Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation

Park, Sein; Steinegger, Martin; Cho, Ho-Seong; Chun, Jongsik

doi:10.3389/fmicb.2020.585622

Cited by 4 publications

(2 citation statements)

References 46 publications

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“…Further differentiation of the L. reuteri isolates using RAPD-PCR revealed 16 different band profile types, indicating gene variation within the species. However, it is striking that about one third of the L. reuteri isolates showed the same band profile, which might reflect that genetically distinct subpopulations of L. reuteri strongly correlate with their host and might indicate a strong host-symbiont association ( Oh et al, 2010 ; Wegmann et al, 2015 ; Yu et al, 2018 ; Park et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Lactobacillus (Limosilactobacillus) reuteri: a probiotic candidate to reduce neonatal diarrhea in calves

Schwaiger,

Storch,

Bauer

et al. 2023

Front. Microbiol.

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BackgroundDiarrhea in newborn calves is considered life-threatening and results in large economic losses in dairy farms. Lactobacilli generally play an important role in intestinal health, and Lactobacillus (Limosilactobacillus; L.) reuteri is the dominant Lactobacillus species in the feces of healthy calves during the first week of life. In calves with diarrhea on day 2 postpartum, lactobacilli are significantly reduced even up to 24 h before the onset of clinical signs. Since the probability of occurrence of diarrheal disease decreases as the L. reuteri count in the feces increases, oral administration of this species might have a protective effect against diarrhea.ObjectiveThese studies were designed to demonstrate whether oral administration of preselected L. reuteri isolates can reduce the incidence of diarrhea in newborn calves on dairy farms.Microorganisms46 L. reuteri isolates from 2-day-old healthy calves were available from a previous study.Animals170 newborn calves of Simmental breed of 10 dairy farms in Bavaria (Germany), were included in the study; of 166 animals the data could be evaluated.MethodsMicrobiological (antibiotic sensitivity test, acid and bile salt stability test, antimicrobial activity of the supernatants), molecular biological (PCR, RAPD-PCR) and toxicological methods (MTT test) were used to select and to characterize suitable L. reuteri isolates. The administration of a suspension of two selected L. reuteri isolates (6–8 × 108 colony forming units per day) to calves was performed from day 2 to day 5 after birth in a double-blinded placebo-controlled study. Clinical monitoring of the calves continued until the 14th day of life.ResultsOut of 46 L. reuteri isolates, only 2 met the set criteria and were used in the feeding trial. In the placebo group, 44 of 83 calves developed diarrhea within the first 2 weeks of life, whereas in the L. reuteri group this was only the case in 31 of 83 animals (p < 0.05).ConclusionL. reuteri appears to be of particular importance for the intestinal health of newborn calves. The diarrhea protective effect could be even more pronounced if an improved administration regimen is developed in terms of start, frequency, and duration.

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Section: Discussionmentioning

confidence: 99%

Lactobacillus (Limosilactobacillus) reuteri: a probiotic candidate to reduce neonatal diarrhea in calves

Schwaiger,

Storch,

Bauer

et al. 2023

Front. Microbiol.

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“…The gut microbiota is a complex and diverse microbial ecosystem that resides in the gastrointestinal (GI) tract of animals [ 9 ]. It contains numerous microorganisms such as bacteria, viruses, fungi, protozoa, and archaea, and plays a significant role in the development and maintenance of the immune system [ 10 , 11 , 12 ]. The absence of microbiota results in the incomplete development of the immune system, as seen in germ-free mice [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

Alteration of the Gut Microbiota in Pigs Infected with African Swine Fever Virus

Tark

Moon

et al. 2023

Veterinary Sciences

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The factors that influence the pathogenicity of African swine fever (ASF) are still poorly understood, and the host’s immune response has been indicated as crucial. Although an increasing number of studies have shown that gut microbiota can control the progression of diseases caused by viral infections, it has not been characterized how the ASF virus (ASFV) changes a pig’s gut microbiome. This study analyzed the dynamic changes in the intestinal microbiome of pigs experimentally infected with the high-virulence ASFV genotype II strain (N = 4) or mock strain (N = 3). Daily fecal samples were collected from the pigs and distributed into the four phases (before infection, primary phase, clinical phase, and terminal phase) of ASF based on the individual clinical features of the pigs. The total DNA was extracted and the V4 region of the 16 s rRNA gene was amplified and sequenced on the Illumina platform. Richness indices (ACE and Chao1) were significantly decreased in the terminal phase of ASF infection. The relative abundances of short-chain-fatty-acids-producing bacteria, such as Ruminococcaceae, Roseburia, and Blautia, were decreased during ASFV infection. On the other hand, the abundance of Proteobacteria and Spirochaetes increased. Furthermore, predicted functional analysis using PICRUSt resulted in a significantly reduced abundance of 15 immune-related pathways in the ASFV-infected pigs. This study provides evidence for further understanding the ASFV–pig interaction and suggests that changes in gut microbiome composition during ASFV infection may be associated with the status of immunosuppression.

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Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

2022

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Mouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Accordingly, the similarity between human and mouse microbiomes at a low taxonomic level is not clear. We construct a comprehensive mouse microbiota genome (CMMG) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 41’798 genomes cluster into 1’573 species, of which 78.1% are uncultured, and we discovered 226 new genera, seven new families, and one new order. CMMG enables an unprecedented coverage of the mouse gut microbiome exceeding 86%, increases the mapping rate over four-fold, and allows functional microbiota analyses of human and mouse linking them to the driver species. Comparing CMMG to microbiota from the unified human gastrointestinal genomes shows an overlap of 62% at the genus but only 10% at the species level, demonstrating that human and mouse gut microbiota are largely distinct. CMMG contains the most comprehensive collection of consistently functionally annotated species of the mouse and human microbiome to date, setting the ground for the analysis of new and reanalysis of existing datasets at an unprecedented depth.

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Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation

Cited by 4 publications

References 46 publications

Lactobacillus (Limosilactobacillus) reuteri: a probiotic candidate to reduce neonatal diarrhea in calves

Lactobacillus (Limosilactobacillus) reuteri: a probiotic candidate to reduce neonatal diarrhea in calves

Alteration of the Gut Microbiota in Pigs Infected with African Swine Fever Virus

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

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