Association of gut microbiota with metabolism in juvenile Atlantic salmon

AbstractThe gut microbiome plays a key role in animal health and metabolism through the intricate functional interconnection between the feed, gut microbes, and the host. Unfortunately, in aquaculture, the links between gut microbes and fish genetics and production phenotypes are not well understood.In this study, we investigate the associations between gut microbial communities, fish feed conversion, and fish genetics in the domestic Atlantic salmon. Microbial community composition was determined for 230 juvenile fish from 23 full-sib families and was then regressed on growth, carbon and nitrogen metabolism, and feed efficiency. We only found weak associations between host genetics and microbial composition. However, we did identify significant (p < 0.05) associations between the abundance of three microbial operational taxonomical units (OTUs) and fish metabolism phenotypes. Two OTUs were associated with both carbon metabolism in adipose tissue and feed efficiency, while a third OTU was associated with weight gain.In conclusion, this study demonstrates an intriguing association between host lipid metabolism and the gut microbiota composition in Atlantic salmon.

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Association of gut microbiota with metabolism in juvenile Atlantic Salmon

10.1101/2020.02.10.941245 ◽

2020 ◽

Cited By ~ 1

Author(s):

H. Dvergedal ◽

S.R. Sandve ◽

I.L. Angell ◽

G. Klemetsdal ◽

K. Rudi

Keyword(s):

Atlantic Salmon ◽

Gut Microbiota ◽

Feed Efficiency ◽

Juvenile Fish ◽

Animal Health ◽

Microbial Community Composition ◽

Fish Feed ◽

Feed Conversion ◽

Microbial Composition ◽

Gut Microbes

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Variations in Microbial Diversity and Metabolite Profiles of Female Landrace Finishing Pigs With Distinct Feed Efficiency

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.702931 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhixin Wang ◽

Yingzhi He ◽

Chuduan Wang ◽

Hong Ao ◽

Zhen Tan ◽

...

Keyword(s):

Gut Microbiota ◽

Feed Efficiency ◽

Growth Traits ◽

Finishing Pigs ◽

Feed Conversion ◽

Microbial Composition ◽

Shotgun Metagenomics ◽

Functional Annotations ◽

Carbohydrate Consumption ◽

High Feed

To enhance pig production, feed efficiency (FE) should be improved; however, the mechanisms by which gut microbes affect FE in pigs have not been fully elucidated. To investigate the differences between the composition and functionality of the gut microbiota associated with low and high FE, microbial compositions were characterized using 16S rRNA sequencing, functional annotations were performed by shotgun metagenomics, and metabolomic profiles were created by GC-TOF-MS from female Landrace finishing pigs with low and high feed conversion ratios (FCRs). Lactobacillus was enriched in the gut microbiota of individuals with low FCRs (and thus high FE), while Prevotella abundance was significantly higher in individuals with high FCRs (and thus low FE). This may be linked to carbohydrate consumption and incomplete digestion. The activity of pathways involved in the metabolism of cofactors and vitamins was greater in pigs with lower FE. We also identified differences in pyruvate-related metabolism, including phenylalanine and lysine metabolism. This suggests that pyruvate metabolism is closely related to microbial fermentation in the colon, which in turn affects glycolysis. This study deepens our understanding of how gut microbiota are related to pig growth traits, and how regulating microbial composition could aid in improving porcine FE. However, these results need to be validated using a larger pig cohort in the future.

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Comparative Analysis of the Gut Microbiota of Adult Mosquitoes From Eight Locations in Hainan, China

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2020.596750 ◽

2020 ◽

Vol 10 ◽

Author(s):

Xun Kang ◽

Yanhong Wang ◽

Siping Li ◽

Xiaomei Sun ◽

Xiangyang Lu ◽

...

Keyword(s):

Gut Microbiota ◽

Disease Control ◽

Bacterial Communities ◽

Mosquito Species ◽

Microbial Community Composition ◽

Variable Region ◽

Rrna Gene ◽

Microbial Composition ◽

Quality Filtering ◽

And Function

The midgut microbial community composition, structure, and function of field-collected mosquitoes may provide a way to exploit microbial function for mosquito-borne disease control. However, it is unclear how adult mosquitoes acquire their microbiome, how the microbiome affects life history traits and how the microbiome influences community structure. We analyzed the composition of 501 midgut bacterial communities from field-collected adult female mosquitoes, including Aedes albopictus, Aedes galloisi, Culex pallidothorax, Culex pipiens, Culex gelidus, and Armigeres subalbatus, across eight habitats using the HiSeq 4000 system and the V3−V4 hyper-variable region of 16S rRNA gene. After quality filtering and rarefaction, a total of 1421 operational taxonomic units, belonging to 29 phyla, 44 families, and 43 genera were identified. Proteobacteria (75.67%) were the most common phylum, followed by Firmicutes (10.38%), Bacteroidetes (6.87%), Thermi (4.60%), and Actinobacteria (1.58%). The genera Rickettsiaceae (33.00%), Enterobacteriaceae (20.27%), Enterococcaceae (7.49%), Aeromonadaceae (7.00%), Thermaceae (4.52%), and Moraxellaceae (4.31%) were dominant in the samples analyzed and accounted for 76.59% of the total genera. We characterized the midgut bacterial communities of six mosquito species in Hainan province, China. The gut bacterial communities were different in composition and abundance, among locations, for all mosquito species. There were significant differences in the gut microbial composition between some species and substantial variation in the gut microbiota between individuals of the same mosquito species. There was a marked variation in different mosquito gut microbiota within the same location. These results might be useful in the identification of microbial communities that could be exploited for disease control.

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Characterization of the Intestinal Microbiota of Broiler Breeders With Different Egg Laying Rate

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.599337 ◽

2020 ◽

Vol 7 ◽

Author(s):

Zengqiao Yang ◽

Chunhua Zhang ◽

Jianping Wang ◽

Pietro Celi ◽

Xuemei Ding ◽

...

Keyword(s):

Intestinal Microbiota ◽

Feed Efficiency ◽

Animal Health ◽

Negative Relationship ◽

Egg Laying ◽

Ovary Cell ◽

Feed Conversion ◽

Broiler Breeders ◽

Gastrointestinal Microbiota

The gastrointestinal microbiota plays a pivotal role in maintaining animal health, immunity and reproductive performances. However, literature about the relationship between microbiota and reproductive performance is limited. The aim of the present study was to determine differences in the intestinal microbiota of broiler breeders with different egg laying rate. A total of 200 AA+ parent broiler breeders (41-week-old) were separated into two groups according to their different egg laying rate [average egg laying rate group (AR: 78.57 ± 0.20%) and high egg laying rate group (HR: 90.79 ± 0.43%). Feed conversion ratio (FCR), ovary cell apoptosis rate (ApoCR) and relative abdominal fat weight were lower (p = 0.01), while the hatchability rate of qualified egg was higher (p = 0.04) in HR group than that in AR group. Phascolarctobacterium abundance were lower (p = 0.012) in ileum of HR birds. Romboutsia (genus) in ileum was negatively related to the feed efficiency (r = −0.58, p < 0.05), Firmicutes (phylum) and Lactobacillus (genus) abundances in cecum were positively related to the egg laying rate (ELR) (r = 0.35 and 0.48, p < 0.05), feed efficiency (r = 0.42 and 0.43, p < 0.05), while Spirochaetes (phylum) and Sphaerochaeta (genus) abundances in cecum were negatively related to the ELR (r = −0.43 and −0.70, p < 0.05), feed efficiency (r = 0.54 and 0.48, p < 0.05), and positively related to ApoCR (r = 0.46 and 0.47, p < 0.05). Our results suggested that microbiota, such as Firmicutes (phylum) and Lactobacillus (genus) have positive relationship, while Spirochaetes (phylum) and Romboutsia (genus) abundances exert negative relationship with broiler breeders' reproductive performances.

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PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

Journal of Animal Science ◽

10.1093/jas/skz258.594 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 293-294

Author(s):

Camila S Marcolla ◽

Benjamin Willing

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Relative Abundance ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Poultry Production ◽

Microbiota Composition ◽

Microbial Composition ◽

The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

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A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo

Scientific Reports ◽

10.1038/s41598-020-75847-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Victor Narat ◽

Katherine R. Amato ◽

Noémie Ranger ◽

Maud Salmona ◽

Séverine Mercier-Delarue ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Diversity ◽

Environmental Conditions ◽

Participant Observation ◽

Feeding Habits ◽

Animal Health ◽

Structured Interviews ◽

Microbial Composition ◽

Species Specific ◽

Free Ranging

Abstract Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats (“wild”, “captive”, “pristine”). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted participant-observation and semi-structured interviews among people living near these great apes to understand better their feeding habits and habitats. Unexpectedly, bacterial diversity (ASV, Faith PD and Shannon) was higher among zoo gorillas than among those in the Cameroonian forest, but zoo and Cameroonian chimpanzees showed no difference. Phylogeny was a strong driver of species-specific microbial composition. Surprisingly, zoo gorilla microbiota more closely resembled that of zoo chimpanzees than of Cameroonian gorillas. Zoo living conditions and dietary similarities may explain these results. We encourage multidisciplinary approach integrating environmental sampling and anthropological evaluation to characterize better diverse environmental conditions of such investigations.

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Comparative Assessment of Growth Performance and Nutrients Utilization of African Catfish (Clarias gariepinus, Burchell 1882) Fed Chicken Offal and Shrimp-Based Diets

Annual Research & Review in Biology ◽

10.9734/arrb/2018/v30i530026 ◽

2019 ◽

pp. 1-11

Author(s):

Elvis Monfung Ayim ◽

Ettah Akpang Ivon ◽

Raymond Odey Ajang ◽

Akaninyene Paul Joseph

Keyword(s):

Growth Rate ◽

Growth Performance ◽

Juvenile Fish ◽

Clarias Gariepinus ◽

Feed Consumption ◽

African Catfish ◽

Fish Feed ◽

Feed Conversion ◽

Treatment Groups ◽

Fish Group

A comparative study on the growth performance of African catfish (Clarias gariepinus) fed shrimp based diet (SBD), chicken offal based diet (COBD) and coppens feed was carried-out for 22 weeks in concrete tanks measuring 3.5 x 1.7 x 1.5 m3. Triplicate groups of 40 juveniles with average length of 9.15 ± 0.17cm and weight of 20.00 ± 2.58g were stored in each tank. A total of 360 juveniles were used throughout the study. Fish were fed daily at 3% of their body weight through-out the duration of the experiment. The nutrient composition of the 3 nutrients differed significantly at p<0.05. Weight gain (WG) (g) was highest (17189.33 ± 506.61g) in fish fed diet A (Coppens feed), followed by 15045.33±202.42 g (diet B) (SBD) and least (14357.33 ± 108.25 g) (diet C) (COBD). The Growth rate (GR) was highest in fish fed with diet A (111.62 ± 3.29 g/day), followed by 97.69±1.31 g/day (diet B), and least (93.23±0.70 g/day) in diet C. Specific growth rate (SGR) was highest in juveniles fed diet A (2.02 ± 0.02 %/day), followed by 1.94±0.01 %/day for diet B, and least (1.91±0.01 %/day) for diet C. Mean growth rate (MGR) was highest in juveniles fed diet A (11.88 ± 0.29 mg/day), followed by 11.74±0.15 mg/day for diet B, and least (11.69±0.09 mg/day) in fish fed diet C. The WG, GR and SGR varied significantly between the juvenile fish group fed the 3 diets at p<0.05, while MGR did not vary significantly between fish group fed the 3 diets at p>0.05. Fish fed diet A had a higher feed consumption (FC) (41650.00 ± 315.34 g/kg), than that fed diet B (39034.24 ± 86.34 g/kg) and then diet C (38276.00 ± 342.97 g/kg). Juveniles fed Coppens feed did better, with a feed conversion ratio (FCR) of 2.42 ± 0.06, followed by 2.59±0.04 for diet B and 2.67 ± 0.03 for fish fed diet C. Feed conversion efficiency (FCE) was higher in fish fed diet A (41.26±0.94 %), followed by 38.54 ± 0.54 % (diet B) and least (37.52 ± 0.51 %) (diet C). The FC and FCR varied significantly between the fish fed the 3 diets at p<0.05, while FCE was not significantly different between the 3 treatment groups at p>0.05. The water parameters of the culture water varied significantly between each treatment groups (p<0.05), and were within the rage suitable for normal growth of fish. Though coppens feed yielded better growth performance and feed utilisation, the use of COBD and SBD is recommended for fish farmers in Nigeria. More researches should be carried out on using chicken offals and shrimps in fish feed formulation.

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Community composition and development of the post-weaning piglet gut microbiome

10.21203/rs.3.rs-60981/v1 ◽

2020 ◽

Author(s):

Daniela Gaio ◽

Matthew Z DeMaere ◽

Kay Anantanawat ◽

Graeme J Eamens ◽

Michael Liu ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Antibiotic Treatment ◽

Gut Microbiome ◽

Treatment Effects ◽

Sequence Data ◽

Microbial Community Composition ◽

Dominant Factor ◽

Microbial Composition

Abstract BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. Studies have previously investigated the effects of probiotics as alternatives to antibiotic treatment for the prevention of post-weaning diarrhea. In order to describe the post-weaning gut microbiota, and the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we processed over 800 faecal time-series samples from 126 piglets and 42 sows, generating over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework.ResultsFactors such as age, litter effects, and breed, by significantly correlating with gut microbial community shifts, can be major confounding factors in the assessment of treatment effects. Intramuscular antibiotic treatment and probiotic treatments were found to correlate with alpha and beta diversity, as well as with a transient establishment of Mollicutes and Lactobacillales, respectively. We found the abundance of certain taxa to correlate with weight gain.ConclusionsOur findings demonstrate that breed, litter, and age, are important contributors to variation in the community composition, and that treatment effects of the antibiotic and probiotic treatments were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The current study shows, by means of a phylogenetic diversity framework, that the post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.

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Potential Role of the Microbiome in Acne: A Comprehensive Review

Journal of Clinical Medicine ◽

10.3390/jcm8070987 ◽

2019 ◽

Vol 8 (7) ◽

pp. 987 ◽

Cited By ~ 24

Author(s):

Lee ◽

Byun ◽

Kim

Keyword(s):

Gut Microbiota ◽

Skin Inflammation ◽

Skin Condition ◽

Metagenomic Sequencing ◽

Depression And Anxiety ◽

Microbial Composition ◽

Gut Microbes ◽

Cutibacterium Acnes ◽

Pathogenic Process

Acne is a highly prevalent inflammatory skin condition involving sebaceous sties. Although it clearly develops from an interplay of multiple factors, the exact cause of acne remains elusive. It is increasingly believed that the interaction between skin microbes and host immunity plays an important role in this disease, with perturbed microbial composition and activity found in acne patients. Cutibacterium acnes (C. acnes; formerly called Propionibacterium acnes) is commonly found in sebum-rich areas and its over-proliferation has long been thought to contribute to the disease. However, information provided by advanced metagenomic sequencing has indicated that the cutaneous microbiota in acne patients and acne-free individuals differ at the virulent-specific lineage level. Acne also has close connections with the gastrointestinal tract, and many argue that the gut microbiota could be involved in the pathogenic process of acne. The emotions of stress (e.g., depression and anxiety), for instance, have been hypothesized to aggravate acne by altering the gut microbiota and increasing intestinal permeability, potentially contributing to skin inflammation. Over the years, an expanding body of research has highlighted the presence of a gut–brain–skin axis that connects gut microbes, oral probiotics, and diet, currently an area of intense scrutiny, to acne severity. This review concentrates on the skin and gut microbes in acne, the role that the gut–brain–skin axis plays in the immunobiology of acne, and newly emerging microbiome-based therapies that can be applied to treat acne.

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