Similarity - ILSI Southeast Asia Region conference proceedings: The gut, its microbes and health: relevance for Asia - Binus e-Thesis

  Asia Pac J Clin Nutr 2017;26(5):957-971

  957

  Seminar Proceeding

  ILSI Southeast Asia Region conference proceedings: The gut, its microbes and health: relevance for Asia

  1

  2

  3 PhD PhD MD, PhD Yuan Kun Lee , Patricia Conway , Sven Pettersson ,

  4,5

  6 PhD, FNA, FASc, FNASc, FTWAS, FAAM PhD G Balakrish Nair

  , Ingrid Surono ,

  7

  8 BSc RD, PhD Yusra Egayanti , Maria Sofia Amarra

  1 Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

  2 University of New South Wales, Sydney, Australia

  3 Karolinska Institute, Sweden and Nanyang Technological University, Singapore

  4 Translational Health Science and Technology Institute, Gurgaon, India

  5 Temporary International Professional, Research Policy Cooperation Unit, Department of Communicable Diseases, World Health Organization, Mahatma Gandhi Marg, Indraprastha Estate, New Delhi, India

  6 Food Technology Department, Bina Nusantara University, Serpong-Tangerang, Indonesia

  7 National Agency of Drug and Food Control (BPOM), Indonesia

  8 International Life Sciences Institute, Southeast Asia (ILSI SEA) Region, Singapore

Background and Objectives: The human being is a complex entity, involving interaction between microbes and

the human host. Evidence shows that the nutritional value of food is influenced in part by the structure and opera-

tions of an individual’s gut microbial community, and food in turn shapes the individual’s microbiome. A confer-

ence was held to promote understanding of the intestinal microbiome and its implications for health and disease,

particularly among Asian populations. Methods and Study Design: Papers describing 1) the intestinal ecosys-

tem in Asian populations, 2) changes in intestinal microbiota through life and its effects, 3) the Asian gut micro-

biota in disease conditions, 4) indigenous probiotics to maintain a healthy gut microbiota, 5) probiotic regulation

in an Asian country, and 6) the results of a panel discussion are included in this report. Conclusions: The gut mi-

crobial inhabitants of Asian people differ from those of Europe and North America. Geographic location, diet,

and ethnic background influence intestinal microbial composition. Urbanization and economic development have

brought changes in traditional Asian diets, which in turn affected the gut microbiome, contributing to a shift in

the region’s health burden from infectious diseases to non-communicable chronic diseases. Novel probiotic

strains of Indonesian origin demonstrated significant enhancement of humoral immune response in human studies.

Knowledge gaps and implications for research to further understand the Asian gut microbiome were discussed.

  Key Words: gut health, nutrition, novel probiotics, Asia, intestinal microbes

  

INTRODUCTION al community, and that food in turn shapes the individu-

  The human intestine carries about 100 trillion microor- al’s microbiome. Changes in cultural traditions and agri- ganisms, representing hundreds of bacterial species, fungi, culture are affecting diets worldwide, resulting in changes

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  parasites and viruses. This colonic microbiota is unique in the intestinal microbial composition among popula- to each individual host, and changes in response to diet, tions and contributing to subsequent health problems. drugs, disease, environmental exposure, and medical or Understanding the intestinal microbiome and approaches surgical intervention. In mammals, the microbiome refers to its structural and functional modification will be essen- to an “extended genome” of millions of microbial genes tial for developing disease prevention strategies and per-

  1 located in the intestine. Intestinal microorganisms carry sonalized health care regimens.

  out an array of enzymatic reactions that are distinct from, but critically augment, human genome-encoded activi-

  Corresponding Author: Dr Maria Sofia Amarra, International

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  ties. This symbiotic condition influences human metabo-

  Life Sciences Institute, Southeast Asia (ILSI SEA) Region, 9 1,2 lism, physiology, and gene expression.

  Mohamad Sultan Road #02-01, Singapore 238959.

  Advances in technology and bioinformatics have made

  Tel: +65 6352 5220; Fax: +65 6352 5536

  it possible to examine the influence of the intestinal eco-

  Email: sofiaamarra@ilsisea.org.sg; amarra.sofia@gmail.com

  system on human health. There is increasing evidencethat

  Manuscript received 15 April 2016. Initial review completed 25 the nutritional value of food is influenced in part by the April 2016. Revision accepted 07 June 2016. doi: 10.6133/apjcn.112016.09

  structure and operations of a consumer’s gut microbi-

  958 YK Lee, P Conway, S Pettersson, GB Nair, I Surono, Y Egayanti and MS Amarra The objectives of the conference were to highlight cur- rent scientific knowledge on the gut microbiome, its in- teractions with diet and nutrition, and implications for health and disease particularly in Asia. The following papers describe the intestinal ecosystem in Asian popula- tions, changes in intestinal microbial composition through the human life cycle and its effects, the Asian gut micro- biota in disease conditions, indigenous probiotics to maintain a healthy gut microbiome and significant en- hancement of humoral immune response, and probiotic regulation in an Asian country. A panel discussion at the end of the sessions is summarized. Since presentations were based on completed studies and published reports and made available online, ethics approval was not re- quired.

  What we know so far is that microbial populations differ between African and Italian children, and this has been associated with differences in diet composition. Bac-

  mained relatively constant in abundance throughout the year, suggesting that genetic contribution might play a greater role than diet, while Faecalibacterium, Bifidobac- terium, Eubacterium changed with the seasons.

  Coprococcus - did not change regardless of diet and re-

  It has been shown that enrichment of the diet with animal protein modulates Bacteroides levels, with change occur- ring slowly within weeks accompanying pH changes in the gut rather than food per se. In a study in Mongolia, we followed changes in gut microbiota over 4 months of seasonal change. Mongolians have an interesting dietary pattern. In winter they consume large amounts of animal meat (lamb) and butter; in summer they consume mainly dairy products with little meat. Their belief is that meat has toxins and therefore shifting to dairy products during summer will reduce the burden of ingested toxins. This food pattern presents a model of dietary change twice every 6 months. Our study showed that the predominant bacterial groups - Prevotella, Bacteroides, Ruminococcus,

  What is the role of meat consumption?

  We also know that dietary plant products facilitate the colonization of Prevotella and that changes in microbi- ome composition are detected within 24 hours of initiat- ing controlled feeding. Consumption of slowly digestible plant carbohydrates (oligosaccharides, wheat arabinoxy- lan) called prebiotics, as well as fruit, vegetables, and milk promote the growth of gut bacteria that metabolize complex carbohydrates, e.g., Bifidobacterium strains in particular B.infantis.

  children while Firmicutes were predominant among Ital- ian children. Italian children had diets that were high in animal protein, sugar, starch and fat and low in fiber while African children had diets that were low in fat and animal protein and rich in starch, fiber and plant polysac- charides.

  teroides were found to be predominant among African

  terobacteriaceae showed a general trend of increase as one ages, and this was observed in all countries. What is the role of diet with respect to changes in gut microbiota structure in Asia?

  RESULTS The intestinal ecosystem Population differences in gut microbiome in relation to diet, environment, and human genes - Yuan Kun Lee, National University of Singapore, Singapore

  The data also show that among different age groups liv- ing in the same location or in the same country, gut mi- crobiota do not change very much except for two micro- bial families - Enterobacteriaceae and Bifidobacteriaceae. In China, as one gets old, Bifidobacteriaceae decrease. The same thing happens in Indonesia, Korea, Mongolia, Thailand. This family of bacteria are the good bacteria associated with sustaining general health and a low level is associated with many diseases. On the other hand, En-

  Random forest clustering using species-level phylotype composition data of 303 Asian children showed that there is a V-shaped clustering of microbial composition. China forms the origin of this v-shape. Taiwan and Bangkok form the two arms of the junction originating from China. KhonKaen and Indonesia cluster onto the Bangkok arm, while Japan cluster onto the Taiwan arm. As shown by their positions on two separate ends of the v-shape, Japa- ferent gut microbiota.

  Bangkok, these same types of bacteria comprise small proportions. Prevotellaceae is the dominant type in Indo- nesia and KhonKaen. This general pattern of clustering was confirmed in a phase 2 study done among 150 adults and 128 elderly in Mongolia, Korea, China, Thailand, and Indonesia.

  Bifidobacteriaceae. However, in Southeast Asia, except

  From the phase 1 study, we observed two distinct clus- ters of populations in Asia – one population with high levels of Prevotella and the other population with high levels of Bifidobacteria and Bacteroides. The family-level gut bacterial composition of children in China, Japan, and Taipei showed high levels of Bacteroidaceae and

  Phase 1 of the study was done among children aged 7 to 11 years. At this age, individuals largely eat at home and in the school canteen, so that foods eaten are mostly traditional and the type of food consumed is easy to check. Data were obtained from 10urban and rural cities in five countries: Japan (Tokyo & Fukuoka), China (Beijing & Lanzhou), Taiwan (Taipei & Taichung), Indonesia (Yog- yakarta & Bali), Thailand (Bangkok & KhonKaen).

  Our intestinal microbiota profile is determined by expo- sure during infancy, the ability of the microbe to adhere to the intestinal surface (adhesion-receptor interaction), and its ability to colonize the intestinal surface, which in turn depends on, the intestinal micro-environment as de- termined by host physiology stage and dietary habits. In 2009, we initiated the Asian Microbiota Program, a re- gional collaboration that seeks to examine how Asians differ in terms of gut microbiota. Asia is different because we cover a large geographic area and we eat very differ- ently.

  The Mongolian diet is similar to the western diet – high in meat, alcohol, fermented milk – but their gut bacterial composition differs from that of western people. The Mongolian Firmicutes to Bacteroidetes (F/B) ratio is 0.71 compared with ratios of 2.81 for urbanized Italian chil- dren and 2.95 for Koreans. Gut microbiome Asia 959 Thailand, Korea, African countries – consume relatively little meat compared with those that carry Bacteroides and Bifidobacterium clusters. The exception is Mongolia, where meat consumption is 108.8 kg per capita. Mongoli- an meat consumption level is very close to that of the U.S. (124.8 kg/capita)and higher than that of other Bacteroides clusters such as Italy, China, and Japan (90.4, 52.4, 43.9 kg/capita, respectively).

  A recent paper in Nature showed that if subjects con- sumed solely animal products, the gut microbiota changes substantially within a short period of time. Subjects given only meat for 4 days shifted their gut microbiota from whatever microbial population was present to Bacteroides. The change was attributed to bile tolerance but can also be interpreted as Bacteroides being the default microbial population in the human intestine.

  Changes in intestinal microbiota through the human life cycle Intestinal microbiota during life - Patricia Conway, University of New South Wales, Australia

  Factors affecting the infant gut microbiota

  Fecal bacteria of breastfed infants are similar to those in breast milk. Whereas fecal bacteria of formula-fed in- fants are similar to maternal fecal bacteria. The particular species of bifidobacteria in infants, Bifidobacteria infantis, differs from that of adults (B. longum). The infant strains can effectively utilize human milk oligosaccharides while the adult species are incapable of doing so. Thus breast milk contributes to the establishment of infantile intesti- nal microbiota by actually feeding the microbes in the infant gut and hence can be considered an important source of bionutrients.

  Molecular profiling of breast milk bacteria has revealed considerable bacterial biodiversity with the composition differing between normal weight and obese mothers. There is also a significant difference in microbial compo- sition of breast milk of mothers after vaginal delivery compared with elective/non-elective caesarean delivery (C-section). Non-elective C-section deliveries, considered as emergencies, have breast milk microbiotas that are more similar to vaginal deliveries. While the mechanisms of change have not been elucidated, it is possible that birthing stresses prior to a non-elective C-section could induce similar responses to vaginal deliveries.

  Analysis of breast milk

  Although previously believed to be sterile at birth, we now know that low levels of colonization can occur in utero. It is reported that bacteria can transfer from the maternal gut into the placenta and amniotic fluid and the newborn can have some gut microbes. However, the greatest impact on the acquisition of microbiota includes the mode of delivery, environmental exposure including other family members, nursing staff, pets, and breast milk. Breast milk has a large population of microbes. Thus, at the time of birth and in the first few weeks of life, the baby is being exposed to microbes that in turn influence his/her individual microbiota throughout life.

  Acquisition of microbiota in the newborn

  The intestinal microbiota is continually evolving in terms of composition and function during life, from birth when the gut has extremely low numbers to the 100s of trillions of microbes in the adult. It is influenced by all aspects of life and in turn impacts on all aspects of life. Understand- through to the adult can help identify factors which can be addressed in order to improve health and well-being as well as to slow the development of the emerging pandem- ic of non-communicable diseases of the modern man.

  geographic location dictates what products are produced, that in turn dictates diet. How much do genetic factors vis-à-vis diet contribute to gut microbiota composition among Asians? These questions pose opportunities for future work in Phase 2 of the Asian Microbiota Program.

  Earlier work showed that in the absence of diet, cells initiate a fucosylation program that provides food for gut

  Prevotella contribute to disease? There is no doubt that

  drives Prevotella in Southeast Asia. One possibility is cereal, a staple food consumed in large amounts in all countries – e.g., wheat bread and potato in U.S., rice in Asia, millet and sorghum in Africa. Prevotella cluster countries differ from Bifidobacteria/Bacteroides coun- tries in terms of the major staple carbohydrate foods con- sumed. The starch fractions of these staple foods – i.e., rapidly digestible starch, slowly digestible starch, re- sistant starch – show the greatest variation in resistant starch content. Can resistant starch consumption be the driving force behind Prevotella clusters? Does change in

  Bacteroides can also digest bran fiber. Something else

  does not differentiate Prevotella from Bacteroides, as

  What drives Prevotella? Prevotella is able to break down bran fiber. But bran fiber

  man diet of fruits and vegetables, evolution and natural selection favoured the establishment of intestinal mi- crobes, which break down plant products. Bacteroides have a complex membrane protein system that catabolizes plant cell wall glycans. Prior to being given solid foods, an infant’s intestinal tract should have a good abundance of Bacteroides obtained from breast milk. However, stud- ies have also shown that abundance of Bacteroides in advanced age is associated with chronic diseases such as cancer.

  Bacteroides. It is hypothesized that, due to an early hu-

  Intrauterine contamination. There is potential for in utero contamination (translocation) of particular groups of or- ganisms (Bifidobacterium, Lactobacillus, Enterococcus). The maternal microbes, antibiotic use, the mother’s diet and lifestyle choices are impacting on the fetus. Babies whose mothers used probiotics prior to birth have mi- crobes influenced by maternal exposure to dietary probi- otics. Mode of delivery. In vaginal delivery, exposure to organ- isms during the birth process allows the infant to establish what is considered normal gut microbes. Caesarean deliv- ery is essentially free of exposure to bacteria, and is con- sidered abnormal microbial introduction. It is reported that about 70% of immune sampling cells are in the intes- tine. Vaginal delivery leads to normal immune develop-

  960 YK Lee, P Conway, S Pettersson, GB Nair, I Surono, Y Egayanti and MS Amarra In C-section babies, delayed development of the intestinal microbes leads to abnormal and disrupted microbial colo- nization making these infants prone to later allergic, di- gestive and inflammatory conditions. Compared with C- section babies, vaginally delivered babies have very dif- ferent bacterial population profiles in various regions of the body. C-section babies have elevated levels of organ- isms that we prefer to avoid (Staphylococcus, Corynebac-

  One study that looked at the proportion of Firmicutes to

  There was also a clear distinction in microbiota de- pending on where the subjects lived (i.e., community vs day-hospital vs rehabilitation vs long stay care or institu- tionalized). Those who lived in institutions or in health service differed from young healthy controls and from those living in their own house or community. Poor health was associated with long-term care. It was con- cluded that microbiota composition is clustered according to residence location and the type of care received. In terms of health indices, microbial composition correlated with fragility as less diverse microbiota profiles were found in those who were more fragile, had poorer nutri- tion (which also tied in with dental health care because if dental health is a problem, food choice is going to differ), and detectable markers of inflammation.

  Another study looked at the major organisms from dif- ferent population groups - elderly centenarians, seniors or elderly, and young adults. Patterns were similar, but quantification of microbial groups differed. Seniors and young adults showed similar microbial profiles while that of centenarians differed dramatically. Certain bacterial groups were elevated in centenarian subjects as were pro- inflammatory cytokines.

  These include lifestyle choices, medications, diet, stress- ors, age, institution care vs. home living, dental health, infection, hygiene, sanitation, urban/rural location. Dif- ferences in microbial diversity are linked to age and cul- ture. Studies that looked at the distribution of different microbial groups in various populations from newborn to age 83 years showed that microbial populations of sub- jects from USA and Europe clustered together while other geographic regions distributed very separately from these countries.

  teroides are reported and can contribute to triggering an inflammatory response. Factors affecting the adult microbiota Potentially whatever we do will influence the microbiota.

  in the ratio of these two organisms correlated with change in the immune system. The elderly are predisposed to inflammatory conditions linked to change in microbiota wherein decrease in Firmicutes and increase in Bac-

  Bacteroides in adults and the elderly revealed that change

  The early microbiota is highly unstable, shifting rapidly in response to diet and illness. The 6th month and early childhood stage are therefore crucial. In healthy individu- als, the microbial community during the early adult stage is highly diverse but stable and slower to react to change. Among the elderly, decreasing microbial diversity is as- sociated with increased fragility and inflammatory mark- ers.

  terium, Propionibacterium) while those vaginally deliv-

  Succession of microbiota Early childhood reflects increasing microbial diversity.

  The infant microbiota starts to resemble that of the adult by age 2 years. The impact of these influencing fac- tors during the first 2 years will influence the health of the infant for future life. In addition to the period of birth there is a window of sensitivity at 6 months of age, when the baby is particularly susceptible to environmental chal- lenges. Before birth, immediately after birth and during breastfeeding, the infant receives antibodies and immune protection from the mother. As breastfeeding decreases and weaning is initiated, protection from the mother’s immune system on the infant is decreasing. Exposure to the environment, dirt, and change in diet are starting. This is when the baby’s immune system starts to develop. The period of susceptibility coincides with the period when the mother’s protection is decreasing and before the ba- by’s immune system is completely developed, which oc- curs at around 6 months of age.

  type of foods chosen also impact on the infant gut micro- biota. Significant changes are found in the microbiota of colicky infants, characterized by lower diversity and slower colonization, elevated levels of Proteobacteria including species producing gas and inflammation, re- duced lactobacilli and bifidobacteria including species with anti-inflammatory effects, and reduced beneficial butyrate-producing species.

  Bifidobacterium, Lactobacillus. The time of weaning and

  Ethnic background. Microbial composition differs by diet and ethnic background and different regions have dramat- ically different microbiota profiles. Antibiotics and diet. There are significant changes in mi- crobes present in babies that received antibiotics during the first 7 days, characterized by a reduction in microbial diversity. Use of prebiotics/probiotics promotes increased

  Bifidobacterium levels while formula feeding promotes increased Enterobacteriaceae levels.

  ered have more favorable ones (Lactobacillus, Prevotella, Sneathia). Impact of gestation time. Pre-term babies are predisposed to harmful intestinal conditions particularly necrotizing enterocolitis with increased risk of potential death. Bac- terial populations differ between preterm and full term babies especially in terms of facultative anaerobes. Even at 3 months, C-section babies have not reached a picture comparable to vaginally delivered babies. Babies who develop necrotizing enterocolitis that ultimately lead to death have dramatically different intestinal microflora compared with control babies. Type of feeding. Breastfeeding promotes increased

  We analysed the microbiota in terms of the type of bac- teria that are present. I would like to emphasize that bac- teria may be unchanged but they may behave differently. Some of our in vitro studies examined the change in lac- tobacillus using microbiota from subjects of different age and sex. Prebiotics such as fructooligosaccharides were used as substrate. Substrate utilization by fecal microbiota Gut microbiome Asia 961 yr old female were similar. But utilization of the same substrate by microbiota from a male of the same age dif- fered. This raises the issue that we need to look at not only what’s there but also what’s the metabolic capacity of the host population.

  To summarize microbial succession with age, during the first month of life bifidobacteria are predominant and gradually over the first year there is increase of Bac-

  Pregnancy and the microbiome – effects on placenta Pregnancy is a period of tremendous metabolic stress.

  big difference in plasma VLDL and triglycerides between GF animals and normal animals, liver concentrations of these compounds do not differ.

  tes are very efficient lipid absorbers. But while there is a

  We examined gluconeogenesis and the enzymes which respond to elevated glucocorticoids in the liver. In GF dams, glucose was immediately absorbed and stored in tissue. It is like they have reduced glucose levels and they are trying to get more energy. GF dams have limited liver glycogen stores that are further reduced by stress. Fatty acids are absorbed in the liver and used as energy through beta-oxidation. One of the key regulators to take up fatty acids is a protein called PPAR alpha. This protein is ele- vated in pregnant GF animals indicating up regulation of the machinery to take up fatty acids in response to energy deficiency. Previous studies have shown that in the ab- sence of bacteria, both GF mice and GF fish are unable to absorb lipids. Fish experiments have shown that Firmicu-

  Mechanism of microbial effects on the placenta

  Pregnancy is associated with increased corticosterone levels because of the need for more glucose to support the developing fetus. Glucocorticoids have anti-inflammatory functions and serve as a metabolic signal to activate glu- coneogenesis. If the host gets too stressed, glucocorti- coids reach a certain threshold indicating insufficient amount of nutrients. This in turn induces the body to con- strain programming in certain organs, including the pla- centa. Signalling pathways shown to be important for placental development are IGF2, PPAR beta, PPAR gamma pathways and these are regulated by glucocorti- coids. When glucocorticoid levels increase, these path- ways are repressed due to insufficient energy. Ongoing investigations are addressing whether placenta display morphological changes. Additional data demonstrate an increased uptake of a labelled tracer in fetus from the GF dam compared with pups from normal specific-pathogen- free (SPF) dams. These preliminary data indicate a possi- ble increased nutritional supply to the GF pups when the maternal microbiome is not present in the GF dam.

  The fetus has to undergo all aspects of development pro- gramming, organ development and subsequently be de- livered. We used germ free (GF) mice to study what hap- pens during pregnancy if microbes are not there. Corti- costerone levels were higher in plasma of pregnant and non-pregnant GF animals compared with normal animals, indicating that GF animals are under constant stress even if they are not pregnant.

  This suggests that other organs may also contain tissue- related regional microbiomes.

  teroides fragilis. In the adolescent age we get contradicto-

  From the holobiont perspective, microbes are part of the machinery for good metabolic regulation in all host species. There is vertical transmission of microbiota from parents to offspring, which seems to be stable, almost like genes. There is also evidence to suggest the existence of a microbiome in the placenta. Its significance is unknown.

  The holobiont is defined as the host and its microbiota. The holobiont contains numerous genes from the host (termed the karyome), the mitochondria (chondriome), the different microbial species (microbiome, virome, fun- giome), and the interactions between the organism and all other genes (epigenome). The holobiont theory sees peo- ple not just as individuals but also as ecosystems, wherein microbes and host share functions in a symbiotic fashion in order to meet their biochemical and biological needs. All genome wide association studies carried out have only looked at the host and ignored the microbiome. But changes in the host influence the microbiome and elicit a response from the microbiome. This part of the equation has not been studied.

  Bacteria have been around for billions of years, way be- fore humans. Hence bacteria have had enough time to adapt and develop within the landscape which they con- trol. In medicine, a paradigm shift has occurred, wherein humans are no longer viewed as a separate entity, but as part of a complex environment involving interaction be- tween microbes and the human host.

  The microbiome influences host physiology in early life- Sven Pettersson, Karolinska Institute, Swe- den/Nanyang Technological University, Singapore

  decrease in biodiversity. It’s a cycle that starts off with very limited diversity and numbers and then finishes with limited biodiversity; and starting with a lot of bifidobacte- ria and finishing with few bifidobacteria. When we talk about human gut composition it is very important to know the age and the history of subjects. We know there are various factors impacting on the composition of gut mi- crobiota and that this composition has an important im- pact on the emerging pandemic of non-communicable diseases. A better understanding of acquisition and suc- cession of the microbiota through life will be valuable in identifying ways of improving health and wellbeing in the future.

  teria). The microbiota of the elderly changes (increase of Bacteroidetes, decrease of Bifidobacteria) with a resulting

  ry results because this population is changing dramatical- ly and is very dependent on exposures including envi- ronmental, diet and emotional factors. Biodiversity is increasing and microbial composition depends on what time samples are taken. The adult stage is mostly stable (Firmicutes >Bacteroidetes >Proteobacteria >Actinobac-

  Another critical component during pregnancy is the ac- tivation of ketone bodies, which serve as an alternative source of energy. The enzymes involved in formation of ketone bodies are massively elevated in GF dams com- pared with SPF control dams. While the steady state level of ketone bodies in plasma of GF mice is about the same as in normal mice, the amount of ketone bodies in liver is more highly elevated in GF dams.

  962 YK Lee, P Conway, S Pettersson, GB Nair, I Surono, Y Egayanti and MS Amarra

  coli collectively cause campylobacteriosis, while Helico- bacter causes peptic/duodenal ulcers and gastric cancer.

  The nutritional status of children was based on anthro- pometric measures using WHO z-scores (weight for age, height for age, weight for height). To obtain an overall measure of nutritional status we calculated a cumulative z-score based on all three anthropometric measures and subdivided subjects into apparently healthy, borderline malnourished, and severely malnourished groups. Micro- bial composition of the 20 gut microbiomes was exam- ined. Abundance of different phyla. Across the 20 microbiomes, 72 % of sequenceswere assigned at phylum level. Eight phyla were present but only four were dominant – Bacte- riodetes, Firmicutes, Proteobacteria, Actinobacteria. These results are similar to those ofother studies. Thirty six percent of sequences were assigned at genus level. Of these, 23 genera belonged to the four dominant phyla. Calculation of rank normalized abundances of the 23 core genera showed the predominance of Prevotella across metagenomes, indicating that majority of gut bacteria in these children were similar to the Enterotype 2 communi- ty established by Arumugam and colleagues.

  The study aimed to determine how undernutrition affects microbiome membership and function. Twenty children aged </=60 months were selected. These children had no history of diarrhea, no acute respiratory infection, and no antibiotics taken for the past 4 weeks before fecal sample collection.

  , was done in a district in West Bengal called Birbhum, a typical rural and agricultural setting. The Birbhum Population Project is a health and demographic surveillance system performing longitudinal observations.

  4

  One

  4 This study, which was published in April 2014 in PLoS

  Gut microbiome of undernourished Indian children

  This simple study showed that there is an overall dif- ference between microbial communities residing in the gut of the malnourished and that of the healthy child. The gut microbiota of the malnourished child is interpreted as aberrant gut microflora, a concept that extends the under- standing of malnutrition beyond nutrition deprivation. Aberration of gut microflora leads to sub-clinical disorder characterized by inflammation and modest malabsorption. The continued aberration of gut microflora leads to un- checked bacterial proliferation, concurrent infection, dis- ruption in community dynamics of commensal intestinal flora, and impaired immunity.

  Other families with higher representation in malnourished samples were Bacteroidaceae (found in obese individuals who lose weight rapidly), and Porphyromonadaceae (found in inflammatory bowel disease). In the healthy child gut metagenome, the predominance of these patho- genic lineages was not observed suggesting that the healthy flora could competitively inhibit and exclude the- se pathogens.

  and 12-folds higher in malnourished children suggesting infection of the intestinal epithelium by pathogens be- longing to these families. Campylobacter both jejuni and

  Maternal microbiome and offspring condition in later life

  Campylobacteriaceae and Helicobacteriaceae were 35-

  we did face-to-face comparison of the metagenome of the gut of a malnourished child versus that of a healthy child. Compared with a healthy child, the malnourished child showed increased incidence of patho- genic members of the phylum Proteobacteria. Families

  3

  In an earlier study,

  Is the gut microbiota altered in undernourished children?

  Undernutrition is defined as the outcome of insufficient food intake and repeated infectious diseases. It includes underweight, stunting, wasting and micronutrient defi- ciency. Progression of undernutrition has been attributed to a variety of causal factors including inadequate dietary intake, which impairs immune responses that in turn pre- disposes to infectious diseases including enteric infec- tions. This in turn alters the microbiota leading to dysreg- ulated gut permeability causing malabsorption. An altered microbiota results in a vicious cycle of diarrhea and un- dernutrition in susceptible children. Undernutrition is influenced by the environment, the human genome, host nutrition and host microbiota. Its effects include impaired vaccine responses, growth failure, stunting, decreased fitness, cognitive and fluency impairment.Globally, South Asia particularly India and sub-Saharan Africa have the highest prevalence of undernutrition (i.e., stunting and wasting).

  Undernutrition and associated problems

  Microbiology is grounded on the basis of culture of mi- croorganisms. We know now that what is cultured is only 2 to 10% of what is there and the rest (90%) are uncul- turable. While clinical decisions regarding diarrhea and gastrointestinal diseases are based on culture results, we know that there are a lot more microorganisms that are actually present but cannot be seen by these results.

  The gut microbiome in health and disease – Asian stud- ies Undernutrition and the gut microbiome - G. Balakrish Nair, Centre for Human Microbial Ecology, Translation- al Health Science and Technology Institute, India

  While outcomes are similar in terms of litter size and birth weight, the conditions under which offspring are generated differ between GF and normal mice. The ques- tion is - after delivery, is there an effect on how these offspring handle stress when exposed to environmental stress factors? Some studies indicate that metabolic status during pregnancy may preset conditions in later life by disrupting the HPA (hypothalamus-pituitary-adrenals) axis. Effects may include psycho-cognitive disorders, metabolic diseases such as obesity and diabetes. In an earlier study we observed that you can change behaviour in a mouse model by changing the maternal microbiome prior to pregnancy. Presumably the maternal microbiome was having an effect on development programming of the brain. It is becoming clear that what we see in the off- spring in terms of susceptibility to environmental stress is set during pregnancy. Using a metabonomic approach, studies should be done in humans to understand what the maternal microbiome does. That is a target to address for the future.

  In 2011, a consortium of investigators combined 22 Gut microbiome Asia 963 four countries with previously published data sets. They identified three robust clusters, which they called entero- types that are nation- or continent-specific. An enterotype is a classification of living organisms based on its bacte- riological ecosystem in the human gut microbiome. En- terotypes are not dictated by age, gender, body weight, or national divisions. The three enterotypes are Enterotype 1 (Bacteroides prevail), Enterotype2 (Prevotella prevail), and Enterotype3 (Ruminococcus prevail). While entero- types are driven by species composition, it must be re- membered that abundant molecular functions are not nec- essarily provided by abundant species, highlighting the importance of functional analysis. Enterotype 2, to which our subjects belonged, is predominantly distributed in Africa and is generally found in populations with high carbohydrate diet. Bacteroides is found where animal fat is rich in the diet. Bacteroides plebeius, found exclusively in Japan, metabolizes seaweeds that form a unique part of the Japanese diet.

  A heat map was created, showing the normalized rank abundances of 23 genera and 8 phyla across the 20 gut microbiomes of subjects classified as healthy and mal- nourished. Taxa were divided into 4 groups based on sim- ilarity in their abundance patterns and labelled as G1, G2, G3, G4.Abundance of G4, predominantly comprising

  Related functional categories. Sixty-four and 112 cluster orthologous genes (COG) groups were shown to have significant positive and negative correlations with the cumulative nutritional indices, respectively. COGs were referred to as Positively Correlated (PC) and Negatively Correlated (NC) COG groups.

  2. Certain functional categories (COG) groups are posi- tively or negatively correlated with nutritional status.

  1. There is a link between the gut microbiome and the nutritional status of children in the Indian setting where impaired nutritional status is not only due to the abundances of likely pathogenic microbial groups but also a result of depletion of several commensal genera.

  I would like to enumerate the following key messages from this study:

  We looked at the abundance patterns of CAZyme fami- lies across gut metagenomes with varying nutritional sta- tus. None of the individual CAZymes were significantly associated with cumulative nutritional index. However, when assemblages of CAZyme families having similar abundance patterns were grouped together,we found that families belonging to groups 3 and 7 had significant posi- tive correlations with at least one nutritional index. Group 3 CAZyme families degrade complex plant carbo- hydrates while those in group 7 degrade mostly pepti- doglycans. Group 6CAZyme families degrade complex plant carbohydrates. When the CAZyme families belong- ing to groups 3, 6, 7 were combined, their cumulative abundances were found to have an even stronger positive correlation with nutritional index. None of the groups had significant negative correlation with nutritional index.

  Carbohydrate active enzymes (CAZymes). Among the genes identified in the human gut microbiome, those that encode CAZymes are of particular interest as these en- zymes digest most of our dietary polysaccharides. The human genome encodes at most only 17 enzymes for the digestion of food glycans, specifically starch, sucrose, lactose. In contrast, the assembled mini-microbiome con- tains 15,882 different CAZyme genes distributed une- qually between glycosyltransferases, carbohydrate ester- ases, glycoside hydrolases, and polysaccharidelyases genes.

  Several functional categories associated with nutrient uptake and metabolism were over-represented or present in the PC COGs. In the NC COG group, over-represented functional categories were those associated with virulence and bacterial pathogenesis, including intracellular traf- ficking, secretion and vesicular transport, cell motility, inorganic ion transport and metabolism. Functionally, virulence appeared to be correlated with low nutritional index whereas functions related to metabolism of nutri- ents correlated positively with improved nutritional index.

  connection between pathogenic forms and beneficial mi- croorganisms and perhaps beneficial microorganisms keep pathogens under check. But as nutritional status declines to borderline malnourishment, pathogenic genera come together in a single connected bar e.g. Enterobacter interdependence among genera is even more pronounced for the severely malnourished group of metagenomes. It is therefore not just microbiomes per se but interconnec- tions that differ when we look at species membership among the three cumulative nutritional indices.

  Proteobacteria, was found to increase from healthy to

  terobacter (G1) associated with genera like Eubacterium, Roseburia, and Dorea (G4). There appears to be inter-

  Take for example the apparently healthy group. There are four distinct connected groups of genera – Strepto- coccus (G4) associated with Faecalibacterium (G1), En-

  Genera co-occurrence networks. The symptomatic charac- teristics of the gut environment depend not only on the presence of specific microbial groups but also on the in- herent inter-microbial co-occurrence networks present therein. Networks of co-occurring genera for the 3 groups of microbiomes were characterized by distinct network architecture.

  abundant in severely malnourished children compared with apparently healthy ones. Although individual genera belonging to G1 did not show any significant differences across the 3 groups, the combined abundances of all the genera belonging to G1 was significantly higher in appar- ently healthy children.

  erichia, Streptococcus, Shigella - were significantly over-

  Among phyla, Proteobacteria correlated negatively while Synergistetes correlated positively with nutritional index. The dominant genus Prevotella and probiotic gen- era like Lactobacillus and Bifidobacterium showed no correlation with nutritional index. Several genera belong- ing to group 4, predominantly Proteobacteria, -i.e. Esch-

  malnourished subjects while G1, comprising beneficial commensals, decreased with decreasing nutritional index and increased with increasing nutritional index. G2 and G3 had no significant association with nutritional index.

  Positively correlated functional groups relate to nutri- ents utilization while negatively correlated functional

  964 YK Lee, P Conway, S Pettersson, GB Nair, I Surono, Y Egayanti and MS Amarra