Lallemand Animal Nutrition
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What's new

Jan 27, 2021

Using OMICS to answer practical shrimp farming questions

Jan 27, 2021

Using omics to answer practical shrimp farming questions

The main microbial components of shrimp farming systems are the water, the soil, and the shrimp gut microbiota. Lallemand Animal Nutrition has developed in-feed probiotics and bioremediation solutions that can help target the modulation of gut and water microbiota, respectively. In turn, it helps secure shrimp farming outcomes. What is their real impact on these microbial ecosystems? Thanks to metagenomics, recent studies conducted by the Lallemand Monogastric Center of Excellence help us to answer some practical questions often asked by shrimp farmers in hatcheries and nurseries. 

Trial setup

We carried out a controlled experiment in Vietnam covering both the hatchery and nursery phases of white leg shrimp (Litopenaeus vannamei). The trial evaluated the use of a water bioremediation product (LALSEA PL Pack, Lallemand Animal Nutrition) alongside an in-feed probiotic (BACTOCELL or LALPACK PROBIO, Lallemand Animal Nutrition) in comparison to, in the hatchery phase, water antibiotic prophylaxis and, in the nursery phase, competitor’s microbial solutions or negative control (Figure 1).

Figure 1. Treatments of water bioremediation and in-feed probiotics in a commercial hatchery and nursery under routine husbandry practices


Bioremediation products

In-feed probiotic


Hatchery (22 days, n = 6/treatment)/

Lallemand (LAL)



Antibiotic (ABX)OTC (5ppm/day)-

Nursery (28 days, n = 4/treatment)

Lallemand (LAL)



Competitor (COMP)Competitor productCompetitor product
Control (CON)No productNo product
BACTOCELL: Pediococcus acidilactici CNCM I-4622 (MA 18/5M); LALSEA PL PACK: Bacillus spp. and BACTOCELL; LALPACK PROBIO: BACTOCELL and Saccharomyces cerevisiae var. boulardii (CNCM I-1079); OTC: oxytetracycline


Answering shrimp farmers questions

Using the amplicon sequencing technique as a metagenomic approach, it was possible to assess the changes in gut and water microbiota induced by the different microbial solutions and the results on performance. Here, the application of state-of-the-art genomic techniques enabled researchers to answer practical questions related to positive microbiota management in shrimp farming:

  • Does the water microbiome impact all life-stages of shrimp similarly? No.

In the early hatchery phases, the gut and water microbial populations were very similar, unlike in the nursery phase.

  • Can we track the added beneficial bacteria in the water and in the shrimp? Yes. (Figure 2)
Relative abundance of Bacillus and Pediococcus in ABX and LAL treatments in hatchery water and nursery shrimp gut microbiota
Relative abundance of Bacillus and Pediococcus in ABX and LAL treatments in hatchery water and nursery shrimp gut microbiota (P<0.05); the individual data, average (straight line), and median (dotted line) for each treatment are shown.


  • Do probiotic and bioremediation products reduce the prevalence of undesirable bacteria and enhance beneficial ones? Yes, both in the nursery and hatchery phase.
  • Are all probiotic and bioremediation products acting the same way? No.

The Lallemand solutions were more effective at enriching the shrimp gut in beneficial microbial groups, and at reducing the relative abundance of undesirable bacteria than the alternative ones. This emphasizes the importance of strain specificity in microbial-based products.

  • Finally, does this translate into performance? Yes.

As a result of improved water and intestinal microbiota, end-point body weight, feed conversion ratio (FCR), and survival improved in the LAL group compared to the COMP group in the nursery phase. The LAL group yielded better and more consistent performance.


For more results, download our White Paper.