The development of probiotics for use in the ostrich farming industry in South Africa

Includes bibliographical references.Ostrich farming in South Africa is an important industry but it often suffers from high mortality rates among the ostrich chicks. This is thought to be due in part to environmental stress, leading to the delay in the development of the microbiota, thus making invasion by pathogens likely. Very little is known about the microorganisms inhabiting the ostrich gastrointestinal tract, however they do play an important role in humans and animals and disturbance of this community can be fatal. It has been established that probiotic bacteria such as Lactobacillus and Bifidobacterium spp. play an important role in the health of the host. In order to discover novel probiotic strains, bacteria should be isolated from the host, identified, characterised in-vitro to screen their potential suitability, and finally these results should be confirmed in-vivo. The aim of this study was to follow these guidelines in order to find a successful probiotic mix to decrease the mortality observed on ostrich farms, and to compare the effects of the probiotic mix to that of the antibiotic, tylosin, on the microbiota of the gastrointestinal tract (GIT)

Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

Careful consideration of experimental artefacts is required in order to successfully apply high-throughput 16S ribosomal ribonucleic acid (rRNA) gene sequencing technology. Here we introduce experimental design, quality control and “denoising” approaches for sequencing low biomass specimens. Results We found that bacterial biomass is a key driver of 16S rRNA gene sequencing profiles generated from bacterial mock communities and that the use of different deoxyribonucleic acid (DNA) extraction methods [DSP Virus/Pathogen Mini Kit® (Kit-QS) and ZymoBIOMICS DNA Miniprep Kit (Kit-ZB)] and storage buffers [PrimeStore® Molecular Transport medium (Primestore) and Skim-milk, Tryptone, Glucose and Glycerol (STGG)] further influence these profiles. Kit-QS better represented hard-to-lyse bacteria from bacterial mock communities compared to Kit-ZB. Primestore storage buffer yielded lower levels of background operational taxonomic units (OTUs) from low biomass bacterial mock community controls compared to STGG. In addition to bacterial mock community controls, we used technical repeats (nasopharyngeal and induced sputum processed in duplicate, triplicate or quadruplicate) to further evaluate the effect of specimen biomass and participant age at specimen collection on resultant sequencing profiles. We observed a positive correlation (r = 0.16) between specimen biomass and participant age at specimen collection: low biomass technical repeats (represented by < 500 16S rRNA gene copies/μl) were primarily collected at < 14 days of age. We found that low biomass technical repeats also produced higher alpha diversities (r = − 0.28); 16S rRNA gene profiles similar to no template controls (Primestore); and reduced sequencing reproducibility. Finally, we show that the use of statistical tools for in silico contaminant identification, as implemented through the decontam package in R, provides better representations of indigenous bacteria following decontamination. Conclusions We provide insight into experimental design, quality control steps and “denoising” approaches for 16S rRNA gene high-throughput sequencing of low biomass specimens. We highlight the need for careful assessment of DNA extraction methods and storage buffers; sequence quality and reproducibility; and in silico identification of contaminant profiles in order to avoid spurious results

Distinct Patterns in Human Milk Microbiota and Fatty Acid Profiles Across Specific Geographic Locations

Breast feeding results in long term health benefits in the prevention of communicable and non-communicable diseases at both individual and population levels. Geographical location directly impacts the composition of breast milk including microbiota and lipids. The aim of this study was to investigate the influence of geographical location, i.e., Europe (Spain and Finland), Africa (South Africa), and Asia (China), on breast milk microbiota and lipid composition in samples obtained from healthy mothers after the 1 month of lactation. Altogether, 80 women (20 from each country) participated in the study, with equal number of women who delivered by vaginal or cesarean section from each country. Lipid composition particularly that of polyunsaturated fatty acids differed between the countries, with the highest amount of n-6 PUFA (25.6%) observed in the milk of Chinese women. Milk microbiota composition also differed significantly between the countries (p = 0.002). Among vaginally delivered women. Spanish women had highest amount of Bacteroidetes (mean relative abundance of 3.75) whereas Chinese women had highest amount of Actinobacteria (mean relative abundance 5.7). Women who had had a cesarean section had higher amount of Proteobacteria as observed in the milk of the Spanish and South African women. Interestingly, the Spanish and South African women had significantly higher bacterial genes mapped to lipid, amino acid and carbohydrate metabolism (p < 0.05). Association of the lipid profile with the microbiota revealed that monounsaturated fatty acids (MUFA) were negatively associated with Proteobacteria (r = 0.43, p < 0.05), while Lactobacillus genus was associated with MUFA (r = 0.23, p = 0.04). These findings reveal that the milk microbiota and lipid composition exhibit differences based on geographical locations in addition to the differences observed due to the mode of delivery

Assessment of the effect of stress-tolerance acquisition on some basic characteristics of specific probiotics

The production of viable functional probiotics presupposes stability of strain features in the final product. We evaluated the impact of acquisition of heat-tolerance and subsequent freeze-drying on the adhesion properties of Lactobacillus rhamnosus GG, Lactobacillus casei Shirota, Bifidobacterium lactis Bb-12 and Bifidobacterium animalis IF20/1 and on their ability to inhibit the adhesion of pathogens in a mucus model. Both fresh and freeze-dried cultures were evaluated. Significant differences were observed between fresh, freeze dried, fresh heat-tolerant and freeze dried heat-tolerant strains, especially in the ability of the freeze dried probiotics to exclude, displace or outcompete pathogens.Based on our study characterizing probiotic properties such as adhesion and competitive exclusion, it seems possible to adapt probiotics to processing stresses, such as heat, without significantly changing the probiotic properties of the strains assessed. This may provide new options for future probiotic production technology. However, our results also emphasize that the properties of the stress-adapted strains, as well as the effect of the production processes should always be assessed as these are strain-specific. © 2013.Peer Reviewe

Human Breast Milk Bacteriome in Health and Disease

It is well-known that, beyond nutritional components, human breast milk (HBM) contains a wide variety of non-nutritive bio-factors perfectly suited for the growing infant. In the pre-2000 era, HBM was considered sterile and devoid of micro-organisms. Though HBM was not included as part of the human microbiome project launched in 2007, great strides have been made in studying the bacterial diversity of HBM in both a healthy state and diseased state, and in understanding their role in infant health. HBM provides a vast array of beneficial micro-organisms that play a key role in colonizing the infant&#8217;s mucosal system, including that of the gut. They also have a role in priming the infant&#8217;s immune system and supporting its maturation. In this review, we provide an in-depth and updated insight into the immunomodulatory, metabolic, and anti-infective role of HBM bacteriome (bacterial community) and its effect on infant health. We also provide key information from the literature by exploring the possible origin of microbial communities in HBM, the bacterial diversity in this niche and the determinants influencing the HBM bacteriome. Lastly, we investigate the role of the HBM bacteriome in maternal infectious disease (human immunodeficiency virus (HIV) and mastitis)), and cancer. Key gaps in HBM bacterial research are also identified

The Determinants of the Human Milk Metabolome and Its Role in Infant Health

Human milk is needed for optimal growth as it satisfies both the nutritional and biological needs of an infant. The established relationship between breastfeeding and an infant&rsquo;s health is attributable to the nutritional and non-nutritional, functional components of human milk including metabolites such as the lipids, amino acids, biogenic amines and carbohydrates. These components have diverse roles, including protecting the infant against infections and guiding the development of the infant&rsquo;s immature immune system. In this review, we provide an in-depth and updated insight into the immune modulatory and anti-infective role of human milk metabolites and their effects on infant health and development. We also review the literature on potential determinants of the human milk metabolome, including maternal infectious diseases such as human immunodeficiency virus and mastitis

Influence of socio-economic and psychosocial profiles on the human breast milk bacteriome of South African women

CITATION: Ojo-Okunola, A. et al. 2019. Influence of Socio-Economic and Psychosocial Profiles on the Human Breast Milk Bacteriome of South African Women. Nutrients, 11(6). doi:10.3390/nu11061390The original publication is available at https://www.mdpi.com/journal/nutrientsThe human breast milk (HBM) bacteriome is an important, continuous source of microbes to the neonate in early life, playing an important role in shaping the infant’s intestinal bacteriome. Study of the composition of the HBM bacteriome is an emerging area of research, with little information available, particularly from low- and middle-income countries. The aim of this study was to characterize the diversity of bacterial communities in HBM samples collected between 6–10 weeks postpartum from lactating South African women and to study potential influencing factors of the bacteriome. Using 16S rRNA gene sequencing of samples from 554 women, we demonstrated that the HBM bacteriome was largely dominated by the phyla Firmicutes (mean relative abundance: 71.1%) and Actinobacteria (mean relative abundance: 16.4%). The most abundant genera identified from the HBM bacteriome were Streptococcus (mean relative abundance: 48.6%), Staphylococcus (mean relative abundance: 17.8%), Rothia (mean relative abundance: 5.8%), and Corynebacterium (mean relative abundance: 4.3%). “Core” bacterial genera including Corynebacterium, Streptococcus, Staphylococcus, Rothia, Veillonella, Gemella, Acinetobacter, Micrococcus and a genus belonging to the Enterobacteriaceae family were present in 80% of samples. HBM samples were classified, according to their bacteriome, into three major clusters, dominated by the genera Staphylococcus (cluster 1), a combination of Staphylococcus and Streptococcus (cluster 2), and Streptococcus (cluster 3). The cluster groups differed significantly for Shannon and chao1 richness indices. Bacterial interactions were studied using co-occurrence networks with positive associations observed between the abundances of Staphylococcus and Corynebacteria (members of the skin microflora) and between Streptococcus, Rothia, Veillonella, and Gemella (members of the oral microflora). HBM from older mothers had a higher Shannon diversity index. The study site was associated with differences in HBM bacteriome composition (permutational multivariate analysis of variance using distance matrices (PERMANOVA), p < 0.05). No other tested socio-demographic or psychosocial factors were associated with HBM bacterial composition.https://www.mdpi.com/2072-6643/11/6/1390Publisher’s versio

Mycobiome Profiles in Breast Milk from Healthy Women Depend on Mode of Delivery, Geographic Location, and Interaction with Bacteria

Recent studies report the presence of fungal species in breast milk of healthy mothers, suggesting a potential role in infant mycobiome development. In the present work, we aimed to determine whether the healthy human breast milk mycobiota is influenced by geographical location and mode of delivery, as well as to investigate its interaction with bacterial profiles in the same samples. A total of 80 mature breast milk samples from 4 different countries were analyzed by Illumina sequencing of the internal transcribed spacer 1 (ITS1) region, joining the 18S and 5.8S regions of the fungal rRNA region. Basidiomycota and Ascomycota were found to be the dominant phyla, with Malassezia and Davidiella being the most prevalent genera across countries. A core formed by Malassezia, Davidiella, Sistotrema, and Penicillium was shared in the milk samples from the different origins, although specific shifts in mycobiome composition were associated with geographic location and delivery mode. The presence of fungi in the breast milk samples was further confirmed by culture and isolate characterization, and fungal loads were estimated by quantitative PCR (qPCR) targeting the fungal ITS1 region. Cooccurrence network analysis of bacteria and fungi showed complex interactions that were influenced by geographical location, mode of delivery, maternal age, and pregestational body mass index. The presence of a breast milk mycobiome was confirmed in all samples analyzed, regardless of the geographic origin. IMPORTANCE During recent years, human breast milk has been documented as a potential source of bacteria for the newborn. Recently, we have reported the presence of fungi in breast milk from healthy mothers. It is well known that environmental and perinatal factors can affect milk bacteria; however, the impact on milk fungi is still unknown. The current report describes fungal communities (mycobiota) in breast milk samples across different geographic locations and the influence of the mode of delivery. We also provide novel insights on bacterium-fungus interactions, taking into account environmental and perinatal factors. We identified a core of four genera shared across locations, consisting of Malassezia, Davidiella, Sistotrema, and Penicillium, which have been reported to be present in the infant gut. Our data confirm the presence of fungi in breast milk across continents and support the potential role of breast milk in the initial seeding of fungal species in the infant gut.A.B.-A. and M.C.C. acknowledge the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (ERC Starting Grant project no. 639226). F.P.-S. was supported by Ministerio de Economía y Competitividad (MINECO) grant no. CTM2016-80095-C2-1-R (NOVAMAR). The Chinese group acknowledges support from Key Projects of Beijing Science and Technology (D141100004814002) and the Natural Scientific Foundation of Beijing (Z140001).Peer reviewe

Breast Milk Polyamines and Microbiota Interactions: Impact of Mode of Delivery and Geographical Location

This is the peer-reviewed but unedited manuscript version of the following article: Ann Nutr Metab 2017;70:184-190 (DOI: 110.1159/000457134) The final, published version is available at http://www.karger.com/?doi=10.1159/000457134Background/Aims: The aim of the present study was to identify and quantify the polyamine levels in human milk obtained from different countries and through different modes of delivery, and to investigate their association with breast milk microbes. Methods: Mature breast milk samples were obtained from 78 healthy mothers after 1 month of lactation from 4 different geographical locations: Finland, Spain (Europe); South Africa (Africa); and China (Asia). Polyamines were determined using HPLC after dansyl derivatization and milk microbiota was obtained by 16S rRNA gene sequencing. Results: The mean values of polyamines in breast milk were 70.0, 424.2, and 610.0 nmol/dL for putrescine, spermidine and spermine, respectively, and 1,170.9 nmol/dL of total polyamines. The levels of putrescine were significantly higher in Spain (p < 0.05) and spermidine levels were significantly higher in Finland (p < 0.05) compared with other countries. Cesarean delivery had an impact on polyamine levels and it was related to an increase in the putrescine concentration being significant in Spanish samples (p < 0.01). Furthermore, putrescine levels were correlated positively with Gammaproteobacteria (r = 0.46, p < 0.001), especially with Pseudomonas fragi (r = 0.40, p < 0.001). Conclusions: The results demonstrate significant effect of geographical variations in human milk polyamine concentrations, being correlated with human milk microbiota composition. These differences may have an impact on infant development during lactation.C. Gómez-Gallego is a recipient of the Seneca Postdoctoral Grant from the Seneca Foundation, the Regional Agency of Science and Technology of the Region of Murcia (funded by the Education and Universities Council – Autonomous Community of the Region of Murcia, Spain). M. Carmen Collado is a recipient of a European Research Council (ERC) Starting Grant 639226-MAMI. Sequencing carried out at CPGR, South Africa, thanks to funding from the National Institutes of Allergy and Infectious Disease 1U01AI110466-01A1, H3Africa Initiative. Chinese group acknowledges the support from Key Projects of Beijing Science and Technology (D141100004814002), and Natural scientific foundation of Beijing (Z140001).Peer reviewe