansenii ◽

Its Region ◽

Rrna Gene ◽

Yeast Strains ◽

Citrus Medica ◽

Amazonian Rainforest ◽

Phenotypic Methods ◽

26S Rrna

Yeasts, commonly present on the surface of fruits, are of industrial interest for the production of enzymes, flavorings, and bioactive compounds, and have many other scientific uses. The Amazonian rainforest may be a good source of new species or strains of yeasts, but their presence on Amazonian fruits is unknown. The aim of this study was to identify and characterize yeasts isolated from Amazonian native fruits using molecular and phenotypic methods. In total, 81 yeast isolates were obtained from 10 fruits species. Rep-PCR showed 29 strain profiles. Using a combination of restriction-fragment length polymorphism (RFLP) of the 5.8S-ITS region and D1/D2 sequencing of the 26S rRNA gene, 16 species were identified belonging to genera Candida, Debaryomyces, Hanseniaspora, Kodamaea, Martiniozyma, and Meyerozyma. The most dominant species were Candida tropicalis, Debaryomyces hansenii, Hanseniaspora opuntiae, and Hanseniaspora thailandica. H. opuntiae and H. thailandica showed the highest number of the strain profiles. Phenotypic profiles were variable between species, and even among strains. Screening for hydrolases showed lipolytic activity in only one isolate, while proteolytic, cellulolytic and amylolytic capabilities were not detected. Yeast presence among fruits varied, with cidra (Citrus medica) and ungurahui (Oenocarpus bataua) having the highest number of species associated. This investigation broadens the understanding and possible biotechnological uses of yeast strains obtained from Amazonian native fruits.

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Polystyrene nanoplastics accumulate in ZFL cell lysosomes and in zebrafish larvae after acute exposure, inducing a synergistic immune response in vitro without affecting larval survival in vivo

Environmental Science Nano ◽

10.1039/d0en00553c ◽

2020 ◽

Vol 7 (8) ◽

pp. 2410-2422

Author(s):

Irene Brandts ◽

Marlid Garcia-Ordoñez ◽

Lluis Tort ◽

Mariana Teles ◽

Nerea Roher

Keyword(s):

Immune Response ◽

Larval Survival ◽

Liver Cells ◽

Acute Exposure ◽

Zebrafish Larvae ◽

Lethal Infection ◽

Zebrafish Liver ◽

Immune Response In Vitro

Polystyrene nanoplastics are internalized in zebrafish liver cells, accumulating in lysosomes, and in zebrafish larvae but do not affect the larval suvival to a lethal infection.

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