Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota

Lee, Sang‐Won; La, Tae-Min; Lee, Hong-Jae; Choi, In‐Soo; Song, Chang‐Seon; Park, Seung‐Yong

doi:10.1038/s41598-019-43280-w

Cited by 123 publications

(161 citation statements)

References 47 publications

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“…These bacteria are likely to be environmental in origin, deriving either from hatchery equipment or workers. Although the possibility of maternal microbiota transfer via the reproductive tract has been claimed the most abundant taxa in embryonic gut and egg albumin was Psuedomonas with no presence of Enterobacteriaceae of Clostridiaceae (26).…”

Section: Introductionmentioning

confidence: 98%

Development of the Ileal Microbiota in Three Broiler Breeds

et al. 2020

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The development and succession of the microbiota in ileal mucus and lumen samples from three breeds of broiler chicken (Cobb 500, n = 36; Hubbard JA87, n = 38; and Ross 308, n = 36) was observed between 3 and 42 days post hatch (d.p.h). Chicks were housed in the same room of a climate-controlled, biosecure chicken housing unit. Between 0 and 14 d.p.h, chicks were kept in three circular brooder pens ensuring a mixture of breeds in each brooder. From 22 d.p.h, chicks were removed from the brooders and kept in the same room. DNA was extracted from a pooled sample of ileal mucus and luminal contents taken from five birds of each breed at 3, 7, 14, 21, 28, and 42 d.p.h. High-throughput Illumina sequencing was performed for the V4 hypervariable region of the 16S rRNA gene. The initial microbiota in the ileum varied between breeds. The common features were a low diversity and general dominance by one or two taxa such as Enterococcus or Escherichia with relatively low numbers of Lactobacillus. Escherichia became the most abundant genus in samples where Enterococcus was previously the dominant taxa. The next phase of development was marked by an increase in the abundance of Candidatus Arthromitus in the mucus and Lactobacillus in the lumen. The high abundance of Candidatus Arthromitus persisted between 7 and 14 d.p.h after which Lactobacillus became the most abundant genus in both the mucus and lumen. Dominance of the ileal microbiota by Lactobacillus was a transient feature. By 42 d.p.h, the relative abundance of Lactobacillus had fallen while a range of other taxa including Escherichia, Turicibacter, and members of Clostridiales increased. This general pattern was followed by all breeds, however, the rate at which succession occurred differed as Ross matured quicker than Cobb with Hubbard as an intermediate.

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Section: Introductionmentioning

confidence: 98%

Development of the Ileal Microbiota in Three Broiler Breeds

et al. 2020

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“…4-6 weeks). It seems reasonable that the microbiome of breeder chickens and laying hens has matured (52,53). These microbiomes may be more competitive and resilient than those in young broilers contributing to less disease and therefore less treatments.…”

Section: Discussionmentioning

confidence: 99%

Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

Suwono

Eckmanns

Kaspar

et al. 2020

Preprint

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Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however, a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics - ampicillin, cefotaxime, ciprofloxacin and gentamicin – for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together and likewise separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might promote a better one-health approach for AR in Germany.

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“…In the postmenopausal samples, some of the bacteria previously reported in the upper reproductive tract (Chen et al, 2017; Lee et al, 2019; Li et al, 2018) and involved in degradation of hormones (Wang et al, 2018b), e.g. Pseudomonas spp.…”

Section: Discussionmentioning

confidence: 99%

The vagino-cervical microbiome as a woman’s life history

Jie

Liang

et al. 2019

Preprint

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The vagina contains at least a billion microbial cells, which are dominated byLactobacilli. Here we perform metagenomic shotgun sequencing on cervical samples from 1148 women. Factors such as pregnancy, delivery histories and breast-feeding were all more important than menstrual cycle in shaping the microbiome. Bifidobacterium breve was seen with older age at sexual debut;Lactobacillus crispatus negatively correlated with pregnancy history; potential markers for lack of menstrual regularity, heavy flow, dysmenorrhea, contraceptives were also identified. Other features such as mood fluctuations and facial speckles could potentially be deduced from the vagino-cervical microbiome. Gut and oral microbiome, plasma vitamins, metals, amino acids and hormones showed associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact. Highlights:Shotgun sequencing of 1148 vagino-cervical samples reveal subtypes; 1Other omics such as moods and skin features could be predicted by the vagino-cervical 2 bacteria; 3Factors such as delivery mode and breast-feeding associate with the vagino-cervical 4 microbiome; 5With dwindled Lactobacilli, postmenopausal samples are relatively enriched for viruses. 6 7 3 4 vulvovaginal candidiasis (Bradford and Ravel, 2017). The over 90% of human 30 sequences in female reproductive tract samples, in contrast to 1% in feces (Li et al., 31 2018; Methé et al., 2012; Wang and Jia, 2016), has made metagenomic shotgun 32 sequencing more expensive. Most studies of the vaginal microbiota used 16S rRNA 33 gene amplicon sequencing, which lacked a view of the overall microorganism 34 communities including bacteria, archaea, viruses and fungi (Byrd et al., 2018), as well 35 as the functional capacity encoded. Besides infection, studies on current sexual activity 36 and the menstrual cycle occurred naturally to the vaginal microbiota field (Gajer et al., 37 2012; Ravel et al., 2010). However, lasting impacts from other potentially important 38 factors such as sexual debut, pregnancy and breast-feeding have not been looked at in 39 a reasonably large cohort. 40 41 As a sizable reservoir of microbes instead of a transient entity, the female reproductive 42 tract microbiota might also reflect conditions in other body sites. It is however not clear 43 whether other omics in circulation or in the intestine cross-talks with the vagino-cervical 44 microbiome. Intersecting with hormones, metabolic and immune functions, we find it 45intriguing to explore the potential link of the vagino-cervical microbiome to the brain and 46 the face. 47 5 data, immune indices, physical fitness test, facial skin imaging, as well as female life 53 history questionnaire, lifestyle questionnaire, and psychological questionnaire (Figure 1). 54Our work pinpoints other metadata or omics that can predict or be predicted from the 55 microbiota in the female reproductive tr...

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Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota

Cited by 123 publications

References 47 publications

Development of the Ileal Microbiota in Three Broiler Breeds

Development of the Ileal Microbiota in Three Broiler Breeds

Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

The vagino-cervical microbiome as a woman’s life history

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