scholarly journals Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi

2021 ◽  
Vol 8 ◽  
Author(s):  
Jeremiah J. Minich ◽  
Barbara Nowak ◽  
Abigail Elizur ◽  
Rob Knight ◽  
Stewart Fielder ◽  
...  
Keyword(s):  
Built Environment ◽  
Marine Fish ◽  
Gut Microbiome ◽  
Animal Health ◽  
Rrna Gene ◽  
Fish Feed ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi ◽  
Microbiome Development ◽  
Over Time

The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment “BE” and feed influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi, over time. For the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish mucous (gill, skin, and digesta), the BE (tank side, water, inlet pipe, airstones, and air diffusers) and feed were sampled from indoor reared fish at three ages (43, 137, and 430 dph; n = 12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. The gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut “allochthonous” microbiome becomes increasingly differentiated from the environment over time. Feed had a relatively low impact on driving microbial communities. Our findings suggest that S. lalandi mucosal microbiomes are differentially influenced by the BE with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to biofouling in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.

scholarly journals Impacts of the Marine Hatchery Built Environment on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola Lalandi

2020 ◽  
Author(s):  
Jeremiah Minich ◽  
Barbara Nowak ◽  
Abigail Elizur ◽  
Rob Knight ◽  
Stewart Fielder ◽  
...  
Keyword(s):  
Built Environment ◽  
Vertical Transmission ◽  
Marine Fish ◽  
Gut Microbiome ◽  
Community Dynamics ◽  
Animal Health ◽  
Rrna Gene ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi ◽  
Microbiome Development

Abstract BackgroundMicrobial succession in vertebrates has primarily focused on vertical transmission and ontogenetic development in the mammalian gut. Teleosts comprise the majority of vertebrate diversity, yet little is known about how the microbiome develops in fish, particularly when vertical transmission is limited or absent for broadcast spawners. Biological factors such as diet, age, phylogeny, and trophic level along with environmental factors such as water salinity, temperature, and depth have been shown to influence the mucosal microbiomes of fish. Here we investigate how various microbial-rich surfaces from the built environment ‘BE’ influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi, over time.ResultsFor the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish microbiomes (gill, skin, and digesta) and the BE (tank side, water, inlet pipe, airstones, and air diffusers) were sampled from indoor reared fish at three ages (43 dph, 137 dph, 430 dph; n=12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. We quantified the change in community dynamics driven by the BE and show that the gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut microbiome becomes increasingly differentiated from the environment over time.ConclusionsOur findings suggest that fish mucosal microbiomes are differentially influenced by the built environment with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to stressors in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.

scholarly journals Adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers

2020 ◽  
Author(s):  
Molly B. El Alam ◽  
Travis T. Sims ◽  
Ramez Kouzy ◽  
Greyson W. G. Biegert ◽  
Joseph Abi Jaoude ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Repeated Measures ◽  
Diversity Index ◽  
Marker Gene ◽  
Hypervariable Region ◽  
Rrna Gene ◽  
Gynecologic Cancers ◽  
Linear Discriminant ◽  
Baseline Levels ◽  
Over Time

ABSTRACTBackgroundA diverse and abundant gut microbiome can improve cancer patients’ treatment response; however, the effect of pelvic chemoradiotherapy (CRT) on gut diversity and composition is unclear. The purpose of this prospective study was to identify changes in the diversity and composition of the gut microbiome during and after pelvic CRT.Materials and MethodsRectal swabs from 58 women with cervical, vaginal, or vulvar cancer from two institutions were prospectively analyzed before CRT (baseline), during CRT (weeks 1, 3, and 5), and at first follow-up (week 12) using 16Sv4 rRNA gene sequencing of the V4 hypervariable region of the bacterial 16S rRNA marker gene. Observed operational taxonomic units (OTUs; representative of richness) and Shannon, Simpson, Inverse Simpson, and Fisher diversity indices were used to characterize alpha (within-sample) diversity. Changes over time were assessed using a paired t-test, repeated measures ANOVA, and linear mixed modeling. Compositional changes in specific bacteria over time were evaluated using linear discriminant analysis effect size.ResultsGut microbiome richness and diversity levels continually decreased throughout CRT (mean Shannon diversity index, 2.52 vs. 2.91; all P <0.01), but were at or near baseline levels in 60% of patients by week 12. Patients with higher gut diversity at baseline had the steepest decline in gut microbiome diversity. Gut microbiome composition was significantly altered during CRT, with increases in Proteobacteria and decreases in Clostridiales, but adapted after CRT, with increases in Bacteroides species.ConclusionAfter CRT, the gut microbiome’s diversity tends to return to baseline levels, but its structure and composition remain significantly altered. These changes should be considered when designing studies to analyze the gut microbiome as a predictive or prognostic biomarker in patients who receive pelvic CRT for gynecologic cancers.

scholarly journals Organ health and development in larval kingfish are unaffected by ocean acidification and warming

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8266 ◽  
Author(s):  
Andrea Y. Frommel ◽  
Colin J. Brauner ◽  
Bridie J.M. Allan ◽  
Simon Nicol ◽  
Darren M. Parsons ◽  
...  
Keyword(s):  
Ocean Acidification ◽  
Marine Fish ◽  
Histological Analysis ◽  
Sublethal Effects ◽  
Developmental Rate ◽  
Organ Damage ◽  
Ocean Warming ◽  
Global Ocean ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi

Anthropogenic CO2 emissions are causing global ocean warming and ocean acidification. The early life stages of some marine fish are vulnerable to elevated ocean temperatures and CO2 concentrations, with lowered survival and growth rates most frequently documented. Underlying these effects, damage to different organs has been found as a response to elevated CO2 in larvae of several species of marine fish, yet the combined effects of acidification and warming on organ health are unknown. Yellowtail kingfish, Seriola lalandi, a circumglobal subtropical pelagic fish of high commercial and recreational value, were reared from fertilization under control (21 °C) and elevated (25 °C) temperature conditions fully crossed with control (500 µatm) and elevated (1,000 µatm) pCO2 conditions. Larvae were sampled at 11 days and 21 days post hatch for histological analysis of the eye, gills, gut, liver, pancreas, kidney and liver. Previous work found elevated temperature, but not elevated CO2, significantly reduced larval kingfish survival while increasing growth and developmental rate. The current histological analysis aimed to determine whether there were additional sublethal effects on organ condition and development and whether underlying organ damage could be responsible for the documented effects of temperature on survivorship. While damage to different organs was found in a number of larvae, these effects were not related to temperature and/or CO2 treatment. We conclude that kingfish larvae are generally vulnerable during organogenesis of the digestive system in their early development, but that this will not be exacerbated by near-future ocean warming and acidification.

scholarly journals Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

2012 ◽  
Vol 78 (17) ◽  
pp. 6153-6160 ◽  
Author(s):  
Elizabeth A. Maga ◽  
Prerak T. Desai ◽  
Bart C. Weimer ◽  
Nguyet Dao ◽  
Dietmar Kültz ◽  
...  
Keyword(s):  
Human Milk ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Gut Health ◽  
Content Type ◽  
Microbiome Composition ◽  
The Impact ◽  
Over Time

ABSTRACTHuman milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk components in gut microbiota modulation and subsequent changes in overall and intestinal health. Using milk from transgenic goats expressing human lysozyme at 68%, the level found in human milk and young pigs as feeding subjects, the fecal microbiota was analyzed over time using 16S rRNA gene sequencing and the G2 Phylochip. The two methods yielded similar results, with the G2 Phylochip giving more comprehensive information by detecting more OTUs. Total community populations remained similar within the feeding groups, and community member diversity was changed significantly upon consumption of lysozyme milk. Levels ofFirmicutes(Clostridia) declined whereas those ofBacteroidetesincreased over time in response to the consumption of lysozyme-rich milk. The proportions of these major phyla were significantly different (P< 0.05) from the proportions seen with control-fed animals after 14 days of feeding. Within phyla, the abundance of bacteria associated with gut health (BifidobacteriaceaeandLactobacillaceae) increased and the abundance of those associated with disease (Mycobacteriaceae,Streptococcaceae,Campylobacterales) decreased with consumption of lysozyme milk. This study demonstrated that a single component of the diet with bioactivity changed the gut microbiome composition. Additionally, this model enabled the direct examination of the impact of lysozyme on beneficial microbe enrichment versus detrimental microbe reduction in the gut microbiome community.

scholarly journals Diet and diet-associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi )

2018 ◽  
Vol 12 (2) ◽  
pp. 275-288 ◽  
Author(s):  
Jackson Wilkes Walburn ◽  
Bernd Wemheuer ◽  
Torsten Thomas ◽  
Elizabeth Copeland ◽  
Wayne O'Connor ◽  
...  
Keyword(s):  
Associated Bacteria ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi ◽  
Microbiome Development

scholarly journals The Gut Microbiota of Naturally Occurring and Laboratory Aquaculture Lytechinus variegatus Revealed Differences in the Community Composition, Taxonomic Co-Occurrence, and Predicted Functional Attributes

2021 ◽  
Vol 1 (2) ◽  
pp. 201-224
Author(s):  
George B. H. Green ◽  
Joseph A. Hakim ◽  
Jiung-Wen Chen ◽  
Hyunmin Koo ◽  
Casey D. Morrow ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Sea Urchins ◽  
Animal Health ◽  
Amplicon Sequencing ◽  
Lytechinus Variegatus ◽  
Rrna Gene ◽  
Taxa Richness ◽  
Scientific Investigations ◽  
Formulated Diet ◽  
Naturally Occurring

Sea urchins, in many instances, are collected from the wild, maintained in the laboratory aquaculture environment, and used as model animals for various scientific investigations. It has been increasingly evident that diet-driven dysbiosis of the gut microbiome could affect animal health and physiology, thereby impacting the outcome of the scientific studies. In this study, we compared the gut microbiome between naturally occurring (ENV) and formulated diet-fed laboratory aquaculture (LAB) sea urchin Lytechinus variegatus by amplicon sequencing of the V4 region of the 16S rRNA gene and bioinformatics tools. Overall, the ENV gut digesta had higher taxa richness with an abundance of Propionigenium, Photobacterium, Roseimarinus, and Flavobacteriales. In contrast, the LAB group revealed fewer taxa richness, but noticeable abundances of Arcobacter, Agarivorans, and Shewanella. However, Campylobacteraceae, primarily represented by Arcobacter spp., was commonly associated with the gut tissues of both ENV and LAB groups whereas the gut digesta had taxa from Gammaproteobacteria, particularly Vibrio spp. Similarly, the co-occurrence network displayed taxonomic organizations interconnected by Arcobacter and Vibrio as being the key taxa in gut tissues and gut digesta, respectively. Predicted functional analysis of the gut tissues microbiota of both ENV and LAB groups showed a higher trend in energy-related metabolisms, whereas amino acids, carbohydrate, and lipid metabolisms heightened in the gut digesta. This study provides an outlook of the laboratory-formulated diet-fed aquaculture L. variegatus gut microbiome and predicted metabolic profile as compared to the naturally occurring animals, which should be taken into consideration for consistency, reproducibility, and translatability of scientific studies.

scholarly journals Alternative Feed Raw Materials Modulate Intestinal Microbiota and Its Relationship with Digestibility in Yellowtail Kingfish Seriola lalandi

Fishes ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. 14
Author(s):  
Chinh Thi My Dam ◽  
Mark Booth ◽  
Igor Pirozzi ◽  
Michael Salini ◽  
Richard Smullen ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Raw Materials ◽  
Nutrient Digestibility ◽  
Rrna Gene ◽  
Distal Intestine ◽  
Alternative Feed ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi

Gut microbiota plays a crucial role in nutrient digestibility and fish health. This study aimed to investigate the effects of alternative feed raw materials on the bacterial communities in the distal intestine and its relationship with nutrient digestibility in yellowtail kingfish (YTK), Seriola lalandi. Two 4-week digestibility trials were conducted to evaluate fish meal (FM), two sources of poultry by-product meal (PBM-1 & PBM-2), blood meal (BLM), faba bean meal (FBM), corn gluten meal (CGM), soy protein concentrate (SPC) and wheat flour (WH). The nutrient digestibility value was determined using the stripping fecal collection method. Bacterial communities were characterized by high-throughput sequencing based on V3-V4 region of the 16S rRNA gene. The most abundant phylum identified in the present study was Proteobacteria. A significant change in the distal intestine was observed in fish fed diets containing CGM and BLM, characterized by a reduction of species richness and diversity. Additionally, significant correlation between nutrient digestibility and intestinal microbiota was observed. Allivibrio, Vibrio, Curvibacter, Ruminococcaceae, and Clostridium were positively correlated, whereas Ralstonia genus was negatively correlated with nutrient digestibility. This study demonstrated that intestinal microbiota could be a useful tool for evaluating the digestibility of feed raw materials; however, further culture-based study is needed to confirm this observation.

scholarly journals Interactions between the gut microbiome and mucosal immunoglobulins A, M and G in the developing infant gut

2019 ◽  
Author(s):  
Anders Janzon ◽  
Julia K. Goodrich ◽  
Omry Koren ◽  
Jillian L. Waters ◽  
Ruth E. Ley ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Gene Profiling ◽  
Secretory Iga ◽  
Rrna Gene ◽  
List Type ◽  
Microbial Cells ◽  
New Findings ◽  
Infant Gut Microbiome ◽  
Antibody Coating ◽  
Microbiome Development

AbstractObjectiveInteractions between the gut microbiome and immunoglobulin (Ig) A in infancy are important for future health. IgM and IgG are also present, however, their interactions with the microbiome in the developing infant are less understood.DesignWe employed stool samples sampled 15 times in infancy from 32 healthy subjects at 4 locations in 3 countries (from the TEDDY study). We characterized patterns of microbiome development in relation to levels of IgA, IgG and IgM. For 8 infants from a single location, we FACS-sorted microbial cells from stool by Ig status. We used 16S rRNA gene profiling on full and sorted microbiomes to assess patterns of antibody coating in relation to age and other factors.ResultsAll antibodies decreased in concentration with age, but were augmented by breastmilk feeding regardless of infant age. Levels of IgA correlated with the relative abundances of OTUs belonging to the Bifidobacteria and Enterobacteriaceae, which dominated the early microbiome, and IgG levels correlated with Haemophilus. The diversity of Ig-coated microbiota was influenced by breastfeeding and age, but birth mode. IgA and IgM coated the same microbiota, while IgG targeted a different subset. Blautia generally evaded antibody coating, while members of the Bifidobacteria and Enterobacteriaceae were high in IgA/M.ConclusionIgA/M have similar dynamics with respect to microbiome development with age, and their interactions with the microbiome are influenced by breastfeeding status. IgG generally does not coat the commensal microbiota.SummaryWhat is already known on this subject?Secretory IgA coats ~50% of microbiota in the gutIgM and IgG are less prevalent and coat a lower fraction in the adult, dynamics in the infant gut are not well characterized.Breastmilk is a source of IgA to the infant gut and decreases with time.IgA coating of microbial cells in infant gut microbiome decreases over time.What are the new findings?Breastfeeding augments the IgA coating of the microbiome at all ages.IgA and IgM coat many of the same cells, whereas few are coated by IgG alone.Bifidobacteria, Enterobacteriaceae, Ruminococcus gnavus are enriched in IgA/M-coated cell fraction, Blautia is enriched in uncoated fraction.IgG levels correlated with Haemophilus.How might it impact on clinical practice in the foreseeable future?Ig-coated fraction of the gut microbiome could serve as a useful tool for tracking development of the infant gut microbiome, and/or identifying aberrations to immune sensing of the microbiome.

scholarly journals A prospective study of the adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247905
Author(s):  
Molly B. El Alam ◽  
Travis T. Sims ◽  
Ramez Kouzy ◽  
Greyson W. G. Biegert ◽  
Joseph A. B. I. Jaoude ◽  
...  
Keyword(s):  
Prospective Study ◽  
Gut Microbiome ◽  
Repeated Measures ◽  
Marker Gene ◽  
Rrna Gene ◽  
Gynecologic Cancers ◽  
Linear Discriminant ◽  
Baseline Levels ◽  
Over Time

Background A diverse and abundant gut microbiome can improve cancer patients’ treatment response; however, the effect of pelvic chemoradiotherapy (CRT) on gut diversity and composition is unclear. The purpose of this prospective study was to identify changes in the diversity and composition of the gut microbiome during and after pelvic CRT. Materials and methods Rectal swabs from 58 women with cervical, vaginal, or vulvar cancer from two institutions were prospectively analyzed before CRT (baseline), during CRT (weeks 1, 3, and 5), and at first follow-up (week 12) using 16Sv4 rRNA gene sequencing of the V4 hypervariable region of the bacterial 16S rRNA marker gene. 42 of these patients received antibiotics during the study period. Observed operational taxonomic units (OTUs; representative of richness) and Shannon, Simpson, Inverse Simpson, and Fisher diversity indices were used to characterize alpha (within-sample) diversity. Changes over time were assessed using a paired t-test, repeated measures ANOVA, and linear mixed modeling. Compositional changes in specific bacteria over time were evaluated using linear discriminant analysis effect size. Results Gut microbiome richness and diversity levels continually decreased throughout CRT (mean Shannon diversity index, 2.52 vs. 2.91; all P <0.01), but were at or near baseline levels in 60% of patients by week 12. Patients with higher gut diversity at baseline had the steepest decline in gut microbiome diversity. Gut microbiome composition was significantly altered during CRT, with increases in Proteobacteria and decreases in Clostridiales, but adapted after CRT, with increases in Bacteroides species. Conclusion After CRT, the diversity of the gut microbiomes in this population tended to return to baseline levels by the 12 week follow-up period, but structure and composition remained significantly altered. These changes should be considered when designing studies to analyze the gut microbiome in patients who receive pelvic CRT for gynecologic cancers.

scholarly journals Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Christian Zenner ◽  
Thomas C. A. Hitch ◽  
Thomas Riedel ◽  
Esther Wortmann ◽  
Stefan Tiede ◽  
...  
Keyword(s):  
Immune System ◽  
Immune Responses ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Animal Health ◽  
Gut Bacteria ◽  
Microbial Colonization ◽  
Rrna Gene ◽  
Colonization Resistance ◽  
The Impact

ABSTRACT The gut microbiome is crucial for both maturation of the immune system and colonization resistance against enteric pathogens. Although chicken are important domesticated animals, the impact of their gut microbiome on the immune system is understudied. Therefore, we investigated the effect of microbiome-based interventions on host mucosal immune responses. Increased levels of IgA and IgY were observed in chickens exposed to maternal feces after hatching compared with strict hygienic conditions. This was accompanied by increased gut bacterial diversity as assessed by 16S rRNA gene amplicon sequencing. Cultivation work allowed the establishment of a collection of 43 bacterial species spanning 4 phyla and 19 families, including the first cultured members of 3 novel genera and 4 novel species that were taxonomically described. This resource is available at www.dsmz.de/chibac. A synthetic community consisting of nine phylogenetically diverse and dominant species from this collection was designed and found to be moderately efficient in boosting immunoglobulin levels when provided to chickens early in life. IMPORTANCE The immune system plays a crucial role in sustaining animal health. Its development is markedly influenced by early microbial colonization of the gastrointestinal tract. As chicken are fully dependent on environmental microbes after hatching, extensive hygienic measures in production facilities are detrimental to the microbiota, resulting in low colonization resistance against pathogens. To combat enteric infections, antibiotics are frequently used, which aggravates the issue by altering gut microbiota colonization. Intervention strategies based on cultured gut bacteria are proposed to influence immune responses in chicken.

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