Microbiology: Learning about the microbes in our body and more of the latest news from Nature

A large-scale resource for investigating microbial communities throughout the human body and an analysis of these data is reported in two studies in this week’s Nature. Microbial communities that live on and in the human body, collectively known as the ‘microbiome’, are thought to have a critical role in human health and disease.

This press release contains:

---Summaries of newsworthy papers:

Genomics: Bonobo genome sequenced

Microbiology: Learning about the microbes in our body

Astrophysics: A starburst galaxy seen 1.1 billion years after the Big Bang

Comment: Climate models at their limit?

Ecology: Transgenic crops let natural born enemies live

Genomics: Monitoring malaria parasites

Immunology: Saturated fat is bad for guts

Comment: India’s sanitation crisis

Planetary science: Titan might have tropical lakes

Comment: Midlife crisis for X-ray astronomy

Oncology: Colorectal cancer treatment resistance mutations identified

Fossils: A fishy family history

Physics: Big Bang theory for atoms

And finally... Small planets don't need heavy metal

---Mention of papers to be published at the same time with the same embargo

---Geographical listing of authors

[1] Genomics: Bonobo genome sequenced (AOP)

DOI: 10.1038/nature11128

The genome sequence of the bonobo, one of our closest relatives along with chimpanzees, and the last great ape to be sequenced, is presented in this week’s Nature. Analysis reveals thatover 3% of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These results shed light on the ancestry of the two ape species and might eventually help understand the genetic basis of traits that humans share with one or the other ape species.

Chimpanzees and bonobos are our two closest living relatives; they are also closely related to each other and their DNA sequences diverged around two million years ago. However, some of their behaviours differ in important ways and they each possess certain characteristics that are more similar to human traits than they are to one another. By sequencing the genome of a female bonobo called Ulindi, Kay Prüfer and colleagues find that the evolutionary relationship of bonobo with human and chimpanzee is complex. The authors suggest that their findings may be of use in understanding the genetic background of behavioural similarities between the ape species.


Kay Prüfer (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany)
Tel: +49 178 5847 443; E-mail: [email protected]

Janet Kelso (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany) co-author
Tel: +49 341 3550 552; E-mail: [email protected]


[2] & [3] Microbiology: Learning about the microbes in our body (pp 215-221; N&V)

A large-scale resource for investigating microbial communities throughout the human body and an analysis of these data is reported in two studies in this week’s Nature. Microbial communities that live on and in the human body, collectively known as the ‘microbiome’, are thought to have a critical role in human health and disease. The data provided by the Human Microbiome Project Consortium provide a platform for future studies of the dynamics of the human microbiome and its impacts on human health.

In one paper, Barbara Methé and colleagues describe various protocols that enabled the generation, processing and interpretation of the vast amount of data acquired. They present resources from a population of 242 healthy adults sampled at up 18 body sites — the airways, skin, mouth, gut and vagina — profiling their microbial communities. In another report, Curtis Huttenhower and co-workers use these resources to examine the structure, function and diversity of the microbiome. Their results reveal that the diversity of microbes in each habitat varies widely: for example, whereas the saliva is the richest ecologically, the vagina is the simplest in this respect. Each site maintains certain specialized metabolic functions despite variation in community structure.

The insights into the microbial communities of a healthy population provided by these studies lay the foundation for future explorations of the links with disease and further characterization of the human microbiome.


Curtis Huttenhower (Harvard University, Boston, MA, USA) Author paper [2]
Tel: +1 617 432 4912; E-mail: [email protected]

Barbara Methé (J. Craig Venter Institute, Rockville, MD, USA) Author paper [3]
Tel: +1 301 795 7818; E-mail: [email protected]

David Relman (Stanford University, CA, USA) N&V author
Tel: +1 650 852 3308; E-mail: [email protected]

Please note:

There are 14 related papers that will be published at the same time and with the same embargo in PLoS ONE, PLoS Genetics and PLoS Computational Biology. Journalists can contact Jen Laloup ([email protected]) for further information about these papers.


[4] Astrophysics: A starburst galaxy seen 1.1 billion years after the Big Bang (pp 233-236; N&V)

A redshift for a distant dusty starburst galaxy, the brightest detected at submillimetre wavelengths, is reported in Nature this week. HDF 850.1 was discovered more than a decade ago but efforts to determine its redshift, and therefore its luminosity and star formation rate, had come up with nothing. The latest study demonstrates that it was bright just 1.1 billion years after the Big Bang, and that it lies in a proto-cluster of galaxies.

HDF 850.1 was found to be the brightest source of submillimetre light in The Hubble Deep Field, one of the deepest multiwavelength views of the distant Universe. However, this galaxy has no counterpart at any other wavelength, and without a redshift (the change in the wavelength of light emitted from distant objects) its physical properties could not be determined.

By using a millimetre line scan, Fabian Walter and co-workers determine the redshift of HDF 850.1 and find it to be much higher than expected. From this information the authors calculate the star formation rate and mass, much of which appears to be in the form of molecular hydrogen.


Fabian Walter (Max-Planck Institut für Astronomie, Heidelberg, Germany)
Tel: +49 6221 528 225; E-mail: [email protected]

Alberto Bolatto (University of Maryland, College Park, MD, USA) N&V author
Tel: +1 301 405 1521; E-mail: [email protected]


Comment: Climate models at their limit? (pp 183-184)

In the run-up to the Rio+20 Earth Summit later this month, Mark Maslin and Patrick Austin predict a serious public-image problem for climate-change scientists in the coming year. The next round of the Intergovernmental Panel on Climate Change’s science assessment, due to be released next year, is likely to produce wider rather than smaller ranges of uncertainty in its predictions of the climate, they say in a Nature Comment piece this week. To the public and to policymakers, this will look as though scientific understanding is becoming less, rather than more, clear.

Many recent climate models contain interactive carbon cycles, better representations of aerosols and atmospheric chemistry and increases in spatial resolution — but that means adding in more ‘known unknowns’. Add to this the difficulties in predicting the economy and in estimating costs to society, and the result it a blurry picture.

None of this means that climate models are useless; in fact they have proven remarkably stable in their core predictions. One way to tackle the public-perception problem, the authors argue, is to subtly rephrase conclusions, emphasizing when change will happen, rather than whether it will happen at all. The weight of scientific evidence is enough to tell us what we need to know, argue Maslin and Austin. “We need governments to just go ahead and take action, as both the United Kingdom and Mexico have done. We do not need to demand impossible levels of certainty from the models to envisage a better, safer future.”


Mark Maslin (University College London, UK)
Tel: +44 20 7679 0556 or: +44 7960 754904; E-mail: [email protected]


[5] Ecology: Transgenic crops let natural born enemies live (AOP)

DOI: 10.1038/nature11153

In addition to reducing the need for pesticide use, transgenic crops that produce a bacterial insecticide can boost populations of beneficial pest-controlling predators, a report in Nature shows. Evidence suggests that this effect may spill over to neighbouring non-transgenic crops. These findings indicate that transgenic crops can promote biological control, which could offer a sustainable way of managing pests.

Bacillus thuringiensis (Bt) protein-producing cotton crops have been used in China to control against the cotton bollworm and have led to a reduction in insecticide use against this pest. Kongming Wu and colleagues report a marked increase in the numbers of ladybirds, lacewings and spiders ― natural enemies of certain pests ― and a decrease in aphid pests associated with the implementation of Bt cotton. Their study also finds evidence that these predators provide biological control against pests in neighbouring non-transgenic maize, soybean and peanut crops. Taken together, these results indicate that the use of Bt cotton promotes biological control in agricultural ecosystems because decreased insecticide use leads to an increase in predator populations.


Kongming Wu (Chinese Academy of Agricultural Sciences, Beijing, China)
Tel: +86 10 6281 5906; E-mail: [email protected]


[6] Genomics: Monitoring malaria parasites (AOP)

DOI: 10.1038/nature11174

Examination of genomic diversity in the parasite responsible for malaria, presented in this week’s Nature, is a way of monitoring genetic variants that have an impact on malaria control, such as those that confer resistance to treatment. Next-generation sequencing is used to analyse genome variation in Plasmodium falciparum clinical blood samples from around the world. This kind of analysis could provide a useful resource for ongoing research to combat malaria.

One of the main obstacles in achieving effective control of malaria is that the parasite genome is continually evolving, allowing it to evade the human immune system and to develop new forms of resistance to antimalarial drugs. To gain insights into the biological characteristics and evolution of malaria parasites, Dominic Kwiatkowski and co-workers performed a large-scale analysis of P. falciparum DNA from the blood of patients with the disease. A total of 227 samples from Africa, Asia and Oceania were assessed, allowing the authors to evaluate regional differences in the P. falciparum genome. This is the first data on within-host diversity at whole-genome scale, and the authors show how this may be used to estimate inbreeding rates, which are important for the evolution of drug resistance.

They demonstrate that, by generating deep sequencing data on hundreds of parasite samples, it is possible to gain deep insights into P. falciparum population biology ranging from the microscopic level — the genetic diversity of parasites carried by single infected individual — to the macroscopic level — the differences that exist between parasite populations on different continents. The authors conclude that large-scale genome sequencing of clinical samples offers opportunities for real-time monitoring of evolutionary changes in the parasite population, which could provide a crucial new surveillance tool in the armamentarium against malaria.


Dominic Kwiatkowski (Wellcome Trust Sanger Institute, Hinxton, UK)
Tel: +44 1865 287654; E-mail: [email protected]


[7] Immunology: Saturated fat is bad for guts (AOP)

DOI: 10.1038/nature11225

A link between diet, bacteria in the gut, and inflammation has been observed in mice and is reported in Nature this week. Milk fat is shown to increase the occurrence of colitis in mice with a specific genetic predisposition to this form of inflammatory disease, an effect associated with an altered balance of gut microbes. These findings provide a possible explanation for how Western diets high in certain saturated fats might increase the prevalence of immune disorders, such as inflammatory bowel disease, in genetically susceptible individuals.

An upward trend in complex immune disorders observed over the past half century is thought to be related to changes in microbial communities within humans caused by environmental factors. Eugene Chang and colleagues provide evidence that in mice one such cause could be diet. They demonstrate that high-fat diets (specifically milk fat) promote the expansion of otherwise less prevalent bacteria in the mouse gut, and these bacteria subsequently drive inflammation in susceptible mice. The authors explain that the milk fat promotes changes in the composition of bile acid, which alters the conditions for microbial communities in the gut.


Eugene Chang (The University of Chicago, IL, USA)
Tel: +1 773 702 6458; E-mail: [email protected]


Comment: India’s sanitation crisis (p. 185)

India is failing to cope with its own excreta, making safe sanitation a top national priority, says Sunita Narain, director general of the Centre for Science and Environment in New Delhi. Her Comment piece in this week’s Nature is followed by a Books and Arts ecodesign special that focuses on sanitation technology for the twenty-first century.

In India, one of the world’s fastest-developing countries, 600 million people still practise open defecation — making up 60% of the global total. Existing sewage systems tend to be ageing and inadequate. With soils, groundwater and waterways often contaminated, the impact on human health — such as outbreaks of diarrhoeal disease and cholera — is severe.

To a degree, India’s sanitation crisis is a class issue. Only the top third of the urban population have sanitation facilities that are connected to underground sewage pipes. But even they still suffer, because the pipes are not always connected to sewage works. Just 20% of the nation’s wastewater is processed, and that is often later mixed with untreated sewage.

New technologies are needed, such as using bioremediation to remove pathogens from effluent. But paramount is a new mindset, reframing sewage as a renewable resource and envisioning toilets for all. In the Books and Arts section, ecosanitation experts give us the nuts and bolts on green toilet systems. Zimbabwe-based environmental scientist Peter Morgan, for instance, talks about his innovative toilet designs — built in their millions in sub-Saharan Africa — and Ed Harrington, general manager of the San Francisco’s water utility, gives the low-down on the organization’s waste-water reuse system, which was inspired by tidal wetlands.


Sunita Narain (Centre for Science and Environment, New Delhi, India)
Tel: +91 112 995 5778; E-mail: [email protected]


[8] Planetary science: Titan might have tropical lakes (pp 237-239)

Regions around the equator of Saturn's moon Titan may be home to lakes of liquid methane, researchers conclude in this week's Nature. Titan has a methane cycle similar to Earth's water cycle, and lakes of methane have been observed at the poles. The suggestion that lakes also exist at lower latitudes indicates that there may be subsurface reservoirs supplying methane to Titan's surface and atmosphere.

Previous examination of Titan's surface has detected liquid at high latitudes and extensive dunes around the tropical regions. Caitlin Griffith and colleagues report an analysis of near-infrared spectral images of an area in the tropics. Their interpretations of the readings point to there being dark terrains, which hint at the existence of liquid methane on the surface at these lower latitudes.

Circulation models indicate that methane is transported from tropical latitudes to the poles, and the authors argue against these areas of liquid being replenished by rain. Instead, the authors propose that such low-latitude lakes are supplied by subterranean sources within a 10,000-year timescale.


Caitlin Griffith (University of Arizona, Tucson, USA)
Tel: +1 520 626 3806; E-mail: [email protected]


Comment: Midlife crisis for X-ray astronomy (pp 181-182)

This month marks the fiftieth anniversary of X-ray astronomy — the window through which we can examine the extremes of the Universe, where gas is more than a thousand times hotter than the surface of the Sun. Yet this window might soon close, argues Martin Elvis in a Nature Comment this week.

Although the US 2010 ‘decadal survey’ for astronomy ranked a next-generation X-ray mission fourth among large-scale space missions, that is low enough, given restricted budgets, to put it on the back-burner for at least a decade. With each space observatory now costing more than US$2 billion, the worldwide budget of about $5 billion a year is just not enough. NASA’s three current ‘Great Observatories’ — Hubble, Chandra and Spitzer — span the infrared to X-ray bands almost without a gap. But they will probably be succeeded by just one next-generation observatory: the James Webb Space Telescope, which works primarily in the infrared. In the rest of the spectrum, astronomers will be blind.

The solution is to drive down the cost of getting equipment into orbit, says Elvis. Launch costs have held steady at some $10,000 per kilogram of payload for more than 50 years. Companies such as SpaceX and Planetary Resources, which seek a larger customer base than just the government for launch services, might finally drive down costs. “Profit is the counterweight to caution,” says Elvis. Only then will new generations of greater observatories become affordable for scientists.


Martin Elvis (Harvard University, Cambridge, MA, USA)
Tel: + 1 617 495 7442 or: +1 617 331 3009; E-mail: [email protected]


[9] & [10] Oncology: Colorectal cancer treatment resistance mutations identified (AOP)

DOI: 10.1038/nature11156

DOI: 10.1038/nature11219

Mutations in a gene called KRAS are causally associated with acquired resistance to targeted therapies for colorectal cancer, a study in Nature reveals. A second study demonstrates that resistance mutations in KRAS and other genes are highly likely to be present in subpopulation of tumour cells before treatment. These mutations can be detected months before there is clinical evidence of treatment failure, which could provide a signal to initiate alternative treatments.

Drugs that target the epidermal growth factor receptors (EGFRs) can be used to treat colon cancer, but patients often develop resistance. Alberto Bardelli and co-workers show in cell-line models that KRAS mutations can confer resistance to an anti-EGFR therapy called cetuximab. They report that these mutations can either be acquired during treatment or may have pre-existed in a small fraction of tumour cells before treatment. In a separate report, Luis Diaz and colleagues use mathematical modelling to provide evidence that KRAS mutations pre-exist in tumour cells before treatment with the anti-EGFR treatment panitumumab. This model may explain why clinical recurrence is usually seen to occur within the same timescale, about 5 to 7 months after treatment began.

Both studies show that DNA from these mutations can be detected in liquid biopsies several months before radiographic evidence of disease progression is observable. This finding may offer an opportunity to anticipate and counter resistance by using combination therapy before patients relapse.


Alberto Bardelli (Institute for Cancer Research and Treatment, Candiolo, Italy) Author paper [9]
Tel: +39 119 933 235; E-mail: [email protected]

Luis Diaz (Johns Hopkins University, Baltimore, MD, USA) Author paper [10]
Tel: +1 410 955 8878; E-mail: [email protected]


[11] Fossils: A fishy family history (pp 247-250)

A re-interpretation of a long-extinct class of fishes called acanthodians, which are among the earliest jawed vertebrates known, is reported in Nature this week. Acanthodians are part of a larger family known as gnathostomes (‘jawed mouths’) and are central to ongoing debates on the origin of their modern relatives. The analysis reveals that acanthodians are anatomically closer to sharks than to bony fish and implies that the evolutionary development and history of gnathostomes needs reappraisal.

Modern gnathostomes are divided into Chondrichthyes (such as sharks and rays) and Osteichthyes (bony fish). Their origin has been interpreted on the basis of examination of acanthodians, which lived around 420 million years ago. Acanthodians had been thought to be anatomically close to bony fishes, but a new analysis of an Acanthodes braincase by Michael Coates and colleagues shows that it is remarkably shark-like. The authors suggest that these findings may assist our understanding of gnathostome evolution. They indicate that changes to the structure of vertebrate heads occurred not only before the emergence of jaws, but also afterwards.


Michael Coates (University of Chicago, Chicago, IL, USA)
Tel: +1 773 834 8417; E-mail: [email protected]


[12] Physics: Big Bang theory for atoms (pp 243-246; N&V)

An electron imaging method that can determine the positions of atoms with sub-ångström (that is, less than one ten-billionth of a metre) resolution inside a crystal is described in this week’s Nature. The technique is called ‘Big Bang’ tomography owing to similarities in the analysis with the Big Bang concept in cosmology that gives a linear relationship between the distance and the speed of distant galaxies.

Obtaining information on the position of individual atoms within objects is challenging, as normally it requires imaging from several angles with high resolution. Dirk Van Dyck and Fu-Rong Chen present an image reconstruction method to extract information about atoms in both the plane of observation and the vertical position from only one viewing direction. Patterns of waves scattered from the atoms provide information on all atoms in the sample that can be retrieved using appropriate algorithms. The concept used to determine the positions of the atoms is similar to those used by astronomers in determining the distances of faraway objects.

The authors demonstrate Big Bang tomography experimentally in a two-layered graphene sample, and consider that it could be of use for other similarly layered materials.


Fu-Rong Chen (Tsing Hua University, Taiwan, China)
Tel: +886 3573 4066; E-mail: [email protected]


[13] And finally... Small planets don't need heavy metal (AOP)

DOI: 10.1038/nature11121

Unlike gas giants, small, terrestrial-like planets do not require a metal-rich environment to form, according to research reported in Nature this week. The authors suggest that the existence of such small planets might be widespread in the disk of our Galaxy. In addition, these findings imply that searches for stars with planets do not have to be restricted to metal-rich stars.

Previous studies have shown that metal-rich stars are more likely to harbour gas giant planets than stars with lower metallicities; metallicity defines the abundance of chemical elements heavier than hydrogen and helium on a logarithmic scale. To understand more about the formation of smaller terrestrial-like planets, Lars Buchhave and colleagues probe the metallicities of 152 stars hosting 226 small exoplanet candidates. They find that planets with a radius smaller than four times the Earth’s radius form around host stars with a wide range of metallicities (though on average close to that of the Sun).

The present study shows that terrestrial-like planets can form at metallicities up to four times lower than the Sun. These findings imply that terrestrial-like planets could have formed early in the history of our Galaxy, the authors note.


Lars Buchhave (University of Copenhagen, Denmark)
Tel: +45 28 91 05 85; E-mail: [email protected]



[14] Visualizing heavy fermions emerging in a quantum critical Kondo lattice (pp 201-206)

[15] Autistic-like social behaviour in Shank2-mutant mice improved by restoring NMDA receptor function (pp 261-265)

[16] Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA (pp 271-275)

[17] Embryonic stem cell potency fluctuates with endogenous retrovirus activity

DOI: 10.1038/nature11244



The following list of places refers to the whereabouts of authors on the papers numbered in this release. For example, London: 4 - this means that on paper number four, there will be at least one author affiliated to an institute or company in London. The listing may be for an author's main affiliation, or for a place where they are working temporarily. Please see the PDF of the paper for full details.

Darwin: 6

Klosterneuburg: 10
Vienna: 1, 4

Antwerp: 12
Brussels: 2, 3
Flanders: 3

São Paulo: 8

Bobo-Dioulasso: 6

Phnom Penh: 6

Guelph: 2, 3
Montreal: 2, 3

Beijing: 5
Taiwan: 12
Xi'an: 10

Aarhus: 1
Copenhagen: 13

Gif-sur-Yvette: 4
Saint-Martin d'Hères: 4
Sophia-Antipolis: 5

Bonn: 4
Heidelberg: 4
Leipzig: 1

Navrongo: 6

Dublin: 11

Bari: 1
Candiolo: 9
Milano: 9
Monte Porzio Catone: 4
Rome: 6
Torino: 9

Kanagawa: 1

Kilifi: 6
Nairobi: 1

Daegu: 15
Daejeon: 15
Seoul: 15

Bamako: 6

Madang: 6

Kinshasa: 1
Pointe-Noire: 1

Barcelona: 1

Lund: 13

Lausanne: 17

Bangkok: 6
Mae Sot Tak: 6

Fajara: 6

Ankara: 1

Cambridge: 4
Hatfield: 13
Hinxton: 6
London: 6
Oxford: 1, 6

Birmingham: 2, 3
Tucson: 4
Berkeley: 2, 3, 4, 13
Irvine: 14
La Jolla: 17
Los Angeles: 2, 3, 10
Moffett Field: 13
Pasadena: 4, 13
San Bruno: 2, 3
San Diego: 2, 3
San Francisco: 2, 3
San Jose: 13
Santa Barbara: 13
Santa Cruz: 4
Thousand Oaks: 10
Tiburon: 2
Walnut Creek: 2, 3
Boulder: 2, 3
Branford: 1
New Haven: 16
West Haven: 16
Gainesville: 13
Boise: 3
Moscow: 2
Argonne: 7
Chicago: 2, 7, 11
Evanston: 3
Bloomington: 2, 3
Notre Dame: 6
Baltimore: 2, 3, 6, 10, 13
Bethesda: 1, 2, 3, 17
Chevy Chase: 3
College Park: 1, 2, 3
Rockville: 1, 2, 3, 6
Boston: 1, 2, 3
Cambridge: 2, 3, 10, 13
Woods Hole: 2, 3
Ann Arbor: 2, 3, 4
Detroit: 2, 3
East Lansing: 2, 3
St Louis: 2, 3
Missoula: 1
New Jersey
Princeton: 14
New Mexico
Los Alamos: 2, 3, 14
Socorro: 4
New York
Ithaca: 2, 3
New York: 2, 3, 9
Troy: 13
North Carolina
Charlotte: 2, 3
Durham: 2, 3
Bowling Green: 13
Cincinnati: 2
Cleveland: 2, 3
Columbus: 1
Norman: 2, 3
Philadelphia: 2, 3
Nashville: 10
Oak Ridge: 2, 3
Austin: 13
Houston: 2, 3
San Antonio: 3
Richmond: 2, 3
Smithfield: 11
Seattle: 1
Tucson: 8

Entebbe: 1



From North America and Canada
Neda Afsarmanesh, Nature New York
Tel: +1 212 726 9231; E-mail: [email protected]

From Japan, Korea, China, Singapore and Taiwan
Eiji Matsuda, Nature Tokyo
Tel: +81 3 3267 8751; E-mail: [email protected]

From the UK
Rebecca Walton, Nature London
Tel: +44 20 7843 4502; E-mail: [email protected]


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Published: 14 Jun 2012

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