Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis

Li, Xin-Meng; Shi, Xiao; Yao, Yao; Shen, Yi-cun; Wu, Xiang-Ling; Cai, Ting; Liang, Luming; Wang, Fen Wei

doi:10.1128/spectrum.04297-22

Cited by 9 publications

(9 citation statements)

References 51 publications

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“…Likewise, larvae from three tanks were sampled to get triplicates for each stage. The larval pools were transferred to 0.5 mL absolute ethanol (HiMedia, India) and frozen at −20°C ( Song et al, 2016 ; Li et al, 2023 ). For the fingerlings, fish from three tanks were sampled with three fish from each tank.…”

Section: Methodsmentioning

confidence: 99%

“…The pooled gut samples from three fish in the same tank constituted a replicate. The gut with the contents was transferred to 0.5 mL absolute ethanol, and preserved at −20°C ( Song et al, 2016 ; Li et al, 2023 ). Accordingly, there were 33 fish samples (11 life stages in triplicates) for sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…In detail, the feed collected included rotifers ( Brachionus plicatilis + Brachionus rotundiformis ) collected on 1, 3, 5, and 7 DPH (12 samples), Artemia nauplii collected on 10 and 12 DPH (6 samples), and different formulated feeds [pellet size of 150 to 200 μM (E-larval 200, Lucky star), 500 μM, 1 mM, 2.5 mM, and 4 mM (Skretting)] (15 feed samples corresponding to five different pellet sizes in triplicates). Around 0.5 g of each feed were collected in 3 mL absolute ethanol at random in triplicates and preserved at −20°C ( Song et al, 2016 ; Li et al, 2023 ). In detail, the sample numbers for fish, water, microalgae, rotifers, artemia, and formulated feed samples for sequencing was 33, 33, 3, 12, 6, and 15, respectively.…”

Section: Methodsmentioning

confidence: 99%

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Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii)

Sumithra,

Sharma,

Suresh

et al. 2024

Front. Microbiol.

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IntroductionDeep investigations of host-associated microbiota can illuminate microbe-based solutions to improve production in an unprecedented manner. The poor larval survival represents the critical bottleneck in sustainable marine aquaculture practices. However, little is known about the microbiota profiles and their governing eco-evolutionary processes of the early life stages of marine teleost, impeding the development of suitable beneficial microbial management strategies. The study provides first-hand mechanistic insights into microbiota and its governing eco-evolutionary processes in early life stages of a tropical marine teleost model, Trachinotus blochii.MethodsThe microbiota profiles and their dynamics from the first day of hatching till the end of metamorphosis and that of fingerling’s gut during the routine hatchery production were studied using 16S rRNA amplicon-based high-throughput sequencing. Further, the relative contributions of various external factors (rearing water, live feed, microalgae, and formulated feed) to the microbiota profiles at different ontogenies was also analyzed.ResultsA less diverse but abundant core microbial community (~58% and 54% in the whole microbiota and gut microbiota, respectively) was observed throughout the early life stages, supporting ‘core microbiota’ hypothesis. Surprisingly, there were two well-differentiated clusters in the whole microbiota profiles, ≤10 DPH (days post-hatching) and > 10 DPH samples. The levels of microbial taxonomic signatures of stress indicated increased stress in the early stages, a possible explanation for increased mortality during early life stages. Further, the results suggested an adaptive mechanism for establishing beneficial strains along the ontogenetic progression. Moreover, the highly transient microbiota in the early life stages became stable along the ontogenetic progression, hypothesizing that the earlier life stages will be the best window to influence the microbiota. The egg microbiota also crucially affected the microbial community. Noteworthily, both water and the feed microbiota significantly contributed to the early microbiota, with the feed microbiota having a more significant contribution to fish microbiota. The results illustrated that rotifer enrichment would be the optimal medium for the early larval microbiota manipulations.ConclusionThe present study highlighted the crucial foundations for the microbial ecology of T. blochii during early life stages with implications to develop suitable beneficial microbial management strategies for sustainable mariculture production.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii)

Sumithra,

Sharma,

Suresh

et al. 2024

Front. Microbiol.

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“…This addresses the logistical barriers of returning a fresh sample immediately to the research team. Furthermore, samples collected with a stabilizing solution have been shown to maintain a stable microbiota, similar to those immediately frozen in À80 degrees (Li et al, 2023). We also suggest protocols include a flexible window for sample collection.…”

Section: Timely Sample Collectionmentioning

confidence: 96%

Challenges and priorities for researching the gut microbiota in individuals living with anorexia nervosa

West,

Hart,

Loughman

et al. 2023

Intl J Eating Disorders

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ObjectiveThe gut microbiota is implicated in several symptoms and biological pathways relevant to anorexia nervosa (AN). Investigations into the role of the gut microbiota in AN are growing, with a specific interest in the changes that occur in response to treatment. Findings suggest that microbial species may be associated with some of the symptoms common in AN, such as depression and gastrointestinal disturbances (GID). Therefore, researchers believe the gut microbiota may have therapeutic relevance. Whilst research in this field is rapidly expanding, the unique considerations relevant to conducting gut microbiota research in individuals with AN must be addressed.MethodWe provide an overview of the published literature investigating the relationship between the gut microbiota and symptoms and behaviors present in AN, discuss important challenges in gut microbiota research, and offer recommendations for addressing these. We conclude by summarizing research design priorities for the field to move forward.ResultsSeveral ways exist to reduce participant burden and accommodate challenges when researching the gut microbiota in individuals with AN.DiscussionRecommendations from this article are foreseen to encourage scientific rigor and thoughtful protocol planning for microbiota research in AN, including ways to reduce participant burden. Employing such methods will contribute to a better understanding of the role of the gut microbiota in AN pathophysiology and treatment.Public SignificanceThe field of gut microbiota research is rapidly expanding, including the role of the gut microbiota in anorexia nervosa. Thoughtful planning of future research will ensure appropriate data collection for meaningful interpretation while providing a positive experience for the participant. We present current challenges, recommendations for research design and priorities to facilitate the advancement of research in this field.

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“…Another study spread over 12 months [25] recommended cryopreservation at -80°C with 10% glycerol as the optimal method for preserving the microbial content of stool samples. Despite this, it is crucial to note that sample conservation influences the taxonomic composition of identified proteins [26].…”

Section: Preservationmentioning

confidence: 99%

Identification of the intestinal microbiota: Methods and applications to Moroccan studies

Semlali,

Benazzouz,

Filali-Zegzouti

et al. 2024

E3S Web Conf.

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The gut microbiota (GM) is a complex microbial community that exerts a considerable influence on human health, and its accurate characterisation has become essential to understanding its roles and implications in various medical conditions. Recent technological advances have paved the way for analytical methods that can uncover this complex microbial community. For these reasons, this review describes the methods used by research teams to discover and understanding the impact of GM in our environment. This paper explores the first phase of collecting and preserving samples, highlighting the impact of storage methods on sample stability and the reliability microbiological analyses. Then, it examines various methods for analysing GM. This diversity of approaches adapted to the specific objectives of each study, whether to characterise diversity using metagenomics, quantify specific micro-organisms using real-time PCR, or use techniques based on microbial targets. These methodologies promise new perspectives for understanding the physiological impact of the microbiota. Finally, concrete examples from Moroccan studies illustrate the application of these techniques to the characterisation of GM. By providing practical advice, this article guides researchers in the judicious choice of methods adapted to their research objectives and budgetary constraints, thereby contributing to the advancement of knowledge about the GM.

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Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis

Cited by 9 publications

References 51 publications

Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii)

Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii)

Challenges and priorities for researching the gut microbiota in individuals living with anorexia nervosa

Identification of the intestinal microbiota: Methods and applications to Moroccan studies

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