Concerns about Marseille’s IHUMI/AMU papers – Part 3

This is Part 3 of a series describing papers from the Institut Hospitalo-Universitaire Méditerranée-Infection (IHUMI or IHU) and Aix-Marseille Université (AMU) — institutions in Marseille, France — with potential problems.

In Part 1, I listed papers with image concerns. In Part 2, I focused on a set of papers describing many different research projects on specimens collected from homeless people — but all run under the same IRB approval number.

In this post, we’ll take a look at IHU/AMU papers describing samples obtained from people in African countries. Many of them lack wording on ethical approval by the local authorities, and all lack authors from these countries. This type of research might fall under the definition of neo-colonial science.

Neo-colonial science

Wikipedia defines neo-colonial science (also referred to as helicopter research or parachute research) as ‘when researchers from wealthier countries go to a developing country, collect information, travel back to their country, analyze the data and samples, and publish the results with no or little involvement of local researchers.‘

Some countries are home to extreme environments, rare plants, almost-extinct animals, or human groups that are unique in their way of living. Many scientists would love to study such places, organisms, and communities because this kind of research is likely to uncover unique and novel results that are easy to publish.

The problem is that some researchers from traditionally high-income countries have studied such interesting places — often located in middle- or low-income countries — without involving the local research community. These researchers might have taken soil samples from the super-dry Atacama Desert in Chile, or the dusty Bodélé Depression in the Republic of Chad, or they could have studied the Hadza people in Tanzania. They traveled to these countries, took some samples, then returned home to analyze and publish — without asking any host-country researchers to collaborate.

A recent Current Biology study found that around 40% of papers about research on coral reef biodiversity conducted in Indonesia and the Philippines listed no host-nation scientists at all. Another paper, published in Earth-Science Reviews, reported that only 30% of African Geosciences papers list an African author. In April 2021, Nature Index reported on these studies, and concluded that although visiting researchers might come with good intentions, their research needs to be more inclusive and diverse.

IHU/AMU papers on human samples without local authors

At least 23 papers by IHU/AMU authors describe novel microbial strains isolated from human subjects in African and South American countries, without mentioning ethical approval by local authorities, and without including local authors. I leave it to the reader to decide if this research could meet the definition of ‘neo-colonial science’ given above.

Unlike most human microbiome papers which typically describe thousands of microbial species isolated from hundreds of human subjects (here, here, and here), most of these IHU/AMU papers describe only one bacterium isolated from one human. The papers were mostly published in New Microbes and New Infections, a journal that was, until recently, heavily controlled by IHU / AMU editors (IHU’s Michel Drancourt founded the journal and was its Editor in Chief. Six other IHU/AMU researchers were on the 2016 editorial board). Of note, the peer review of some of these papers was remarkably fast — often taking less than a month between first submission and online publication.

In twenty of these papers (listed below), novel bacterial species isolated from stool samples of one or several Pygmy people are described. These papers are mostly brief, and lack descriptions of factors such as living conditions, diet, place of residence, or genetic lineages of the human subject(s). Because the composition of the gut microbiome is greatly determined by dietary and genetic factors, this makes a description of these novel gut bacteria of limited value for the microbiome research field.

The text of these papers state that the samples were collected in ‘Congo’, without clarifying if the authors mean the Republic of the Congo or the neighboring Democratic Republic of the Congo. Despite originating from Congo, the bacteria are often named after the city of Marseille or its surrounding area (species names timonensis, massiliensis, bouchesdurhonensis, mediterraneensis) and after the authors (genus names Raoultibacter, Libanicoccus). In one case, though, a strain was given the species name minihominis, a reference to the short height of Pygmy people.

The corresponding 16S rRNA gene Genbank entries often only state that the samples were isolated in Marseille, not mentioning Congo or Pygmy people at all (see e.g. LT623900, LT598568, or LT598573 )

There are no details of how stool samples were transported back to Marseille. Most bacteria described in these papers are anaerobic, which involves tricky transportation techniques, in particular during long-distance travel. Some details appear to be missing. Was the stool sample transported from Congo back to France at a low temperature, and then stored in a freezer? Or was the stool sample added to a blood culture bottle first? And was this done locally, or in France?

Most of these studies include wording such as ‘The culturomics study was approved by the ethics committee of the Institut Fédératif de Recherche 48 under number 09–022’. But that is a committee in France, not in one of the Congo Republics. There is no word about obtaining IRB approval, e.g. on consent wording with the local authorities, or a permit to perform a study on a small and unique human community. In addition, there appear to be hundreds of IHU/AMU papers that use this same ethics permit number.

Finally, and perhaps most relevant for this particular blog post, the authors of these 23 papers list affiliations in France, Lebanon, and Saudi Arabia.

But none of them list affiliations in the host-country.

List of the 23 papers:

• Melhem Bilen et al. – Genomic and phenotypic description of the newly isolated human species Collinsella bouchesdurhonensis sp. nov. – MicrobiologyOpen. 2018;7:e580. – DOI:10.1002/mbo3.580 – [PubPeer] – 50-year old Pygmy woman
• Melhem Bilen et al. – Taxonogenomics description of Parabacteroides timonensis sp. nov. isolated from a human stool sample – MicrobiologyOpen. 2019;8:e702. – DOI:10.1002/mbo3.702 – [PubPeer] – 39-year old Pygmy man
• Melhem Bilen et al. – Miniphocibacter massiliensis gen. nov., sp. nov., a new species isolated from the human gut and its taxono‐genomics description – MicrobiologyOpen. 2019;8:e735. – DOI:10.1002/mbo3.735 – [PubPeer] – 39-year old Pygmy man
• Melhem Bilen et al. – Phoenicibacter congonensis gen. nov., sp. nov., a new genus isolated from the human gut and its description using a taxonogenomic approach – Antonie van Leeuwenhoek 2019 – DOI:10.1007/s10482-018-01211-1 – [PubPeer] – 45-year old Pygmy woman
• Melhem Bilen et al. – Parabacteroides timonensis sp. nov., identified in human stool – Human Microbiome Journal 2 (2016) 1-2 – DOI:10.1016/j.humic.2016.10.002 – [PubPeer] – 39-year old Pygmy man
• Melhem Bilen et al. – “Libanicoccus massiliensis” gen. nov., sp. nov., a new bacterium isolated from a stool sample from a pygmy woman – New Microbe and New Infect 2017; 15: 40–41 – DOI:10.1016/j.nmni.2016.10.006 – [PubPeer] – 35-year old Pygmy woman
• Melhem Bilen et al. – Eggerthella timonensis» gen.nov., isolated from a human stool sample – New Microbe and New Infect – DOI:10.1016/j.nmni.2016.11.001 – [PubPeer] – 8-year old Pygmy girl
• Melhem Bilen et al. – «Collinsella bouchesdurhonensis» sp.nov., identified in human stool sample – New Microbes and New Infections – DOI:10.1016/j.nmni.2016.11.004 – [PubPeer] – 50-year old Pygmy woman
• Melhem Bilen et al. – ‘Congobacterium massiliense ’ gen. nov. sp. nov., a new bacterium isolated from the gut of a pygmy ( Baka ) woman – New Microbe and New Infect 2017; 15: 63–64 – DOI:10.1016/j.nmni.2016.11.005 – [PubPeer] – 50-year old Pygmy woman
• Melhem Bilen et al. – ‘Mobilibacterium massiliense’ gen. nov. and ‘Mobilibacterium timonense’ sp. nov., identified in a human stool specimen – New Microbe and New Infect 2017; 15: 61–62 – DOI:10.1016/j.nmni.2016.11.008 – [PubPeer] – 50-year old Pygmy woman
• Melhem Bilen et al. – ‘Pygmaiobacter massiliensis’ sp. nov., a new bacterium isolated from the human gut of a Pygmy woman – New Microbe and New Infect 2017; 16: 37–38 – DOI:10.1016/j.nmni.2016.12.015 – [PubPeer] – 47-year old Pygmy woman
• Melhem Bilen et al. – ‘Raoultibacter timonensis’ gen. nov., sp. nov. , a new bacterium isolated from the human gut of a Pygmy woman – New Microbe and New Infect 2017; 16: 45–46 – DOI:10.1016/j.nmni.2016.12.016 – [PubPeer] – 11-year old Pygmy girl
• Melhem Bilen et al. – ‘Gabonibacter timonensis’ sp. nov., a new bacterium isolated from the human gut of a Pygmy woman – New Microbe and New Infect 2017; 16: 39–40 – DOI:10.1016/j.nmni.2016.12.017 – [PubPeer] – 47-year old Pygmy woman
• Melhem Bilen et al. – ‘Phoenicibacter massiliensis’ gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman – New Microbe and New Infect 2017; 19: 43–44 – DOI:10.1016/j.nmni.2017.04.003 – [PubPeer] – 47-year old Pygmy woman
• Melhem Bilen et al. – ‘Olsenella congonensis’ sp.nov., identified in human stool sample – New Microbe and New Infect 2017; 19: 132–133 – DOI:10.1016/j.nmni.2017.05.013 – [PubPeer] – 47-year old Pygmy woman
• Melhem Bilen et al. – Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool – New Microbe and New Infect 2018; 21: 63–71 – DOI:10.1016/j.nmni.2017.11.001 – [PubPeer] – 35-year old Pygmy woman
• Melhem Bilen et al. – Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples – New Microbe and New Infect 2018; 24: 21–25 – DOI:10.1016/j.nmni.2018.03.002 – [PubPeer] – 12-year-old Pygmy girl, a 39-year old Pygmy man, and a Senegalese man
• T. Takakura et al. – Enterococcus mediterraneensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy – New Microbe and New Infect 2019; 32: 100599 – DOI:10.1016/j.nmni.2019.100599 – [PubPeer] – 39-year old Pygmy man
• T. Takakura et al. – Anaerosphaera massiliensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy – New Microbe and New Infect 2020; 33: 100633 – DOI:10.1016/j.nmni.2019.100633 – [PubPeer] – 39-year old Pygmy man
• M. Boxberger et al. – Corynebacterium neomassiliense sp. nov., a new bacterium isolated in a stool sample from a healthy male pygmy – New Microbe and New Infect – DOI:10.1016/j.nmni.2019.100644 – [PubPeer] – 49-year old Pygmy man
• Awa Diop et al. – Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille‐P2481 T , a moderate halophilic bacterium isolated from the human gut microflora – MicrobiologyOpen. 2019;8:e638. – DOI:10.1002/mbo3.638 – [PubPeer] – 10-year old boy from Senegal
• S. Khelaifia and D. Raoult – Haloferax massiliensis sp. nov., the first human-associated halophilic archaea – New Microbe and New Infect 2016; 12: 96–98 – DOI:10.1016/j.nmni.2016.05.007 – [PubPeer] – 22-year old Amazonian woman
• Nina Gouba et al. – Eukaryote Culturomics of the Gut Reveals New Species – PLoS ONE 9(9): e106994 – DOI:10.1371/journal.pone.0106994 – [PubPeer] – 3 subjects in Polynesia, 2 from Amazonia, 1 from Senegal, 1 from India (all adults, all men)